Index: /issm/trunk/src/c/Container/Constraints.cpp =================================================================== --- /issm/trunk/src/c/Container/Constraints.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Constraints.cpp (revision 12330) @@ -48,10 +48,11 @@ /*figure out total number of constraints combining all the cpus (no clones here)*/ - #ifdef _PARALLEL_ - MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); - MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); #else - numberofconstraints=localconstraints; + numberofconstraints=localconstraints; #endif + return numberofconstraints; Index: /issm/trunk/src/c/Container/DataSet.cpp =================================================================== --- /issm/trunk/src/c/Container/DataSet.cpp (revision 12329) +++ /issm/trunk/src/c/Container/DataSet.cpp (revision 12330) @@ -11,4 +11,5 @@ #endif +#include #include #include @@ -84,329 +85,4 @@ /*}}}*/ -/*I/O*/ -#ifdef _SERIAL_ -/*FUNCTION DataSet::Marshall{{{1*/ -char* DataSet::Marshall(){ - - vector::iterator object; - int object_size; - int marshalled_dataset_size=0; - char* marshalled_dataset=NULL; - char* old_marshalled_dataset=NULL; - - /*First get size of marshalled dataset: */ - object_size=(int)objects.size(); - - marshalled_dataset_size=MarshallSize(); - - /*Allocate marshalled dataset: */ - marshalled_dataset=(char*)xmalloc(marshalled_dataset_size*sizeof(char)); - - /*Keep track of old_marshalled_dataset: */ - old_marshalled_dataset=marshalled_dataset; - - /*Store internals of dataset first: */ - memcpy(marshalled_dataset,&object_size,sizeof(int)); marshalled_dataset+=sizeof(int); - memcpy(marshalled_dataset,&sorted,sizeof(int)); marshalled_dataset+=sizeof(int); - if(sorted){ - if(object_size)memcpy(marshalled_dataset,sorted_ids,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); - if(object_size)memcpy(marshalled_dataset,id_offsets,object_size*sizeof(int)); marshalled_dataset+=object_size*sizeof(int); - } - - for ( object=objects.begin() ; object < objects.end(); object++ ){ - (*object)->Marshall(&marshalled_dataset); - } - - /* Ok, marshalled_dataset now points to the end of the original marshalled_dataset pointer - * before we started the loop on objects. Get object to point right again: */ - marshalled_dataset-=marshalled_dataset_size; - - /*We should be back to old_marshalled_dataset: check and abort if that's not the case, - * because this is a nasty error: */ - if (marshalled_dataset!=old_marshalled_dataset){ - _error_("final marshalled dataset \"%s\" is different from initial one!",EnumToStringx(enum_type)); - abort(); - } - - /*Return: */ - return marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DataSet::MarshallSize{{{1*/ -int DataSet::MarshallSize(){ - - vector::iterator object; - int marshalled_dataset_size=0; - - - for ( object=objects.begin() ; object < objects.end(); object++ ){ - marshalled_dataset_size+= (*object)->MarshallSize(); - } - - marshalled_dataset_size+=sizeof(int); //objects size - marshalled_dataset_size+=sizeof(int); //sorted size - if(sorted){ - marshalled_dataset_size+=(int)objects.size()*sizeof(int); //sorted ids - marshalled_dataset_size+=(int)objects.size()*sizeof(int); //id offsets - } - - return marshalled_dataset_size; -} -/*}}}*/ -/*FUNCTION DataSet::Demarshall{{{1*/ -DataSet* DataSetDemarshall(char* marshalled_dataset){ - - return DataSetDemarshallRaw(&marshalled_dataset); - -} -/*}}}*/ -/*FUNCTION DataSet::DemarshallRaw{{{1*/ -DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset){ - - int i; - - DataSet* dataset=NULL; - int numobjects=0; - int enum_type; - Object* object=NULL; - int sorted; - int* sorted_ids=NULL; - int* id_offsets=NULL; - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset pointer: */ - marshalled_dataset=*pmarshalled_dataset; - - /*initialize dataset: */ - dataset=new DataSet(); - - /*Get internals first: */ - memcpy(&numobjects,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - memcpy(&sorted,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(sorted){ - if(numobjects){ - sorted_ids=(int*)xmalloc(numobjects*sizeof(int)); - id_offsets=(int*)xmalloc(numobjects*sizeof(int)); - memcpy(sorted_ids,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); - memcpy(id_offsets,marshalled_dataset,numobjects*sizeof(int)); marshalled_dataset+=numobjects*sizeof(int); - } - dataset->SetSorting(sorted_ids,id_offsets); - } - - for(i=0;iDemarshall(&marshalled_dataset); - dataset->AddObject(node);} - break; - case VertexEnum:{ - Vertex* vertex=NULL; - vertex=new Vertex(); - vertex->Demarshall(&marshalled_dataset); - dataset->AddObject(vertex);} - break; - case DoubleParamEnum:{ - DoubleParam* doubleparam=NULL; - doubleparam=new DoubleParam(); - doubleparam->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleparam);} - break; - case TriaEnum:{ - Tria* tria=NULL; - tria=new Tria(); - tria->Demarshall(&marshalled_dataset); - dataset->AddObject(tria);} - break; - case TriaP1InputEnum:{ - TriaP1Input* triavertexinput=NULL; - triavertexinput=new TriaP1Input(); - triavertexinput->Demarshall(&marshalled_dataset); - dataset->AddObject(triavertexinput);} - break; - #ifdef _HAVE_3D_ - case PentaP1InputEnum:{ - PentaP1Input* pentavertexinput=NULL; - pentavertexinput=new PentaP1Input(); - pentavertexinput->Demarshall(&marshalled_dataset); - dataset->AddObject(pentavertexinput);} - break; - #endif - case TransientInputEnum:{ - TransientInput* transientinput=NULL; - transientinput=new TransientInput(); - transientinput->Demarshall(&marshalled_dataset); - dataset->AddObject(transientinput);} - break; - #ifdef _HAVE_CONTROL_ - case ControlInputEnum:{ - ControlInput* controlinputinput=NULL; - controlinputinput=new ControlInput(); - controlinputinput->Demarshall(&marshalled_dataset); - dataset->AddObject(controlinputinput);} - break; - #endif - case DatasetInputEnum:{ - DatasetInput* datasetinputinput=NULL; - datasetinputinput=new DatasetInput(); - datasetinputinput->Demarshall(&marshalled_dataset); - dataset->AddObject(datasetinputinput);} - break; - case TriaP1ElementResultEnum:{ - TriaP1ElementResult* triavertexelementresult=NULL; - triavertexelementresult=new TriaP1ElementResult(); - triavertexelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(triavertexelementresult);} - break; - #ifdef _HAVE_3D_ - case PentaP1ElementResultEnum:{ - PentaP1ElementResult* pentavertexelementresult=NULL; - pentavertexelementresult=new PentaP1ElementResult(); - pentavertexelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(pentavertexelementresult);} - break; - case PentaEnum:{ - Penta* penta=NULL; - penta=new Penta(); - penta->Demarshall(&marshalled_dataset); - dataset->AddObject(penta);} - break; - #endif - case MaticeEnum:{ - Matice* matice=NULL; - matice=new Matice(); - matice->Demarshall(&marshalled_dataset); - dataset->AddObject(matice);} - break; - case MatparEnum:{ - Matpar* matpar=NULL; - matpar=new Matpar(); - matpar->Demarshall(&marshalled_dataset); - dataset->AddObject(matpar);} - break; - case SpcStaticEnum:{ - SpcStatic* spcstatic=NULL; - spcstatic=new SpcStatic(); - spcstatic->Demarshall(&marshalled_dataset); - dataset->AddObject(spcstatic);} - break; - case SpcDynamicEnum:{ - SpcDynamic* spcdynamic=NULL; - spcdynamic=new SpcDynamic(); - spcdynamic->Demarshall(&marshalled_dataset); - dataset->AddObject(spcdynamic);} - break; - case SpcTransientEnum:{ - SpcTransient* spctransient=NULL; - spctransient=new SpcTransient(); - spctransient->Demarshall(&marshalled_dataset); - dataset->AddObject(spctransient);} - break; - case PengridEnum:{ - Pengrid* pengrid=NULL; - pengrid=new Pengrid(); - pengrid->Demarshall(&marshalled_dataset); - dataset->AddObject(pengrid);} - break; - case PenpairEnum:{ - Penpair* penpair=NULL; - penpair=new Penpair(); - penpair->Demarshall(&marshalled_dataset); - dataset->AddObject(penpair);} - break; - case IcefrontEnum:{ - Icefront* icefront=NULL; - icefront=new Icefront(); - icefront->Demarshall(&marshalled_dataset); - dataset->AddObject(icefront);} - break; - case NumericalfluxEnum:{ - Numericalflux* numericalflux=NULL; - numericalflux=new Numericalflux(); - numericalflux->Demarshall(&marshalled_dataset); - dataset->AddObject(numericalflux);} - break; - #ifdef _HAVE_RIFTS_ - case RiftfrontEnum:{ - Riftfront* riftfront=NULL; - riftfront=new Riftfront(); - riftfront->Demarshall(&marshalled_dataset); - dataset->AddObject(riftfront);} - break; - #endif - case DoubleInputEnum:{ - DoubleInput* doubleinput=NULL; - doubleinput=new DoubleInput(); - doubleinput->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleinput);} - break; - case IntInputEnum:{ - IntInput* intinput=NULL; - intinput=new IntInput(); - intinput->Demarshall(&marshalled_dataset); - dataset->AddObject(intinput);} - break; - case BoolInputEnum:{ - BoolInput* boolinput=NULL; - boolinput=new BoolInput(); - boolinput->Demarshall(&marshalled_dataset); - dataset->AddObject(boolinput);} - break; - case IntParamEnum:{ - IntParam* intparam=NULL; - intparam=new IntParam(); - intparam->Demarshall(&marshalled_dataset); - dataset->AddObject(intparam);} - break; - case BoolParamEnum:{ - BoolParam* boolparam=NULL; - boolparam=new BoolParam(); - boolparam->Demarshall(&marshalled_dataset); - dataset->AddObject(boolparam);} - break; - case StringParamEnum:{ - StringParam* stringparam=NULL; - stringparam=new StringParam(); - stringparam->Demarshall(&marshalled_dataset); - dataset->AddObject(stringparam);} - break; - case DoubleVecExternalResultEnum:{ - DoubleVecExternalResult* doublevecexternalresult=NULL; - doublevecexternalresult=new DoubleVecExternalResult(); - doublevecexternalresult->Demarshall(&marshalled_dataset); - dataset->AddObject(doublevecexternalresult);} - break; - case DoubleExternalResultEnum:{ - DoubleExternalResult* doubleexternalresult=NULL; - doubleexternalresult=new DoubleExternalResult(); - doubleexternalresult->Demarshall(&marshalled_dataset); - dataset->AddObject(doubleexternalresult);} - break; - #ifdef _HAVE_GROUNDINGLINE_ - case BoolElementResultEnum:{ - BoolElementResult* boolelementresult=NULL; - boolelementresult=new BoolElementResult(); - boolelementresult->Demarshall(&marshalled_dataset); - dataset->AddObject(boolelementresult);} - break; - #endif - default: - _error_("could not recognize enum type: %s",EnumToStringx(enum_type)); - } - } - - /*Assign output pointers:*/ - *pmarshalled_dataset=marshalled_dataset; - - return dataset; -} -/*}}}*/ -#endif - /*Specific methods*/ /*FUNCTION DataSet::AddObject{{{1*/ Index: /issm/trunk/src/c/Container/DataSet.h =================================================================== --- /issm/trunk/src/c/Container/DataSet.h (revision 12329) +++ /issm/trunk/src/c/Container/DataSet.h (revision 12330) @@ -49,8 +49,4 @@ void Echo(); void DeepEcho(); - #ifdef _SERIAL_ - char* Marshall(); - int MarshallSize(); - #endif int AddObject(Object* object); int DeleteObject(int id); @@ -69,11 +65,3 @@ }; -/*This routine cannot be object oriented, but need for demarshalling: */ -#ifdef _SERIAL_ -DataSet* DataSetDemarshall(char* marshalled_dataset); -DataSet* DataSetDemarshallRaw(char** pmarshalled_dataset); #endif - - - -#endif Index: /issm/trunk/src/c/Container/Elements.cpp =================================================================== --- /issm/trunk/src/c/Container/Elements.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Elements.cpp (revision 12330) @@ -124,6 +124,6 @@ } - #ifdef _PARALLEL_ /*Synchronize across cluster, so as to not end up with different sizes for each patch on each cpu: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&numvertices,&max_numvertices,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&max_numvertices,1,MPI_INT,0,MPI_COMM_WORLD); @@ -193,7 +193,11 @@ /*Get rank of first cpu that has results*/ + #ifdef _HAVE_MPI_ if(this->Size()) rank=my_rank; else rank=num_procs; MPI_Allreduce (&rank,&minrank,1,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + minrank=my_rank; + #endif /*see what the first element of this partition has in stock (this is common to all partitions)*/ @@ -203,8 +207,11 @@ element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numberofresults,1,MPI_DOUBLE,minrank,MPI_COMM_WORLD); + #endif /*Get out if there is no results. Otherwise broadcast info*/ if(!numberofresults) return; + #ifdef _HAVE_MPI_ if(my_rank!=minrank){ resultsenums=(int*)xmalloc(numberofresults*sizeof(int)); @@ -217,4 +224,5 @@ MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,minrank,MPI_COMM_WORLD); MPI_Bcast(resultssteps,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); + #endif /*Loop over all results and get nodal vector*/ @@ -250,7 +258,5 @@ /*Gather onto master cpu 0, if needed: */ -#ifdef _PARALLEL_ if(io_gather)patch->Gather(); -#endif /*create result object and add to results dataset:*/ @@ -276,9 +282,9 @@ int numberofelements; - #ifdef _PARALLEL_ local_nelem=this->Size(); + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&local_nelem,(void*)&numberofelements,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); #else - numberofelements=this->Size(); + numberofelements=local_nelem; #endif Index: /issm/trunk/src/c/Container/Loads.cpp =================================================================== --- /issm/trunk/src/c/Container/Loads.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Loads.cpp (revision 12330) @@ -63,5 +63,5 @@ /*figure out total number of loads combining all the cpus (no clones here)*/ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce(&localloads,&numberofloads,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&numberofloads,1,MPI_INT,0,MPI_COMM_WORLD); @@ -69,4 +69,5 @@ numberofloads=localloads; #endif + return numberofloads; Index: /issm/trunk/src/c/Container/Nodes.cpp =================================================================== --- /issm/trunk/src/c/Container/Nodes.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Nodes.cpp (revision 12330) @@ -83,8 +83,12 @@ * 0. This means the dofs between all the cpus are not unique. We now offset the dofs of eache * cpus by the total last dofs of the previus cpu, starting from 0. - * First: bet number of dofs for each cpu*/ + * First: get number of dofs for each cpu*/ alldofcount=(int*)xmalloc(num_procs*sizeof(int)); + #ifdef _HAVE_MPI_ MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else + alldofcount[0]=dofcount; + #endif /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ @@ -119,5 +123,10 @@ } } - MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + + #ifdef _HAVE_MPI_ + MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;iNumberOfNodes(analysis_type); @@ -162,5 +170,9 @@ * dealt with by another cpu. We take the minimum because we are going to manage dof assignment in increasing * order of cpu rank. This is also why we initialized this array to num_procs.*/ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)ranks,(void*)minranks,numnodes,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include + +#include "./DataSet.h" +#include "./Observations.h" +#include "../shared/shared.h" +#include "../include/include.h" +#include "../EnumDefinitions/EnumDefinitions.h" + +using namespace std; +/*}}}*/ + +/*Object constructors and destructor*/ +/*FUNCTION Observations::Observations(){{{*/ +Observations::Observations(){ + this->quadtree = NULL; + return; +} +/*}}}*/ +/*FUNCTION Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){{{*/ +Observations::Observations(double* observations_list,double* x,double* y,int n,Options* options){ + + /*Intermediaries*/ + int i,j,maxdepth,level,counter,index; + int xi,yi; + double xmin,xmax,ymin,ymax; + double offset,minlength,minspacing,mintrimming,maxtrimming; + int *indices = NULL; + Observation *observation = NULL; + + /*Get extrema*/ + xmin=x[0]; ymin=y[0]; + xmax=x[0]; ymax=y[0]; + for(i=1;iGet(&mintrimming,"mintrimming",-1.e+21); + options->Get(&maxtrimming,"maxtrimming",+1.e+21); + options->Get(&minspacing,"minspacing",0.01); + if(minspacing<=0) _error_("minspacing must > 0"); + + /*Get Minimum box size*/ + if(options->GetOption("boxlength")){ + options->Get(&minlength,"boxlength"); + if(minlength<=0)_error_("boxlength should be a positive number"); + maxdepth=int(log(max(xmax-xmin,ymax-ymin)/minlength +1)/log(2.0)); + } + else{ + maxdepth = 30; + minlength=max(xmax-xmin,ymax-ymin)/double((1L<quadtree = new Quadtree(xmin,xmax,ymin,ymax,maxdepth); + + /*Add observations one by one*/ + counter = 0; + for(i=0;imaxtrimming) continue; + if(observations_list[i]quadtree->ClosestObs(&index,x[i],y[i]); + if(index>=0){ + observation=(Observation*)this->GetObjectByOffset(index); + if(pow(observation->x-x[i],2)+pow(observation->y-y[i],2) < minspacing) continue; + } + + this->quadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth2(&level,xi,yi); + if((int)level <= maxdepth){ + observation = new Observation(x[i],y[i],xi,yi,counter++,observations_list[i]); + this->quadtree->Add(observation); + this->AddObject(observation); + } + else{ + /*We need to average with the current observations*/ + this->quadtree->AddAndAverage(x[i],y[i],observations_list[i]); + } + } + printf("done\n"); + printf("Initial number of observations: %i\n",n); + printf(" Final number of observations: %i\n",this->quadtree->NbObs); +} +/*}}}*/ +/*FUNCTION Observations::~Observations(){{{*/ +Observations::~Observations(){ + delete quadtree; + return; +} +/*}}}*/ + +/*Methods*/ +/*FUNCTION Observations::ObservationList{{{*/ +void Observations::ObservationList(double **px,double **py,double **pobs,int* pnobs,double x_interp,double y_interp,double radius,int maxdata){ + + /*Output and Intermediaries*/ + bool stop; + int nobs,tempnobs,i,j,k,n,counter; + double h2,radius2; + int *indices = NULL; + int *tempindices = NULL; + double *dists = NULL; + double *x = NULL; + double *y = NULL; + double *obs = NULL; + Observation *observation = NULL; + + /*Compute radius square*/ + if(radius==0) radius=this->quadtree->root->length; + radius2 = radius*radius; + + /*Find all observations that are in radius*/ + this->quadtree->RangeSearch(&tempindices,&tempnobs,x_interp,y_interp,radius); + if(tempnobs){ + indices = (int*)xmalloc(tempnobs*sizeof(int)); + dists = (double*)xmalloc(tempnobs*sizeof(double)); + } + nobs = 0; + for (i=0;iGetObjectByOffset(tempindices[i]); + h2 = (observation->x-x_interp)*(observation->x-x_interp) + (observation->y-y_interp)*(observation->y-y_interp); + + if(nobs==maxdata && h2>radius2) continue; + if(nobs<=maxdata){ + indices[nobs] = tempindices[i]; + dists[nobs] = h2; + nobs++; + } + if(nobs==1) continue; + + /*Sort all dists up to now*/ + n=nobs-1; + stop = false; + for(k=0;kGetObjectByOffset(indices[i]); + observation->WriteXYObs(&x[i],&y[i],&obs[i]); + } + } + + /*Assign output pointer*/ + xfree((void**)&indices); + *px=x; + *py=y; + *pobs=obs; + *pnobs=nobs; +}/*}}}*/ +/*FUNCTION Observations::QuadtreeColoring{{{*/ +void Observations::QuadtreeColoring(double* A,double *x,double *y,int n){ + + int xi,yi,level; + + for(int i=0;iquadtree->IntergerCoordinates(&xi,&yi,x[i],y[i]); + this->quadtree->QuadtreeDepth(&level,xi,yi); + A[i]=(double)level; + } + +}/*}}}*/ +/*FUNCTION Observations::Variomap{{{*/ +void Observations::Variomap(double* gamma,double *x,int n){ + + /*Output and Intermediaries*/ + int i,j,k; + double distance; + Observation *observation1 = NULL; + Observation *observation2 = NULL; + + int *counter= (int*)xmalloc(n*sizeof(int)); + for(j=0;jSize();i++){ + observation1=(Observation*)this->GetObjectByOffset(i); + + for(j=i+1;jSize();j++){ + observation2=(Observation*)this->GetObjectByOffset(j); + + distance=sqrt(pow(observation1->x - observation2->x,2.) + pow(observation1->y - observation2->y,2.)); + if(distance>x[n-1]) continue; + + int index = int(distance/(x[1]-x[0])); + if(index>n-1) index = n-1; + if(index<0) index = 0; + + gamma[index] += 1./2.*pow(observation1->value - observation2->value,2.); + counter[index] += 1; + } + } + + /*Normalize semivariogram*/ + gamma[0]=0; + for(k=0;k #include +#include #include "./DataSet.h" @@ -20,7 +21,5 @@ #include "../shared/shared.h" #include "../EnumDefinitions/EnumDefinitions.h" -#if _SERIAL_ #include "../io/io.h" -#endif /*}}}*/ @@ -31,30 +30,4 @@ } /*}}}*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION Options::Options(int istart, int nrhs, const mxArray* prhs[]){{{1*/ -Options::Options(int istart, int nrhs, const mxArray* prhs[]){ - - int i; - char *name = NULL; - Option *option = NULL; - - /*loop over each name and value*/ - for (i=istart; iAddOption(option); - option=NULL; - } - - /*echo the dataset */ - //if (this->Size()) for(i=0;iSize();i++) ((Option*)this->GetObjectByOffset(i))->Echo(); -} -/*}}}*/ -#endif /*FUNCTION Options::~Options(){{{1*/ Options::~Options(){ @@ -93,4 +66,42 @@ return 1; +} +/*}}}*/ +/*FUNCTION Options::Get(int* pvalue, char* name){{{1*/ +void Options::Get(int* pvalue,const char* name){ + + vector::iterator object; + Option* option=NULL; + + /*Get option*/ + option=GetOption(name); + + /*If the pointer is not NULL, the option has been found*/ + if(option){ + option->Get(pvalue); + } + /*Else, the Option does not exist, no default provided*/ + else{ + _error_("option of name \"%s\" not found, and no default value has been provided",name); + } +} +/*}}}*/ +/*FUNCTION Options::Get(int* pvalue, char* name,int default_value){{{1*/ +void Options::Get(int* pvalue,const char* name,int default_value){ + + vector::iterator object; + Option* option=NULL; + + /*Get option*/ + option=GetOption(name); + + /*If the pointer is not NULL, the option has been found*/ + if(option){ + option->Get(pvalue); + } + /*Else, the Option does not exist, a default is provided here*/ + else{ + *pvalue=default_value; + } } /*}}}*/ Index: /issm/trunk/src/c/Container/Options.h =================================================================== --- /issm/trunk/src/c/Container/Options.h (revision 12329) +++ /issm/trunk/src/c/Container/Options.h (revision 12330) @@ -15,7 +15,4 @@ /*constructors, destructors*/ Options(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - Options(int istart, int nrhs, const mxArray* prhs[]); - #endif ~Options(); @@ -25,4 +22,6 @@ void Get(double* pvalue,const char* name); void Get(double* pvalue,const char* name,double default_value); + void Get(int* pvalue,const char* name); + void Get(int* pvalue,const char* name,int default_value); void Get(bool* pvalue,const char* name); void Get(bool* pvalue,const char* name,bool default_value); Index: /issm/trunk/src/c/Container/Parameters.h =================================================================== --- /issm/trunk/src/c/Container/Parameters.h (revision 12329) +++ /issm/trunk/src/c/Container/Parameters.h (revision 12330) @@ -5,4 +5,5 @@ #ifndef _CONTAINER_PARAMETERS_H_ #define _CONTAINER_PARAMETERS_H_ +#include /*forward declarations */ Index: /issm/trunk/src/c/Container/Results.cpp =================================================================== --- /issm/trunk/src/c/Container/Results.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Results.cpp (revision 12330) @@ -65,88 +65,4 @@ /*}}}*/ /*FUNCTION Results::Write{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Results::Write(mxArray** pdataref){ - - int i,j; - int count; - - /*output: */ - mxArray* dataref=NULL; - mxArray* processeddataref=NULL; - mwSize nfields; - mwSize maxfields; - mwSize nsteps; - mwSize step; - const char **fnames = NULL; - int *enums = NULL; - int baseenum; - mwSize onebyone[2] = {1,1}; - mwSize ndim = 2; - - /*How many time steps do we have? : */ - nsteps=0; - for(i=0;iSize();i++){ - ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); - step=result->GetStep(); - if(step>nsteps)nsteps=step; - } - onebyone[0]=nsteps; - - /*How many field names do we have. First, figure out how many result types we have: */ - maxfields=(mwSize)this->Size(); - enums=(int*)xmalloc(maxfields*sizeof(int)); - for(i=0;iGetObjectByOffset(i); - enums[i]=result->InstanceEnum(); - } - /*Now, make result types unique: */ - for(i=0;i=0){//if <0, it means this enum was found to replicate another one previously - baseenum=enums[i]; - /*is the baseenum repeated later on?:*/ - for(j=i+1;j0)nfields++; - - /*Add 2 fields for time and step: */ - nfields=nfields+2; - - /*Fill the names of the structure field: */ - fnames=(const char**)xmalloc(nfields*sizeof(char*)); - count=0; - for(i=0;i0){ - fnames[count]=EnumToStringx(enums[i]); - count++; - } - } - /*don't forget the extra fields "time" and "step":*/ - fnames[nfields-2]="time"; - fnames[nfields-1]="step"; - - /*Initialize structure: */ - dataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); - - /*Fill each field: */ - for(i=0;iSize();i++){ //do not include the last one used for time - ExternalResult* result=(ExternalResult*)this->GetObjectByOffset(i); - result->SetMatlabField(dataref); - } - - /*Now, process the patch in the dataref structure, by calling MatlabProcessPatch.m - *on the current dataref structure: */ - mexCallMATLAB(1,&processeddataref,1,&dataref, "MatlabProcessPatch"); - - /*Assign output pointers:*/ - *pdataref=processeddataref; -} -#else void Results::Write(Parameters* parameters){ @@ -167,4 +83,3 @@ } -#endif /*}}}*/ Index: /issm/trunk/src/c/Container/Results.h =================================================================== --- /issm/trunk/src/c/Container/Results.h (revision 12329) +++ /issm/trunk/src/c/Container/Results.h (revision 12330) @@ -26,9 +26,5 @@ /*numerics: {{{1*/ Results* SpawnTriaResults(int* indices); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void Write(mxArray** pdataref); - #else void Write(Parameters* parameters); - #endif /*}}}*/ }; Index: /issm/trunk/src/c/Container/Vertices.cpp =================================================================== --- /issm/trunk/src/c/Container/Vertices.cpp (revision 12329) +++ /issm/trunk/src/c/Container/Vertices.cpp (revision 12330) @@ -61,6 +61,10 @@ * First: bet number of dofs for each cpu*/ alldofcount=(int*)xmalloc(num_procs*sizeof(int)); + #ifdef _HAVE_MPI_ MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else + alldofcount[0]=dofcount; + #endif /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ @@ -85,5 +89,9 @@ vertex->ShowTrueDofs(truedofs); } + #ifdef _HAVE_MPI_ MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;i put everything in file temp -cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,//g" | awk '{ printf "%s %s\n", NR, $0 }' > temp +#Get all lines of EnumDefinitions2.h which hold Enum | remove all comas > put everything in file temp +cat EnumDefinitions.h | grep -e "[0-9]Enum," -e "[a-zA-Z]Enum," | grep -v include | sed -e "s/,/ /g" | awk '{print $1}' > temp #Removed existing files -rm $ISSM_TIER/src/m/enum/*.m -rm $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp -rm $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp +rm $ISSM_DIR/src/m/enum/*.m +rm $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp +rm $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp #Get number of enums NUMENUMS=$(wc -l temp | awk '{printf("%s",$1);}'); -#Build EnumToStringx.cpp {{{1 +#Build EnumToStringx.cpp {{{ #Header -cat < $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat < $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp /* * \file EnumToStringx.cpp: @@ -35,7 +35,7 @@ END #core -cat temp | awk '{print "\t\t" "case " $2" : return \"" substr($2,1,length($2)-4) "\";"}' >> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat temp | awk '{print "\t\t" "case " $1" : return \"" substr($1,1,length($1)-4) "\";"}' >> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp #Footer -cat <> $ISSM_TIER/src/c/modules/EnumToStringx/EnumToStringx.cpp +cat <> $ISSM_DIR/src/c/modules/EnumToStringx/EnumToStringx.cpp default : return "unknown"; @@ -57,5 +57,5 @@ #Build StringToEnumx.cpp {{{1 #Header -cat < $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp +cat < $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp /* * \file StringToEnumx.cpp: @@ -81,9 +81,9 @@ i2=120; for (( i=1 ; i<=100 ; i++ )); do - echo " if(stage==$i){" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " if(stage==$i){" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp awk -v i1=$i1 -v i2=$i2 '{if(NR>=i1 && NR<=i2) print $0 }' temp | - awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($2,1,length($2)-4) "\")==0) return " $2 ";"}' >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp - echo " else stage=$(($i+1));" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp - echo " }" >> $ISSM_TIER//src/c/modules/StringToEnumx/StringToEnumx.cpp + awk '{print "\t" ((NR==1)?" if":" else if") " (strcmp(name,\"" substr($1,1,length($1)-4) "\")==0) return " $1 ";"}' >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " else stage=$(($i+1));" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp + echo " }" >> $ISSM_DIR//src/c/modules/StringToEnumx/StringToEnumx.cpp if [ $i2 -ge $NUMENUMS ]; then break; fi @@ -93,5 +93,5 @@ #footer -cat <> $ISSM_TIER/src/c/modules/StringToEnumx/StringToEnumx.cpp +cat <> $ISSM_DIR/src/c/modules/StringToEnumx/StringToEnumx.cpp /*If we reach this point, the string provided has not been found*/ _error_("Enum %s not found",name); @@ -101,31 +101,30 @@ # go through the lines of temp -for (( i=1 ; i<=$NUMENUMS ; i++ )); do +ENUM=0; +for NAMEENUM in $(cat temp); do #Get name and enum of the line i - NAMEENUM=$(cat temp | grep "^[ ]*$i " | awk '{printf("%s",$2);}'); NAME=$(echo $NAMEENUM | sed -e "s/Enum//g") - ENUM=$i; #offset Enum by one (Enum begins with 0 and not 1!) - let ENUM=$ENUM-1 + let ENUM=$ENUM+1 #print info {{{ - if [ $i -lt 10 ] + if [ $ENUM -lt 10 ] then printf "\r " - printf "\r $i/$NUMENUMS Adding "$NAME"..." + printf "\r $ENUM/$NUMENUMS Adding "$NAME"..." else - if [ $i -lt 100 ] + if [ $ENUM -lt 100 ] then printf "\r " - printf "\r $i/$NUMENUMS Adding "$NAME"..." + printf "\r $ENUM/$NUMENUMS Adding "$NAME"..." else printf "\r " - printf "\r$i/$NUMENUMS Adding "$NAME"..." + printf "\r$ENUM/$NUMENUMS Adding "$NAME"..." fi fi #}}} #Add case to matlabenum file{{{ - cat < $ISSM_TIER"/src/m/enum/"$(echo $NAMEENUM".m") + cat < $ISSM_DIR"/src/m/enum/"$(echo $NAMEENUM".m") function macro=$(echo $NAMEENUM)() %$(echo $NAMEENUM | awk {'print toupper($1)'}) - Enum of $(echo $NAME) @@ -143,4 +142,21 @@ done +#MaximumNumberOfEnums{{{ +cat < $ISSM_DIR/src/m/enum/MaximumNumberOfEnums.m +function macro=MaximumNumberOfEnums() +%$(echo "MaximumNumberOfEnums" | awk {'print toupper($1)'}) - Enum of MaximumNumberOfEnums +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=MaximumNumberOfEnums() + +macro=$(cat EnumDefinitions.h | grep -e "[0-9]Enum" -e "[a-zA-Z]Enum" | grep -v include \ + | awk '{ printf "%s %s\n", NR-1, $0 }' \ + | grep "MaximumNumberOfEnums" | awk '{print $1}'); +END +#}}} #clean up{{{ Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 12329) +++ /issm/trunk/src/c/Makefile.am (revision 12330) @@ -4,17 +4,13 @@ #Library declaration {{{1 -#Compile serial library, and then try and compile parallel library -if NOSERIAL -if NOPARALLEL -lib_LIBRARIES = -else -lib_LIBRARIES = libpISSM.a libOverload.a -endif -else -if NOPARALLEL -lib_LIBRARIES = libISSM.a libOverload.a -else -lib_LIBRARIES = libISSM.a libpISSM.a libOverload.a -endif +lib_LIBRARIES = libISSMCore.a libISSMOverload.a +if PYTHON +lib_LIBRARIES += libISSMPython.a +endif +if MATLAB +lib_LIBRARIES += libISSMMatlab.a +endif +if MODULES +lib_LIBRARIES += libISSMModules.a endif #}}} @@ -22,5 +18,7 @@ #sources #Core sources{{{1 -core_sources = ./include/macros.h\ +core_sources = ./issm.h\ + ./issm-binding.h\ + ./include/macros.h\ ./include/typedefs.h\ ./include/types.h\ @@ -211,10 +209,4 @@ ./shared/Wrapper/ModuleBoot.cpp\ ./shared/Wrapper/ModuleEnd.cpp\ - ./toolkits/mpi/mpiincludes.h\ - ./toolkits/mpi/patches/mpipatches.h\ - ./toolkits/mpi/patches/DetermineLocalSize.cpp\ - ./toolkits/mpi/patches/MPI_Upperrow.cpp\ - ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ - ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp\ ./toolkits/metis/metisincludes.h\ ./toolkits/issm/issmtoolkit.h\ @@ -223,6 +215,4 @@ ./toolkits/issm/SeqMat.h\ ./toolkits/issm/SeqMat.cpp\ - ./toolkits/metis/patches/metispatches.h\ - ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp\ ./toolkits/triangle/triangleincludes.h\ ./toolkitsenums.h\ @@ -362,14 +352,14 @@ ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ - ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h -dakota_psources= ./modules/Dakotax/SpawnCoreParallel.cpp + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ + ./modules/Dakotax/SpawnCoreParallel.cpp #}}} #Transient sources {{{1 -transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp -transient_psources = ./solutions/transient_core.cpp +transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp \ + ./solutions/transient_core.cpp #}}} #Steadystate sources {{{1 -steadystate_psources = ./solutions/steadystate_core.cpp\ - ./solutions/steadystateconvergence.cpp +steadystate_sources = ./solutions/steadystate_core.cpp\ + ./solutions/steadystateconvergence.cpp #}}} #Prognostic sources {{{1 @@ -377,6 +367,6 @@ ./modules/ModelProcessorx/Prognostic/CreateNodesPrognostic.cpp\ ./modules/ModelProcessorx/Prognostic/CreateConstraintsPrognostic.cpp\ - ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp -prognostic_psources = ./solutions/prognostic_core.cpp + ./modules/ModelProcessorx/Prognostic/CreateLoadsPrognostic.cpp\ + ./solutions/prognostic_core.cpp #}}} #Thermal sources {{{1 @@ -395,9 +385,8 @@ ./modules/ConstraintsStatex/ThermalConstraintsState.cpp\ ./modules/ConstraintsStatex/ThermalIsPresent.cpp\ - ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp - -thermal_psources = ./solutions/thermal_core.cpp\ - ./solutions/enthalpy_core.cpp\ - ./solvers/solver_thermal_nonlinear.cpp + ./modules/ResetConstraintsx/ThermalConstraintsReset.cpp \ + ./solutions/thermal_core.cpp\ + ./solutions/enthalpy_core.cpp\ + ./solvers/solver_thermal_nonlinear.cpp #}}} #Control sources {{{1 @@ -443,8 +432,6 @@ ./objects/Inputs/ControlInput.cpp\ ./shared/Numerics/BrentSearch.cpp\ - ./shared/Numerics/OptimalSearch.cpp\ - ./shared/Numerics/OptFunc.cpp - -control_psources=./solutions/control_core.cpp\ + ./shared/Numerics/OptimalSearch.cpp \ + ./solutions/control_core.cpp\ ./solutions/controltao_core.cpp\ ./solutions/controlrestart.cpp\ @@ -462,8 +449,7 @@ ./modules/ModelProcessorx/Hydrology/CreateNodesHydrology.cpp\ ./modules/ModelProcessorx/Hydrology/CreateConstraintsHydrology.cpp\ - ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp - -hydrology_psources = ./solutions/hydrology_core.cpp\ - ./solutions/hydrology_core_step.cpp + ./modules/ModelProcessorx/Hydrology/CreateLoadsHydrology.cpp \ + ./solutions/hydrology_core.cpp\ + ./solutions/hydrology_core_step.cpp #}}} #Diagnostic sources {{{1 @@ -480,11 +466,11 @@ ./modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp \ ./modules/ModelProcessorx/DiagnosticHutter/CreateLoadsDiagnosticHutter.cpp \ - ./shared/Elements/CoordinateSystemTransform.cpp\ - ./shared/Elements/TransformLoadVectorCoord.cpp \ - ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ - ./shared/Elements/TransformSolutionCoord.cpp -diagnostic_psources =./solutions/diagnostic_core.cpp\ - ./solvers/solver_stokescoupling_nonlinear.cpp + ./shared/Elements/CoordinateSystemTransform.cpp\ + ./shared/Elements/TransformLoadVectorCoord.cpp \ + ./shared/Elements/TransformStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformInvStiffnessMatrixCoord.cpp \ + ./shared/Elements/TransformSolutionCoord.cpp\ + ./solutions/diagnostic_core.cpp\ + ./solvers/solver_stokescoupling_nonlinear.cpp #}}} #Balanced sources {{{1 @@ -492,6 +478,6 @@ ./modules/ModelProcessorx/Balancethickness/CreateNodesBalancethickness.cpp\ ./modules/ModelProcessorx/Balancethickness/CreateConstraintsBalancethickness.cpp\ - ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp -balanced_psources = ./solutions/balancethickness_core.cpp + ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ + ./solutions/balancethickness_core.cpp #}}} #Responses sources {{{1 @@ -533,6 +519,6 @@ ./modules/ModelProcessorx/SurfaceSlope/CreateNodesSurfaceSlope.cpp \ ./modules/ModelProcessorx/SurfaceSlope/CreateConstraintsSurfaceSlope.cpp\ - ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp -slope_psources = ./solutions/surfaceslope_core.cpp\ + ./modules/ModelProcessorx/SurfaceSlope/CreateLoadsSurfaceSlope.cpp\ + ./solutions/surfaceslope_core.cpp\ ./solutions/bedslope_core.cpp #}}} @@ -589,6 +575,6 @@ ./objects/Bamg/Metric.cpp\ ./objects/Bamg/Metric.h\ - ./objects/Bamg/QuadTree.cpp\ - ./objects/Bamg/QuadTree.h\ + ./objects/Bamg/BamgQuadtree.cpp\ + ./objects/Bamg/BamgQuadtree.h\ ./objects/Bamg/R2.h\ ./objects/Bamg/SetOfE4.cpp\ @@ -625,4 +611,24 @@ ./modules/BamgTriangulatex/BamgTriangulatex.cpp\ ./modules/BamgTriangulatex/BamgTriangulatex.h +#}}} +#Kriging sources {{{1 +kriging_sources = ./Container/Observations.h\ + ./Container/Observations.cpp\ + ./objects/Kriging/Variogram.h \ + ./objects/Kriging/GaussianVariogram.h\ + ./objects/Kriging/GaussianVariogram.cpp\ + ./objects/Kriging/ExponentialVariogram.h\ + ./objects/Kriging/ExponentialVariogram.cpp\ + ./objects/Kriging/SphericalVariogram.h\ + ./objects/Kriging/SphericalVariogram.cpp\ + ./objects/Kriging/PowerVariogram.h\ + ./objects/Kriging/PowerVariogram.cpp\ + ./objects/Kriging/Quadtree.h\ + ./objects/Kriging/Quadtree.cpp\ + ./objects/Kriging/Observation.h\ + ./objects/Kriging/Observation.cpp\ + ./modules/Krigingx/Krigingx.cpp\ + ./modules/Krigingx/Krigingx.h + #}}} #Kml sources {{{1 @@ -694,23 +700,4 @@ ./objects/KML/KMLFileReadUtils.h #}}} -#Matlab sources {{{1 -matlab_sources= ./toolkits/matlab/matlabincludes.h\ - ./toolkits/matlab/MatlabNArrayToNArray.cpp\ - ./toolkits/double/MatlabVectorToDoubleVector.cpp\ - ./toolkits/double/double.h\ - ./toolkits/double/MatlabMatrixToDoubleMatrix.cpp\ - ./io/Matlab/matlabio.h\ - ./io/Matlab/CheckNumMatlabArguments.cpp\ - ./io/Matlab/mxGetAssignedField.cpp\ - ./io/Matlab/WriteMatlabData.cpp\ - ./io/Matlab/FetchMatlabData.cpp\ - ./io/Matlab/OptionParse.cpp -#}}} -#Python sources {{{1 -python_sources= ./io/Python/pythonio.h\ - ./io/Python/WritePythonData.cpp\ - ./io/Python/CheckNumPythonArguments.cpp\ - ./io/Python/FetchPythonData.cpp -#}}} #Petsc sources {{{1 petsc_sources= ./toolkits/petsc\ @@ -718,8 +705,4 @@ ./toolkits/petsc/patches/SolverEnum.h\ ./toolkits/petsc/patches/petscpatches.h\ - ./toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp\ - ./toolkits/petsc/patches/MatlabVectorToPetscVector.cpp\ - ./toolkits/petsc/patches/PetscMatrixToMatlabMatrix.cpp\ - ./toolkits/petsc/patches/PetscVectorToMatlabVector.cpp\ ./toolkits/petsc/patches/VecTranspose.cpp\ ./toolkits/petsc/patches/VecToMPISerial.cpp\ @@ -732,4 +715,6 @@ ./toolkits/petsc/patches/SerialToVec.cpp\ ./toolkits/petsc/patches/VecFree.cpp\ + ./toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp\ + ./toolkits/petsc/patches/PetscVectorToDoubleVector.cpp\ ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ ./toolkits/petsc/patches/KSPFree.cpp\ @@ -754,6 +739,48 @@ #}}} -#Serialsources {{{1 -serial_sources= ./objects/Options/Option.cpp\ +#Mpi sources {{{1 +mpi_sources= ./toolkits/mpi/mpiincludes.h\ + ./toolkits/mpi/patches/mpipatches.h\ + ./toolkits/mpi/patches/DetermineLocalSize.cpp\ + ./toolkits/mpi/patches/MPI_Upperrow.cpp\ + ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ + ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp +#}}} +#Metis sources {{{1 +metis_sources= ./toolkits/metis/patches/metispatches.h\ + ./toolkits/metis/patches/METIS_PartMeshNodalPatch.cpp +#}}} +#Python sources {{{1 +python_sources= ./python/io/pythonio.h\ + ./python/python-binding.h\ + ./python/io/WritePythonData.cpp\ + ./python/io/CheckNumPythonArguments.cpp\ + ./python/io/FetchPythonData.cpp + +#}}} +#Matlab sources {{{1 +matlab_sources= ./toolkits/matlab/matlabincludes.h\ + ./matlab/matlab-binding.h\ + ./matlab/io/matlabio.h\ + ./matlab/io/MatlabNArrayToNArray.cpp\ + ./matlab/io/CheckNumMatlabArguments.cpp\ + ./matlab/io/mxGetAssignedField.cpp\ + ./matlab/io/WriteMatlabData.cpp\ + ./matlab/io/FetchMatlabData.cpp\ + ./matlab/io/OptionParse.cpp\ + ./matlab/io/MatlabMatrixToMatrix.cpp\ + ./matlab/io/MatlabVectorToVector.cpp\ + ./matlab/io/MatlabVectorToDoubleVector.cpp\ + ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\ + ./matlab/io/MatlabMatrixToSeqMat.cpp\ + ./matlab/io/MatlabVectorToSeqVec.cpp +#}}} +#Matlab and Petsc sources {{{1 +matlabpetsc_sources= ./matlab/io/MatlabMatrixToPetscMatrix.cpp\ + ./matlab/io/MatlabVectorToPetscVector.cpp + +#}}} +#Modules sources{{{1 +module_sources= ./objects/Options/Option.cpp\ ./objects/Options/Option.h\ ./objects/Options/OptionDouble.cpp\ @@ -769,4 +796,6 @@ ./objects/Options/OptionUtilities.cpp\ ./objects/Options/OptionUtilities.h\ + ./shared/Alloc/alloc_module.h\ + ./shared/Alloc/alloc_module.cpp\ ./shared/Threads/issm_threads.h\ ./shared/Threads/LaunchThread.cpp\ @@ -790,5 +819,4 @@ ./modules/Chacox/chaco_seconds.cpp\ ./modules/Chacox/user_params.cpp\ - ./modules/Dakotax/SpawnCoreSerial.cpp\ ./modules/TriaSearchx/TriaSearchx.h\ ./modules/TriaSearchx/TriaSearchx.cpp\ @@ -841,67 +869,55 @@ #}}} +#{{{1 Conditional build-up of sources #ISSM sources are a combination of core sources and sources related to specific capabilities (which can #be activated by autotools conditionals -#{{{1 + #First the core issm_sources = $(core_sources) -issm_psources = #Now the optional source if DAKOTA issm_sources += $(dakota_sources) -issm_psources += $(dakota_psources) endif if PETSC issm_sources += $(petsc_sources) -issm_psources += $(petsc_psources) endif if GSL issm_sources += $(gsl_sources) -issm_psources += $(gsl_psources) -endif - +endif if TRANSIENT issm_sources += $(transient_sources) -issm_psources += $(transient_psources) endif if STEADYSTATE issm_sources += $(steadystate_sources) -issm_psources += $(steadystate_psources) endif if PROGNOSTIC issm_sources += $(prognostic_sources) -issm_psources += $(prognostic_psources) endif if THERMAL issm_sources += $(thermal_sources) -issm_psources += $(thermal_psources) endif if CONTROL issm_sources += $(control_sources) -issm_psources += $(control_psources) endif if HYDROLOGY issm_sources += $(hydrology_sources) -issm_psources += $(hydrology_psources) endif if DIAGNOSTIC issm_sources += $(diagnostic_sources) -issm_psources += $(diagnostic_psources) endif if BALANCED issm_sources += $(balanced_sources) -issm_psources += $(balanced_psources) endif @@ -912,5 +928,4 @@ if SLOPE issm_sources += $(slope_sources) -issm_psources += $(slope_psources) endif @@ -926,70 +941,82 @@ issm_sources += $(threed_sources) endif -#}}} - -#ISSM serial library {{{1 -if SERIAL -libISSM_a_SOURCES = $(issm_sources) -libISSM_a_SOURCES += $(serial_sources) -libISSM_a_SOURCES += $(bamg_sources) -libISSM_a_SOURCES += $(kml_sources) -libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) -#libISSM_a_CXXFLAGS = -D_SERIAL_ -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER $(CXXFLAGS) $(CXXOPTFLAGS) + +if MPI +issm_sources += $(mpi_sources) +endif + +if METIS +issm_sources += $(metis_sources) +endif + +if PETSC +if MATLAB +issm_sources += $(matlabpetsc_sources) +endif +endif + + +#}}} +#Library flags and sources {{{1 +ALLCXXFLAGS= -fPIC -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) + +libISSMCore_a_SOURCES = $(issm_sources) +libISSMCore_a_CXXFLAGS = $(ALLCXXFLAGS) + +if MODULES +libISSMModules_a_SOURCES = $(module_sources) +libISSMModules_a_SOURCES += $(bamg_sources) +libISSMModules_a_SOURCES += $(kriging_sources) +libISSMModules_a_SOURCES += $(kml_sources) +libISSMModules_a_CXXFLAGS = $(ALLCXXFLAGS) +endif if PYTHON -libISSM_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API -libISSM_a_SOURCES += $(python_sources) +libISSMPython_a_SOURCES = $(python_sources) +libISSMPython_a_CXXFLAGS= $(ALLCXXFLAGS) endif if MATLAB -libISSM_a_SOURCES += $(matlab_sources) -endif - -endif -#}}} -#ISSM parallel library {{{1 -if PARALLEL -libpISSM_a_SOURCES = $(issm_sources) -libpISSM_a_SOURCES += $(issm_psources) -libpISSM_a_CXXFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(CXXFLAGS) $(CXXOPTFLAGS) -endif +libISSMMatlab_a_SOURCES = $(matlab_sources) +libISSMMatlab_a_CXXFLAGS= $(ALLCXXFLAGS) +endif + #}}} #Overload library, to overload any non-standard symbols. {{{1 -libOverload_a_SOURCES = ./shared/String/stricmp.c -libOverload_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) $(CFLAGS) +libISSMOverload_a_SOURCES = ./shared/String/stricmp.c +libISSMOverload_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) $(CFLAGS) #}}} #Executable {{{1 -if NOPARALLEL -bin_PROGRAMS = -else bin_PROGRAMS = issm -endif #Standard libraries -LDADD = ./libpISSM.a ./libOverload.a +LDADD = ./libISSMCore.a ./libISSMOverload.a #External packages -LDADD += $(PETSCLIB) $(TAOLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) +LDADD += $(PETSCLIB) $(TAOLIB) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) + +if FORTRAN +LDADD += $(FLIBS) +endif issm_SOURCES = solutions/issm.cpp -issm_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) +issm_CXXFLAGS= -fPIC $(CXXFLAGS) $(CXXOPTFLAGS) $(COPTFLAGS) #}}} #Automatic differentiation: append this fold to the end of the src/c/Makefile.am to get this Makefile.am {{{ if ADIC2 -lib_LIBRARIES += libAD.a libpISSMRose.a +lib_LIBRARIES += libAD.a libISSMRose.a #ADIC2 library, for automatic differentiation #libAD_a_SOURCES = ./mini1.ad.c libAD_a_SOURCES = -libAD_a_CFLAGS = -fPIC -D_PARALLEL_ -D_C_ $(COPTFLAGS) - +libAD_a_CFLAGS = -fPIC -D_C_ $(COPTFLAGS) #test rose preprocessing %.r2cpp.cpp : %.cpp - testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_PARALLEL_ -D_C_ -I. -I../.. $(INCLUDES) $< -libpISSMRose_a_SOURCES = $(libpISSM_a_SOURCES:.cpp=.r2cpp.cpp) -libpISSMRose_a_CXXFLAGS= -fPIC -D_PARALLEL_ -D_C_ $(CXXOPTFLAGS) + testTranslator -rose:o $@ -rose:skipfinalCompileStep -DHAVE_CONFIG_H -D_C_ -I. -I../.. $(INCLUDES) $< +libISSMRose_a_SOURCES = $(libISSMCore_a_SOURCES:.cpp=.r2cpp.cpp) +libISSMRose_a_CXXFLAGS= -fPIC -D_C_ $(CXXOPTFLAGS) @@ -1003,7 +1030,7 @@ #Executable bin_PROGRAMS += issmRose.exe -issmRose_exe_LDADD = ./libpISSMRose.a $(LDADD) +issmRose_exe_LDADD = ./libISSMRose.a $(LDADD) issmRose_exe_SOURCES = solutions/issm.cpp -issmRose_exe_CXXFLAGS= -fPIC -D_PARALLEL_ $(CXXOPTFLAGS) $(COPTFLAGS) +issmRose_exe_CXXFLAGS= -fPIC $(CXXOPTFLAGS) $(COPTFLAGS) LDADD += $(ADIC2LIB) Index: /issm/trunk/src/c/include/macros.h =================================================================== --- /issm/trunk/src/c/include/macros.h (revision 12329) +++ /issm/trunk/src/c/include/macros.h (revision 12330) @@ -40,39 +40,14 @@ #endif /*}}}*/ - -/* MODULEBOOT/MODULEEND {{{1*/ +/* ISSMBOOT/ISSMEND {{{1*/ /*The following macros hide the error exception handling in a matlab module. Just put - * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * ISSMBOOT(); and ISSMEND(); at the beginning and end of a module, and c++ exceptions * will be trapped. Really nifty!*/ -#ifdef _SERIAL_ -#ifdef _HAVE_MATLAB_ //{{{2 -#define MODULEBOOT(); ModuleBoot(); \ +#define ISSMBOOT(); \ try{ -#define MODULEEND(); ModuleEnd(); }\ - catch(ErrorException &exception){\ - exception.Report(); \ - mexErrMsgTxt(""); \ - }\ - catch (exception& e) {\ - _printf_(true,"Standard exception: %s\n",e.what());\ - mexErrMsgTxt(" ");\ - } -#endif //}}} -#ifdef _HAVE_PYTHON_ //{{{2 -#define MODULEBOOT(); ModuleBoot(); \ - PyObject* output = PyTuple_New(NLHS); if (!output) return NULL; - -#define MODULEEND(); ModuleEnd(); \ - return output; -#endif //}}} -#else -//{{{2 -#define MODULEBOOT(); \ - try{ - -#define MODULEEND(); }\ +#define ISSMEND(); }\ catch(ErrorException &exception){\ exception.Report(); \ @@ -82,50 +57,9 @@ _printf_(true,"Standard exception: %s\n",e.what());\ return 1;\ + }\ + catch(...){\ + _printf_(true,"An unexpected error occurred");\ } -//}}} -#endif /*}}}*/ -/* WRAPPER {{{1*/ -#ifdef _HAVE_MATLAB_ -#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) -#endif -#ifdef _HAVE_PYTHON_ -#define WRAPPER(modulename,...) \ -\ -static PyObject* modulename(PyObject* self,PyObject* args);\ -static PyMethodDef modulename##_funcs[] = {\ - {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ - {NULL,NULL,0,NULL}\ -};\ -\ -static struct PyModuleDef modulename##module= {\ - PyModuleDef_HEAD_INIT,\ - #modulename, /* name of module */\ - NULL, /* module documentation, may be NULL */\ - -1, /* size of per-interpreter state of the module,\ - or -1 if the module keeps state in global variables. */\ - modulename##_funcs\ -};\ -\ -PyMODINIT_FUNC PyInit_##modulename(void){\ -\ - import_array();\ - return PyModule_Create(&modulename##module);\ -}\ -\ -static PyObject* modulename(PyObject* self,PyObject* args) #endif - -/*}}}*/ -/* CHECKARGUMENTS {{{1*/ -#ifdef _HAVE_MATLAB_ -#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) -#endif -#ifdef _HAVE_PYTHON_ -#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) -#endif -/*}}}*/ - - -#endif Index: /issm/trunk/src/c/include/types.h =================================================================== --- /issm/trunk/src/c/include/types.h (revision 12329) +++ /issm/trunk/src/c/include/types.h (revision 12330) @@ -16,12 +16,4 @@ /*Define abstract type for I/O: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -typedef const mxArray* ConstDataHandle; //serially, we are reading data from a matlab array. -typedef mxArray* DataHandle; -#else -typedef FILE* ConstDataHandle; //in parallel, we are reading data from a file. -typedef FILE* DataHandle; -#endif enum param_type { STRING, INTEGER, STRINGARRAY, DOUBLE, DOUBLEVEC, DOUBLEMAT, PETSCVEC, PETSCMAT }; @@ -35,5 +27,10 @@ #endif -typedef double IssmDouble; +#ifdef _HAVE_ADOLC_ +typedef adouble IssmDouble; +#else +typedef double IssmDouble; +#endif + typedef bool IssmBool; Index: /issm/trunk/src/c/io/PrintfFunction.cpp =================================================================== --- /issm/trunk/src/c/io/PrintfFunction.cpp (revision 12329) +++ /issm/trunk/src/c/io/PrintfFunction.cpp (revision 12330) @@ -8,8 +8,4 @@ #include "../shared/shared.h" #include "../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif int PrintfFunction(const char* format,...){ @@ -53,9 +49,5 @@ /*Ok, if we are running in parallel, get node 0 to print*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mexPrintf(buffer); -#else if(my_rank==0)printf(buffer); -#endif /*Clean up and return*/ Index: /issm/trunk/src/c/io/io.h =================================================================== --- /issm/trunk/src/c/io/io.h (revision 12329) +++ /issm/trunk/src/c/io/io.h (revision 12330) @@ -15,12 +15,4 @@ #include "./Disk/diskio.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "./Matlab/matlabio.h" -#endif - -#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) -#include "./Python/pythonio.h" -#endif - /*printf: */ int PrintfFunction(const char* format,...); Index: /issm/trunk/src/c/issm-binding.h =================================================================== --- /issm/trunk/src/c/issm-binding.h (revision 12330) +++ /issm/trunk/src/c/issm-binding.h (revision 12330) @@ -0,0 +1,18 @@ +#ifndef _ISSM_BINDING_H_ +#define _ISSM_BINDING_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#ifdef _HAVE_MATLAB_MODULES_ +#include "./matlab/matlab-binding.h" +#endif + +#ifdef _HAVE_PYTHON_MODULES_ +#include "./python/python-binding.h" +#endif + +#endif Index: /issm/trunk/src/c/matlab/include/matlab_macros.h =================================================================== --- /issm/trunk/src/c/matlab/include/matlab_macros.h (revision 12330) +++ /issm/trunk/src/c/matlab/include/matlab_macros.h (revision 12330) @@ -0,0 +1,47 @@ +/* \file matlab macros.h + * \brief: macros used for the matlab bindings + */ + +/*Header {{{1*/ +#ifndef _MATLAB_MACROS_H_ +#define _MATLAB_MACROS_H_ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +/*}}}*/ + +#ifdef _HAVE_MATLAB_ +/* MODULEBOOT/MODULEEND {{{1*/ + +/*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ +//exception.Report(); + +#define MODULEBOOT(); ModuleBoot(); \ + try{ + +#define MODULEEND(); ModuleEnd(); }\ + catch(ErrorException &exception){\ + mexErrMsgTxt("ISSM Error"); \ + }\ + catch (exception &e){\ + mexErrMsgTxt(exprintf("Standard exception: %s\n",e.what()));\ + }\ + catch(...){\ + mexErrMsgTxt("An unexpected error occurred");\ + } +//}}} +/* WRAPPER {{{1*/ +#define WRAPPER(modulename,...) void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) + +/*}}}*/ +/* CHECKARGUMENTS {{{1*/ +#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,functionpointer) +/*}}}*/ +#endif + +#endif Index: /issm/trunk/src/c/matlab/io/CheckNumMatlabArguments.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/CheckNumMatlabArguments.cpp (revision 12330) @@ -0,0 +1,31 @@ +/*!\file CheckNumMatlabArguments.cpp: + * \brief: check number of arguments and report an usage error message. + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "../../shared/Exceptions/exceptions.h" +#include "../../include/include.h" +#include "mex.h" + +int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* __FUNCT__, void (*function)( void )){ + + /*checks on arguments on the matlab side: */ + if (nrhs==0 && nlhs==0) { + /*unless NLHS=0 and NRHS=0, we are just asking for documentation: */ + if (NRHS==0 && NLHS==0)return 1; + /* special case: */ + function(); + _error_("usage: see above"); + } + else if (nlhs!=NLHS || nrhs!=NRHS ) { + function(); + _error_("usage error."); + } + return 1; +} Index: /issm/trunk/src/c/matlab/io/FetchMatlabData.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/FetchMatlabData.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/FetchMatlabData.cpp (revision 12330) @@ -0,0 +1,628 @@ +/*\file FetchData.cpp: + * \brief: general I/O interface to fetch data in matlab + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "./matlabio.h" + +/*Primitive data types*/ +/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ +void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){ + + double* outmatrix=NULL; + int outmatrix_rows,outmatrix_cols; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else if(mxIsClass(dataref,"double") || mxIsClass(dataref,"single")){ + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else{ + /*Convert matlab matrix to double* matrix: */ + MatlabMatrixToDoubleMatrix(&outmatrix,&outmatrix_rows,&outmatrix_cols,dataref); + } + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pmatrix=outmatrix; + if (pM)*pM=outmatrix_rows; + if (pN)*pN=outmatrix_cols; + +} +/*}}}*/ +/*FUNCTION FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){{{1*/ +void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref){ + + double* outmatrix=NULL; + int outmatrix_numel,outmatrix_ndims; + int* outmatrix_size=NULL; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_numel=0; + outmatrix_ndims=0; + outmatrix_size =NULL; + outmatrix=NULL; + } + else if (mxIsClass(dataref,"double") ){ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetNumberOfElements(dataref)==1) ){ + outmatrix_numel=0; + outmatrix_ndims=0; + outmatrix_size =NULL; + outmatrix=NULL; + } + else{ + + /*Convert matlab n-dim array to double* matrix: */ + MatlabNArrayToNArray(&outmatrix,&outmatrix_numel,&outmatrix_ndims,&outmatrix_size,dataref); + } + } + else{ + /*This is an error: we don't have the correct input!: */ + _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref)); + } + + /*Assign output pointers:*/ + *pmatrix=outmatrix; + if (pnumel)*pnumel=outmatrix_numel; + if (pndims)*pndims=outmatrix_ndims; + if (psize )*psize =outmatrix_size; + else xfree((void**)&outmatrix_size); + +} +/*}}}*/ +/*FUNCTION FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/ +void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref){ + + int i,outmatrix_rows,outmatrix_cols; + double *doublematrix=NULL; + int *outmatrix=NULL; + + if(mxIsEmpty(dataref) ){ + /*Nothing to pick up. Just initialize matrix pointer to NULL: */ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else if (mxIsClass(dataref,"double") ){ + + /*Check dataref is not pointing to NaN: */ + if ( mxIsNaN(*(mxGetPr(dataref))) && (mxGetM(dataref)==1) && (mxGetN(dataref)==1) ){ + outmatrix_rows=0; + outmatrix_cols=0; + outmatrix=NULL; + } + else{ + + /*Convert matlab matrix to double* matrix: */ + MatlabMatrixToDoubleMatrix(&doublematrix,&outmatrix_rows,&outmatrix_cols,dataref); + + /*Convert double matrix into integer matrix: */ + outmatrix=(int*)xmalloc(outmatrix_rows*outmatrix_cols*sizeof(int)); + for(i=0;iVertices,&bamggeom->VerticesSize[0],&bamggeom->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); + FetchData(&bamggeom->Edges, &bamggeom->EdgesSize[0], &bamggeom->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); + FetchData(&bamggeom->Corners, &bamggeom->CornersSize[0], &bamggeom->CornersSize[1], mxGetAssignedField(dataref,0,"Corners")); + FetchData(&bamggeom->RequiredVertices,&bamggeom->RequiredVerticesSize[0],&bamggeom->RequiredVerticesSize[1],mxGetAssignedField(dataref,0,"RequiredVertices")); + FetchData(&bamggeom->RequiredEdges, &bamggeom->RequiredEdgesSize[0], &bamggeom->RequiredEdgesSize[1], mxGetAssignedField(dataref,0,"RequiredEdges")); + FetchData(&bamggeom->CrackedEdges,&bamggeom->CrackedEdgesSize[0],&bamggeom->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); + FetchData(&bamggeom->SubDomains,&bamggeom->SubDomainsSize[0],&bamggeom->SubDomainsSize[1],mxGetAssignedField(dataref,0,"SubDomains")); + + /*Assign output pointers:*/ + *pbamggeom=bamggeom; +} +/*}}}*/ +/*FUNCTION FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){{{1*/ +void FetchData(BamgMesh** pbamgmesh,const mxArray* dataref){ + + /*Initialize output*/ + BamgMesh* bamgmesh=new BamgMesh(); + + /*Fetch all fields*/ + FetchData(&bamgmesh->Vertices,&bamgmesh->VerticesSize[0],&bamgmesh->VerticesSize[1],mxGetAssignedField(dataref,0,"Vertices")); + FetchData(&bamgmesh->Edges, &bamgmesh->EdgesSize[0], &bamgmesh->EdgesSize[1], mxGetAssignedField(dataref,0,"Edges")); + FetchData(&bamgmesh->Triangles, &bamgmesh->TrianglesSize[0], &bamgmesh->TrianglesSize[1], mxGetAssignedField(dataref,0,"Triangles")); + FetchData(&bamgmesh->CrackedEdges,&bamgmesh->CrackedEdgesSize[0],&bamgmesh->CrackedEdgesSize[1],mxGetAssignedField(dataref,0,"CrackedEdges")); + FetchData(&bamgmesh->VerticesOnGeomEdge,&bamgmesh->VerticesOnGeomEdgeSize[0],&bamgmesh->VerticesOnGeomEdgeSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomEdge")); + FetchData(&bamgmesh->VerticesOnGeomVertex,&bamgmesh->VerticesOnGeomVertexSize[0],&bamgmesh->VerticesOnGeomVertexSize[1],mxGetAssignedField(dataref,0,"VerticesOnGeomVertex")); + FetchData(&bamgmesh->EdgesOnGeomEdge, &bamgmesh->EdgesOnGeomEdgeSize[0], &bamgmesh->EdgesOnGeomEdgeSize[1], mxGetAssignedField(dataref,0,"EdgesOnGeomEdge")); + FetchData(&bamgmesh->IssmSegments,&bamgmesh->IssmSegmentsSize[0],&bamgmesh->IssmSegmentsSize[1],mxGetAssignedField(dataref,0,"IssmSegments")); + + /*Assign output pointers:*/ + *pbamgmesh=bamgmesh; +} +/*}}}*/ +/*FUNCTION FetchData(BamgOpts** pbamgopts,const mxArray* dataref){{{1*/ +void FetchData(BamgOpts** pbamgopts,const mxArray* dataref){ + + /*Initialize output*/ + BamgOpts* bamgopts=new BamgOpts(); + + /*Fetch all fields*/ + FetchData(&bamgopts->anisomax,mxGetField(dataref,0,"anisomax")); + FetchData(&bamgopts->cutoff,mxGetField(dataref,0,"cutoff")); + FetchData(&bamgopts->coeff,mxGetField(dataref,0,"coeff")); + FetchData(&bamgopts->errg,mxGetField(dataref,0,"errg")); + FetchData(&bamgopts->gradation,mxGetField(dataref,0,"gradation")); + FetchData(&bamgopts->Hessiantype,mxGetField(dataref,0,"Hessiantype")); + FetchData(&bamgopts->MaxCornerAngle,mxGetField(dataref,0,"MaxCornerAngle")); + FetchData(&bamgopts->maxnbv,mxGetField(dataref,0,"maxnbv")); + FetchData(&bamgopts->maxsubdiv,mxGetField(dataref,0,"maxsubdiv")); + FetchData(&bamgopts->Metrictype,mxGetField(dataref,0,"Metrictype")); + FetchData(&bamgopts->nbjacobi,mxGetField(dataref,0,"nbjacobi")); + FetchData(&bamgopts->nbsmooth,mxGetField(dataref,0,"nbsmooth")); + FetchData(&bamgopts->omega,mxGetField(dataref,0,"omega")); + FetchData(&bamgopts->power,mxGetField(dataref,0,"power")); + FetchData(&bamgopts->verbose,mxGetField(dataref,0,"verbose")); + + FetchData(&bamgopts->Crack,mxGetField(dataref,0,"Crack")); + FetchData(&bamgopts->geometricalmetric,mxGetField(dataref,0,"geometricalmetric")); + FetchData(&bamgopts->KeepVertices,mxGetField(dataref,0,"KeepVertices")); + FetchData(&bamgopts->splitcorners,mxGetField(dataref,0,"splitcorners")); + + FetchData(&bamgopts->hmin,mxGetField(dataref,0,"hmin")); + FetchData(&bamgopts->hmax,mxGetField(dataref,0,"hmax")); + FetchData(&bamgopts->hminVertices,&bamgopts->hminVerticesSize[0],&bamgopts->hminVerticesSize[1],mxGetField(dataref,0,"hminVertices")); + FetchData(&bamgopts->hmaxVertices,&bamgopts->hmaxVerticesSize[0],&bamgopts->hmaxVerticesSize[1],mxGetField(dataref,0,"hmaxVertices")); + FetchData(&bamgopts->hVertices,&bamgopts->hVerticesSize[0],&bamgopts->hVerticesSize[1],mxGetField(dataref,0,"hVertices")); + FetchData(&bamgopts->metric,&bamgopts->metricSize[0],&bamgopts->metricSize[1],mxGetField(dataref,0,"metric")); + FetchData(&bamgopts->field,&bamgopts->fieldSize[0],&bamgopts->fieldSize[1],mxGetField(dataref,0,"field")); + FetchData(&bamgopts->err,&bamgopts->errSize[0],&bamgopts->errSize[1],mxGetField(dataref,0,"err")); + + /*Additional checks*/ + bamgopts->Check(); + + /*Assign output pointers:*/ + *pbamgopts=bamgopts; +} +/*}}}*/ +/*FUNCTION FetchData(Options** poptions,const mxArray* dataref){{{1*/ +void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref){ + + char *name = NULL; + Option *option = NULL; + + /*Initialize output*/ + Options* options=new Options(); + + /*Fetch all options*/ + for (int i=istart; iAddOption(option); + option=NULL; + } + + /*Assign output pointers:*/ + *poptions=options; +} +/*}}}*/ Index: /issm/trunk/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/MatlabMatrixToDoubleMatrix.cpp (revision 12330) @@ -0,0 +1,101 @@ +/* \file MatlabMatrixToDoubleMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a double* pointer + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + + int i,j,count,rows,cols; + double *pmxdoublematrix = NULL; + float *pmxsinglematrix = NULL; + + /*output: */ + double* matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ + pmxdoublematrix=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); + + if(rows*cols){ + matrix=(double*)xcalloc(rows*cols,sizeof(double)); + + /*Now, get ir,jc and pr: */ + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + + /*Now, start inserting data into double* matrix: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "./matlabio.h" +#include "../../objects/objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" + +/*}}}*/ + +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ + + int dummy; + Matrix* matrix=NULL; + + /*allocate matrix object: */ + matrix=new Matrix(); + + #ifdef _HAVE_PETSC_ + MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); + #else + matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); + #endif + + return matrix; +} Index: /issm/trunk/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp (revision 12330) @@ -0,0 +1,120 @@ +/* \file MatlabMatrixToPetscMatrix.cpp + * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix: + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ + + int rows, cols; + double* mxmatrix_ptr=NULL; + double* tmatrix=NULL; + int ierr; + int i,j; + + /*output: */ + Mat matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*petsc indices: */ + int* idxm=NULL; + int* idxn=NULL; + + /*Ok, first check if we are dealing with a sparse or full matrix: */ + if (mxIsSparse(mxmatrix)){ + + /*Dealing with sparse matrix: recover size first: */ + mxmatrix_ptr=(double*)mxGetPr(mxmatrix); + rows=mxGetM(mxmatrix); + cols=mxGetN(mxmatrix); + nnz=mxGetNzmax(mxmatrix); + if(rows){ + nz=(int)((double)nnz/(double)rows); + } + else{ + nz=0; + } + + ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxmatrix); + ir=mxGetIr(mxmatrix); + jc=mxGetJc(mxmatrix); + + /*Now, start inserting data into sparse matrix: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "../../toolkits/toolkits.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +/*}}}*/ + +SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ + + SeqMat* output=NULL; + + output=new SeqMat(); + MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); + return output; + +} Index: /issm/trunk/src/c/matlab/io/MatlabNArrayToNArray.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/MatlabNArrayToNArray.cpp (revision 12330) @@ -0,0 +1,272 @@ +/* \file MatlabNArrayToNArray.cpp + * \brief: convert a sparse or dense matlab n-dimensional array to cpp n-dimensional array + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../shared/shared.h" +#include "../../include/include.h" + +#include + +/*FUNCTION MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){{{1*/ +int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix){ + + int i,j,rows,cols; + int numel,ndims; + int *size,*dims; + double* mxmatrix_ptr=NULL; + const mwSize* ipt=NULL; + + /*output: */ + double* matrix=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*get Matlab matrix information: */ + numel=mxGetNumberOfElements(mxmatrix); + ndims=mxGetNumberOfDimensions(mxmatrix); + ipt =mxGetDimensions(mxmatrix); + size =(int *) xcalloc(ndims,sizeof(int)); + for (i=0; i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector){ + + int rows,cols; + double* mxvector_ptr=NULL; + int ierr; + int i,j; + + /*output: */ + double* vector=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*Ok, first check if we are dealing with a sparse or full vector: */ + if (mxIsSparse(mxvector)){ + + /*Dealing with sparse vector: recover size first: */ + mxvector_ptr=(double*)mxGetPr(mxvector); + rows=mxGetM(mxvector); + cols=mxGetN(mxvector); + nnz=mxGetNzmax(mxvector); + + /*Check that input is actualy a vector*/ + if (cols!=1) _error_("input vector of size %ix%i should have only one column",rows,cols); + + nz=(int)((double)nnz/(double)rows); + + if(rows){ + vector=(double*)xcalloc(rows,sizeof(double)); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxvector); + ir=mxGetIr(mxvector); + jc=mxGetJc(mxvector); + + /*Now, start inserting data into sparse vector: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Matlab includes: */ +#include "mex.h" + +#include "../../shared/shared.h" + +int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ + + int rows, cols; + double* mxvector_ptr=NULL; + int ierr; + int i,j; + + /*output: */ + Vec vector=NULL; + + /*matlab indices: */ + mwIndex* ir=NULL; + mwIndex* jc=NULL; + double* pr=NULL; + int count; + int nnz; + int nz; + + /*petsc indices: */ + int* idxm=NULL; + + /*Ok, first check if we are dealing with a sparse or full vector: */ + if (mxIsSparse(mxvector)){ + + /*Dealing with sparse vector: recover size first: */ + mxvector_ptr=(double*)mxGetPr(mxvector); + rows=mxGetM(mxvector); + cols=mxGetN(mxvector); + nnz=mxGetNzmax(mxvector); + nz=(int)((double)nnz/(double)rows); + + ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr); + + /*Now, get ir,jc and pr: */ + pr=mxGetPr(mxvector); + ir=mxGetIr(mxvector); + jc=mxGetJc(mxvector); + + /*Now, start inserting data into sparse vector: */ + count=0; + for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "../../toolkits/toolkits.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +/*}}}*/ + +SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ + + SeqVec* output=NULL; + + output=new SeqVec(); + MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); + return output; + +} Index: /issm/trunk/src/c/matlab/io/MatlabVectorToVector.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/MatlabVectorToVector.cpp (revision 12330) @@ -0,0 +1,39 @@ +/*!\file MatlabVectorToVector.cpp + */ + +/*Headers:*/ +/*{{{1*/ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include +#include "./matlabio.h" +#include "../../objects/objects.h" +#include "../../shared/shared.h" +#include "../../Container/Container.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" + +/*}}}*/ + +Vector* MatlabVectorToVector(const mxArray* mxvector){ + + int dummy; + Vector* vector=NULL; + + /*allocate vector object: */ + vector=new Vector(); + + #ifdef _HAVE_PETSC_ + MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); + #else + vector->vector=MatlabVectorToSeqVec(mxvector); + #endif + + return vector; +} Index: /issm/trunk/src/c/matlab/io/OptionParse.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/OptionParse.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/OptionParse.cpp (revision 12330) @@ -0,0 +1,191 @@ +/*\file OptionParse.c + *\brief: functions to parse the mex options. + */ +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../shared/shared.h" +#include "../../io/io.h" +#include "../../include/include.h" +#include "./matlabio.h" + +#include + +/*FUNCTION OptionDoubleParse {{{1*/ +OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]){ + + OptionDouble *odouble = NULL; + + /*check and parse the name */ + odouble=new OptionDouble; + odouble->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(odouble->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"double")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",odouble->name,"double",odouble->name,mxGetClassName(prhs[0])); + } + + FetchData(&odouble->values,&odouble->numel,&odouble->ndims,&odouble->size,prhs[0]); + + return(odouble); +}/*}}}*/ +/*FUNCTION OptionLogicalParse {{{1*/ +OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]){ + + OptionLogical *ological = NULL; + + /*check and parse the name */ + ological=new OptionLogical; + ological->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ological->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"logical")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ological->name,"logical",ological->name,mxGetClassName(prhs[0])); + } + + FetchData(&ological->values,&ological->numel,&ological->ndims,&ological->size,prhs[0]); + + return(ological); +}/*}}}*/ +/*FUNCTION OptionCharParse {{{1*/ +OptionChar* OptionCharParse( char* name, const mxArray* prhs[]){ + + OptionChar *ochar = NULL; + + /*check and parse the name */ + ochar=new OptionChar(); + ochar->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ochar->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"char")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ochar->name,"char",ochar->name,mxGetClassName(prhs[0])); + } + + FetchData(&ochar->values,&ochar->numel,&ochar->ndims,&ochar->size,prhs[0]); + + return(ochar); +}/*}}}*/ +/*FUNCTION OptionStructParse {{{1*/ +OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]){ + + int i; + char namei[161]; + OptionStruct *ostruct = NULL; + Option *option = NULL; + const mwSize *ipt = NULL; + const mxArray *structi; + mwIndex sindex; + + /*check and parse the name */ + ostruct=new OptionStruct; + ostruct->name =(char*)xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ostruct->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"struct")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ostruct->name,"struct",ostruct->name,mxGetClassName(prhs[0])); + } + + ostruct->numel=mxGetNumberOfElements(prhs[0]); + ostruct->ndims=mxGetNumberOfDimensions(prhs[0]); + ipt =mxGetDimensions(prhs[0]); + ostruct->size =(int *) xmalloc(ostruct->ndims*sizeof(int)); + for (i=0; indims; i++) ostruct->size[i]=(int)ipt[i]; + if (ostruct->numel) ostruct->values=(Options**) xmalloc(ostruct->numel*sizeof(Options *)); + + /*loop through and process each element of the struct array */ + for (sindex=0; sindexnumel; sindex++) { + ostruct->values[sindex]=new Options; + + /*loop through and process each field for the element */ + for (i=0; ivalues[sindex]->AddObject((Object*)option); + option=NULL; + } + } + + return(ostruct); +}/*}}}*/ +/*FUNCTION OptionCellParse {{{1*/ +OptionCell* OptionCellParse( char* name, const mxArray* prhs[]){ + + int i; + int *dims; + char namei[161]; + char cstr[81]; + OptionCell *ocell = NULL; + Option *option = NULL; + const mwSize *ipt = NULL; + const mxArray *celli; + mwIndex cindex; + + /*check and parse the name */ + ocell=new OptionCell; + ocell->name =(char *) xmalloc((strlen(name)+1)*sizeof(char)); + memcpy(ocell->name,name,(strlen(name)+1)*sizeof(char)); + + /*check and parse the value */ + if (!mxIsClass(prhs[0],"cell")){ + _error_("Value of option \"%s\" must be class \"%s\", not class \"%s\".",ocell->name,"cell",ocell->name,mxGetClassName(prhs[0])); + } + + ocell->numel=mxGetNumberOfElements(prhs[0]); + ocell->ndims=mxGetNumberOfDimensions(prhs[0]); + ipt =mxGetDimensions(prhs[0]); + ocell->size =(int *) xmalloc(ocell->ndims*sizeof(int)); + for (i=0; indims; i++) ocell->size[i]=(int)ipt[i]; + ocell->values=new Options; + + /*loop through and process each element of the cell array */ + dims=(int *) xmalloc(ocell->ndims*sizeof(int)); + for (cindex=0; cindexnumel; cindex++) { + ColumnWiseDimsFromIndex(dims,(int)cindex,ocell->size,ocell->ndims); + StringFromDims(cstr,dims,ocell->ndims); + #ifdef _INTEL_WIN_ + _snprintf(namei,161,"%s%s",name,cstr); + #else + snprintf(namei,161,"%s%s",name,cstr); + #endif + celli=mxGetCell(prhs[0],cindex); + + option=(Option*)OptionParse(namei,&celli); + ocell->values->AddObject((Object*)option); + option=NULL; + } + xfree((void**)&dims); + + return(ocell); +}/*}}}*/ +/*FUNCTION OptionParse{{{1*/ +Option* OptionParse(char* name, const mxArray* prhs[]){ + + Option *option = NULL; + mxArray *lhs[1]; + + /*parse the value according to the matlab data type */ + if (mxIsClass(prhs[0],"double")) option=(Option*)OptionDoubleParse(name,prhs); + else if(mxIsClass(prhs[0],"logical")) option=(Option*)OptionLogicalParse(name,prhs); + else if(mxIsClass(prhs[0],"char")) option=(Option*)OptionCharParse(name,prhs); + else if(mxIsClass(prhs[0],"struct")) option=(Option*)OptionStructParse(name,prhs); + else if(mxIsClass(prhs[0],"cell")) option=(Option*)OptionCellParse(name,prhs); + else { + _printf_(true," Converting value of option \"%s\" from unrecognized class \"%s\" to class \"%s\".\n",name,mxGetClassName(prhs[0]),"struct"); + if (!mexCallMATLAB(1,lhs,1,(mxArray**)prhs,"struct")) { + option=(Option*)OptionStructParse(name,(const mxArray**)lhs); + mxDestroyArray(lhs[0]); + } + else _error_("Second argument value of option \"%s\" is of unrecognized class \"%s\".",name,mxGetClassName(prhs[0])); + } + + return(option); +}/*}}}*/ Index: /issm/trunk/src/c/matlab/io/PrintfFunction.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/PrintfFunction.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/PrintfFunction.cpp (revision 12330) @@ -0,0 +1,58 @@ +/*\file PrintfFunction.c + *\brief: this function is used by the _printf_ macro, to take into account the + *fact we may be running on a cluster. + */ + +#include +#include +#include "../../shared/shared.h" +#include "../../include/include.h" + +#include "mex.h" + +int PrintfFunction(char* format,...){ + /*http://linux.die.net/man/3/vsnprintf*/ + + /*string to be printed: */ + char *buffer = NULL; + int n,size = 100; + int string_size; + extern int my_rank; + extern int num_procs; + + //variable list of arguments + va_list args; + + while(true){ + + /*allocate buffer for given string size*/ + buffer=(char*)xmalloc(size*sizeof(char)); + + /* Try to print in the allocated space. */ + va_start(args, format); +#ifndef WIN32 + n=vsnprintf(buffer,size,format,args); +#else + n=vsnprintf(buffer,size,format,args); +#endif + va_end(args); + + /* If that worked, return the string. */ + if(n>-1 && n-1) /* glibc 2.1 */ + size=n+1; /* precisely what is needed */ + else /* glibc 2.0 */ + size*=2; /* twice the old size */ + + xfree((void**)&buffer); + } + + /*Ok, if we are running in parallel, get node 0 to print*/ + if(my_rank==0)printf(buffer); + + /*Clean up and return*/ + xfree((void**)&buffer); + return 1; +} Index: /issm/trunk/src/c/matlab/io/WriteMatlabData.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/WriteMatlabData.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/WriteMatlabData.cpp (revision 12330) @@ -0,0 +1,310 @@ +/* \file WriteData.c: + * \brief: general interface for writing data + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../include/include.h" +#include "../../shared/shared.h" +#include "./matlabio.h" + +#include + + +/*Primitive data types*/ +/*FUNCTION WriteData(mxArray** pdataref,double* matrix, int M,int N){{{1*/ +void WriteData(mxArray** pdataref,double* matrix, int M,int N){ + + mxArray *dataref = NULL; + double *tmatrix = NULL; + + if(matrix){ + /*create the matlab matrixwith Matlab's memory manager */ + tmatrix=(double*)mxMalloc(M*N*sizeof(double)); + for(int i=0;iVerticesSize[0], bamggeom->VerticesSize[1], bamggeom->Vertices); + i++; SetStructureField(dataref,"Edges", bamggeom->EdgesSize[0], bamggeom->EdgesSize[1], bamggeom->Edges); + i++; SetStructureField(dataref,"TangentAtEdges", bamggeom->TangentAtEdgesSize[0], bamggeom->TangentAtEdgesSize[1], bamggeom->TangentAtEdges); + i++; SetStructureField(dataref,"RequiredVertices",bamggeom->RequiredVerticesSize[0],bamggeom->RequiredVerticesSize[1],bamggeom->RequiredVertices); + i++; SetStructureField(dataref,"RequiredEdges", bamggeom->RequiredEdgesSize[0], bamggeom->RequiredEdgesSize[1], bamggeom->RequiredEdges); + i++; SetStructureField(dataref,"CrackedEdges", bamggeom->CrackedEdgesSize[0], bamggeom->CrackedEdgesSize[1], bamggeom->CrackedEdges); + i++; SetStructureField(dataref,"SubDomains", bamggeom->SubDomainsSize[0], bamggeom->SubDomainsSize[1], bamggeom->SubDomains); + _assert_(i==numfields); + + /*Assign output*/ + *pdataref=dataref; +} +/*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,BamgMesh* bamgmesh){{{1*/ +void WriteData(mxArray** pdataref,BamgMesh* bamgmesh){ + + /*Intermediary*/ + int i; + mxArray *dataref = NULL; + const int numfields = 16; + const char *fnames[numfields]; + mwSize ndim = 2; + mwSize dimensions[2] = {1,1}; + + /*Initialize field names*/ + i=0; + fnames[i++] = "Triangles"; + fnames[i++] = "Vertices"; + fnames[i++] = "Edges"; + fnames[i++] = "IssmSegments"; + fnames[i++] = "IssmEdges"; + fnames[i++] = "Quadrilaterals"; + fnames[i++] = "VerticesOnGeomVertex"; + fnames[i++] = "VerticesOnGeomEdge"; + fnames[i++] = "EdgesOnGeomEdge"; + fnames[i++] = "SubDomains"; + fnames[i++] = "SubDomainsFromGeom"; + fnames[i++] = "ElementConnectivity"; + fnames[i++] = "NodalConnectivity"; + fnames[i++] = "NodalElementConnectivity"; + fnames[i++] = "CrackedVertices"; + fnames[i++] = "CrackedEdges"; + _assert_(i==numfields); + + /*Initialize Matlab structure*/ + dataref=mxCreateStructArray(ndim,dimensions,numfields,fnames); + + /*set each matlab each field*/ + i=0; + i++; SetStructureField(dataref,"Triangles", bamgmesh->TrianglesSize[0],bamgmesh->TrianglesSize[1], bamgmesh->Triangles); + i++; SetStructureField(dataref,"Vertices",bamgmesh->VerticesSize[0], bamgmesh->VerticesSize[1],bamgmesh->Vertices); + i++; SetStructureField(dataref,"Edges", bamgmesh->EdgesSize[0],bamgmesh->EdgesSize[1], bamgmesh->Edges); + i++; SetStructureField(dataref,"IssmSegments",bamgmesh->IssmSegmentsSize[0], bamgmesh->IssmSegmentsSize[1],bamgmesh->IssmSegments); + i++; SetStructureField(dataref,"IssmEdges", bamgmesh->IssmEdgesSize[0],bamgmesh->IssmEdgesSize[1], bamgmesh->IssmEdges); + i++; SetStructureField(dataref,"Quadrilaterals",bamgmesh->QuadrilateralsSize[0], bamgmesh->QuadrilateralsSize[1],bamgmesh->Quadrilaterals); + i++; SetStructureField(dataref,"VerticesOnGeomVertex",bamgmesh->VerticesOnGeomVertexSize[0],bamgmesh->VerticesOnGeomVertexSize[1], bamgmesh->VerticesOnGeomVertex); + i++; SetStructureField(dataref,"VerticesOnGeomEdge",bamgmesh->VerticesOnGeomEdgeSize[0],bamgmesh->VerticesOnGeomEdgeSize[1], bamgmesh->VerticesOnGeomEdge); + i++; SetStructureField(dataref,"EdgesOnGeomEdge", bamgmesh->EdgesOnGeomEdgeSize[0], bamgmesh->EdgesOnGeomEdgeSize[1],bamgmesh->EdgesOnGeomEdge); + i++; SetStructureField(dataref,"SubDomains",bamgmesh->SubDomainsSize[0], bamgmesh->SubDomainsSize[1],bamgmesh->SubDomains); + i++; SetStructureField(dataref,"SubDomainsFromGeom", bamgmesh->SubDomainsFromGeomSize[0], bamgmesh->SubDomainsFromGeomSize[1],bamgmesh->SubDomainsFromGeom); + i++; SetStructureField(dataref,"ElementConnectivity",bamgmesh->ElementConnectivitySize[0],bamgmesh->ElementConnectivitySize[1], bamgmesh->ElementConnectivity); + i++; SetStructureField(dataref,"NodalConnectivity",bamgmesh->NodalConnectivitySize[0],bamgmesh->NodalConnectivitySize[1], bamgmesh->NodalConnectivity); + i++; SetStructureField(dataref,"NodalElementConnectivity", bamgmesh->NodalElementConnectivitySize[0], bamgmesh->NodalElementConnectivitySize[1],bamgmesh->NodalElementConnectivity); + i++; SetStructureField(dataref,"CrackedVertices", bamgmesh->CrackedVerticesSize[0],bamgmesh->CrackedVerticesSize[1], bamgmesh->CrackedVertices); + i++; SetStructureField(dataref,"CrackedEdges",bamgmesh->CrackedEdgesSize[0], bamgmesh->CrackedEdgesSize[1],bamgmesh->CrackedEdges); + _assert_(i==numfields); + + /*Assign output*/ + *pdataref=dataref; +} +/*}}}*/ +/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/ +void WriteData(mxArray** pdataref,Matrix* matrix){ + + int i,j; + int rows,cols; + mxArray *dataref = NULL; + double *matrix_ptr = NULL; + double *tmatrix_ptr = NULL; + + if(matrix){ + + #ifdef _HAVE_PETSC_ + PetscMatrixToDoubleMatrix(&matrix_ptr,&rows,&cols,matrix->matrix); + #else + matrix_ptr=matrix->matrix->ToSerial(); + matrix->matrix->GetSize(&rows,&cols); + #endif + + /*Now transpose the matrix and allocate with Matlab's memory manager: */ + tmatrix_ptr=(double*)mxMalloc(rows*cols*sizeof(double)); + for(i=0;ivector); + #else + vector_ptr=vector->vector->ToMPISerial(); + vector->vector->GetSize(&rows); + #endif + + /*now create the matlab vector with Matlab's memory manager */ + vector_matlab=(double*)mxMalloc(rows*sizeof(double)); + for(int i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "../../objects/objects.h" +#include "../../Container/Container.h" +#include "../../include/include.h" + +#include + +void WriteData(mxArray** pdataref,Matrix* matrix); +void WriteData(mxArray** pdataref,double* matrix, int M,int N); +void WriteData(mxArray** pdataref,int* matrix, int M,int N); +void WriteData(mxArray** pdataref,Vector* vector); +void WriteData(mxArray** pdataref,double* vector, int M); +void WriteData(mxArray** pdataref,int integer); +void WriteData(mxArray** pdataref,bool boolean); +void WriteData(mxArray** pdataref,double scalar); +void WriteData(mxArray** pdataref,char* string); +void WriteData(mxArray** pdataref,BamgGeom* bamggeom); +void WriteData(mxArray** pdataref,BamgMesh* bamgmesh); + +void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(int** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(bool** pmatrix,int* pM,int *pN,const mxArray* dataref); +void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(Matrix** pmatrix,const mxArray* dataref); +void FetchData(int** pvector,int* pM,const mxArray* dataref); +void FetchData(float** pvector,int* pM,const mxArray* dataref); +void FetchData(double** pvector,int* pM,const mxArray* dataref); +void FetchData(bool** pvector,int* pM,const mxArray* dataref); +void FetchData(Vector** pvector,const mxArray* dataref); +void FetchData(char** pstring,const mxArray* dataref); +void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref); +void FetchData(double* pscalar,const mxArray* dataref); +void FetchData(int* pinteger,const mxArray* dataref); +void FetchData(bool* pbool,const mxArray* dataref); +void FetchData(BamgGeom** bamggeom,const mxArray* dataref); +void FetchData(BamgMesh** bamgmesh,const mxArray* dataref); +void FetchData(BamgOpts** bamgopts,const mxArray* dataref); +void FetchData(Options** poptions,int istart, int nrhs,const mxArray** pdataref); + +Option* OptionParse(char* name, const mxArray* prhs[]); +OptionDouble* OptionDoubleParse( char* name, const mxArray* prhs[]); +OptionLogical* OptionLogicalParse( char* name, const mxArray* prhs[]); +OptionChar* OptionCharParse( char* name, const mxArray* prhs[]); +OptionStruct* OptionStructParse( char* name, const mxArray* prhs[]); +OptionCell* OptionCellParse( char* name, const mxArray* prhs[]); + +mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number, const char* field); +void SetStructureField(mxArray* dataref,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); +int CheckNumMatlabArguments(int nlhs,int NLHS, int nrhs,int NRHS, const char* THISFUNCTION, void (*function)( void )); + +/*Matlab to Matrix routines: */ +Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); +Vector* MatlabVectorToVector(const mxArray* mxvector); + +/*Matlab to double* routines: */ +int MatlabVectorToDoubleVector(double** pvector,int* pvector_rows,const mxArray* mxvector); +int MatlabMatrixToDoubleMatrix(double** pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix); +int MatlabNArrayToNArray(double** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); +int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); + +/*Matlab to SeqMat routines: */ +SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); +SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); + +/*Matlab to Petsc routines: */ +#ifdef _HAVE_PETSC_ +int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); +int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); +#endif + + +#endif /* _IO_H_ */ Index: /issm/trunk/src/c/matlab/io/mxGetAssignedField.cpp =================================================================== --- /issm/trunk/src/c/matlab/io/mxGetAssignedField.cpp (revision 12330) +++ /issm/trunk/src/c/matlab/io/mxGetAssignedField.cpp (revision 12330) @@ -0,0 +1,45 @@ +/*!\file: mxGetAssignedField.c: + * \brief: abstract interface on parallel side for i/o, so it ressembles the serial i/o. + * + * In serial mode, this routine takes care of returning the field coming + * from the model. If largesize is 1, we are running out of core models in + * matlab, and we need to call the subsref private method from the model object + * in order to correctly load the data from disk. + */ + +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include "mex.h" + +mxArray* mxGetAssignedField(const mxArray* pmxa_array,int number,const char* field){ + + //output + mxArray* mxfield=NULL; + + //input + mxArray *inputs[2]; + mxArray *pindex = NULL; + const char *fnames[2]; + mwSize ndim = 2; + mwSize onebyone[2] = {1,1}; + + //We want to call the subsasgn method, and get the returned array.This ensures that if we are running + //large sized problems, the data is truly loaded from disk by the model subsasgn class method. + inputs[0]=(mxArray*)pmxa_array; //this is the model + + //create index structure used in the assignment (index.type='.' and index.subs='x' for field x for ex) + fnames[0] = "type"; + fnames[1] = "subs"; + pindex=mxCreateStructArray( ndim,onebyone,2,fnames); + mxSetField( pindex, 0, "type",mxCreateString(".")); + mxSetField( pindex, 0, "subs",mxCreateString(field)); + inputs[1]=pindex; + + mexCallMATLAB( 1, &mxfield, 2, (mxArray**)inputs, "subsref"); + + return mxfield; +} Index: /issm/trunk/src/c/matlab/matlab-binding.h =================================================================== --- /issm/trunk/src/c/matlab/matlab-binding.h (revision 12330) +++ /issm/trunk/src/c/matlab/matlab-binding.h (revision 12330) @@ -0,0 +1,7 @@ +#ifndef _MATLAB_BINDING_H_ +#define _MATLAB_BINDING_H_ + +#include "./io/matlabio.h" +#include "./include/matlab_macros.h" + +#endif Index: /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp =================================================================== --- /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/Bamgx/Bamgx.cpp (revision 12330) @@ -92,5 +92,5 @@ //Make Quadtree from background mesh - BTh.MakeQuadTree(); + BTh.MakeBamgQuadtree(); //Bound hmin and hmax Index: /issm/trunk/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp =================================================================== --- /issm/trunk/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12330) @@ -32,5 +32,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -95,5 +95,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); @@ -135,5 +135,5 @@ /*Is there just one found? that would mean we have frozen! : */ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -195,5 +195,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -228,5 +228,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); @@ -289,5 +289,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); @@ -329,5 +329,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&max_penetration,&mpi_max_penetration,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_max_penetration,1,MPI_DOUBLE,0,MPI_COMM_WORLD); @@ -368,5 +368,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp =================================================================== --- /issm/trunk/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12330) @@ -36,5 +36,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp =================================================================== --- /issm/trunk/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12330) @@ -28,5 +28,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.cpp =================================================================== --- /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.cpp (revision 12330) @@ -11,5 +11,5 @@ #include "./ContourToMeshx.h" -int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue) { +int ContourToMeshx( Vector** pin_nod,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue) { int noerr=1; @@ -37,5 +37,4 @@ /*initialize thread parameters: */ - gate.numcontours=numcontours; gate.contours=contours; gate.nods=nods; Index: /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.h =================================================================== --- /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12329) +++ /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshx.h (revision 12330) @@ -13,6 +13,5 @@ typedef struct{ - int numcontours; - Contour** contours; + DataSet* contours; int nods; int edgevalue; @@ -25,5 +24,5 @@ /* local prototypes: */ -int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,Contour** contours,int numcontours,char* interptype,int nel,int nods, int edgevalue); +int ContourToMeshx( Vector** pin_nods,Vector** pin_elem, double* index, double* x, double* y,DataSet* contours,char* interptype,int nel,int nods, int edgevalue); void* ContourToMeshxt(void* vContourToMeshxThreadStruct); Index: /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp =================================================================== --- /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ContourToMeshx/ContourToMeshxt.cpp (revision 12330) @@ -26,13 +26,7 @@ /*Contour:*/ - Contour* contouri=NULL; - int numnodes; - double* xc=NULL; - double* yc=NULL; - + DataSet* contours=NULL; /*parameters: */ - int numcontours; - Contour** contours=NULL; int nods; int edgevalue; @@ -49,5 +43,4 @@ /*recover parameters :*/ - numcontours=gate->numcontours; contours=gate->contours; nods=gate->nods; @@ -61,10 +54,7 @@ /*Loop through all contours: */ - for (i=0;inods; - xc=contouri->x; - yc=contouri->y; - IsInPoly(in_nod,xc,yc,numnodes,x,y,i0,i1,edgevalue); + for (i=0;iSize();i++){ + Contour* contour=(Contour*)contours->GetObjectByOffset(i); + IsInPoly(in_nod,contour->x,contour->y,contour->nods,x,y,i0,i1,edgevalue); } Index: /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.cpp =================================================================== --- /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.cpp (revision 12330) @@ -38,2 +38,36 @@ return 1; } + +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue){ + + int i; + int m,n; + + /*Contour:*/ + Contour* contouri=NULL; + int numnodes; + double* xc=NULL; + double* yc=NULL; + double value; + + /*output: */ + Vector* flags=NULL; + + flags=new Vector(nods); + + /*Loop through all contours: */ + if(contours){ + for (i=0;iSize();i++){ + Contour* contour=(Contour*)contours->GetObjectByOffset(i); + IsInPoly(flags,contour->x,contour->y,contour->nods,x,y,0,nods,edgevalue); + } + } + + /*Assemble vector: */ + flags->Assemble(); + + /*Assign output pointers: */ + *pflags=flags; + + return 1; +} Index: /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.h =================================================================== --- /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 12329) +++ /issm/trunk/src/c/modules/ContourToNodesx/ContourToNodesx.h (revision 12330) @@ -12,4 +12,5 @@ /* local prototypes: */ int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, Contour** contours,int numcontours,int edgevalue); +int ContourToNodesx( Vector** pflags,double* x, double* y, int nods, DataSet* contours, int edgevalue); #endif /* _CONTOURTONODESX_H */ Index: /issm/trunk/src/c/modules/Dakotax/Dakotax.cpp =================================================================== --- /issm/trunk/src/c/modules/Dakotax/Dakotax.cpp (revision 12329) +++ /issm/trunk/src/c/modules/Dakotax/Dakotax.cpp (revision 12330) @@ -51,9 +51,5 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Dakotax(mxArray* femmodel){ -#else void Dakotax(FemModel* femmodel){ -#endif @@ -69,9 +65,5 @@ /*Retrieve parameters: */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - FetchData((Parameters**)¶meters,mxGetField((mxArray*)femmodel,0,"parameters")); - #else parameters=femmodel->parameters; - #endif /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ @@ -80,15 +72,9 @@ parameters->FindParam(&dakota_error_file,QmuErrNameEnum); - #ifdef _PARALLEL_ if(my_rank==0){ - #endif // Instantiate/initialize the parallel library and problem description // database objects. - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - Dakota::ParallelLibrary parallel_lib; //use Dakota's standard library mode constructor - #else - Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. - #endif + Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. Dakota::ProblemDescDB problem_db(parallel_lib); @@ -123,10 +109,7 @@ selected_strategy.run_strategy(); - #ifdef _PARALLEL_ //Warn other cpus that we are done running the dakota iterator, by setting the counter to -1: SpawnCore(NULL,0, NULL,NULL,0,femmodel,-1); - #endif - #ifdef _PARALLEL_ } else{ @@ -136,5 +119,4 @@ } } - #endif //#ifdef _PARALLEL_ /*Free ressources:*/ @@ -143,8 +125,4 @@ xfree((void**)&dakota_output_file); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - delete parameters; - #endif - #endif //#ifdef _HAVE_DAKOTA_ } Index: /issm/trunk/src/c/modules/Dakotax/Dakotax.h =================================================================== --- /issm/trunk/src/c/modules/Dakotax/Dakotax.h (revision 12329) +++ /issm/trunk/src/c/modules/Dakotax/Dakotax.h (revision 12330) @@ -10,14 +10,9 @@ /* local prototypes: */ -int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); +int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); int DescriptorIndex(char* root, int* pindex,char* descriptor); -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void Dakotax(mxArray* femmodel); -void SpawnCoreSerial(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, mxArray* femmodel,int counter); -#else void Dakotax(FemModel* femmodel); void SpawnCoreParallel(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, FemModel* femmodel,int counter); -#endif void DakotaResponses(double* responses,char** responses_descriptors,int numresponses,FemModel* femmodel); void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses); Index: /issm/trunk/src/c/modules/Dakotax/SpawnCore.cpp =================================================================== --- /issm/trunk/src/c/modules/Dakotax/SpawnCore.cpp (revision 12329) +++ /issm/trunk/src/c/modules/Dakotax/SpawnCore.cpp (revision 12330) @@ -21,12 +21,9 @@ /*Branch into a serial SpawnCore and a parallel SpawnCore: */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - SpawnCoreSerial(responses, numresponses, variables, variables_descriptors,numvariables, (mxArray*)femmodel, counter); - #else - /*Call SpawnCoreParallel unless counter=-1 on cpu0, in which case, bail out and return 0: */ - MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); - if(counter==-1)return 0; - SpawnCoreParallel(responses, numresponses, variables, variables_descriptors,numvariables, (FemModel*)femmodel,counter); - #endif + /*Call SpawnCoreParallel unless counter=-1 on cpu0, in which case, bail out and return 0: */ + MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); + if(counter==-1)return 0; + + SpawnCoreParallel(responses, numresponses, variables, variables_descriptors,numvariables, (FemModel*)femmodel,counter); return 1; } Index: sm/trunk/src/c/modules/Dakotax/SpawnCoreSerial.cpp =================================================================== --- /issm/trunk/src/c/modules/Dakotax/SpawnCoreSerial.cpp (revision 12329) +++ (revision ) @@ -1,71 +1,0 @@ -/*!\file: SpawnCoreSerial.cpp - * \brief: run core ISSM solution using Dakota inputs. Call the Serial core solution, using mexCallMATLAB - * \sa SpawnCore.cpp SpawnCoreParallel.cpp - * - */ - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include "../../objects/objects.h" -#include "../../io/io.h" -#include "../../EnumDefinitions/EnumDefinitions.h" -#include "../../shared/shared.h" -#include "./Dakotax.h" -#include "../../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void SpawnCoreSerial(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, mxArray* femmodel, int counter){ - - int i; - - //inputs to matlab routine - mxArray* mxvariables=NULL; - double* variables_copy=NULL; - mxArray* mxvariabledescriptors=NULL; - mxArray* mxcounter=NULL; - mwSize dims[2]={0}; - - //mexCallMATLAB arrays - mxArray* array[4]; - - //output from SpawnCore in matlab routine. - mxArray* mxresponses=NULL; - - /*Create variables and variable descriptors mxArrays that we will feed to the core solution for update of the inputs: */ - mxvariables=mxCreateDoubleMatrix(numvariables,1,mxREAL); - variables_copy=(double*)xmalloc(numvariables*sizeof(double)); - memcpy(variables_copy,variables,numvariables*sizeof(double)); - mxSetPr(mxvariables,variables_copy); - - dims[0]=numvariables; - dims[1]=1; - mxvariabledescriptors=mxCreateCellArray(2,dims); - for(i=0;iAssemble(); + #ifdef _HAVE_MPI_ MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); _printf_(VerboseConvergence()," Additional number of vertices allowed to unground: %i\n",nflipped); + #else + nflipped=local_nflipped; + #endif /*Avoid leaks: */ Index: /issm/trunk/src/c/modules/IceVolumex/IceVolumex.cpp =================================================================== --- /issm/trunk/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12329) +++ /issm/trunk/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12330) @@ -19,6 +19,10 @@ local_ice_volume+=element->IceVolume(); } + #ifdef _HAVE_MPI_ MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #else + total_ice_volume=local_ice_volume; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/InputConvergencex/InputConvergencex.cpp =================================================================== --- /issm/trunk/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12329) +++ /issm/trunk/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12330) @@ -30,5 +30,5 @@ /*In parallel, we need to gather the converged status: */ - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&num_notconverged,(void*)&total_notconverged,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); num_notconverged=total_notconverged; Index: /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (revision 12330) @@ -14,5 +14,5 @@ int InterpFromMeshToMesh2dx(double** pdata_interp,double* index_data,double* x_data,double* y_data,int nods_data,int nels_data, - double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values, Contour** contours, int numcontours){ + double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values, DataSet* contours){ /*Output*/ @@ -36,5 +36,4 @@ bool skip_bamg=false; - /*Checks*/ if (data_cols<=0){ @@ -50,5 +49,5 @@ /*If default values supplied, figure out which nodes are inside the contour, including the border of the contour: */ if(num_default_values){ - ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,numcontours,1); + ContourToNodesx( &vec_incontour,x_interp,y_interp,nods_interp,contours,1); incontour=vec_incontour->ToMPISerial(); } Index: /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h =================================================================== --- /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 12329) +++ /issm/trunk/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.h (revision 12330) @@ -10,5 +10,5 @@ /* local prototypes: */ int InterpFromMeshToMesh2dx(double** pdata_interp,double* index_data,double* x_data,double* y_data,int nods_data,int nels_data, - double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values,Contour** contours, int numcontours ); + double* data,int data_rows,int data_cols,double* x_interp,double* y_interp,int nods_interp,double* default_values,int num_default_values,DataSet* contours); #endif Index: /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp =================================================================== --- /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp (revision 12330) +++ /issm/trunk/src/c/modules/Krigingx/Krigingx.cpp (revision 12330) @@ -0,0 +1,263 @@ +/*!\file: Kriging.cpp + * \brief "c" core code for Kriging + */ + +#include "./Krigingx.h" +#include "../../shared/shared.h" +#include "../../include/include.h" +#include "../../toolkits/toolkits.h" +#include "../../objects/objects.h" +#include "../../Container/Observations.h" +#include "../modules.h" + +#ifdef _HAVE_GSL_ +#include +#endif + +#include "../../objects/Kriging/GaussianVariogram.h" +/*FUNCTION Krigingx{{{*/ +int Krigingx(double** ppredictions,double **perror,double* obs_x, double* obs_y, double* obs_list, int obs_length,double* x_interp,double* y_interp,int n_interp,Options* options){ + + /*output*/ + double *predictions = NULL; + double *error = NULL; + + /*Intermediaries*/ + int mindata,maxdata; + double radius; + char *output = NULL; + Variogram *variogram = NULL; + Observations *observations = NULL; + + /*threading: */ + KrigingxThreadStruct gate; + int num=1; +#ifdef _MULTITHREADING_ + num=_NUMTHREADS_; +#endif + + /*Get Variogram from Options*/ + ProcessVariogram(&variogram,options); + options->Get(&radius,"searchradius",0.); + options->Get(&mindata,"mindata",1); + options->Get(&maxdata,"maxdata",50); + + /*Process observation dataset*/ + observations=new Observations(obs_list,obs_x,obs_y,obs_length,options); + + /*Allocate output*/ + predictions =(double*)xcalloc(n_interp,sizeof(double)); + error =(double*)xcalloc(n_interp,sizeof(double)); + + /*Get output*/ + options->Get(&output,"output","prediction"); + + if(strcmp(output,"quadtree")==0){ + observations->QuadtreeColoring(predictions,x_interp,y_interp,n_interp); + } + else if(strcmp(output,"variomap")==0){ + observations->Variomap(predictions,x_interp,n_interp); + } + else if(strcmp(output,"prediction")==0){ + + /*initialize thread parameters: */ + gate.n_interp = n_interp; + gate.x_interp = x_interp; + gate.y_interp = y_interp; + gate.radius = radius; + gate.mindata = mindata; + gate.maxdata = maxdata; + gate.variogram = variogram; + gate.observations = observations; + gate.predictions = predictions; + gate.error = error; + gate.percent = (double*)xcalloc(num,sizeof(double)); + + /*launch the thread manager with Krigingxt as a core: */ + LaunchThread(Krigingxt,(void*)&gate,num); + printf("\r interpolation progress: 100.00%%\n"); + xfree((void**)&gate.percent); + } + else{ + _error_("output '%s' not supported yet",output); + } + + /*clean-up and Assign output pointer*/ + delete variogram; + delete observations; + xfree((void**)&output); + *ppredictions = predictions; + *perror = error; + return 1; +}/*}}}*/ +/*FUNCTION Krigingxt{{{*/ +void* Krigingxt(void* vpthread_handle){ + + /*gate variables :*/ + KrigingxThreadStruct *gate = NULL; + pthread_handle *handle = NULL; + int my_thread; + int num_threads; + int i0,i1; + + /*recover handle and gate: */ + handle = (pthread_handle*)vpthread_handle; + gate = (KrigingxThreadStruct*)handle->gate; + my_thread = handle->id; + num_threads = handle->num; + + /*recover parameters :*/ + int n_interp = gate->n_interp; + double *x_interp = gate->x_interp; + double *y_interp = gate->y_interp; + double radius = gate->radius; + int mindata = gate->mindata; + int maxdata = gate->maxdata; + Variogram *variogram = gate->variogram; + Observations *observations = gate->observations; + double *predictions = gate->predictions; + double *error = gate->error; + double *percent = gate->percent; + + /*Intermediaries*/ + int i,j,n_obs; + double numerator,denominator,ratio,localpercent; + double *x = NULL; + double *y = NULL; + double *obs = NULL; + double *Gamma = NULL; + double *GinvG0 = NULL; + double *Ginv1 = NULL; + double *GinvZ = NULL; + double *gamma0 = NULL; + double *ones = NULL; + + /*partition loop across threads: */ + PartitionRange(&i0,&i1,n_interp,num_threads,my_thread); + for(int idx=i0;idxObservationList(&x,&y,&obs,&n_obs,x_interp[idx],y_interp[idx],radius,maxdata); + if(n_obsSemiVariogram(x[i]-x[j],y[i]-y[j]); + Gamma[i*n_obs+j] = variogram->Covariance(x[i]-x[j],y[i]-y[j]); + Gamma[j*n_obs+i] = Gamma[i*n_obs+j]; + } + } + for(i=0;iSemiVariogram(x[i]-x_interp[idx],y[i]-y_interp[idx]); + for(i=0;iCovariance(x[i]-x_interp[idx],y[i]-y_interp[idx]); + + /*Solve the three linear systems*/ + GslSolve(&GinvG0,Gamma,gamma0,n_obs); // Gamma^-1 gamma0 + GslSolve(&Ginv1, Gamma,ones,n_obs); // Gamma^-1 ones + GslSolve(&GinvZ, Gamma,obs,n_obs); // Gamma^-1 Z + + /*Prepare predictor*/ + numerator=-1.; denominator=0.; + for(i=0;iGetOption("model")){ + options->Get(&model,"model"); + if (strcmp(model,"gaussian")==0) variogram = new GaussianVariogram(options); + else if(strcmp(model,"exponential")==0) variogram = new ExponentialVariogram(options); + else if(strcmp(model,"spherical")==0) variogram = new SphericalVariogram(options); + else if(strcmp(model,"power")==0) variogram = new PowerVariogram(options); + else _error_("variogram %s not supported yet (list of supported variogram: gaussian, exponential, spherical and power)",model); + } + else variogram = new GaussianVariogram(options); + + /*Assign output pointer*/ + xfree((void**)&model); + *pvariogram = variogram; +}/*}}}*/ +void GslSolve(double** pX,double* A,double* B,int n){/*{{{*/ +#ifdef _HAVE_GSL_ + + /*GSL Matrices and vectors: */ + int s; + gsl_matrix_view a; + gsl_vector_view b; + gsl_vector *x = NULL; + gsl_permutation *p = NULL; + + /*A will be modified by LU decomposition. Use copy*/ + double* Acopy = (double*)xmalloc(n*n*sizeof(double)); + memcpy(Acopy,A,n*n*sizeof(double)); + + /*Initialize gsl matrices and vectors: */ + a = gsl_matrix_view_array (Acopy,n,n); + b = gsl_vector_view_array (B,n); + x = gsl_vector_alloc (n); + + /*Run LU and solve: */ + p = gsl_permutation_alloc (n); + gsl_linalg_LU_decomp (&a.matrix, p, &s); + gsl_linalg_LU_solve (&a.matrix, p, &b.vector, x); + + //printf ("x = \n"); + //gsl_vector_fprintf (stdout, x, "%g"); + + /*Copy result*/ + double* X = (double*)xmalloc(n*sizeof(double)); + memcpy(X,gsl_vector_ptr(x,0),n*sizeof(double)); + + /*Clean up and assign output pointer*/ + xfree((void**)&Acopy); + gsl_permutation_free(p); + gsl_vector_free(x); + *pX=X; +#else + _error_("GSL support required"); +#endif + }/*}}}*/ Index: /issm/trunk/src/c/modules/Krigingx/Krigingx.h =================================================================== --- /issm/trunk/src/c/modules/Krigingx/Krigingx.h (revision 12330) +++ /issm/trunk/src/c/modules/Krigingx/Krigingx.h (revision 12330) @@ -0,0 +1,34 @@ +/*!\file Kriging.h + * \brief: header file for Kriging + */ + +#ifndef _KRIGINGX_H +#define _KRIGINGX_H + +#include "../../objects/objects.h" +#include "../../toolkits/toolkits.h" + +class Observations; +class Variogram; + +int Krigingx(double** ppredictions,double **perror,double* x, double* y, double* observations, int n_obs,double* x_interp,double* y_interp,int n_interp,Options* options); +void ProcessVariogram(Variogram **pvariogram,Options* options); +void GslSolve(double** pX,double* A,double* B,int n); + +/*threading: */ +typedef struct{ + int n_interp; + double *x_interp; + double *y_interp; + double radius; + int mindata; + int maxdata; + Variogram *variogram; + Observations *observations; + double *predictions; + double *error; + double *percent; +}KrigingxThreadStruct; + +void* Krigingxt(void*); +#endif /* _KRIGINGX_H */ Index: /issm/trunk/src/c/modules/MassFluxx/MassFluxx.cpp =================================================================== --- /issm/trunk/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12330) @@ -59,5 +59,5 @@ } - #ifdef _PARALLEL_ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&mass_flux,(void*)&all_mass_flux,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD); mass_flux=all_mass_flux; Index: /issm/trunk/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvx,&node_maxabsvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12330) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvy,&node_maxabsvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvz,&node_maxabsvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxVelx/MaxVelx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12330) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvel,&node_maxvel,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxVxx/MaxVxx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvx,&node_maxvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxVyx/MaxVyx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvy,&node_maxvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MaxVzx/MaxVzx.cpp =================================================================== --- /issm/trunk/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12330) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvz,&node_maxvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MeshPartitionx/MeshPartitionx.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12330) @@ -42,5 +42,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements,&numberofnodes, index, &etype, &numflag, &num_procs, &edgecut, epart, npart); + #endif } else if (num_procs==1){ @@ -67,5 +69,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements2d,&numberofnodes2d, index2d, &etype2d, &numflag, &num_procs, &edgecut, epart2d, npart2d); + #endif } else if (num_procs==1){ Index: /issm/trunk/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp =================================================================== --- /issm/trunk/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MeshProfileIntersectionx/SegmentIntersect.cpp (revision 12330) @@ -6,5 +6,5 @@ int SegmentIntersect(double* palpha, double* pbeta, double* x1, double* y1, double* x2, double* y2){ - /*See ISSM_TIER/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ + /*See ISSM_DIR/src/m/utils/Geometry/SegIntersect.m for matlab routine from which we take this routine: */ /*output: */ Index: /issm/trunk/src/c/modules/MinVelx/MinVelx.cpp =================================================================== --- /issm/trunk/src/c/modules/MinVelx/MinVelx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MinVelx/MinVelx.cpp (revision 12330) @@ -32,6 +32,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvel,&node_minvel,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MinVxx/MinVxx.cpp =================================================================== --- /issm/trunk/src/c/modules/MinVxx/MinVxx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MinVxx/MinVxx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MinVyx/MinVyx.cpp =================================================================== --- /issm/trunk/src/c/modules/MinVyx/MinVyx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MinVyx/MinVyx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvy,&node_minvy,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/MinVzx/MinVzx.cpp =================================================================== --- /issm/trunk/src/c/modules/MinVzx/MinVzx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/MinVzx/MinVzx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (revision 12330) @@ -63,5 +63,4 @@ else elements_width=6; //penta elements - #ifdef _PARALLEL_ /*Determine parallel partitioning of elements: we use Metis for now. First load the data, then partition*/ if(dim==2){ @@ -79,9 +78,4 @@ xfree((void**)&elements); xfree((void**)&elements2d); - - #else - /*In serial mode, epart is full of 0: all elements belong to cpu 0: */ - epart=(int*)xcalloc(numberofelements,sizeof(int)); - #endif /*Deal with rifts, they have to be included into one partition only, not several: */ Index: /issm/trunk/src/c/modules/NodalValuex/NodalValuex.cpp =================================================================== --- /issm/trunk/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12329) +++ /issm/trunk/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12330) @@ -36,10 +36,16 @@ /*Broadcast whether we found the element: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); if(!sumfound)_error_("%s%i%s%s","could not find element with vertex with id",index," to compute nodal value ",EnumToStringx(natureofdataenum)); + #endif /*Broadcast and plug into response: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); MPI_Bcast(&value,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); + #else + value=cpu_found; + #endif *pnodalvalue=value; Index: /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp =================================================================== --- /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.cpp (revision 12330) @@ -16,9 +16,5 @@ #include "../../objects/objects.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ -#else void OutputResultsx( Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,Results* results){ -#endif extern int my_rank; @@ -31,11 +27,4 @@ bool dakota_analysis = false; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - const char **fnames = NULL; - mwSize onebyone[2] = {0,0}; - mwSize ndim = 2; - int nfields=0; - #endif - /*retrieve parameters: */ parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); @@ -43,7 +32,4 @@ if(dakota_analysis){ //no need to output anything, Dakota analysis has different outputs - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - *pdataref=mxCreateStructArray( ndim,onebyone,nfields,fnames); - #endif return; } @@ -56,5 +42,4 @@ /*Results do not include the type of solution being run . In parallel, we output results to a filename, *therefore, we need to include the solutiontype into the filename: */ - #ifdef _PARALLEL_ if(my_rank==0){ parameters->FindParam(&solutiontype,SolutionTypeEnum); @@ -88,26 +73,19 @@ parameters->SetParam(fid,OutputFilePointerEnum); } - #endif - /*Write results to disk (in parallel), or to memory (in serial mode): */ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - results->Write(pdataref); - #else - results->Write(parameters); - #endif + /*Write results to disk: */ + results->Write(parameters); /*Delete and reinitialize results, in parallel: */ - #ifdef _PARALLEL_ - results->clear(); + results->clear(); - /*Close output file? :*/ - /*WARNING: issm.cpp is taking care of it for now (quick fix) - if((step==1) && (time==0)){ - if(io_gather){ - if(my_rank==0) pfclose(fid,outputfilename); - } - else pfclose(fid,cpu_outputfilename); - } - */ - #endif + /*Close output file? :*/ + /*WARNING: issm.cpp is taking care of it for now (quick fix) + if((step==1) && (time==0)){ + if(io_gather){ + if(my_rank==0) pfclose(fid,outputfilename); + } + else pfclose(fid,cpu_outputfilename); + } + */ } Index: /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.h =================================================================== --- /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12329) +++ /issm/trunk/src/c/modules/OutputResultsx/OutputResultsx.h (revision 12330) @@ -14,10 +14,5 @@ #include "../../Container/Container.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -void OutputResultsx(mxArray** pdataref, Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); -#else void OutputResultsx(Elements* elements, Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, Results* results); -#endif #endif /* _OUTPUTRESULTS_H */ Index: /issm/trunk/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp =================================================================== --- /issm/trunk/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12330) @@ -10,4 +10,6 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif + +#include #include "./ParsePetscOptionsx.h" @@ -92,6 +94,6 @@ } - #ifdef _PARALLEL_ /*Ok, broadcast to other cpus: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&numanalyses,1,MPI_INT,0,MPI_COMM_WORLD); if(my_rank!=0){ @@ -100,4 +102,5 @@ } MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif for(i=0;iFindParam(&analysis_type,AnalysisTypeEnum); - PetscOptionsFromAnalysis(parameters,analysis_type); - #endif SolverxPetsc(&uf_vector,Kff->matrix,pf->vector,uf0_vector,df_vector,parameters); Index: /issm/trunk/src/c/modules/Solverx/SolverxPetsc.cpp =================================================================== --- /issm/trunk/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12329) +++ /issm/trunk/src/c/modules/Solverx/SolverxPetsc.cpp (revision 12330) @@ -43,5 +43,4 @@ #endif - /*Display message*/ _printf_(VerboseModule()," Solving\n"); @@ -52,5 +51,5 @@ #endif - /*First, check that f-set is not NULL, i.e. model is fully constrained: {{{*/ + /*First, check that f-set is not NULL, i.e. model is fully constrained:*/ _assert_(Kff); MatGetSize(Kff,&global_m,&global_n); _assert_(global_m==global_m); @@ -58,6 +57,6 @@ *puf=NULL; return; } - /*}}}*/ - /*Initial guess logic here: {{{1*/ + + /*Initial guess */ /*Now, check that we are not giving an initial guess to the solver, if we are running a direct solver: */ #if _PETSC_MAJOR_ >= 3 @@ -74,54 +73,23 @@ MatGetLocalSize(Kff,&local_m,&local_n);uf=NewVec(local_n,fromlocalsize); } - /*}}}*/ - /*Process petsc options to see if we are using special types of external solvers: {{{1*/ + + /*Process petsc options to see if we are using special types of external solvers*/ PetscOptionsDetermineSolverType(&solver_type); - /*In serial mode, the matrices have been loaded as MPIAIJ or AIJ matrices. - We need to convert them if we are going to run the solvers successfully: */ - #ifdef _SERIAL_ - #if _PETSC_MAJOR_ == 2 - if (solver_type==MUMPSPACKAGE_LU){ - /*Convert Kff to MATTAIJMUMPS: */ - MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); + /*Check the solver is available*/ + if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ + #if _PETSC_MAJOR_ >=3 + #ifndef _HAVE_MUMPS_ + _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); + #endif + #endif } - if (solver_type==MUMPSPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_LU){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SUPERLUDISTPACKAGE){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==StokesSolverEnum){ - _error_("Petsc 2 does not support multi-physics solvers"); - } - #endif - #endif - /*}}}*/ - /*Check the solver is available: {{{1*/ - if(solver_type==MUMPSPACKAGE_LU || solver_type==MUMPSPACKAGE_CHOL){ - #if _PETSC_MAJOR_ >=3 - #ifndef _HAVE_MUMPS_ - _error_("requested MUMPS solver, which was not compiled into ISSM!\n"); - #endif - #endif - } - /*}}}*/ - /*Prepare solver:{{{1*/ + /*Prepare solver*/ KSPCreate(MPI_COMM_WORLD,&ksp); KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); KSPSetFromOptions(ksp); - #if defined(_SERIAL_) && _PETSC_MAJOR_==3 + #if _PETSC_MAJOR_==3 /*Specific solver?: */ KSPGetPC(ksp,&pc); @@ -133,7 +101,5 @@ #endif } - #endif - #if defined(_PARALLEL_) && _PETSC_MAJOR_==3 /*Stokes: */ if (solver_type==StokesSolverEnum){ @@ -155,16 +121,15 @@ #endif - /*}}}*/ - /*If there is an initial guess for the solution, use it, except if we are using the MUMPS direct solver, where any initial guess will crash Petsc: {{{1*/ + /*If there is an initial guess for the solution, use it + * except if we are using the MUMPS direct solver + * where any initial guess will crash Petsc*/ if (uf0){ - if( (solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ + if((solver_type!=MUMPSPACKAGE_LU) && (solver_type!=MUMPSPACKAGE_CHOL) && (solver_type!=SPOOLESPACKAGE_LU) && (solver_type!=SPOOLESPACKAGE_CHOL) && (solver_type!=SUPERLUDISTPACKAGE)){ KSPSetInitialGuessNonzero(ksp,PETSC_TRUE); } } - /*}}}*/ - - if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); /*Solve: */ + if(VerboseSolver())KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD); KSPSolve(ksp,pf,uf); Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 12330) @@ -161,4 +161,5 @@ else if (strcmp(name,"PetscProfilingCurrentFlops")==0) return PetscProfilingCurrentFlopsEnum; else if (strcmp(name,"PetscProfilingSolutionTime")==0) return PetscProfilingSolutionTimeEnum; + else if (strcmp(name,"MaxIterationConvergenceFlag")==0) return MaxIterationConvergenceFlagEnum; else if (strcmp(name,"SteadystateMaxiter")==0) return SteadystateMaxiterEnum; else if (strcmp(name,"SteadystateNumRequestedOutputs")==0) return SteadystateNumRequestedOutputsEnum; @@ -259,9 +260,9 @@ else if (strcmp(name,"Input")==0) return InputEnum; else if (strcmp(name,"IntInput")==0) return IntInputEnum; - else if (strcmp(name,"IntParam")==0) return IntParamEnum; else stage=3; } if(stage==3){ - if (strcmp(name,"IntVecParam")==0) return IntVecParamEnum; + if (strcmp(name,"IntParam")==0) return IntParamEnum; + else if (strcmp(name,"IntVecParam")==0) return IntVecParamEnum; else if (strcmp(name,"MacAyeal2dIceFront")==0) return MacAyeal2dIceFrontEnum; else if (strcmp(name,"MacAyeal3dIceFront")==0) return MacAyeal3dIceFrontEnum; @@ -382,9 +383,9 @@ else if (strcmp(name,"StressTensoryz")==0) return StressTensoryzEnum; else if (strcmp(name,"StressTensorzz")==0) return StressTensorzzEnum; - else if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; else stage=4; } if(stage==4){ - if (strcmp(name,"P0")==0) return P0Enum; + if (strcmp(name,"IceVolume")==0) return IceVolumeEnum; + else if (strcmp(name,"P0")==0) return P0Enum; else if (strcmp(name,"P1")==0) return P1Enum; else if (strcmp(name,"P1DG")==0) return P1DGEnum; Index: /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/SurfaceAreax/SurfaceAreax.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceAreax/SurfaceAreax.cpp (revision 12330) @@ -28,7 +28,9 @@ /*Sum all J from all cpus of the cluster:*/ - MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); + #ifdef _HAVE_MPI_ + MPI_Reduce (&S,&S_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&S_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); S=S_sum; + #endif /*add surface area to element inputs:*/ Index: /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceAverageVelMisfitx/SurfaceAverageVelMisfitx.cpp (revision 12330) @@ -31,7 +31,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceLogVxVyMisfitx/SurfaceLogVxVyMisfitx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp =================================================================== --- /issm/trunk/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ThicknessAbsGradientx/ThicknessAbsGradientx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp =================================================================== --- /issm/trunk/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/ThicknessAbsMisfitx/ThicknessAbsMisfitx.cpp (revision 12330) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk/src/c/modules/TimeAdaptx/TimeAdaptx.cpp =================================================================== --- /issm/trunk/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/TimeAdaptx/TimeAdaptx.cpp (revision 12330) @@ -31,6 +31,6 @@ } - #ifdef _PARALLEL_ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&min_dt,&node_min_dt,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_min_dt,1,MPI_DOUBLE,0,MPI_COMM_WORLD); Index: /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp =================================================================== --- /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12329) +++ /issm/trunk/src/c/modules/TriMeshx/TriMeshx.cpp (revision 12330) @@ -10,8 +10,15 @@ #include "../../toolkits/toolkits.h" #include "../../EnumDefinitions/EnumDefinitions.h" +/*ANSI_DECLARATORS needed to call triangle library: */ +#ifndef ANSI_DECLARATORS +#define ANSI_DECLARATORS +#include "triangle.h" +#undef ANSI_DECLARATORS +#else +#include "triangle.h" +#endif /*}}}*/ - -void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,double area,bool order){ +void TriMeshx(Matrix** pindex,Vector** px,Vector** py,Matrix** psegments,Vector** psegmentmarkerlist,DataSet* domain,DataSet* rifts,double area){ /*indexing: */ @@ -28,5 +35,5 @@ /*intermediary: */ - int counter,backcounter; + int counter,counter2,backcounter; Contour* contour=NULL; @@ -39,6 +46,11 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); + in.numberofpoints+=contour->nods-1; + } + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); in.numberofpoints+=contour->nods; } + /*number of point attributes: */ in.numberofpointattributes=1; @@ -50,4 +62,12 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); + for (j=0;jnods-1;j++){ + in.pointlist[2*counter+0]=contour->x[j]; + in.pointlist[2*counter+1]=contour->y[j]; + counter++; + } + } + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); for (j=0;jnods;j++){ in.pointlist[2*counter+0]=contour->x[j]; @@ -58,5 +78,5 @@ /*fill in the point attribute list: */ - in.pointattributelist = (REAL *) xmalloc(in.numberofpoints * in.numberofpointattributes * sizeof(REAL)); + in.pointattributelist = (REAL*)xmalloc(in.numberofpoints*in.numberofpointattributes*sizeof(REAL)); for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); - in.numberofsegments+=contour->nods; + in.numberofsegments+=contour->nods-1; + } + for(i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); + /*for rifts, we have one less segment as we have vertices*/ + in.numberofsegments+=contour->nods-1; } @@ -79,5 +103,5 @@ for (i=0;iSize();i++){ contour=(Contour*)domain->GetObjectByOffset(i); - for (j=0;jnods-1;j++){ + for (j=0;jnods-2;j++){ in.segmentlist[2*counter+0]=counter; in.segmentlist[2*counter+1]=counter+1; @@ -92,5 +116,16 @@ backcounter=counter; } - + counter2=counter; + for (i=0;iSize();i++){ + contour=(Contour*)rifts->GetObjectByOffset(i); + for (j=0;j<(contour->nods-1);j++){ + in.segmentlist[2*counter2+0]=counter; + in.segmentlist[2*counter2+1]=counter+1; + in.segmentmarkerlist[counter2]=2+i; + counter2++; + counter++; + } + counter++; + } /*Build regions: */ @@ -103,20 +138,19 @@ for (i=0;iSize()-1;i++){ contour=(Contour*)domain->GetObjectByOffset(i+1); - GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods,contour->x,contour->y); + GridInsideHole(&in.holelist[2*i+0],&in.holelist[2*i+1],contour->nods-1,contour->x,contour->y); } } /* Make necessary initializations so that Triangle can return a triangulation in `out': */ - - out.pointlist = (REAL *) NULL; - out.pointattributelist = (REAL *) NULL; - out.pointmarkerlist = (int *) NULL; - out.trianglelist = (int *) NULL; - out.triangleattributelist = (REAL *) NULL; - out.neighborlist = (int *) NULL; - out.segmentlist = (int *) NULL; - out.segmentmarkerlist = (int *) NULL; - out.edgelist = (int *) NULL; - out.edgemarkerlist = (int *) NULL; + out.pointlist = (REAL*)NULL; + out.pointattributelist = (REAL*)NULL; + out.pointmarkerlist = (int *)NULL; + out.trianglelist = (int *)NULL; + out.triangleattributelist = (REAL*)NULL; + out.neighborlist = (int *)NULL; + out.segmentlist = (int *)NULL; + out.segmentmarkerlist = (int *)NULL; + out.edgelist = (int *)NULL; + out.edgemarkerlist = (int *)NULL; /* Triangulate the points:. Switches are chosen to read and write a */ @@ -125,12 +159,7 @@ /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ /* neighbor list (n). */ - sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/ - - triangulate(options, &in, &out, NULL); - /*report(&out, 0, 1, 1, 1, 1, 0);*/ - /*Allocate index, x and y: */ @@ -141,15 +170,14 @@ segmentmarkerlist=(double*)xmalloc(out.numberofsegments*sizeof(double)); - for (i = 0; i < out.numberoftriangles; i++) { + for (i = 0; i< out.numberoftriangles; i++) { for (j = 0; j < out.numberofcorners; j++) { - *(index+3*i+j)=(double)out.trianglelist[i * out.numberofcorners + j]+1; - } - } - for (i = 0; i < out.numberofpoints; i++) { - x[i]=out.pointlist[i * 2 + 0]; - y[i]=out.pointlist[i * 2 + 1]; - } - - for (i = 0; i < out.numberofsegments; i++) { + index[3*i+j]=(double)out.trianglelist[i*out.numberofcorners+j]+1; + } + } + for (i = 0; i< out.numberofpoints; i++){ + x[i]=out.pointlist[i*2+0]; + y[i]=out.pointlist[i*2+1]; + } + for (i = 0; iVertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); - FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); - this->TangentAtEdgesSize[0]=0, this->TangentAtEdgesSize[1]=0; this->TangentAtEdges=NULL; - FetchData(&this->Corners, &this->CornersSize[0], &this->CornersSize[1], mxGetAssignedField(matlab_struct,0,"Corners")); - FetchData(&this->RequiredVertices,&this->RequiredVerticesSize[0],&this->RequiredVerticesSize[1],mxGetAssignedField(matlab_struct,0,"RequiredVertices")); - FetchData(&this->RequiredEdges, &this->RequiredEdgesSize[0], &this->RequiredEdgesSize[1], mxGetAssignedField(matlab_struct,0,"RequiredEdges")); - FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); - FetchData(&this->SubDomains, &this->SubDomainsSize[0], &this->SubDomainsSize[1], mxGetAssignedField(matlab_struct,0,"SubDomains")); - -} -#endif -/*}}}*/ /*FUNCTION BamgGeom::~BamgGeom(){{{1*/ BamgGeom::~BamgGeom(){ @@ -49,77 +33,2 @@ } /*}}}*/ - -/*Methods*/ -/*FUNCTION BamgGeom::SetMatlabStructureFields{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgGeom::SetMatlabStructureFields(mxArray** matlab_struct){ - - /*Intermediary*/ - int i; - mxArray* output=NULL; - const int numfields=7; - const char* fnames[numfields]; - mwSize ndim=2; - mwSize dimensions[2]={1,1}; - - /*Initialize field names*/ - i=0; - fnames[i++] = "Vertices"; - fnames[i++] = "Edges"; - fnames[i++] = "TangentAtEdges"; - fnames[i++] = "RequiredVertices"; - fnames[i++] = "RequiredEdges"; - fnames[i++] = "CrackedEdges"; - fnames[i++] = "SubDomains"; - _assert_(i==numfields); - - /*Initialize Matlab structure*/ - output=mxCreateStructArray(ndim,dimensions,numfields,fnames); - - /*set each matlab each field*/ - i=0; - i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); - i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); - i++; SetMatlabStructureField(output,"TangentAtEdges", this->TangentAtEdgesSize[0], this->TangentAtEdgesSize[1], this->TangentAtEdges); - i++; SetMatlabStructureField(output,"RequiredVertices",this->RequiredVerticesSize[0],this->RequiredVerticesSize[1],this->RequiredVertices); - i++; SetMatlabStructureField(output,"RequiredEdges", this->RequiredEdgesSize[0], this->RequiredEdgesSize[1], this->RequiredEdges); - i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); - i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); - _assert_(i==numfields); - - /*Assign output*/ - *matlab_struct=output; - -} -#endif -/*}}}*/ -/*FUNCTION BamgGeom::SetMatlabStructureField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgGeom::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ - - /*Intermediary*/ - int i1,i2; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - - /*Copy field*/ - double* fieldcopy=NULL; - if (fieldrows*fieldcols){ - fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); - for(i1=0;i1 -#endif class BamgGeom{ @@ -30,13 +26,5 @@ BamgGeom(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgGeom(mxArray* matlab_struct); - #endif ~BamgGeom(); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabStructureFields(mxArray** matlab_struct); - void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); - #endif }; Index: /issm/trunk/src/c/objects/Bamg/BamgMesh.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/BamgMesh.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/BamgMesh.cpp (revision 12330) @@ -18,7 +18,7 @@ this->CrackedEdgesSize[0]=0, this->CrackedEdgesSize[1]=0; this->CrackedEdges=NULL; - this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0;this->VerticesOnGeomVertex=NULL; - this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; - this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; + this->VerticesOnGeomVertexSize[0]=0, this->VerticesOnGeomVertexSize[1]=0; this->VerticesOnGeomVertex=NULL; + this->VerticesOnGeomEdgeSize[0]=0, this->VerticesOnGeomEdgeSize[1]=0; this->VerticesOnGeomEdge=NULL; + this->EdgesOnGeomEdgeSize[0]=0, this->EdgesOnGeomEdgeSize[1]=0; this->EdgesOnGeomEdge=NULL; this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; @@ -28,37 +28,5 @@ this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; - - } -/*}}}*/ -/*FUNCTION BamgMesh::BamgMesh(mxArray* matlab_struct){{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -BamgMesh::BamgMesh(mxArray* matlab_struct){ - - int lines,cols; - - FetchData(&this->Vertices, &this->VerticesSize[0], &this->VerticesSize[1], mxGetAssignedField(matlab_struct,0,"Vertices")); - FetchData(&this->Edges, &this->EdgesSize[0], &this->EdgesSize[1], mxGetAssignedField(matlab_struct,0,"Edges")); - FetchData(&this->Triangles, &this->TrianglesSize[0], &this->TrianglesSize[1], mxGetAssignedField(matlab_struct,0,"Triangles")); - this->QuadrilateralsSize[0]=0, this->QuadrilateralsSize[1]=0; this->Quadrilaterals=NULL; - - this->SubDomainsSize[0]=0, this->SubDomainsSize[1]=0; this->SubDomains=NULL; - this->SubDomainsFromGeomSize[0]=0, this->SubDomainsFromGeomSize[1]=0; this->SubDomainsFromGeom=NULL; - this->CrackedVerticesSize[0]=0, this->CrackedVerticesSize[1]=0; this->CrackedVertices=NULL; - FetchData(&this->CrackedEdges, &this->CrackedEdgesSize[0], &this->CrackedEdgesSize[1], mxGetAssignedField(matlab_struct,0,"CrackedEdges")); - - FetchData(&this->VerticesOnGeomEdge, &this->VerticesOnGeomEdgeSize[0], &this->VerticesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"VerticesOnGeomEdge")); - FetchData(&this->VerticesOnGeomVertex,&this->VerticesOnGeomVertexSize[0],&this->VerticesOnGeomVertexSize[1],mxGetAssignedField(matlab_struct,0,"VerticesOnGeomVertex")); - FetchData(&this->EdgesOnGeomEdge, &this->EdgesOnGeomEdgeSize[0], &this->EdgesOnGeomEdgeSize[1], mxGetAssignedField(matlab_struct,0,"EdgesOnGeomEdge")); - - this->IssmEdgesSize[0]=0, this->IssmEdgesSize[1]=0; this->IssmEdges=NULL; - FetchData(&this->IssmSegments, &this->IssmSegmentsSize[0], &this->IssmSegmentsSize[1], mxGetAssignedField(matlab_struct,0,"IssmSegments")); - - this->ElementConnectivitySize[0]=0, this->ElementConnectivitySize[1]=0; this->ElementConnectivity=NULL; - this->NodalConnectivitySize[0]=0, this->NodalConnectivitySize[1]=0; this->NodalConnectivity=NULL; - this->NodalElementConnectivitySize[0]=0, this->NodalElementConnectivitySize[1]=0; this->NodalElementConnectivity=NULL; - -} -#endif /*}}}*/ /*FUNCTION BamgMesh::~BamgMesh(){{{1*/ @@ -89,95 +57,2 @@ } /*}}}*/ - -/*Methods*/ -/*FUNCTION BamgMesh::SetMatlabStructureFields{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgMesh::SetMatlabStructureFields(mxArray** matlab_struct){ - - /*Intermediary*/ - int i; - mxArray* output=NULL; - const int numfields=16; - const char* fnames[numfields]; - mwSize ndim=2; - mwSize dimensions[2]={1,1}; - - /*Initialize field names*/ - i=0; - fnames[i++] = "Triangles"; - fnames[i++] = "Vertices"; - fnames[i++] = "Edges"; - fnames[i++] = "IssmSegments"; - fnames[i++] = "IssmEdges"; - fnames[i++] = "Quadrilaterals"; - fnames[i++] = "VerticesOnGeomVertex"; - fnames[i++] = "VerticesOnGeomEdge"; - fnames[i++] = "EdgesOnGeomEdge"; - fnames[i++] = "SubDomains"; - fnames[i++] = "SubDomainsFromGeom"; - fnames[i++] = "ElementConnectivity"; - fnames[i++] = "NodalConnectivity"; - fnames[i++] = "NodalElementConnectivity"; - fnames[i++] = "CrackedVertices"; - fnames[i++] = "CrackedEdges"; - _assert_(i==numfields); - - /*Initialize Matlab structure*/ - output=mxCreateStructArray(ndim,dimensions,numfields,fnames); - - /*set each matlab each field*/ - i=0; - i++; SetMatlabStructureField(output,"Triangles", this->TrianglesSize[0], this->TrianglesSize[1], this->Triangles); - i++; SetMatlabStructureField(output,"Vertices", this->VerticesSize[0], this->VerticesSize[1], this->Vertices); - i++; SetMatlabStructureField(output,"Edges", this->EdgesSize[0], this->EdgesSize[1], this->Edges); - i++; SetMatlabStructureField(output,"IssmSegments", this->IssmSegmentsSize[0], this->IssmSegmentsSize[1], this->IssmSegments); - i++; SetMatlabStructureField(output,"IssmEdges", this->IssmEdgesSize[0], this->IssmEdgesSize[1], this->IssmEdges); - i++; SetMatlabStructureField(output,"Quadrilaterals", this->QuadrilateralsSize[0], this->QuadrilateralsSize[1], this->Quadrilaterals); - i++; SetMatlabStructureField(output,"VerticesOnGeomVertex",this->VerticesOnGeomVertexSize[0],this->VerticesOnGeomVertexSize[1], this->VerticesOnGeomVertex); - i++; SetMatlabStructureField(output,"VerticesOnGeomEdge", this->VerticesOnGeomEdgeSize[0], this->VerticesOnGeomEdgeSize[1], this->VerticesOnGeomEdge); - i++; SetMatlabStructureField(output,"EdgesOnGeomEdge", this->EdgesOnGeomEdgeSize[0], this->EdgesOnGeomEdgeSize[1], this->EdgesOnGeomEdge); - i++; SetMatlabStructureField(output,"SubDomains", this->SubDomainsSize[0], this->SubDomainsSize[1], this->SubDomains); - i++; SetMatlabStructureField(output,"SubDomainsFromGeom", this->SubDomainsFromGeomSize[0], this->SubDomainsFromGeomSize[1], this->SubDomainsFromGeom); - i++; SetMatlabStructureField(output,"ElementConnectivity", this->ElementConnectivitySize[0], this->ElementConnectivitySize[1], this->ElementConnectivity); - i++; SetMatlabStructureField(output,"NodalConnectivity", this->NodalConnectivitySize[0], this->NodalConnectivitySize[1], this->NodalConnectivity); - i++; SetMatlabStructureField(output,"NodalElementConnectivity", this->NodalElementConnectivitySize[0], this->NodalElementConnectivitySize[1], this->NodalElementConnectivity); - i++; SetMatlabStructureField(output,"CrackedVertices", this->CrackedVerticesSize[0], this->CrackedVerticesSize[1], this->CrackedVertices); - i++; SetMatlabStructureField(output,"CrackedEdges", this->CrackedEdgesSize[0], this->CrackedEdgesSize[1], this->CrackedEdges); - _assert_(i==numfields); - - /*Assign output*/ - *matlab_struct=output; - -} -#endif -/*}}}*/ -/*FUNCTION BamgMesh::SetMatlabStructureField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BamgMesh::SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer){ - - /*Intermediary*/ - int i1,i2; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - - /*Copy field*/ - double* fieldcopy=NULL; - if (fieldrows*fieldcols){ - fieldcopy=(double*)xmalloc(fieldrows*fieldcols*sizeof(double)); - for(i1=0;i1 -#endif class BamgMesh{ @@ -51,14 +47,5 @@ BamgMesh(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgMesh(mxArray* matlab_struct); - #endif ~BamgMesh(); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabStructureFields(mxArray** matlab_struct); - void SetMatlabStructureField(mxArray* matlab_struct,const char* fieldname,int fieldrows,int fieldcols,double* fieldpointer); - #endif - }; Index: /issm/trunk/src/c/objects/Bamg/BamgOpts.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/BamgOpts.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/BamgOpts.cpp (revision 12330) @@ -40,44 +40,4 @@ } -/*}}}*/ -/*FUNCTION BamgOpts::BamgOpts(mxArray* matlab_struct){{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -BamgOpts::BamgOpts(mxArray* matlab_struct){ - - FetchData(&this->anisomax,mxGetField(matlab_struct,0,"anisomax")); - FetchData(&this->cutoff,mxGetField(matlab_struct,0,"cutoff")); - FetchData(&this->coeff,mxGetField(matlab_struct,0,"coeff")); - FetchData(&this->errg,mxGetField(matlab_struct,0,"errg")); - FetchData(&this->gradation,mxGetField(matlab_struct,0,"gradation")); - FetchData(&this->Hessiantype,mxGetField(matlab_struct,0,"Hessiantype")); - FetchData(&this->MaxCornerAngle,mxGetField(matlab_struct,0,"MaxCornerAngle")); - FetchData(&this->maxnbv,mxGetField(matlab_struct,0,"maxnbv")); - FetchData(&this->maxsubdiv,mxGetField(matlab_struct,0,"maxsubdiv")); - FetchData(&this->Metrictype,mxGetField(matlab_struct,0,"Metrictype")); - FetchData(&this->nbjacobi,mxGetField(matlab_struct,0,"nbjacobi")); - FetchData(&this->nbsmooth,mxGetField(matlab_struct,0,"nbsmooth")); - FetchData(&this->omega,mxGetField(matlab_struct,0,"omega")); - FetchData(&this->power,mxGetField(matlab_struct,0,"power")); - FetchData(&this->verbose,mxGetField(matlab_struct,0,"verbose")); - - FetchData(&this->Crack,mxGetField(matlab_struct,0,"Crack")); - FetchData(&this->geometricalmetric,mxGetField(matlab_struct,0,"geometricalmetric")); - FetchData(&this->KeepVertices,mxGetField(matlab_struct,0,"KeepVertices")); - FetchData(&this->splitcorners,mxGetField(matlab_struct,0,"splitcorners")); - - FetchData(&this->hmin,mxGetField(matlab_struct,0,"hmin")); - FetchData(&this->hmax,mxGetField(matlab_struct,0,"hmax")); - FetchData(&this->hminVertices,&this->hminVerticesSize[0],&this->hminVerticesSize[1],mxGetField(matlab_struct,0,"hminVertices")); - FetchData(&this->hmaxVertices,&this->hmaxVerticesSize[0],&this->hmaxVerticesSize[1],mxGetField(matlab_struct,0,"hmaxVertices")); - FetchData(&this->hVertices,&this->hVerticesSize[0],&this->hVerticesSize[1],mxGetField(matlab_struct,0,"hVertices")); - FetchData(&this->metric,&this->metricSize[0],&this->metricSize[1],mxGetField(matlab_struct,0,"metric")); - FetchData(&this->field,&this->fieldSize[0],&this->fieldSize[1],mxGetField(matlab_struct,0,"field")); - FetchData(&this->err,&this->errSize[0],&this->errSize[1],mxGetField(matlab_struct,0,"err")); - - /*Additional checks*/ - this->Check(); - -} -#endif /*}}}*/ /*FUNCTION BamgOpts::~BamgOpts() {{{1*/ Index: /issm/trunk/src/c/objects/Bamg/BamgOpts.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/BamgOpts.h (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/BamgOpts.h (revision 12330) @@ -5,8 +5,4 @@ #ifndef _BAMGOPTS_H_ #define _BAMGOPTS_H_ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif class BamgOpts{ @@ -54,7 +50,4 @@ BamgOpts(); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - BamgOpts(mxArray* matlab_struct); - #endif ~BamgOpts(); Index: /issm/trunk/src/c/objects/Bamg/BamgQuadtree.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/BamgQuadtree.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Bamg/BamgQuadtree.cpp (revision 12330) @@ -0,0 +1,598 @@ +#include +#include +#include + +#include "../objects.h" + +namespace bamg { + + /*MACROS {{{1*/ + /* + * + * J j + * ^ ^ + * | | +--------+--------+ + * | | | | | + * 1X | | | 2 | 3 | + * | | | | | + * | | +--------+--------+ + * | | | | | + * 0X | | | 0 | 1 | + * | | | | | + * | | +--------+--------+ + * | +-----------------------> i + * | + * |----------------------------> I + * X0 X1 + * + * box 0 -> I=0 J=0 IJ=00 = 0 + * box 1 -> I=1 J=0 IJ=01 = 1 + * box 2 -> I=0 J=1 IJ=10 = 2 + * box 3 -> I=1 J=1 IJ=11 = 3 + */ +#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b))) +#define ABS(i) ((i)<0 ?-(i) :(i)) +#define MAX1(i,j) ((i)>(j) ?(i) :(j)) +#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2))) + + //IJ(i,j,l) returns the box number of i and j with respect to l + //if !j&l and !i&l -> 0 (box zero: lower left ) + //if !j&l and i&l -> 1 (box one: lower right) + //if j&l and !i&l -> 2 (box two: upper left ) + //if j&l and i&l -> 3 (box three:upper right) +#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) + + //I_IJ(k,l) returns l if first bit of k is 1, else 0 +#define I_IJ(k,l) ((k&1) ? l:0) + //J_IJ(k,l) returns l if second bit of k is 1, else 0 +#define J_IJ(k,l) ((k&2) ? l:0) + /*}}}*/ + /*DOCUMENTATION What is a BamgQuadtree? {{{1 + * A Quadtree is a very simple way to group vertices according + * to their locations. A square that holds all the points of the mesh + * (or the geometry) is divided into 4 boxes. As soon as one box + * hold more than 4 vertices, it is divided into 4 new boxes, etc... + * There cannot be more than MAXDEEP (=30) subdivision. + * This process is like a Dichotomy in dimension 2 + * + * + - - - - - - - - + - - + - + - + - - - - + + * | | | | X | | + * + - + - + + * | | | | | | + * + - - + - + - + + + * | | | | | + * + * | | | | | + * + - - - - - - - - + - - + - - + - - - - + + * | | | | + * + * | | | | + * + * | | | | + * | | | | + * + - - - - - - - - + - - - - + - - - - + + * | | | + * + * | | | + * + * | | | + * + * | | | + * | | | + * | | | + * | | | + * | | | + * + - - - - - - - - + - - - - - - - - + + * + * The coordinate system used in a quadtree are integers to avoid + * round-off errors. The vertex in the lower left box has the coordinates + * (0 0) + * The upper right vertex has the follwing coordinates: + * 2^30 -1 2^30 -1 in decimal + * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary + * \-- 29 --/ \-- 29 --/ + * Using binaries is therefore very easy to locate a vertex in a box: + * we just need to look at the bits from the left to the right (See ::Add) + }}}1*/ + + /*Constructors/Destructors*/ + /*FUNCTION BamgQuadtree::BamgQuadtree(){{{1*/ + BamgQuadtree::BamgQuadtree(){ + + /*Number of boxes and vertices*/ + NbBamgQuadtreeBox=0; + NbVertices=0; + + /*Create container*/ + boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + root=NewBamgQuadtreeBox(); + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){{{1*/ + BamgQuadtree::BamgQuadtree(Mesh * t,long nbv){ + + /*Number of boxes and vertices*/ + NbBamgQuadtreeBox=0; + NbVertices=0; + + /*Create container*/ + boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + root=NewBamgQuadtreeBox(); + + /*Check Sizes*/ + _assert_(MaxISize>MaxICoor); + + /*Add all vertices of the mesh*/ + if (nbv==-1) nbv=t->nbv; + for (int i=0;ivertices[i]); + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::~BamgQuadtree(){{{1*/ + BamgQuadtree::~BamgQuadtree() { + delete boxcontainer; + root=NULL; + } + /*}}}1*/ + + /*Methods*/ + /*FUNCTION BamgQuadtree::Add{{{1*/ + void BamgQuadtree::Add(BamgVertex &w){ + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/Add)*/ + BamgQuadtreeBox** pb=NULL; + BamgQuadtreeBox* b=NULL; + + /*Get integer coodinate of current point w*/ + register long i=w.i.x, j=w.i.y; + + /*Initialize level*/ + register long level=MaxISize; + + /*Get inital box (the largest)*/ + pb = &root; + + /*Find the smallest box where w is located*/ + while((b=*pb) && (b->nbitems<0)){ + + //shift b->nbitems by -1 + b->nbitems--; + + //shifted righ by one bit: level=00000010 -> 00000001 + level >>= 1; + + //Get next subbox according to the bit value (level) + pb = &b->b[IJ(i,j,level)]; + } + + /*OK, we have found b, a Subbox holding vertices (might be full) + check that the vertex is not already in the box*/ + if (b){ + if (b->nbitems > 3 && b->v[3] == &w) return; + if (b->nbitems > 2 && b->v[2] == &w) return; + if (b->nbitems > 1 && b->v[1] == &w) return; + if (b->nbitems > 0 && b->v[0] == &w) return; + } + + /*check that l is not 0 (this should not happen as MaxDepth = 30)*/ + _assert_(level>0); + + /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it + in 4 new subboxes*/ + while ((b= *pb) && (b->nbitems == 4)){ // the BamgQuadtreeBox is full + + /*Copy the 4 vertices in the current BamgQuadtreebox*/ + BamgVertex* v4[4]; + v4[0]= b->v[0]; + v4[1]= b->v[1]; + v4[2]= b->v[2]; + v4[3]= b->v[3]; + + /*set nbitems as negative + * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ + b->nbitems = -b->nbitems; + + /*Initialize the 4 pointers toward the 4 subboxes*/ + b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; + + /*level = 0010000 -> 0001000*/ + level >>= 1; + + /*Put the four vertices in the new boxes*/ + for (int k=0;k<4;k++){ + + int ij; + /*bb is the new "sub"box of b where v4[k] is located*/ + BamgQuadtreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; + + // alloc the BamgQuadtreeBox + if (!bb) bb=b->b[ij]=NewBamgQuadtreeBox(); + + /*Copy the current vertex*/ + bb->v[bb->nbitems++] = v4[k]; + } + + /*Get the subbox where w (i,j) is located*/ + pb = &b->b[IJ(i,j,level)]; + } + + /*alloc the BamgQuadtreeBox if necessary*/ + if (!(b=*pb)) b=*pb= NewBamgQuadtreeBox(); + + /*Add w*/ + b->v[b->nbitems++]=&w; + + //Increase NbVertices by one (we have one new vertex) + NbVertices++; + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NearestVertex{{{1*/ + BamgVertex* BamgQuadtree::NearestVertex(Icoor1 i,Icoor1 j) { + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertex)*/ + + /*Intermediaries*/ + BamgQuadtreeBox *pb[MaxDepth]; + int pi[MaxDepth]; + Icoor1 ii[MaxDepth]; + Icoor1 jj[MaxDepth]; + int level; + long n0; + BamgQuadtreeBox *b; + long h0; + long h = MaxISize; + long hb= MaxISize; + Icoor1 i0=0,j0=0; + + /*initial output as NULL (no vertex found)*/ + BamgVertex* nearest_v=NULL; + + /*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/ + Icoor1 iplus( inbitems) return nearest_v; + + /*else, find the smallest non-empty BamgQuadtreeBox containing the point (i,j)*/ + while((n0=b->nbitems)<0){ + + Icoor1 hb2 = hb >> 1; //size of the current box + int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) + BamgQuadtreeBox *b0 = b->b[k]; //pointer toward current box + + /* break if NULL box or empty (Keep previous box b)*/ + if (( b0 == NULL) || (b0->nbitems == 0)) break; + + /*Get next Quadtree box*/ + b=b0; + i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox (macro) + j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox + hb = hb2; // size of the box (in Int) + } + + /*The box b, is the smallest box containing the point (i,j) and + * has the following properties: + * - n0: number of items (>0 if vertices, else boxes) + * - hb: box size (int) + * - i0: x coordinate of the lower left corner + * - j0: y coordinate of the lower left corner*/ + + /* if the current subbox is holding vertices, we are almost done*/ + if (n0>0){ + //loop over the vertices of the box and find the closest vertex + for(int k=0;kv[k]->i; + + /*Compute norm with w*/ + h0=NORM(iplus,i2.x,jplus,i2.y); + + /*is it smaller than previous value*/ + if (h0v[k]; + } + } + /*return closest vertex*/ + return nearest_v; + } + + /* general case: the current box is empty, we have to go backwards + and find the closest not-empty box and find the closest vertex*/ + + /*Initialize search variables*/ + pb[0]=b; //pointer toward the box b + pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b + ii[0]=i0; //i coordinate of the box lowest left corner + jj[0]=j0; //j coordinate of the box lowest left corner + + /*initialize h: smallest box size, containing a vertex close to w*/ + h=hb; + + /*Main loop*/ + level=0; + do { + + /*get current box*/ + b= pb[level]; + + /*Loop over the items in current box (if not empty!)*/ + while (pi[level]){ + + /*We are looping now over the items of b. k is the current index (in [0 3])*/ + pi[level]--; + int k=pi[level]; + + /*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/ + if (b->nbitems>0){ + I2 i2=b->v[k]->i; + h0 = NORM(iplus,i2.x,jplus,i2.y); + if (h0v[k]; + } + } + /*else: current box b is pointing toward 4 boxes + * test sub-box k and go deeper into the tree if it is non empty + * and contains the point w modulo a size h that is either the size of the smallest + * non empty box containing w, or the closest point to w (so far) */ + else{ + BamgQuadtreeBox* b0=b; + + /*if the next box exists:*/ + if (b=b->b[k]){ + + /*Get size (hb) and coordinates of the current sub-box lowest left corner*/ + hb>>=1; + Icoor1 iii = ii[level]+I_IJ(k,hb); + Icoor1 jjj = jj[level]+J_IJ(k,hb); + + /*if the current point (iplus,jplus) is in b (modulo h), this box is good: + * it is holding vertices that are close to w */ + if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){ + level++; + pb[level]= b; + pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[level]= iii; + jj[level]= jjj; + } + + //else go backwards + else{ + //shifted righ by one bit: hb=001000000 -> 01000000 + b=b0; + hb<<=1; + } + } + else{ + /*Current box is NULL, go to next subbox of b (k=k-1)*/ + b=b0; + } + } + } + + /*We have found a vertex, now, let's try the other boxes of the previous level + * in case there is a vertex closest to w that has not yet been tested*/ + hb <<= 1; + } while (level--); + + /*return nearest_v, nearest vertex*/ + return nearest_v; + + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NearestVertexWithNormal{{{1*/ + BamgVertex* BamgQuadtree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/NearestVertexWithNormal)*/ + + BamgQuadtreeBox * pb[ MaxDepth ]; + int pi[ MaxDepth ]; + Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + int l; // level + BamgQuadtreeBox * b; + long h =MaxISize,h0; + long hb=MaxISize; + Icoor1 i0=0,j0=0; + Icoor1 iplus( inbitems) + return vn; // empty tree + + while( (n0 = b->nbitems) < 0) + { + // search the non empty + // BamgQuadtreeBox containing the point (i,j) + register Icoor1 hb2 = hb >> 1 ; + register int k = IJ(iplus,jplus,hb2);// BamgQuadtreeBox number of size hb2 contening i;j + register BamgQuadtreeBox * b0= b->b[k]; + if ( ( b0 == 0) || (b0->nbitems == 0) ) + break; // null box or empty => break + b=b0; + i0 += I_IJ(k,hb2); // i orign of BamgQuadtreeBox + j0 += J_IJ(k,hb2); // j orign of BamgQuadtreeBox + hb = hb2; + } + + + if ( n0 > 0) + { + for(register int k=0;kv[k]->i; + // try if is in the right direction -- + h0 = NORM(iplus,i2.x,jplus,i2.y); + if (h0 v[k];} + } + if (vn) return vn; + } + // general case ----- + // INITIALISATION OF THE HEAP + l =0; // level + pb[0]= b; + pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[0]=i0; + jj[0]=j0; + h=hb; + do { // walk on the tree + b= pb[l]; + while (pi[l]--) // loop on 4 element of the box + { + int k = pi[l]; + + if (b->nbitems>0) // BamgVertex BamgQuadtreeBox none empty + { + I2 i2 = b->v[k]->i; + // if good direction when try -- + + h0 = NORM(iplus,i2.x,jplus,i2.y); + if (h0 v[k]; + } + } + else // Pointer BamgQuadtreeBox + { + register BamgQuadtreeBox *b0=b; + if ((b=b->b[k])) + { + hb >>=1 ; // div by 2 + register Icoor1 iii = ii[l]+I_IJ(k,hb); + register Icoor1 jjj = jj[l]+J_IJ(k,hb); + + if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) + { + pb[++l]= b; + pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[l]= iii; + jj[l]= jjj; + + } + else + b=b0, hb <<=1 ; + } + else + b=b0; + } + } + hb <<= 1; // mul by 2 + } while (l--); + + return vn; + } + /*}}}1*/ + /*FUNCTION BamgQuadtree::NewBamgQuadtreeBox {{{1*/ + BamgQuadtree::BamgQuadtreeBox* BamgQuadtree::NewBamgQuadtreeBox(void){ + + /*Output*/ + BamgQuadtreeBox* newbox=NULL; + + /*Create and initialize a new box*/ + newbox=new BamgQuadtreeBox; + newbox->nbitems=0; + newbox->b[0]=NULL; + newbox->b[1]=NULL; + newbox->b[2]=NULL; + newbox->b[3]=NULL; + + /*Add root to the container*/ + boxcontainer->AddObject(newbox); + + /*Increase counter*/ + NbBamgQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; + }/*}}}*/ + /*FUNCTION BamgQuadtree::ToClose {{{1*/ + BamgVertex* BamgQuadtree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){ + /*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.cpp/ToClose)*/ + + const Icoor1 i=v.i.x; + const Icoor1 j=v.i.y; + const R2 X(v.r); + const Metric Mx(v.m); + + BamgQuadtreeBox * pb[ MaxDepth ]; + int pi[ MaxDepth ]; + Icoor1 ii[ MaxDepth ], jj [ MaxDepth]; + register int l=0; // level + register BamgQuadtreeBox * b; + Icoor1 h=MaxISize; + Icoor1 hb = MaxISize; + Icoor1 i0=0,j0=0; + + // BamgVertex *vn=0; + + if (!root->nbitems) + return 0; // empty tree + + // general case ----- + pb[0]=root; + pi[0]=root->nbitems>0 ?(int) root->nbitems : 4 ; + ii[0]=i0; + jj[0]=j0; + h=hb; + do { + b= pb[l]; + while (pi[l]--){ + register int k = pi[l]; + + if (b->nbitems>0){ // BamgVertex BamgQuadtreeBox none empty + I2 i2 = b->v[k]->i; + if ( ABS(i-i2.x) v[k]->r); + double dd; + if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ + return b->v[k]; + } + } + } + else{ // Pointer BamgQuadtreeBox + register BamgQuadtreeBox *b0=b; + if ((b=b->b[k])){ + hb >>=1 ; // div by 2 + register long iii = ii[l]+I_IJ(k,hb); + register long jjj = jj[l]+J_IJ(k,hb); + + if (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){ + pb[++l]= b; + pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; + ii[l]= iii; + jj[l]= jjj; + + } + else{ + b=b0; + hb <<=1 ; + } + } + else{ + b=b0; + } + } + } + hb <<= 1; // mul by 2 + } while (l--); + + return 0; + } + /*}}}1*/ +} Index: /issm/trunk/src/c/objects/Bamg/BamgQuadtree.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/BamgQuadtree.h (revision 12330) +++ /issm/trunk/src/c/objects/Bamg/BamgQuadtree.h (revision 12330) @@ -0,0 +1,60 @@ +/*Original code from Frederic Hecht (BAMG v1.01, BamgQuadtree.h)*/ +#ifndef _BAMGQUADTREE_H +#define _BAMGQUADTREE_H + +#include "./include.h" + +namespace bamg { + + const int MaxDepth = 30; + const long MaxISize = ( 1L << MaxDepth); // = 2^30 : 010000000000..000 (bitwise operation) + + class BamgVertex; + + class BamgQuadtree{ + + private: + + /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are + * created if a fifth vertex is added to the same box. A Quadtree box is therefore + * composed of EITHER: + * - up to 4 vertices + * - 4 "sub" quadtree boxes*/ + class BamgQuadtreeBox: public Object{ + public: + int nbitems; // number of current vertices in the box + union{ + BamgQuadtreeBox* b[4]; + BamgVertex* v[4]; + }; + /*Object functions*/ + void Echo() {_error_("not implemented yet"); }; + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; + int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum() {_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + }; + + /*BamgQuadtree private Fields*/ + DataSet* boxcontainer; + + public: + + /*BamgQuadtree public Fields*/ + BamgQuadtreeBox* root; + long NbBamgQuadtreeBox; + long NbVertices; + + BamgQuadtree(); + BamgQuadtree(Mesh *t,long nbv=-1); + ~BamgQuadtree(); + + BamgVertex *NearestVertex(Icoor1 i,Icoor1 j); + BamgVertex *NearestVertexWithNormal(Icoor1 i,Icoor1 j); + BamgQuadtreeBox *NewBamgQuadtreeBox(void); + BamgVertex *ToClose(BamgVertex &,double ,Icoor1,Icoor1); + void Add(BamgVertex &w); + }; +} +#endif Index: /issm/trunk/src/c/objects/Bamg/Geometry.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/Geometry.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/Geometry.cpp (revision 12330) @@ -505,5 +505,5 @@ float *eangle = new float[nbe]; double eps = 1e-20; - QuadTree quadtree; // build quadtree to find duplicates + BamgQuadtree quadtree; // build quadtree to find duplicates BamgVertex *v0 = vertices; GeomVertex *v0g = (GeomVertex*) (void*)v0; Index: /issm/trunk/src/c/objects/Bamg/Geometry.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/Geometry.h (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/Geometry.h (revision 12330) @@ -12,5 +12,5 @@ class Triangle; - class QuadTree; + class BamgQuadtree; class GeomSubDomain; class Edge; @@ -20,17 +20,17 @@ public: - long NbRef; // counter of ref on the this class if 0 we can delete - long nbv; // number of vertices - long nbe; // number of edges - long nbsubdomains; - long nbcurves; + long NbRef; // counter of ref on the this class if 0 we can delete + long nbv; // number of vertices + long nbe; // number of edges + long nbsubdomains; + long nbcurves; GeomVertex *vertices; GeomEdge *edges; - QuadTree *quadtree; + BamgQuadtree *quadtree; GeomSubDomain *subdomains; - Curve *curves; - R2 pmin,pmax; // domain extrema coordinates - double coefIcoor; // coef to integer Icoor1; - double MaxCornerAngle; + Curve *curves; + R2 pmin,pmax; // domain extrema coordinates + double coefIcoor; // coef to integer Icoor1; + double MaxCornerAngle; //Constructor/Destructors @@ -44,5 +44,5 @@ GeomVertex &operator[](long i) { return vertices[i]; }; const GeomEdge &operator()(long i) const { return edges[i]; }; - GeomEdge &operator()(long i) { return edges[i]; }; + GeomEdge &operator()(long i) { return edges[i]; }; //Methods Index: /issm/trunk/src/c/objects/Bamg/Mesh.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/Mesh.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/Mesh.cpp (revision 12330) @@ -2885,5 +2885,5 @@ //build quadtree - if (!quadtree) quadtree = new QuadTree(this,0); + if (!quadtree) quadtree = new BamgQuadtree(this,0); quadtree->Add(*v0); quadtree->Add(*v1); @@ -3107,10 +3107,10 @@ } /*}}}1*/ - /*FUNCTION Mesh::MakeQuadTree{{{1*/ - void Mesh::MakeQuadTree() { - /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeQuadTree)*/ + /*FUNCTION Mesh::MakeBamgQuadtree{{{1*/ + void Mesh::MakeBamgQuadtree() { + /*Original code from Frederic Hecht (BAMG v1.01, Mesh2.cpp/MakeBamgQuadtree)*/ long int verbose=0; - if ( !quadtree ) quadtree = new QuadTree(this); + if ( !quadtree ) quadtree = new BamgQuadtree(this); } @@ -3622,5 +3622,5 @@ if (!quadtree) delete quadtree; //ReInitialise; - quadtree = new QuadTree(this,0); + quadtree = new BamgQuadtree(this,0); quadtree->Add(*v0); quadtree->Add(*v1); @@ -3900,5 +3900,5 @@ if (quadtree){ delete quadtree; - quadtree = new QuadTree(this); + quadtree = new BamgQuadtree(this); } @@ -4116,5 +4116,5 @@ delete [] tstart; - if (quadtree) quadtree= new QuadTree(this); + if (quadtree) quadtree= new BamgQuadtree(this); } /*}}}1*/ Index: /issm/trunk/src/c/objects/Bamg/Mesh.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/Mesh.h (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/Mesh.h (revision 12330) @@ -17,5 +17,5 @@ class Geometry; class CrackedEdge; - class QuadTree; + class BamgQuadtree; class SubDomain; @@ -29,5 +29,5 @@ Triangle *triangles; Edge *edges; - QuadTree *quadtree; + BamgQuadtree *quadtree; BamgVertex **orderedvertices; SubDomain *subdomains; @@ -94,5 +94,5 @@ void MakeQuadrangles(double costheta); int SplitElement(int choice); - void MakeQuadTree(); + void MakeBamgQuadtree(); void NewPoints(Mesh &,BamgOpts* bamgopts,int KeepVertices=1); long InsertNewPoints(long nbvold,long & NbTSwap) ; Index: /issm/trunk/src/c/objects/Bamg/Metric.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/Metric.h (revision 12329) +++ /issm/trunk/src/c/objects/Bamg/Metric.h (revision 12330) @@ -5,4 +5,5 @@ #include "../../shared/Bamg/shared.h" #include "R2.h" +#include namespace bamg { Index: sm/trunk/src/c/objects/Bamg/QuadTree.cpp =================================================================== --- /issm/trunk/src/c/objects/Bamg/QuadTree.cpp (revision 12329) +++ (revision ) @@ -1,598 +1,0 @@ -#include -#include -#include - -#include "../objects.h" - -namespace bamg { - - /*MACROS {{{1*/ - /* - * - * J j - * ^ ^ - * | | +--------+--------+ - * | | | | | - * 1X | | | 2 | 3 | - * | | | | | - * | | +--------+--------+ - * | | | | | - * 0X | | | 0 | 1 | - * | | | | | - * | | +--------+--------+ - * | +-----------------------> i - * | - * |----------------------------> I - * X0 X1 - * - * box 0 -> I=0 J=0 IJ=00 = 0 - * box 1 -> I=1 J=0 IJ=01 = 1 - * box 2 -> I=0 J=1 IJ=10 = 2 - * box 3 -> I=1 J=1 IJ=11 = 3 - */ -#define INTER_SEG(a,b,x,y) (((y) > (a)) && ((x) <(b))) -#define ABS(i) ((i)<0 ?-(i) :(i)) -#define MAX1(i,j) ((i)>(j) ?(i) :(j)) -#define NORM(i1,j1,i2,j2) MAX1(ABS((i1)-(j1)),ABS((i2)-(j2))) - - //IJ(i,j,l) returns the box number of i and j with respect to l - //if !j&l and !i&l -> 0 (box zero: lower left ) - //if !j&l and i&l -> 1 (box one: lower right) - //if j&l and !i&l -> 2 (box two: upper left ) - //if j&l and i&l -> 3 (box three:upper right) -#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) - - //I_IJ(k,l) returns l if first bit of k is 1, else 0 -#define I_IJ(k,l) ((k&1) ? l:0) - //J_IJ(k,l) returns l if second bit of k is 1, else 0 -#define J_IJ(k,l) ((k&2) ? l:0) - /*}}}*/ - /*DOCUMENTATION What is a QuadTree? {{{1 - * A Quadtree is a very simple way to group vertices according - * to their locations. A square that holds all the points of the mesh - * (or the geometry) is divided into 4 boxes. As soon as one box - * hold more than 4 vertices, it is divided into 4 new boxes, etc... - * There cannot be more than MAXDEEP (=30) subdivision. - * This process is like a Dichotomy in dimension 2 - * - * + - - - - - - - - + - - + - + - + - - - - + - * | | | | X | | - * + - + - + - * | | | | | | - * + - - + - + - + + - * | | | | | - * - * | | | | | - * + - - - - - - - - + - - + - - + - - - - + - * | | | | - * - * | | | | - * - * | | | | - * | | | | - * + - - - - - - - - + - - - - + - - - - + - * | | | - * - * | | | - * - * | | | - * - * | | | - * | | | - * | | | - * | | | - * | | | - * + - - - - - - - - + - - - - - - - - + - * - * The coordinate system used in a quadtree are integers to avoid - * round-off errors. The vertex in the lower left box has the coordinates - * (0 0) - * The upper right vertex has the follwing coordinates: - * 2^30 -1 2^30 -1 in decimal - * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary - * \-- 29 --/ \-- 29 --/ - * Using binaries is therefore very easy to locate a vertex in a box: - * we just need to look at the bits from the left to the right (See ::Add) - }}}1*/ - - /*Constructors/Destructors*/ - /*FUNCTION QuadTree::QuadTree(){{{1*/ - QuadTree::QuadTree(){ - - /*Number of boxes and vertices*/ - NbQuadTreeBox=0; - NbVertices=0; - - /*Create container*/ - boxcontainer=new DataSet(); - - /*Create Root, pointer toward the main box*/ - root=NewQuadTreeBox(); - - } - /*}}}1*/ - /*FUNCTION QuadTree::QuadTree(Mesh * t,long nbv){{{1*/ - QuadTree::QuadTree(Mesh * t,long nbv){ - - /*Number of boxes and vertices*/ - NbQuadTreeBox=0; - NbVertices=0; - - /*Create container*/ - boxcontainer=new DataSet(); - - /*Create Root, pointer toward the main box*/ - root=NewQuadTreeBox(); - - /*Check Sizes*/ - _assert_(MaxISize>MaxICoor); - - /*Add all vertices of the mesh*/ - if (nbv==-1) nbv=t->nbv; - for (int i=0;ivertices[i]); - - } - /*}}}1*/ - /*FUNCTION QuadTree::~QuadTree(){{{1*/ - QuadTree::~QuadTree() { - delete boxcontainer; - root=NULL; - } - /*}}}1*/ - - /*Methods*/ - /*FUNCTION QuadTree::Add{{{1*/ - void QuadTree::Add(BamgVertex &w){ - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/Add)*/ - QuadTreeBox** pb=NULL; - QuadTreeBox* b=NULL; - - /*Get integer coodinate of current point w*/ - register long i=w.i.x, j=w.i.y; - - /*Initialize level*/ - register long level=MaxISize; - - /*Get inital box (the largest)*/ - pb = &root; - - /*Find the smallest box where w is located*/ - while((b=*pb) && (b->nbitems<0)){ - - //shift b->nbitems by -1 - b->nbitems--; - - //shifted righ by one bit: level=00000010 -> 00000001 - level >>= 1; - - //Get next subbox according to the bit value (level) - pb = &b->b[IJ(i,j,level)]; - } - - /*OK, we have found b, a Subbox holding vertices (might be full) - check that the vertex is not already in the box*/ - if (b){ - if (b->nbitems > 3 && b->v[3] == &w) return; - if (b->nbitems > 2 && b->v[2] == &w) return; - if (b->nbitems > 1 && b->v[1] == &w) return; - if (b->nbitems > 0 && b->v[0] == &w) return; - } - - /*check that l is not 0 (this should not happen as MaxDeep = 30)*/ - _assert_(level>0); - - /*Now, try to add the vertex, if the subbox is full (nbitems=4), we have to divide it - in 4 new subboxes*/ - while ((b= *pb) && (b->nbitems == 4)){ // the QuadTreeBox is full - - /*Copy the 4 vertices in the current QuadTreebox*/ - BamgVertex* v4[4]; - v4[0]= b->v[0]; - v4[1]= b->v[1]; - v4[2]= b->v[2]; - v4[3]= b->v[3]; - - /*set nbitems as negative - * (box full -> holds 4 pointers toward subboxes and not 4 vertices)*/ - b->nbitems = -b->nbitems; - - /*Initialize the 4 pointers toward the 4 subboxes*/ - b->b[0]=b->b[1]=b->b[2]=b->b[3]=NULL; - - /*level = 0010000 -> 0001000*/ - level >>= 1; - - /*Put the four vertices in the new boxes*/ - for (int k=0;k<4;k++){ - - int ij; - /*bb is the new "sub"box of b where v4[k] is located*/ - QuadTreeBox *bb = b->b[ij=IJ(v4[k]->i.x,v4[k]->i.y,level)]; - - // alloc the QuadTreeBox - if (!bb) bb=b->b[ij]=NewQuadTreeBox(); - - /*Copy the current vertex*/ - bb->v[bb->nbitems++] = v4[k]; - } - - /*Get the subbox where w (i,j) is located*/ - pb = &b->b[IJ(i,j,level)]; - } - - /*alloc the QuadTreeBox if necessary*/ - if (!(b=*pb)) b=*pb= NewQuadTreeBox(); - - /*Add w*/ - b->v[b->nbitems++]=&w; - - //Increase NbVertices by one (we have one new vertex) - NbVertices++; - } - /*}}}1*/ - /*FUNCTION QuadTree::NearestVertex{{{1*/ - BamgVertex* QuadTree::NearestVertex(Icoor1 i,Icoor1 j) { - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertex)*/ - - /*Intermediaries*/ - QuadTreeBox *pb[MaxDeep]; - int pi[MaxDeep]; - Icoor1 ii[MaxDeep]; - Icoor1 jj[MaxDeep]; - int level; - long n0; - QuadTreeBox *b; - long h0; - long h = MaxISize; - long hb= MaxISize; - Icoor1 i0=0,j0=0; - - /*initial output as NULL (no vertex found)*/ - BamgVertex* nearest_v=NULL; - - /*Project w coordinates (i,j) onto [0,MaxISize-1] x [0,MaxISize-1] -> (iplus,jplus)*/ - Icoor1 iplus( inbitems) return nearest_v; - - /*else, find the smallest non-empty QuadTreeBox containing the point (i,j)*/ - while((n0=b->nbitems)<0){ - - Icoor1 hb2 = hb >> 1; //size of the current box - int k = IJ(iplus,jplus,hb2); //box number (0,1,2 or 3) - QuadTreeBox *b0 = b->b[k]; //pointer toward current box - - /* break if NULL box or empty (Keep previous box b)*/ - if (( b0 == NULL) || (b0->nbitems == 0)) break; - - /*Get next Quadtree box*/ - b=b0; - i0 += I_IJ(k,hb2); // i orign of QuadTreeBox (macro) - j0 += J_IJ(k,hb2); // j orign of QuadTreeBox - hb = hb2; // size of the box (in Int) - } - - /*The box b, is the smallest box containing the point (i,j) and - * has the following properties: - * - n0: number of items (>0 if vertices, else boxes) - * - hb: box size (int) - * - i0: x coordinate of the lower left corner - * - j0: y coordinate of the lower left corner*/ - - /* if the current subbox is holding vertices, we are almost done*/ - if (n0>0){ - //loop over the vertices of the box and find the closest vertex - for(int k=0;kv[k]->i; - - /*Compute norm with w*/ - h0=NORM(iplus,i2.x,jplus,i2.y); - - /*is it smaller than previous value*/ - if (h0v[k]; - } - } - /*return closest vertex*/ - return nearest_v; - } - - /* general case: the current box is empty, we have to go backwards - and find the closest not-empty box and find the closest vertex*/ - - /*Initialize search variables*/ - pb[0]=b; //pointer toward the box b - pi[0]=b->nbitems>0?(int)b->nbitems:4;//number of boxes in b - ii[0]=i0; //i coordinate of the box lowest left corner - jj[0]=j0; //j coordinate of the box lowest left corner - - /*initialize h: smallest box size, containing a vertex close to w*/ - h=hb; - - /*Main loop*/ - level=0; - do { - - /*get current box*/ - b= pb[level]; - - /*Loop over the items in current box (if not empty!)*/ - while (pi[level]){ - - /*We are looping now over the items of b. k is the current index (in [0 3])*/ - pi[level]--; - int k=pi[level]; - - /*if the current subbox is holding vertices (b->nbitems<0 is subboxes)*/ - if (b->nbitems>0){ - I2 i2=b->v[k]->i; - h0 = NORM(iplus,i2.x,jplus,i2.y); - if (h0v[k]; - } - } - /*else: current box b is pointing toward 4 boxes - * test sub-box k and go deeper into the tree if it is non empty - * and contains the point w modulo a size h that is either the size of the smallest - * non empty box containing w, or the closest point to w (so far) */ - else{ - QuadTreeBox* b0=b; - - /*if the next box exists:*/ - if (b=b->b[k]){ - - /*Get size (hb) and coordinates of the current sub-box lowest left corner*/ - hb>>=1; - Icoor1 iii = ii[level]+I_IJ(k,hb); - Icoor1 jjj = jj[level]+J_IJ(k,hb); - - /*if the current point (iplus,jplus) is in b (modulo h), this box is good: - * it is holding vertices that are close to w */ - if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)){ - level++; - pb[level]= b; - pi[level]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[level]= iii; - jj[level]= jjj; - } - - //else go backwards - else{ - //shifted righ by one bit: hb=001000000 -> 01000000 - b=b0; - hb<<=1; - } - } - else{ - /*Current box is NULL, go to next subbox of b (k=k-1)*/ - b=b0; - } - } - } - - /*We have found a vertex, now, let's try the other boxes of the previous level - * in case there is a vertex closest to w that has not yet been tested*/ - hb <<= 1; - } while (level--); - - /*return nearest_v, nearest vertex*/ - return nearest_v; - - } - /*}}}1*/ - /*FUNCTION QuadTree::NearestVertexWithNormal{{{1*/ - BamgVertex* QuadTree::NearestVertexWithNormal(Icoor1 i,Icoor1 j) { - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/NearestVertexWithNormal)*/ - - QuadTreeBox * pb[ MaxDeep ]; - int pi[ MaxDeep ]; - Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; - int l; // level - QuadTreeBox * b; - long h =MaxISize,h0; - long hb=MaxISize; - Icoor1 i0=0,j0=0; - Icoor1 iplus( inbitems) - return vn; // empty tree - - while( (n0 = b->nbitems) < 0) - { - // search the non empty - // QuadTreeBox containing the point (i,j) - register Icoor1 hb2 = hb >> 1 ; - register int k = IJ(iplus,jplus,hb2);// QuadTreeBox number of size hb2 contening i;j - register QuadTreeBox * b0= b->b[k]; - if ( ( b0 == 0) || (b0->nbitems == 0) ) - break; // null box or empty => break - b=b0; - i0 += I_IJ(k,hb2); // i orign of QuadTreeBox - j0 += J_IJ(k,hb2); // j orign of QuadTreeBox - hb = hb2; - } - - - if ( n0 > 0) - { - for(register int k=0;kv[k]->i; - // try if is in the right direction -- - h0 = NORM(iplus,i2.x,jplus,i2.y); - if (h0 v[k];} - } - if (vn) return vn; - } - // general case ----- - // INITIALISATION OF THE HEAP - l =0; // level - pb[0]= b; - pi[0]=b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[0]=i0; - jj[0]=j0; - h=hb; - do { // walk on the tree - b= pb[l]; - while (pi[l]--) // loop on 4 element of the box - { - int k = pi[l]; - - if (b->nbitems>0) // BamgVertex QuadTreeBox none empty - { - I2 i2 = b->v[k]->i; - // if good direction when try -- - - h0 = NORM(iplus,i2.x,jplus,i2.y); - if (h0 v[k]; - } - } - else // Pointer QuadTreeBox - { - register QuadTreeBox *b0=b; - if ((b=b->b[k])) - { - hb >>=1 ; // div by 2 - register Icoor1 iii = ii[l]+I_IJ(k,hb); - register Icoor1 jjj = jj[l]+J_IJ(k,hb); - - if (INTER_SEG(iii,iii+hb,iplus-h,iplus+h) && INTER_SEG(jjj,jjj+hb,jplus-h,jplus+h)) - { - pb[++l]= b; - pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[l]= iii; - jj[l]= jjj; - - } - else - b=b0, hb <<=1 ; - } - else - b=b0; - } - } - hb <<= 1; // mul by 2 - } while (l--); - - return vn; - } - /*}}}1*/ - /*FUNCTION QuadTree::NewQuadTreeBox {{{1*/ - QuadTree::QuadTreeBox* QuadTree::NewQuadTreeBox(void){ - - /*Output*/ - QuadTreeBox* newbox=NULL; - - /*Create and initialize a new box*/ - newbox=new QuadTreeBox; - newbox->nbitems=0; - newbox->b[0]=NULL; - newbox->b[1]=NULL; - newbox->b[2]=NULL; - newbox->b[3]=NULL; - - /*Add root to the container*/ - boxcontainer->AddObject(newbox); - - /*Increase counter*/ - NbQuadTreeBox++; - - /*currentbox now points toward next quadtree box*/ - return newbox; - }/*}}}*/ - /*FUNCTION QuadTree::ToClose {{{1*/ - BamgVertex* QuadTree::ToClose(BamgVertex & v,double seuil,Icoor1 hx,Icoor1 hy){ - /*Original code from Frederic Hecht (BAMG v1.01, QuadTree.cpp/ToClose)*/ - - const Icoor1 i=v.i.x; - const Icoor1 j=v.i.y; - const R2 X(v.r); - const Metric Mx(v.m); - - QuadTreeBox * pb[ MaxDeep ]; - int pi[ MaxDeep ]; - Icoor1 ii[ MaxDeep ], jj [ MaxDeep]; - register int l=0; // level - register QuadTreeBox * b; - Icoor1 h=MaxISize; - Icoor1 hb = MaxISize; - Icoor1 i0=0,j0=0; - - // BamgVertex *vn=0; - - if (!root->nbitems) - return 0; // empty tree - - // general case ----- - pb[0]=root; - pi[0]=root->nbitems>0 ?(int) root->nbitems : 4 ; - ii[0]=i0; - jj[0]=j0; - h=hb; - do { - b= pb[l]; - while (pi[l]--){ - register int k = pi[l]; - - if (b->nbitems>0){ // BamgVertex QuadTreeBox none empty - I2 i2 = b->v[k]->i; - if ( ABS(i-i2.x) v[k]->r); - double dd; - if( (dd= LengthInterpole(Mx(XY), b->v[k]->m(XY))) < seuil ){ - return b->v[k]; - } - } - } - else{ // Pointer QuadTreeBox - register QuadTreeBox *b0=b; - if ((b=b->b[k])){ - hb >>=1 ; // div by 2 - register long iii = ii[l]+I_IJ(k,hb); - register long jjj = jj[l]+J_IJ(k,hb); - - if (INTER_SEG(iii,iii+hb,i-hx,i+hx) && INTER_SEG(jjj,jjj+hb,j-hy,j+hy)){ - pb[++l]= b; - pi[l]= b->nbitems>0 ?(int) b->nbitems : 4 ; - ii[l]= iii; - jj[l]= jjj; - - } - else{ - b=b0; - hb <<=1 ; - } - } - else{ - b=b0; - } - } - } - hb <<= 1; // mul by 2 - } while (l--); - - return 0; - } - /*}}}1*/ -} Index: sm/trunk/src/c/objects/Bamg/QuadTree.h =================================================================== --- /issm/trunk/src/c/objects/Bamg/QuadTree.h (revision 12329) +++ (revision ) @@ -1,66 +1,0 @@ -/*Original code from Frederic Hecht (BAMG v1.01, QuadTree.h)*/ -#ifndef _QUADTREE_H -#define _QUADTREE_H - -#include "./include.h" - -namespace bamg { - - const int MaxDeep = 30; - const long MaxISize = ( 1L << MaxDeep); // = 2^30 : 010000000000..000 (bitwise operation) - - class BamgVertex; - - class QuadTree{ - - private: - - /*A quadtree box contains a maximum of 4 vertices. 4 other quadtree boxes are - * created if a fifth vertex is added to the same box. A Quadtree box is therefore - * composed of EITHER: - * - up to 4 vertices - * - 4 "sub" quadtree boxes*/ - class QuadTreeBox: public Object{ - public: - int nbitems; // number of current vertices in the box - union{ - QuadTreeBox* b[4]; - BamgVertex* v[4]; - }; - /*Object functions*/ - void Echo(){_error_("not implemented yet");}; - void DeepEcho(){_error_("not implemented yet");}; - int Id(){_error_("not implemented yet");}; - int MyRank(){_error_("not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("not implemented yet");}; - int MarshallSize(){_error_("not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("not implemented yet");}; - #endif - int ObjectEnum(){_error_("not implemented yet");}; - Object* copy(){_error_("not implemented yet");}; - }; - - /*QuadTree private Fields*/ - DataSet* boxcontainer; - - public: - - /*QuadTree public Fields*/ - QuadTreeBox* root; - long NbQuadTreeBox; - long NbVertices; - - QuadTree(); - QuadTree(Mesh *t,long nbv=-1); - ~QuadTree(); - - BamgVertex* NearestVertex(Icoor1 i,Icoor1 j); - BamgVertex* NearestVertexWithNormal(Icoor1 i,Icoor1 j); - QuadTreeBox* NewQuadTreeBox(void); - BamgVertex* ToClose(BamgVertex & ,double ,Icoor1,Icoor1); - void Add( BamgVertex & w); - - }; -} -#endif Index: /issm/trunk/src/c/objects/Constraints/Constraint.h =================================================================== --- /issm/trunk/src/c/objects/Constraints/Constraint.h (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/Constraint.h (revision 12330) @@ -11,8 +11,6 @@ /*Headers:*/ /*{{{1*/ +class Nodes; #include "../Object.h" - -class Nodes; - #include "../../toolkits/toolkits.h" /*}}}*/ Index: /issm/trunk/src/c/objects/Constraints/SpcDynamic.cpp =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcDynamic.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcDynamic.cpp (revision 12330) @@ -72,68 +72,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcDynamic::Marshall {{{1*/ -void SpcDynamic::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcDynamic: */ - enum_type=SpcDynamicEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcDynamic data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&isset,sizeof(isset));marshalled_dataset+=sizeof(isset); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcDynamic::MarshallSize {{{1*/ -int SpcDynamic::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(value) - +sizeof(isset) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcDynamic::Demarshall {{{1*/ -void SpcDynamic::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&isset,marshalled_dataset,sizeof(isset));marshalled_dataset+=sizeof(isset); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcDynamic::ObjectEnum{{{1*/ int SpcDynamic::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Constraints/SpcDynamic.h =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcDynamic.h (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcDynamic.h (revision 12330) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Constraints/SpcStatic.cpp =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcStatic.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcStatic.cpp (revision 12330) @@ -75,65 +75,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcStatic::Marshall {{{1*/ -void SpcStatic::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcStatic: */ - enum_type=SpcStaticEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcStatic data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcStatic::MarshallSize {{{1*/ -int SpcStatic::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(value) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcStatic::Demarshall {{{1*/ -void SpcStatic::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcStatic::ObjectEnum{{{1*/ int SpcStatic::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Constraints/SpcStatic.h =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcStatic.h (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcStatic.h (revision 12330) @@ -33,9 +33,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Constraints/SpcTransient.cpp =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcTransient.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcTransient.cpp (revision 12330) @@ -87,76 +87,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION SpcTransient::Marshall {{{1*/ -void SpcTransient::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of SpcTransient: */ - enum_type=SpcTransientEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall SpcTransient data: */ - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&nodeid,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&nsteps,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - if(nsteps){ - memcpy(marshalled_dataset,values,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - memcpy(marshalled_dataset,times,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - } - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION SpcTransient::MarshallSize {{{1*/ -int SpcTransient::MarshallSize(){ - - return sizeof(sid) - +sizeof(nodeid) - +sizeof(dof) - +sizeof(nsteps) - +nsteps*2*sizeof(double) - +sizeof(analysis_type) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION SpcTransient::Demarshall {{{1*/ -void SpcTransient::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&nodeid,marshalled_dataset,sizeof(nodeid));marshalled_dataset+=sizeof(nodeid); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&nsteps,marshalled_dataset,sizeof(nsteps));marshalled_dataset+=sizeof(nsteps); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - if(nsteps){ - values=(double*)xmalloc(nsteps*sizeof(double)); - times=(double*)xmalloc(nsteps*sizeof(double)); - memcpy(values,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - memcpy(times,marshalled_dataset,nsteps*sizeof(double));marshalled_dataset+=nsteps*sizeof(double); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION SpcTransient::ObjectEnum{{{1*/ int SpcTransient::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Constraints/SpcTransient.h =================================================================== --- /issm/trunk/src/c/objects/Constraints/SpcTransient.h (revision 12329) +++ /issm/trunk/src/c/objects/Constraints/SpcTransient.h (revision 12330) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Contour.cpp =================================================================== --- /issm/trunk/src/c/objects/Contour.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Contour.cpp (revision 12330) @@ -9,4 +9,5 @@ #endif +#include #include "./objects.h" #include "../include/include.h" @@ -79,71 +80,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Contour::Marshall{{{1*/ -void Contour::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputssize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Contour: */ - enum_type=ContourEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Contour data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&nods,sizeof(nods));marshalled_dataset+=sizeof(nods); - memcpy(marshalled_dataset,&closed,sizeof(closed));marshalled_dataset+=sizeof(closed); - memcpy(marshalled_dataset,x,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - memcpy(marshalled_dataset,y,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Contour::MarshallSize{{{1*/ -int Contour::MarshallSize(){ - - return sizeof(id)+ - sizeof(nods)+ - sizeof(closed)+ - 2*nods*sizeof(double)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Contour::Demarshall{{{1*/ -void Contour::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&nods,marshalled_dataset,sizeof(nods));marshalled_dataset+=sizeof(nods); - memcpy(&closed,marshalled_dataset,sizeof(closed));marshalled_dataset+=sizeof(closed); - - if(nods){ - this->x=(double*)xmalloc(nods*sizeof(double)); - this->y=(double*)xmalloc(nods*sizeof(double)); - memcpy(x,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - memcpy(y,marshalled_dataset,nods*sizeof(double));marshalled_dataset+=nods*sizeof(double); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Contour::ObjectEnum{{{1*/ int Contour::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Contour.h =================================================================== --- /issm/trunk/src/c/objects/Contour.h (revision 12329) +++ /issm/trunk/src/c/objects/Contour.h (revision 12330) @@ -20,11 +20,11 @@ int id; int nods; //number of vertices in the contour - double* x; - double* y; + IssmDouble* x; + IssmDouble* y; bool closed; //is this contour closed? /*Contour constructors, destructors {{{1*/ Contour(); - Contour(int id, int nods, double* x, double* y,bool closed); + Contour(int id, int nods, IssmDouble* x, IssmDouble* y,bool closed); ~Contour(); /*}}}*/ @@ -34,9 +34,4 @@ int Id(void); int MyRank(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(void); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(void); Object* copy(void); Index: /issm/trunk/src/c/objects/DofIndexing.cpp =================================================================== --- /issm/trunk/src/c/objects/DofIndexing.cpp (revision 12329) +++ /issm/trunk/src/c/objects/DofIndexing.cpp (revision 12330) @@ -208,128 +208,3 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DofIndexing::Marshall{{{1*/ -void DofIndexing::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - bool flagdoftype; //to indicate if there are some doftype or if NULL - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*preliminary: */ - if(this->doftype)flagdoftype=true; - else flagdoftype=false; - - /*get enum type of DofIndexing: */ - enum_type=DofIndexingEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall DofIndexing data: */ - memcpy(marshalled_dataset,&gsize,sizeof(gsize));marshalled_dataset+=sizeof(gsize); - memcpy(marshalled_dataset,&fsize,sizeof(fsize));marshalled_dataset+=sizeof(fsize); - memcpy(marshalled_dataset,&ssize,sizeof(ssize));marshalled_dataset+=sizeof(ssize); - memcpy(marshalled_dataset,&flagdoftype,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); - memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); - - if(this->gsize>0){ - memcpy(marshalled_dataset,f_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(marshalled_dataset,s_set,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(marshalled_dataset,svalues,gsize*sizeof(double)); marshalled_dataset+=gsize*sizeof(double); - if(flagdoftype){ memcpy(marshalled_dataset,doftype,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); } - memcpy(marshalled_dataset,gdoflist,gsize*sizeof(int)); marshalled_dataset+=gsize*sizeof(int); - } - if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(marshalled_dataset,fdoflist,fsize*sizeof(int)); marshalled_dataset+=fsize*sizeof(int);} - if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(marshalled_dataset,sdoflist,ssize*sizeof(int)); marshalled_dataset+=ssize*sizeof(int);} - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION DofIndexing::MarshallSize{{{1*/ -int DofIndexing::MarshallSize(){ - - int size=0; - - size+=4*sizeof(int)+sizeof(bool); - if(this->gsize>0){ - size+= 2*this->gsize*sizeof(bool)+ - this->gsize*sizeof(double)+ - this->gsize*sizeof(int); - if(this->doftype)size+=this->gsize*sizeof(int); - } - if(this->fsize>0 && this->fsize!=UNDEF)size+=this->fsize*sizeof(int); - if(this->ssize>0 && this->ssize!=UNDEF)size+=this->ssize*sizeof(int); - - size+=sizeof(int); //sizeof(int) for enum type - - return size; -} -/*}}}*/ -/*FUNCTION DofIndexing::Demarshall{{{1*/ -void DofIndexing::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type; - bool flagdoftype; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of object since DofIndexing is not directly called by DataSet: */ - memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - - /*easy part: */ - memcpy(&gsize,marshalled_dataset,sizeof(gsize));marshalled_dataset+=sizeof(gsize); - memcpy(&fsize,marshalled_dataset,sizeof(fsize));marshalled_dataset+=sizeof(fsize); - memcpy(&ssize,marshalled_dataset,sizeof(ssize));marshalled_dataset+=sizeof(ssize); - memcpy(&flagdoftype,marshalled_dataset,sizeof(flagdoftype));marshalled_dataset+=sizeof(flagdoftype); - memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); - - /*Allocate: */ - if(this->gsize>0){ - this->f_set=(bool*)xmalloc(this->gsize*sizeof(bool)); - this->s_set=(bool*)xmalloc(this->gsize*sizeof(bool)); - this->svalues=(double*)xmalloc(this->gsize*sizeof(double)); - if(flagdoftype)this->doftype=(int*)xmalloc(this->gsize*sizeof(int)); - else this->doftype=NULL; - this->gdoflist=(int*)xmalloc(this->gsize*sizeof(int)); - } - else{ - this->f_set=NULL; - this->s_set=NULL; - this->svalues=NULL; - this->doftype=NULL; - this->gdoflist=NULL; - } - if(this->fsize>0) - this->fdoflist=(int*)xmalloc(this->fsize*sizeof(int)); - else - this->fdoflist=NULL; - if(this->ssize>0) - this->sdoflist=(int*)xmalloc(this->ssize*sizeof(int)); - else - this->sdoflist=NULL; - - /*Copy arrays: */ - if(this->gsize>0){ - memcpy(f_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(s_set,marshalled_dataset,gsize*sizeof(bool));marshalled_dataset+=gsize*sizeof(bool); - memcpy(svalues,marshalled_dataset,gsize*sizeof(double));marshalled_dataset+=gsize*sizeof(double); - if(flagdoftype){memcpy(doftype,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); } - memcpy(gdoflist,marshalled_dataset,gsize*sizeof(int));marshalled_dataset+=gsize*sizeof(int); - } - - if(this->fsize>0 && this->fsize!=UNDEF){ memcpy(this->fdoflist,marshalled_dataset,this->fsize*sizeof(int));marshalled_dataset+=this->fsize*sizeof(int); } - if(this->ssize>0 && this->ssize!=UNDEF){ memcpy(this->sdoflist,marshalled_dataset,this->ssize*sizeof(int));marshalled_dataset+=this->ssize*sizeof(int); } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif - + Index: /issm/trunk/src/c/objects/DofIndexing.h =================================================================== --- /issm/trunk/src/c/objects/DofIndexing.h (revision 12329) +++ /issm/trunk/src/c/objects/DofIndexing.h (revision 12330) @@ -5,4 +5,6 @@ #ifndef _DOFINDEXING_H_ #define _DOFINDEXING_H_ + +#include "../include/include.h" class DofIndexing{ @@ -21,5 +23,5 @@ bool* f_set; //is dof on f-set (on which we solve) bool* s_set; //is dof on s-set (on which boundary conditions -dirichlet- are applied) - double* svalues; //list of constraint values. size g_size, for ease of use. + IssmDouble* svalues; //list of constraint values. size g_size, for ease of use. /*types of dofs: */ @@ -43,9 +45,4 @@ void Echo(void); void DeepEcho(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif void copy(DofIndexing* properties); /*}}}*/ Index: /issm/trunk/src/c/objects/ElementResults/BoolElementResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/BoolElementResult.cpp (revision 12330) @@ -64,61 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolElementResult::Marshall{{{1*/ -void BoolElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolElementResult: */ - enum_value=BoolElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolElementResult::Demarshall{{{1*/ -void BoolElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION BoolElementResult::MarshallSize{{{1*/ -int BoolElementResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -#endif /*FUNCTION BoolElementResult::ObjectEnum{{{1*/ int BoolElementResult::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/ElementResults/BoolElementResult.h =================================================================== --- /issm/trunk/src/c/objects/ElementResults/BoolElementResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/BoolElementResult.h (revision 12330) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.cpp (revision 12330) @@ -64,61 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleElementResult::Marshall{{{1*/ -void DoubleElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleElementResult: */ - enum_value=DoubleElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleElementResult::Demarshall{{{1*/ -void DoubleElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION DoubleElementResult::MarshallSize{{{1*/ -int DoubleElementResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -#endif /*FUNCTION DoubleElementResult::ObjectEnum{{{1*/ int DoubleElementResult::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.h =================================================================== --- /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/DoubleElementResult.h (revision 12330) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.cpp (revision 12330) @@ -67,61 +67,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PentaP1ElementResult::Marshall{{{1*/ -void PentaP1ElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PentaP1ElementResult: */ - enum_value=PentaP1ElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PentaP1ElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PentaP1ElementResult::MarshallSize{{{1*/ -int PentaP1ElementResult::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PentaP1ElementResult::Demarshall{{{1*/ -void PentaP1ElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION PentaP1ElementResult::ObjectEnum{{{1*/ int PentaP1ElementResult::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.h =================================================================== --- /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/PentaP1ElementResult.h (revision 12330) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.cpp (revision 12330) @@ -66,62 +66,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TriaP1ElementResult::Marshall{{{1*/ -void TriaP1ElementResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TriaP1ElementResult: */ - enum_value=TriaP1ElementResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TriaP1ElementResult data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION TriaP1ElementResult::MarshallSize{{{1*/ -int TriaP1ElementResult::MarshallSize(){ - - return sizeof(values) - +sizeof(enum_type) - +sizeof(time) - +sizeof(step) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TriaP1ElementResult::Demarshall{{{1*/ -void TriaP1ElementResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION TriaP1ElementResult::ObjectEnum{{{1*/ int TriaP1ElementResult::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.h =================================================================== --- /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ElementResults/TriaP1ElementResult.h (revision 12330) @@ -33,9 +33,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 12330) @@ -142,161 +142,4 @@ } /*}}}*/ - -/*Marshall*/ -#ifdef _SERIAL_ -/*FUNCTION Penta::Marshall {{{1*/ -void Penta::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - char* marshalled_results=NULL; - int marshalled_results_size; - int flaghook; //to indicate if hook is NULL or exists - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Penta: */ - enum_type=PentaEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Penta data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*Mershall Ref: */ - for(i=0;iMarshall(&marshalled_dataset); - } - else{ - /*Set flag to 0 and do not marshall flag as there is no Hook */ - flaghook=0; - memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); - } - } - hmatice->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - hneighbors->Marshall(&marshalled_dataset); - - /*Marshall inputs and results: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - marshalled_results_size=results->MarshallSize(); - marshalled_results=results->Marshall(); - memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); - marshalled_dataset+=marshalled_results_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - xfree((void**)&marshalled_results); - - /*marshall horizontal neighbors: */ - memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Penta::MarshallSize {{{1*/ -int Penta::MarshallSize(){ - - int i; - int hnodes_size=0;; - - for(i=0;iMarshallSize(); - } - - return sizeof(id) - +sizeof(sid) - +hnodes_size - +sizeof(numanalyses) - +numanalyses*sizeof(int) //element_type_lists - +hmatice->MarshallSize() - +hmatpar->MarshallSize() - +hneighbors->MarshallSize() - +inputs->MarshallSize() - +results->MarshallSize() - +3*sizeof(int) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Penta::Demarshall {{{1*/ -void Penta::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int flaghook; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*demarshall Ref: */ - this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); - for(i=0;ihnodes=new Hook*[this->numanalyses]; - /*demarshall hooks: */ - for(i=0;iDemarshall(&marshalled_dataset); - } - else hnodes[i]=NULL; //There is no hook so it is NULL - } - hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - hneighbors=new Hook(); hneighbors->Demarshall(&marshalled_dataset); - - /*pointers are garbage, until configuration is carried out: */ - nodes=NULL; - matice=NULL; - matpar=NULL; - verticalneighbors=NULL; - - /*demarshall inputs and results: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*neighbors: */ - memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*Other*/ Index: /issm/trunk/src/c/objects/Elements/Penta.h =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.h (revision 12329) +++ /issm/trunk/src/c/objects/Elements/Penta.h (revision 12330) @@ -55,9 +55,4 @@ int ObjectEnum(); int Id(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int MyRank(); /*}}}*/ Index: /issm/trunk/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 12330) @@ -122,158 +122,4 @@ } /*}}}*/ - -/*Marshall*/ -#ifdef _SERIAL_ -/*FUNCTION Tria::Marshall {{{1*/ -void Tria::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - char* marshalled_results=NULL; - int marshalled_results_size; - int flaghook; //to indicate if hook is NULL or exists - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Tria: */ - enum_type=TriaEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Tria data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&numanalyses,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*Mershall Ref: */ - for(i=0;iMarshall(&marshalled_dataset); - } - else{ - /*Set flag to 0 and do not marshall flag as there is no Hook */ - flaghook=0; - memcpy(marshalled_dataset,&flaghook,sizeof(flaghook));marshalled_dataset+=sizeof(flaghook); - } - } - hmatice->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*Marshall results: */ - marshalled_results_size=results->MarshallSize(); - marshalled_results=results->Marshall(); - memcpy(marshalled_dataset,marshalled_results,marshalled_results_size*sizeof(char)); - marshalled_dataset+=marshalled_results_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - xfree((void**)&marshalled_results); - - /*marshall horizontal neighbors: */ - memcpy(marshalled_dataset,horizontalneighborsids,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Tria::MarshallSize {{{1*/ -int Tria::MarshallSize(){ - - int i; - int hnodes_size=0;; - - for(i=0;iMarshallSize(); - } - - return sizeof(id) - +sizeof(sid) - +hnodes_size - +sizeof(numanalyses) - +numanalyses*sizeof(int) //element_type_lists - +hmatice->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +results->MarshallSize() - +3*sizeof(int) - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Tria::Demarshall {{{1*/ -void Tria::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int flaghook; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&numanalyses,marshalled_dataset,sizeof(numanalyses));marshalled_dataset+=sizeof(numanalyses); - - /*demarshall Ref: */ - this->element_type_list=(int*)xmalloc(this->numanalyses*sizeof(int)); - for(i=0;ihnodes=new Hook*[this->numanalyses]; - /*demarshall hooks: */ - for(i=0;iDemarshall(&marshalled_dataset); - } - else hnodes[i]=NULL; //There is no hook so it is NULL - } - hmatice=new Hook(); hmatice->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - matice=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - results=(Results*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*neighbors: */ - memcpy(&this->horizontalneighborsids,marshalled_dataset,3*sizeof(int));marshalled_dataset+=3*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*Other*/ @@ -783,5 +629,8 @@ basal_melting_input->GetInputValue(&basal_melting_g,gauss); thickness_input->GetInputValue(&thickness_g,gauss); - if(basal_melting_correction_input) basal_melting_correction_input->GetInputValue(&basal_melting_correction_g,gauss); + if(basal_melting_correction_input) + basal_melting_correction_input->GetInputValue(&basal_melting_correction_g,gauss); + else + basal_melting_correction_g=0.; for(i=0;ivalues[i]+=Jdettria*gauss->weight*(thickness_g+dt*(surface_mass_balance_g-basal_melting_g-basal_melting_correction_g))*L[i]; Index: /issm/trunk/src/c/objects/Elements/Tria.h =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.h (revision 12329) +++ /issm/trunk/src/c/objects/Elements/Tria.h (revision 12330) @@ -51,9 +51,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.cpp (revision 12330) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolExternalResult::Marshall{{{1*/ -void BoolExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolExternalResult: */ - enum_value=BoolExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolExternalResult::MarshallSize{{{1*/ -int BoolExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolExternalResult::Demarshall{{{1*/ -void BoolExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolExternalResult::ObjectEnum{{{1*/ int BoolExternalResult::ObjectEnum(void){ @@ -185,17 +125,4 @@ } /*}}}*/ -/*FUNCTION BoolExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BoolExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar((double)value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); -} -#endif -/*}}}*/ /*FUNCTION BoolExternalResult::GetStep{{{1*/ int BoolExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/BoolExternalResult.h (revision 12330) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -47,9 +42,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -59,9 +49,6 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ }; -#endif /* _BOOLEXTERNALRESULT_H */ +#endif Index: /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.cpp (revision 12330) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleExternalResult::Marshall{{{1*/ -void DoubleExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleExternalResult: */ - enum_value=DoubleExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleExternalResult::MarshallSize{{{1*/ -int DoubleExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleExternalResult::Demarshall{{{1*/ -void DoubleExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleExternalResult::ObjectEnum{{{1*/ int DoubleExternalResult::ObjectEnum(void){ @@ -181,17 +121,4 @@ } /*}}}*/ -/*FUNCTION DoubleExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - mxSetField( dataref,this->step-1, name,mxCreateDoubleScalar(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION DoubleExternalResult::GetStep{{{1*/ int DoubleExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleExternalResult.h (revision 12330) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -48,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +51,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.cpp (revision 12330) @@ -96,73 +96,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatExternalResult::Marshall{{{1*/ -void DoubleMatExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatExternalResult: */ - enum_value=DoubleMatExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatExternalResult::MarshallSize{{{1*/ -int DoubleMatExternalResult::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleMatExternalResult::Demarshall{{{1*/ -void DoubleMatExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - values=(double*)xmalloc(M*N*sizeof(double)); - memcpy(values,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatExternalResult::ObjectEnum{{{1*/ int DoubleMatExternalResult::ObjectEnum(void){ @@ -222,37 +153,4 @@ } /*}}}*/ -/*FUNCTION DoubleMatExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatExternalResult::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - char* name=NULL; - double* doublemat=NULL; - - /*Make a copy of the value, to be used by matlab: */ - doublemat=(double*)xmalloc(M*N*sizeof(double)); - memcpy(doublemat,values,M*N*sizeof(double)); - - /*recover name: */ - this->GetResultName(&name); - - /*create matlab matrix: */ - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,N); - mxSetN(pfield,M); - mxSetPr(pfield,doublemat); - - /*transpose the matrix, from c to matlab format */ - mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); - - /*set tranpose matrix inside the dataref structure: */ - mxSetField( dataref, this->step-1, name,pfield2); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION DoubleMatExternalResult::GetStep{{{1*/ int DoubleMatExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleMatExternalResult.h (revision 12330) @@ -14,9 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -49,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -61,7 +51,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.cpp (revision 12330) @@ -87,70 +87,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleVecExternalResult::Marshall{{{1*/ -void DoubleVecExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleVecExternalResult: */ - enum_value=DoubleVecExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleVecExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleVecExternalResult::MarshallSize{{{1*/ -int DoubleVecExternalResult::MarshallSize(){ - - return sizeof(M) - +M*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleVecExternalResult::Demarshall{{{1*/ -void DoubleVecExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - values=(double*)xmalloc(M*sizeof(double)); - memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleVecExternalResult::ObjectEnum{{{1*/ int DoubleVecExternalResult::ObjectEnum(void){ @@ -206,32 +140,4 @@ } /*}}}*/ -/*FUNCTION DoubleVecExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleVecExternalResult::SetMatlabField(mxArray* dataref){ - - mxArray *pfield = NULL; - double *doublemat = NULL; - char *name = NULL; - double *doublevec = NULL; - - /*Make a copy of the value, to be used by matlab: */ - doublevec=(double*)xmalloc(M*sizeof(double)); - memcpy(doublevec,values,M*sizeof(double)); - - /*recover name: */ - this->GetResultName(&name); - - /*create matlab matrix: */ - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, this->step-1, name,pfield); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); -} -#endif -/*}}}*/ /*FUNCTION DoubleVecExternalResult::GetStep{{{1*/ int DoubleVecExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/DoubleVecExternalResult.h (revision 12330) @@ -14,9 +14,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/ExternalResult.h (revision 12330) @@ -16,8 +16,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "../Object.h" #include "../Node.h" @@ -33,7 +29,4 @@ virtual void WriteData(FILE* fid,bool io_gather)=0; virtual void GetResultName(char**)=0; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - virtual void SetMatlabField(mxArray* dataref)=0; - #endif virtual int GetStep(void)=0; /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.cpp (revision 12330) @@ -68,64 +68,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntExternalResult::Marshall{{{1*/ -void IntExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntExternalResult: */ - enum_value=IntExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntExternalResult::MarshallSize{{{1*/ -int IntExternalResult::MarshallSize(){ - - return sizeof(value)+ - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntExternalResult::Demarshall{{{1*/ -void IntExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntExternalResult::ObjectEnum{{{1*/ int IntExternalResult::ObjectEnum(void){ @@ -185,18 +125,4 @@ } /*}}}*/ -/*FUNCTION IntExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name,mxCreateDoubleScalar(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION IntExternalResult::GetStep{{{1*/ int IntExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/IntExternalResult.h (revision 12330) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -46,9 +42,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -58,7 +49,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.cpp (revision 12330) @@ -80,108 +80,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PetscVecExternalResult::Marshall{{{1*/ -void PetscVecExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M; - double* serial_value=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PetscVecExternalResult: */ - enum_value=PetscVecExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PetscVecExternalResult data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - if(value){ - VecGetSize(value,&M); - VecToMPISerial(&serial_value,value); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - } - else{ - M=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - } - /*Free ressources:*/ - xfree((void**)&serial_value); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PetscVecExternalResult::MarshallSize{{{1*/ -int PetscVecExternalResult::MarshallSize(){ - - int M=0; - if(value)VecGetSize(value,&M); - - return sizeof(M)+M*sizeof(double) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PetscVecExternalResult::Demarshall{{{1*/ -void PetscVecExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int M; - double* serial_vec=NULL; - int* idxm=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - serial_vec=(double*)xmalloc(M*sizeof(double)); - memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - - value=NewVec(M); - idxm=(int*)xmalloc(M*sizeof(int)); - for(i=0;iGetResultName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, this->step-1, name, pfield); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION PetscVecExternalResult::GetStep{{{1*/ int PetscVecExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/PetscVecExternalResult.h (revision 12330) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.cpp (revision 12330) @@ -71,77 +71,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringExternalResult::Marshall{{{1*/ -void StringExternalResult::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringExternalResult: */ - enum_value=StringExternalResultEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - stringsize=strlen(this->value)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - memcpy(marshalled_dataset,&step,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(marshalled_dataset,&time,sizeof(time));marshalled_dataset+=sizeof(time); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringExternalResult::MarshallSize{{{1*/ -int StringExternalResult::MarshallSize(){ - - int stringsize; - stringsize=strlen(this->value)+1; - - return sizeof(int)+ - +stringsize*sizeof(char) - +sizeof(id) - +sizeof(enum_type) - +sizeof(step) - +sizeof(time) - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION StringExternalResult::Demarshall{{{1*/ -void StringExternalResult::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - - this->value=(char*)xmalloc(stringsize*sizeof(char)); - memcpy(value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - memcpy(&step,marshalled_dataset,sizeof(step));marshalled_dataset+=sizeof(step); - memcpy(&time,marshalled_dataset,sizeof(time));marshalled_dataset+=sizeof(time); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringExternalResult::ObjectEnum{{{1*/ int StringExternalResult::ObjectEnum(void){ @@ -197,19 +124,4 @@ } /*}}}*/ -/*FUNCTION StringExternalResult::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringExternalResult::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - - this->GetResultName(&name); - - mxSetField( dataref, this->step-1, name, mxCreateString(value)); - mxSetField( dataref, this->step-1, "time",mxCreateDoubleScalar((double)this->time)); - mxSetField( dataref, this->step-1, "step",mxCreateDoubleScalar((double)this->step)); - -} -#endif -/*}}}*/ /*FUNCTION StringExternalResult::GetStep{{{1*/ int StringExternalResult::GetStep(void){ Index: /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h =================================================================== --- /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h (revision 12329) +++ /issm/trunk/src/c/objects/ExternalResults/StringExternalResult.h (revision 12330) @@ -15,9 +15,4 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif - #include "./ExternalResult.h" @@ -48,9 +43,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -60,7 +50,4 @@ void WriteData(FILE* fid,bool io_gather); void GetResultName(char**); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif int GetStep(void); /*}}}*/ Index: /issm/trunk/src/c/objects/FemModel.cpp =================================================================== --- /issm/trunk/src/c/objects/FemModel.cpp (revision 12329) +++ /issm/trunk/src/c/objects/FemModel.cpp (revision 12330) @@ -22,5 +22,4 @@ /*FUNCTION FemModel::constructor {{{1*/ FemModel::FemModel(char* inputfilename, char* outputfilename, const int in_solution_type,const int* analyses,const int nummodels){ -#ifdef _PARALLEL_ /*intermediary*/ @@ -75,6 +74,4 @@ /*Add output file name to parameters: */ this->parameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename)); - -#endif } Index: /issm/trunk/src/c/objects/Hook.cpp =================================================================== --- /issm/trunk/src/c/objects/Hook.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Hook.cpp (revision 12330) @@ -118,91 +118,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Hook::Marshall{{{1*/ -void Hook::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Hook: */ - enum_type=HookEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Hook data: */ - memcpy(marshalled_dataset,&num,sizeof(num));marshalled_dataset+=sizeof(num); - for(i=0;iids[i],sizeof(int));marshalled_dataset+=sizeof(int); - memcpy(marshalled_dataset,&this->offsets[i],sizeof(int));marshalled_dataset+=sizeof(int); - } - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Hook::MarshallSize{{{1*/ -int Hook::MarshallSize(){ - - return - sizeof(num)+ - num*sizeof(int)+ - num*sizeof(int)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Hook::Demarshall{{{1*/ -void Hook::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int enum_type; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of object since Hook is not directly called by DataSet: */ - memcpy(&enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - - memcpy(&num,marshalled_dataset,sizeof(num));marshalled_dataset+=sizeof(num); - - /*allocate: */ - if (num<0){ - _error_("cannot demarshall Hook as num<=0"); - } - else if (num==0){ - this->ids=NULL; - this->offsets=NULL; - this->objects=NULL; - } - else{ - - this->ids=(int*)xmalloc(num*sizeof(int)); - this->offsets=(int*)xmalloc(num*sizeof(int)); - - /*demarshall allocated ids and offsets: */ - _assert_(num<1000); - for (i=0;iids[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - memcpy(&this->offsets[i],marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - } - - /*nullify object pointers */ - this->objects=(Object**)xmalloc(num*sizeof(Object*)); - for (i=0;iobjects[i]=NULL; - } - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Hook::copy {{{1*/ Object* Hook::copy(void){ Index: /issm/trunk/src/c/objects/Hook.h =================================================================== --- /issm/trunk/src/c/objects/Hook.h (revision 12329) +++ /issm/trunk/src/c/objects/Hook.h (revision 12330) @@ -34,9 +34,4 @@ void Echo(void); void DeepEcho(void); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif Object* copy(void); /*}}}*/ Index: /issm/trunk/src/c/objects/Inputs/BoolInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/BoolInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/BoolInput.cpp (revision 12330) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolInput::Marshall{{{1*/ -void BoolInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolInput: */ - enum_value=BoolInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolInput::MarshallSize{{{1*/ -int BoolInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolInput::Demarshall{{{1*/ -void BoolInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolInput::ObjectEnum{{{1*/ int BoolInput::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/BoolInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/BoolInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/BoolInput.h (revision 12330) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/ControlInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/ControlInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/ControlInput.cpp (revision 12330) @@ -90,212 +90,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION ControlInput::Marshall{{{1*/ -void ControlInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int flag; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of ControlInput: */ - enum_value=ControlInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall enum_type: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&control_id,sizeof(control_id));marshalled_dataset+=sizeof(control_id); - - /*marshal values*/ - if(!values){ - flag=0; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - } - else{ - flag=1; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - this->values->Marshall(&marshalled_dataset); - } - - /*marshal savedvalues*/ - if(!savedvalues){ - flag=0; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - } - else{ - flag=1; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - this->savedvalues->Marshall(&marshalled_dataset); - } - - /*marshal minvalues*/ - if(!minvalues){ - flag=0; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - } - else{ - flag=1; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - this->minvalues->Marshall(&marshalled_dataset); - } - - /*marshal maxvalues*/ - if(!maxvalues){ - flag=0; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - } - else{ - flag=1; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - this->maxvalues->Marshall(&marshalled_dataset); - } - - /*marshal gradient*/ - if(!gradient){ - flag=0; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - } - else{ - flag=1; - memcpy(marshalled_dataset,&flag,sizeof(flag));marshalled_dataset+=sizeof(flag); - this->gradient->Marshall(&marshalled_dataset); - } - - /*clean up and assign output pointer*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION ControlInput::MarshallSize{{{1*/ -int ControlInput::MarshallSize(){ - - int size=0; - - size=sizeof(enum_type)+ - +sizeof(control_id) - +5*sizeof(int) //5 flags - +sizeof(int); //sizeof(int) for enum value - - if(values) size+=values->MarshallSize(); - if(savedvalues)size+=savedvalues->MarshallSize(); - if(minvalues)size+=minvalues->MarshallSize(); - if(maxvalues)size+=maxvalues->MarshallSize(); - if(gradient) size+=gradient->MarshallSize(); - return size; -} -/*}}}*/ -/*FUNCTION ControlInput::Demarshall{{{1*/ -void ControlInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int flag,input_enum_type; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&control_id,marshalled_dataset,sizeof(control_id));marshalled_dataset+=sizeof(control_id); - - /*Demarshal values*/ - memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(flag){ - memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(input_enum_type==PentaP1InputEnum){ - values=new PentaP1Input(); - values->Demarshall(&marshalled_dataset); - } - else if(input_enum_type==TriaP1InputEnum){ - values=new TriaP1Input(); - values->Demarshall(&marshalled_dataset); - } - else _error_("Not supported yet"); - } - else{ - values=NULL; - } - - /*Demarshal savedvalues*/ - memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(flag){ - memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(input_enum_type==PentaP1InputEnum){ - savedvalues=new PentaP1Input(); - savedvalues->Demarshall(&marshalled_dataset); - } - else if(input_enum_type==TriaP1InputEnum){ - savedvalues=new TriaP1Input(); - savedvalues->Demarshall(&marshalled_dataset); - } - else _error_("Not supported yet"); - } - else{ - savedvalues=NULL; - } - - /*Demarshal minvalues*/ - memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(flag){ - memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(input_enum_type==PentaP1InputEnum){ - minvalues=new PentaP1Input(); - minvalues->Demarshall(&marshalled_dataset); - } - else if(input_enum_type==TriaP1InputEnum){ - minvalues=new TriaP1Input(); - minvalues->Demarshall(&marshalled_dataset); - } - else _error_("Not supported yet"); - } - else{ - minvalues=NULL; - } - - /*Demarshal maxvalues*/ - memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(flag){ - memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(input_enum_type==PentaP1InputEnum){ - maxvalues=new PentaP1Input(); - maxvalues->Demarshall(&marshalled_dataset); - } - else if(input_enum_type==TriaP1InputEnum){ - maxvalues=new TriaP1Input(); - maxvalues->Demarshall(&marshalled_dataset); - } - else _error_("Not supported yet"); - } - else{ - maxvalues=NULL; - } - - /*Demarshal gradient*/ - memcpy(&flag,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(flag){ - memcpy(&input_enum_type,marshalled_dataset,sizeof(int)); marshalled_dataset+=sizeof(int); - if(input_enum_type==PentaP1InputEnum){ - gradient=new PentaP1Input(); - gradient->Demarshall(&marshalled_dataset); - } - else if(input_enum_type==TriaP1InputEnum){ - gradient=new TriaP1Input(); - gradient->Demarshall(&marshalled_dataset); - } - else _error_("Not supported yet"); - } - else{ - gradient=NULL; - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION ControlInput::ObjectEnum{{{1*/ int ControlInput::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/ControlInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/ControlInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/ControlInput.h (revision 12330) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/DatasetInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/DatasetInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/DatasetInput.cpp (revision 12330) @@ -61,68 +61,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DatasetInput::Marshall{{{1*/ -void DatasetInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DatasetInput: */ - enum_value=DatasetInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall enum_type: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshal inputs*/ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*clean up and assign output pointer*/ - xfree((void**)&marshalled_inputs); - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DatasetInput::MarshallSize{{{1*/ -int DatasetInput::MarshallSize(){ - - int size=0; - - size=sizeof(enum_type)+ - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum value - - return size; -} -/*}}}*/ -/*FUNCTION DatasetInput::Demarshall{{{1*/ -void DatasetInput::Demarshall(char** pmarshalled_dataset){ - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*Demarshal values*/ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DatasetInput::ObjectEnum{{{1*/ int DatasetInput::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/DatasetInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/DatasetInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/DatasetInput.h (revision 12330) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/DoubleInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/DoubleInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/DoubleInput.cpp (revision 12330) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleInput::Marshall{{{1*/ -void DoubleInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleInput: */ - enum_value=DoubleInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleInput::MarshallSize{{{1*/ -int DoubleInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleInput::Demarshall{{{1*/ -void DoubleInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleInput::ObjectEnum{{{1*/ int DoubleInput::ObjectEnum(void){ @@ -159,9 +108,5 @@ /*FUNCTION DoubleInput::GetInputValue(bool* pvalue) {{{1*/ void DoubleInput::GetInputValue(bool* pvalue){ -#ifdef _SERIAL_ - *pvalue=(bool)value; -#else _error_("Double input of enum %s cannot return a boolean",EnumToStringx(enum_type)); -#endif } @@ -169,9 +114,5 @@ /*FUNCTION DoubleInput::GetInputValue(int* pvalue){{{1*/ void DoubleInput::GetInputValue(int* pvalue){ -#ifdef _SERIAL_ - *pvalue=(int)value; -#else _error_("Double input of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type)); -#endif } Index: /issm/trunk/src/c/objects/Inputs/DoubleInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/DoubleInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/DoubleInput.h (revision 12330) @@ -30,9 +30,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/IntInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/IntInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/IntInput.cpp (revision 12330) @@ -54,55 +54,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntInput::Marshall{{{1*/ -void IntInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntInput: */ - enum_value=IntInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntInput::MarshallSize{{{1*/ -int IntInput::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntInput::Demarshall{{{1*/ -void IntInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntInput::ObjectEnum{{{1*/ int IntInput::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/IntInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/IntInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/IntInput.h (revision 12330) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/PentaP1Input.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/PentaP1Input.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/PentaP1Input.cpp (revision 12330) @@ -70,55 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION PentaP1Input::Marshall{{{1*/ -void PentaP1Input::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of PentaP1Input: */ - enum_value=PentaP1InputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall PentaP1Input data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION PentaP1Input::MarshallSize{{{1*/ -int PentaP1Input::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION PentaP1Input::Demarshall{{{1*/ -void PentaP1Input::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION PentaP1Input::ObjectEnum{{{1*/ int PentaP1Input::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/PentaP1Input.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/PentaP1Input.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/PentaP1Input.h (revision 12330) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/TransientInput.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/TransientInput.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/TransientInput.cpp (revision 12330) @@ -85,77 +85,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TransientInput::Marshall{{{*/ -void TransientInput::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TransientInput: */ - enum_value=TransientInputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TransientInput data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&numtimesteps,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); - memcpy(marshalled_dataset,timesteps,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); - - /*marshal inputs*/ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*clean up and assign output pointer*/ - xfree((void**)&marshalled_inputs); - *pmarshalled_dataset=marshalled_dataset; - -} -/*}}}* -/*FUNCTION TransientInput::MarshallSize{{{*/ -int TransientInput::MarshallSize(){ - - return - +sizeof(enum_type)+ - +sizeof(numtimesteps)+ - +inputs->MarshallSize() - +numtimesteps*sizeof(double)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TransientInput::Demarshall{{{*/ -void TransientInput::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&numtimesteps,marshalled_dataset,sizeof(numtimesteps));marshalled_dataset+=sizeof(numtimesteps); - - /*allocate: */ - timesteps=(double*)xmalloc(numtimesteps*sizeof(double)); - memcpy(timesteps,marshalled_dataset,numtimesteps*sizeof(double));marshalled_dataset+=numtimesteps*sizeof(double); - - /*Demarshal values*/ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; - -} -/*}}}*/ -#endif /*FUNCTION TransientInput::ObjectEnum{{{*/ int TransientInput::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/TransientInput.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/TransientInput.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/TransientInput.h (revision 12330) @@ -34,9 +34,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Inputs/TriaP1Input.cpp =================================================================== --- /issm/trunk/src/c/objects/Inputs/TriaP1Input.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/TriaP1Input.cpp (revision 12330) @@ -70,55 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION TriaP1Input::Marshall{{{1*/ -void TriaP1Input::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of TriaP1Input: */ - enum_value=TriaP1InputEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall TriaP1Input data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&values,sizeof(values));marshalled_dataset+=sizeof(values); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION TriaP1Input::MarshallSize{{{1*/ -int TriaP1Input::MarshallSize(){ - - return sizeof(values)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION TriaP1Input::Demarshall{{{1*/ -void TriaP1Input::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&values,marshalled_dataset,sizeof(values));marshalled_dataset+=sizeof(values); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION TriaP1Input::ObjectEnum{{{1*/ int TriaP1Input::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Inputs/TriaP1Input.h =================================================================== --- /issm/trunk/src/c/objects/Inputs/TriaP1Input.h (revision 12329) +++ /issm/trunk/src/c/objects/Inputs/TriaP1Input.h (revision 12330) @@ -31,9 +31,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/IoModel.cpp =================================================================== --- /issm/trunk/src/c/objects/IoModel.cpp (revision 12329) +++ /issm/trunk/src/c/objects/IoModel.cpp (revision 12330) @@ -45,4 +45,7 @@ this->fid=iomodel_handle; + /*Check that Enums are Synchronized*/ + this->CheckEnumSync(); + /*Initialize and read constants:*/ this->constants=new Parameters(); @@ -89,4 +92,47 @@ /*}}}*/ +/*FUNCTION IoModel::CheckEnumSync{{{1*/ +void IoModel::CheckEnumSync(void){ + + extern int my_rank; + int record_enum = 0; + + + /*Check that some fields have been allocated*/ + _assert_(this->fid || my_rank); + + + /*Go find in the binary file, the position of the data we want to fetch: */ + if(my_rank==0){ //cpu 0 + + /*First set FILE* position to the beginning of the file: */ + fseek(this->fid,0,SEEK_SET); + + /*Get first Enum*/ + if(fread(&record_enum,sizeof(int),1,this->fid)==0){ + _error_("Marshalled file is empty"); + } + else{ + if(record_enum!=MaximumNumberOfEnums){ + printf("\n"); + printf("=========================================================================\n"); + printf(" Enums in marshalled file are not compatible with compiled code \n"); + printf(" \n"); + printf(" * If you are running ISSM on a remote cluster: \n"); + printf(" make sure that you are using the same version of ISSM on your local \n"); + printf(" machine and remote cluster (you might need to run svn update) \n"); + printf(" * If you are running ISSM on your local machine: \n"); + printf(" make sure that all the code is compiled (modules and executables) \n"); + printf(" * If you are a developer and just added a new Enum: \n"); + printf(" you might need to run ./Synchronize.sh in src/c/EnumDefinitions \n"); + printf(" and recompile \n"); + printf("=========================================================================\n"); + printf("\n"); + _error_("Enums not consistent (See error message above)"); + } + } + } +} +/*}}}*/ /*FUNCTION IoModel::Constant(bool* poutput,int constant_enum){{{1*/ void IoModel::Constant(bool* poutput,int constant_enum){ @@ -198,5 +244,7 @@ /*Ok, we have reached the end of the file. break: */ record_code=0; //0 means bailout + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell others cpus we are bailing: */ + #endif break; } @@ -207,4 +255,5 @@ fread(&record_code,sizeof(int),1,this->fid); + #ifdef _HAVE_MPI_ /*Tell other cpus what we are doing: */ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell other cpus what we are going to do: */ @@ -213,11 +262,13 @@ MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD); + #endif - switch(record_code){ case 1: /*Read the boolean and broadcast it to other cpus:*/ if(fread(&booleanint,sizeof(int),1,this->fid)!=1) _error_(" could not read boolean "); + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create BoolParam: */ @@ -228,5 +279,7 @@ /*Read the integer and broadcast it to other cpus:*/ if(fread(&integer,sizeof(int),1,this->fid)!=1) _error_(" could not read integer "); + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create IntParam: */ @@ -237,5 +290,7 @@ /*Read the scalar and broadcast it to other cpus:*/ if(fread(&scalar,sizeof(double),1,this->fid)!=1) _error_(" could not read scalar "); + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*create DoubleParam: */ @@ -246,5 +301,7 @@ /*We have to read a string from disk. First read the dimensions of the string, then the string: */ if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_(" could not read length of string "); + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ @@ -254,5 +311,7 @@ /*Read string, then broadcast: */ if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -308,4 +367,5 @@ } } //}}} + #ifdef _HAVE_MPI_ else{ //cpu ~0 {{{2 for(;;){ //wait on cpu 0 @@ -377,4 +437,5 @@ } } //}}} + #endif } /*}}}*/ @@ -399,5 +460,7 @@ if(fread(&booleanint,sizeof(int),1,fid)!=1) _error_(" could not read boolean "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*cast to bool: */ @@ -428,5 +491,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -456,5 +521,7 @@ if(fread(&scalar,sizeof(double),1,fid)!=1)_error_(" could not read scalar "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -487,5 +554,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string: */ @@ -498,5 +567,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -538,10 +609,14 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } - MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -554,5 +629,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -602,10 +679,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -617,5 +698,7 @@ if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -652,5 +735,7 @@ if(fread(&numstrings,sizeof(int),1,fid)!=1) _error_(" could not read length of string array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numstrings,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string array: */ @@ -665,5 +750,7 @@ if(fread(&string_size,sizeof(int),1,fid)!=1) _error_(" could not read length of string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ string=(char*)xmalloc((string_size+1)*sizeof(char)); @@ -674,5 +761,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -717,5 +806,7 @@ if(fread(&numrecords,sizeof(int),1,fid)!=1) _error_("could not read number of records in matrix array "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numrecords,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(numrecords){ @@ -738,10 +829,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of rows in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of columns in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -754,5 +849,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -1047,11 +1144,15 @@ } } + #ifdef _HAVE_MPI_ MPI_Bcast(&found,1,MPI_INT,0,MPI_COMM_WORLD); if(!found)_error_("%s %s ","could not find data with name",EnumToStringx(data_enum)); + #endif /*Broadcast code and vector type: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); if(record_code==5) MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers:*/ Index: /issm/trunk/src/c/objects/IoModel.h =================================================================== --- /issm/trunk/src/c/objects/IoModel.h (revision 12329) +++ /issm/trunk/src/c/objects/IoModel.h (revision 12330) @@ -19,6 +19,6 @@ private: FILE *fid; //pointer to input file - double **data; //this dataset holds temporary data, memory intensive. - Parameters *constants; //this dataset holds all double, int, bool and char *parameters read in from the input file.* + IssmDouble **data; //this dataset holds temporary data, memory intensive. + Parameters *constants; //this dataset holds all IssmDouble, int, bool and char *parameters read in from the input file.* public: @@ -41,23 +41,24 @@ /*Input/Output*/ - void Constant(bool *poutput,int constant_enum); - void Constant(int *poutput,int constant_enum); - void Constant(double *poutput,int constant_enum); - void Constant(char **poutput,int constant_enum); - Param *CopyConstantObject(int constant_enum); - double *Data(int dataenum); - void DeleteData(int num,...); - void FetchConstants(void); - void FetchData(bool* pboolean,int data_enum); - void FetchData(int* pinteger,int data_enum); - void FetchData(double* pscalar,int data_enum); - void FetchData(char** pstring,int data_enum); - void FetchData(int** pmatrix,int* pM,int* pN,int data_enum); - void FetchData(double** pscalarmatrix,int* pM,int* pN,int data_enum); - void FetchData(char*** pstringarray,int* pnumstrings,int data_enum); - void FetchData(double*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,int data_enum); - void FetchData(int num,...); - void FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,double default_value=0); - FILE* SetFilePointerToData(int* pcode,int* pvector_type, int data_enum); + void CheckEnumSync(void); + void Constant(bool *poutput,int constant_enum); + void Constant(int *poutput,int constant_enum); + void Constant(IssmDouble *poutput,int constant_enum); + void Constant(char **poutput,int constant_enum); + Param *CopyConstantObject(int constant_enum); + IssmDouble *Data(int dataenum); + void DeleteData(int num,...); + void FetchConstants(void); + void FetchData(bool* pboolean,int data_enum); + void FetchData(int* pinteger,int data_enum); + void FetchData(IssmDouble* pscalar,int data_enum); + void FetchData(char** pstring,int data_enum); + void FetchData(int** pmatrix,int* pM,int* pN,int data_enum); + void FetchData(IssmDouble** pscalarmatrix,int* pM,int* pN,int data_enum); + void FetchData(char*** pstringarray,int* pnumstrings,int data_enum); + void FetchData(IssmDouble*** pmatrixarray,int** pmdims,int** pndims, int* pnumrecords,int data_enum); + void FetchData(int num,...); + void FetchDataToInput(Elements* elements,int vector_enum,int default_vector_enum=NoneEnum,IssmDouble default_value=0); + FILE* SetFilePointerToData(int* pcode,int* pvector_type, int data_enum); }; Index: /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.cpp (revision 12330) @@ -0,0 +1,92 @@ +/*!\file ExponentialVariogram.c + * \brief: implementation of the ExponentialVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*ExponentialVariogram constructors and destructor*/ +/*FUNCTION ExponentialVariogram::ExponentialVariogram(){{{1*/ +ExponentialVariogram::ExponentialVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION ExponentialVariogram::ExponentialVariogram(Options* options){{{1*/ +ExponentialVariogram::ExponentialVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION ExponentialVariogram::~ExponentialVariogram(){{{1*/ +ExponentialVariogram::~ExponentialVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION ExponentialVariogram::Echo {{{1*/ +void ExponentialVariogram::Echo(void){ + printf("ExponentialVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION ExponentialVariogram::Covariance{{{1*/ +double ExponentialVariogram::Covariance(double deltax,double deltay){ + /*The covariance can be deduced from the variogram from the following + * relationship: + * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) + * so + * C(h) = sill - gamma */ + double h,a,cova; + + /*Calculate length*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return covariance*/ + a = 1./3.; + cova = (sill-nugget)*exp(-h/(a*range)); + return cova; +} +/*}}}*/ +/*FUNCTION ExponentialVariogram::SemiVariogram{{{1*/ +double ExponentialVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,a,gamma; + + /*Calculate length*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + a = 1./3.; + gamma = (sill-nugget)*(1-exp(-h/(a*range))) + nugget; + return gamma; +} +/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/ExponentialVariogram.h (revision 12330) @@ -0,0 +1,35 @@ +/*! \file ExponentialVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _EXPONENTIALVARIOGRAM_H_ +#define _EXPONENTIALVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class ExponentialVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*ExponentialVariogram constructors, destructors*/ + ExponentialVariogram(); + ExponentialVariogram(Options* options); + ~ExponentialVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); + double Covariance(double deltax,double deltay); +}; +#endif /* _EXPONENTIALVARIOGRAM_H */ Index: /issm/trunk/src/c/objects/Kriging/GaussianVariogram.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/GaussianVariogram.cpp (revision 12330) @@ -0,0 +1,98 @@ +/*!\file GaussianVariogram.c + * \brief: implementation of the GaussianVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*GaussianVariogram constructors and destructor*/ +/*FUNCTION GaussianVariogram::GaussianVariogram(){{{1*/ +GaussianVariogram::GaussianVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION GaussianVariogram::GaussianVariogram(Options* options){{{1*/ +GaussianVariogram::GaussianVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION GaussianVariogram::~GaussianVariogram(){{{1*/ +GaussianVariogram::~GaussianVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION GaussianVariogram::Echo {{{1*/ +void GaussianVariogram::Echo(void){ + printf("GaussianVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION GaussianVariogram::Covariance{{{1*/ +double GaussianVariogram::Covariance(double deltax,double deltay){ + /*The covariance can be deduced from the variogram from the following + * relationship: + * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) + * so + * C(h) = sill - gamma */ + double h2,a,cova; + + /*Calculate length square*/ + h2=pow(deltax,2.)+pow(deltay,2.); + + /*return covariance*/ + a = 1./3.; + cova = (sill-nugget)*exp(-h2/(a*range*range)); + + if(h2<0.0000001) cova = sill; + + return cova; +} +/*}}}*/ +/*FUNCTION GaussianVariogram::SemiVariogram{{{1*/ +double GaussianVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h2,a,gamma; + + /*Calculate length square*/ + h2=pow(deltax,2.)+pow(deltay,2.); + + /*return semi-variogram*/ + a = 1./3.; + gamma = (sill-nugget)*(1.-exp(-h2/(a*range*range))) + nugget; + + //if(h2>1000*1000) printf("gamma = %g h= %g\n",gamma,sqrt(h2)); + printf("h = %g gamma = %g\n",sqrt(h2),gamma); + return gamma; +} +/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/GaussianVariogram.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/GaussianVariogram.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/GaussianVariogram.h (revision 12330) @@ -0,0 +1,35 @@ +/*! \file GaussianVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _GAUSSIANVARIOGRAM_H_ +#define _GAUSSIANVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class GaussianVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*GaussianVariogram constructors, destructors*/ + GaussianVariogram(); + GaussianVariogram(Options* options); + ~GaussianVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); + double Covariance(double deltax,double deltay); +}; +#endif /* _GAUSSIANVARIOGRAM_H */ Index: /issm/trunk/src/c/objects/Kriging/Observation.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/Observation.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/Observation.cpp (revision 12330) @@ -0,0 +1,57 @@ +/*!\file Observation.c + * \brief: implementation of the Observation object + */ + +#include +#include "../objects.h" + +/*Observation constructors and destructor*/ +/*FUNCTION Observation::Observation(){{{1*/ +Observation::Observation(){ + return; +} +/*}}}*/ +/*FUNCTION Observation::Observation(double x,double y,int xi,int yi,int index,double value){{{1*/ +Observation::Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in){ + + this->x = x_in; + this->y = y_in; + this->xi = xi_in; + this->yi = yi_in; + this->index = index_in; + this->value = value_in; + this->weight = 1.; + +} +/*}}}*/ +/*FUNCTION Observation::~Observation(){{{1*/ +Observation::~Observation(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION Observation::Echo {{{1*/ +void Observation::Echo(void){ + + int bit; + + printf("Observation\n"); + printf(" index : %i\n",this->index); + printf(" x : %g\n",this->x); + printf(" y : %g\n",this->y); + printf(" xi : "); printbinary(this->xi); printf("\n"); + printf(" yi : "); printbinary(this->yi); printf("\n"); + printf(" weight: %g\n",this->weight); + printf(" value : %g\n",this->value); +} +/*}}}*/ + +/*Observations functions*/ +/*FUNCTION Observation::WriteXYObs(double* px,double* py,double* pobs){{{1*/ +void Observation::WriteXYObs(double* px,double* py,double* pobs){ + *px = this->x; + *py = this->y; + *pobs = this->value; +} +/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/Observation.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/Observation.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/Observation.h (revision 12330) @@ -0,0 +1,35 @@ +/*! \file Observation.h + * \brief: header file for Observation object + */ + +#ifndef _OBSERVATION_H_ +#define _OBSERVATION_H_ + +#include "../Object.h" + +class Observation: public Object{ + + public: + double x,y; + int xi,yi; + int index; + double weight; + double value; + + /*Observation constructors, destructors*/ + Observation(); + Observation(double x_in,double y_in,int xi_in,int yi_in,int index_in,double value_in); + ~Observation(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho() {_error_("Not implemented yet"); }; + int Id() {_error_("Not implemented yet"); }; + int MyRank() {_error_("Not implemented yet"); }; + int ObjectEnum(){_error_("Not implemented yet"); }; + Object *copy() {_error_("Not implemented yet"); }; + + /*Management*/ + void WriteXYObs(double* px,double* py,double* pobs); +}; +#endif /* _OBSERVATION_*/ Index: /issm/trunk/src/c/objects/Kriging/PowerVariogram.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/PowerVariogram.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/PowerVariogram.cpp (revision 12330) @@ -0,0 +1,94 @@ +/*!\file PowerVariogram.c + * \brief: implementation of the PowerVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*PowerVariogram constructors and destructor*/ +/*FUNCTION PowerVariogram::PowerVariogram(){{{1*/ +PowerVariogram::PowerVariogram(){ + this->nugget = 0.2; + this->slope = 1.; + this->power = 1.; + return; +} +/*}}}*/ +/*FUNCTION PowerVariogram::PowerVariogram(Options* options){{{1*/ +PowerVariogram::PowerVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->slope = 1.; + this->power = 1.; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("slope")) options->Get(&this->slope,"slope"); + if(options->GetOption("power")) options->Get(&this->power,"power"); + + /*Checks*/ + if(power<=0 || power>=2) _error_("power must be betwwen 0 and 2 (0 < power < 2)"); + if(slope<=0) _error_("slope must be positive"); +} +/*}}}*/ +/*FUNCTION PowerVariogram::~PowerVariogram(){{{1*/ +PowerVariogram::~PowerVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION PowerVariogram::Echo {{{1*/ +void PowerVariogram::Echo(void){ + printf("PowerVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" slope : %g\n",this->slope); + printf(" power : %g\n",this->power); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION PowerVariogram::Covariance{{{1*/ +double PowerVariogram::Covariance(double deltax,double deltay){ + /*The covariance can be deduced from the variogram from the following + * relationship: + * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) + * so + * C(h) = sill - gamma */ + double h,cova; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return covariance*/ + cova = 9999. - this->slope*pow(h,this->power); + + return cova; +} +/*}}}*/ +/*FUNCTION PowerVariogram::SemiVariogram{{{1*/ +double PowerVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,gamma; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + gamma = this->nugget + this->slope*pow(h,this->power); + + //if(h>1000) printf("gamma = %g h=%g\n",gamma,h); + return gamma; +} +/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/PowerVariogram.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/PowerVariogram.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/PowerVariogram.h (revision 12330) @@ -0,0 +1,35 @@ +/*! \file PowerVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _POWERVARIOGRAM_H_ +#define _POWERVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class PowerVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double slope; + double power; + + /*PowerVariogram constructors, destructors*/ + PowerVariogram(); + PowerVariogram(Options* options); + ~PowerVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); + double Covariance(double deltax,double deltay); +}; +#endif /* _POWERVARIOGRAM_H */ Index: /issm/trunk/src/c/objects/Kriging/Quadtree.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/Quadtree.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/Quadtree.cpp (revision 12330) @@ -0,0 +1,606 @@ +#include "../objects.h" +/*DOCUMENTATION What is a Quadtree? {{{1 + * A Quadtree is a very simple way to group vertices according + * to their locations. A square that holds all the points of the mesh + * (or the geometry) is divided into 4 boxes. As soon as one box + * hold more than 4 vertices, it is divided into 4 new boxes, etc... + * There cannot be more than MAXDEEP (=30) subdivision. + * This process is like a Dichotomy in dimension 2 + * + * + - - - - - - - - + - - + - + - + - - - - + + * | | | | X | | + * + - + - + + * | | | | | | + * + - - + - + - + + + * | | | | | + * + * | | | | | + * + - - - - - - - - + - - + - - + - - - - + + * | | | | + * + * | | | | + * + * | | | | + * | | | | + * + - - - - - - - - + - - - - + - - - - + + * | | | + * + * | | | + * + * | | | + * + * | | | + * | | | + * | | | + * | | | + * | | | + * + - - - - - - - - + - - - - - - - - + + * + * The coordinate system used in a quadtree are integers to avoid + * round-off errors. The vertex in the lower left box has the coordinates + * (0 0) + * The upper right vertex has the follwing coordinates: + * 2^30 -1 2^30 -1 in decimal + * 0 1 1 1 .... 1 0 1 1 1 .... 1 in binary + * \-- 29 --/ \-- 29 --/ + * Using binaries is therefore very easy to locate a vertex in a box: + * we just need to look at the bits from the left to the right (See ::Add) + }}}1*/ +/*MACROS {{{1*/ +/* + * + * J j + * ^ ^ + * | | +--------+--------+ + * | | | | | + * 1X | | | 2 | 3 | + * | | | | | + * | | +--------+--------+ + * | | | | | + * 0X | | | 0 | 1 | + * | | | | | + * | | +--------+--------+ + * | +-----------------------> i + * | + * |----------------------------> I + * X0 X1 + * + * box 0 -> I=0 J=0 IJ=00 = 0 + * box 1 -> I=1 J=0 IJ=01 = 1 + * box 2 -> I=0 J=1 IJ=10 = 2 + * box 3 -> I=1 J=1 IJ=11 = 3 + */ +//IJ(i,j,l) returns the box number of i and j with respect to l +//if !j&l and !i&l -> 0 (box zero: lower left ) +//if !j&l and i&l -> 1 (box one: lower right) +//if j&l and !i&l -> 2 (box two: upper left ) +//if j&l and i&l -> 3 (box three:upper right) +#define IJ(i,j,l) ((j&l) ? ((i&l) ? 3:2 ) :((i&l) ? 1:0 )) +/*}}}*/ + + /*Constructors/Destructors*/ +/*FUNCTION Quadtree::Quadtree(){{{1*/ +Quadtree::Quadtree(){ + _error_("Constructor not supported"); + +} +/*}}}1*/ +/*FUNCTION Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){{{1*/ +Quadtree::Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth){ + + /*Intermediaries*/ + double length; + + /*Initialize fields*/ + this->MaxDepth=maxdepth; + this->NbQuadtreeBox=0; + this->NbObs=0; + + /*Create container*/ + this->boxcontainer=new DataSet(); + + /*Create Root, pointer toward the main box*/ + length=max(xmax-xmin,ymax-ymin); + this->root=NewQuadtreeBox(xmin+length/2,ymin+length/2,length); +} +/*}}}1*/ + /*FUNCTION Quadtree::~Quadtree(){{{1*/ + Quadtree::~Quadtree(){ + + delete boxcontainer; + root=NULL; + + } + /*}}}1*/ + + /*Methods*/ +/*FUNCTION Quadtree::Add{{{1*/ +void Quadtree::Add(Observation* observation){ + + /*Intermediaries*/ + int xi,yi,ij,level,levelbin; + QuadtreeBox **pbox = NULL; // pointer toward current box b + QuadtreeBox **pmaster = NULL; // pointer toward master of b + QuadtreeBox *box = NULL; // current box b + QuadtreeBox *slave = NULL; // suslaveox of b (if necessary) + Observation *obs[4]; + + /*Get integer coodinates*/ + xi = observation->xi; + yi = observation->yi; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pmaster = &root; + pbox = &root; + + /*Find the smallest box where the observation is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + /*Go down one level (levelbin = 00100 -> 00010)*/ + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + /*Get next box according to the bit value (levelbin)*/ + pmaster = pbox; + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + _assert_(levelbin>0); + + /*Now, try to add the vertex, if the box is full (nbitems=4), we have to divide it in 4 new boxes*/ + while((box=*pbox) && (box->nbitems==4)){ + + /*Copy the 4 observation in the current Quadtreebox*/ + obs[0] = box->obs[0]; + obs[1] = box->obs[1]; + obs[2] = box->obs[2]; + obs[3] = box->obs[3]; + + /*set nbitems as -1 (now holding boxes instead of observations)*/ + box->nbitems = -1; + box->box[0] = NULL; + box->box[1] = NULL; + box->box[2] = NULL; + box->box[3] = NULL; + + /*Go down one level (levelbin = 00010 -> 00001)*/ + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + /*Put the four observations in the new boxes*/ + for (int k=0;k<4;k++){ + + /*Get box for observation number k*/ + ij = IJ(obs[k]->xi,obs[k]->yi,levelbin); + slave = box->box[ij]; + if(!slave){ + box->box[ij] = NewQuadtreeBox(box,ij); + slave = box->box[ij]; + } + slave->obs[slave->nbitems++] = obs[k]; + } + + /*Get the suslaveox where the current observation is located*/ + ij = IJ(xi,yi,levelbin); + pmaster = pbox; + pbox = &box->box[ij]; + } + + /*alloc the QuadtreeBox if necessary and add current observation*/ + box = *pbox; + if(!box){ + ij = IJ(xi,yi,levelbin); + box = *pbox = NewQuadtreeBox(*pmaster,ij); + } + box->obs[box->nbitems++]=observation; + NbObs++; + +}/*}}}*/ +/*FUNCTION Quadtree::AddAndAverage{{{1*/ +void Quadtree::AddAndAverage(double x,double y,double value){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int xi,yi; + int level,levelbin; + int index; + double length,length2; + + /*Get integer coodinates*/ + this->IntergerCoordinates(&xi,&yi,x,y); + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + + /*Add obervation in this box (should be full)*/ + if(box && box->nbitems==4){ + index = 0; + length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.); + for(int i=1;i<4;i++){ + length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.); + if(length2obs[index]->x = (box->obs[index]->weight*box->obs[index]->x + x)/(box->obs[index]->weight+1); + box->obs[index]->y = (box->obs[index]->weight*box->obs[index]->y + y)/(box->obs[index]->weight+1); + box->obs[index]->xi= int((box->obs[index]->weight*double(box->obs[index]->xi) + double(xi))/(box->obs[index]->weight+1)); + box->obs[index]->yi= int((box->obs[index]->weight*double(box->obs[index]->yi) + double(yi))/(box->obs[index]->weight+1)); + box->obs[index]->value = (box->obs[index]->weight*box->obs[index]->value + value)/(box->obs[index]->weight+1); + box->obs[index]->weight += 1; + } + else{ + _error_("Box is not full"); + } +}/*}}}*/ +/*FUNCTION Quadtree::ClosestObs{{{1*/ +void Quadtree::ClosestObs(int *pindex,double x,double y){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int xi,yi; + int level,levelbin; + int index = -1; + double length,length2; + + /*Get integer coodinates*/ + this->IntergerCoordinates(&xi,&yi,x,y); + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + + /*Add obervation in this box (should be full)*/ + if(box && box->nbitems>0){ + index = box->obs[0]->index; + length = pow(box->obs[0]->x - x,2.) + pow(box->obs[0]->y - y,2.); + for(int i=1;inbitems;i++){ + length2 = pow(box->obs[i]->x - x,2.) + pow(box->obs[i]->y - y,2.); + if(length2obs[i]->index; + length = length2; + } + } + } + + *pindex=index; +}/*}}}*/ +/*FUNCTION Quadtree::Echo{{{1*/ +void Quadtree::Echo(void){ + + printf("Quadtree:\n"); + printf(" MaxDepth = %i\n",this->MaxDepth); + printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); + printf(" NbObs = %i\n",this->NbObs); + printf(" root = %p\n",this->root); + +}/*}}}*/ +/*FUNCTION Quadtree::DeepEcho{{{1*/ +void Quadtree::DeepEcho(void){ + + printf("Quadtree:\n"); + printf(" MaxDepth = %i\n",this->MaxDepth); + printf(" NbQuadtreeBox = %i\n",this->NbQuadtreeBox); + printf(" NbObs = %i\n",this->NbObs); + printf(" root = %p\n",this->root); + boxcontainer->Echo(); + +}/*}}}*/ +/*FUNCTION Quadtree::IntergerCoordinates{{{1*/ +void Quadtree::IntergerCoordinates(int *xi,int *yi,double x,double y){ + + /*Intermediaries*/ + double coefficient; + double xmin,ymin; + + /*Checks in debugging mode*/ + _assert_(xi && yi); + _assert_(this->root); + + /*coeffIcoor is the coefficient used for integer coordinates: + * (x-xmin) + * xi = (2^30 -1) --------- + * length + * coefficient = (2^30 -1)/length + */ + coefficient = double((1L<MaxDepth)-1)/(this->root->length); + xmin = this->root->xcenter - this->root->length/2; + ymin = this->root->ycenter - this->root->length/2; + + *xi=int(coefficient*(x - xmin)); + *yi=int(coefficient*(y - ymin)); +}/*}}}*/ +/*FUNCTION Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){{{1*/ +Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(double xcenter,double ycenter,double length){ + + /*Output*/ + QuadtreeBox* newbox=NULL; + + /*Create and initialize a new box*/ + newbox=new QuadtreeBox(); + newbox->nbitems=0; + newbox->xcenter=xcenter; + newbox->ycenter=ycenter; + newbox->length=length; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; + newbox->box[3]=NULL; + + /*Add to container*/ + this->boxcontainer->AddObject(newbox); + NbQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; +}/*}}}*/ +/*FUNCTION Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index) {{{1*/ +Quadtree::QuadtreeBox* Quadtree::NewQuadtreeBox(QuadtreeBox* master,int index){ + + /*Output*/ + QuadtreeBox* newbox=NULL; + + /*Checks in debugging mode*/ + _assert_(master); + + /*Create and initialize a new box*/ + newbox=new QuadtreeBox(); + newbox->nbitems=0; + newbox->box[0]=NULL; + newbox->box[1]=NULL; + newbox->box[2]=NULL; + newbox->box[3]=NULL; + switch(index){ + case 0: + newbox->xcenter=master->xcenter - master->length/4; + newbox->ycenter=master->ycenter - master->length/4; + break; + case 1: + newbox->xcenter=master->xcenter + master->length/4; + newbox->ycenter=master->ycenter - master->length/4; + break; + case 2: + newbox->xcenter=master->xcenter - master->length/4; + newbox->ycenter=master->ycenter + master->length/4; + break; + case 3: + newbox->xcenter=master->xcenter + master->length/4; + newbox->ycenter=master->ycenter + master->length/4; + break; + default: + _error_("Case %i not supported",index); + } + newbox->length=master->length/2; + + /*Add to container*/ + this->boxcontainer->AddObject(newbox); + NbQuadtreeBox++; + + /*currentbox now points toward next quadtree box*/ + return newbox; +}/*}}}*/ +/*FUNCTION Quadtree::QuadtreeDepth{{{1*/ +void Quadtree::QuadtreeDepth(int* A,int xi,int yi){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int level,levelbin; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; _assert_(levelMaxDepth); + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + if(box && box->nbitems>0){ + /*This box is not empty, add one level*/ + level+=1; + } + + *A=level; +}/*}}}*/ +/*FUNCTION Quadtree::QuadtreeDepth2{{{1*/ +void Quadtree::QuadtreeDepth2(int* A,int xi,int yi){ + + QuadtreeBox **pbox = NULL; + QuadtreeBox *box = NULL; + int level,levelbin; + + /*Initialize levels*/ + level = 0; + levelbin = (1L<MaxDepth);// = 2^30 + + /*Get inital box (the largest)*/ + pbox=&root; + + /*Find the smallest box where this point is located*/ + while((box=*pbox) && (box->nbitems<0)){ + + levelbin>>=1; level+=1; + + pbox = &box->box[IJ(xi,yi,levelbin)]; + } + if(box && box->nbitems>0){ + /*This box is not empty, add one level*/ + level+=1; + } + + /*If we were to add the vertex, get level*/ + if(box && box->nbitems==4){ + int ij; + bool flag=true; + while(flag){ + + levelbin>>=1; level+=1; + if(level>this->MaxDepth){ + level+=1; + break; + } + + /*loop over the four observations*/ + ij=IJ(box->obs[0]->xi,box->obs[0]->yi,levelbin); + for (int k=1;k<4;k++){ + if(IJ(box->obs[k]->xi,box->obs[k]->yi,levelbin) != ij){ + flag = false; + } + } + if(IJ(xi,yi,levelbin)!=ij){ + flag = false; + } + } + } + + *A=level; +}/*}}}*/ +/*FUNCTION Quadtree::RangeSearch{{{1*/ +void Quadtree::RangeSearch(int **pindices,int *pnobs,double x,double y,double range){ + + /*Intermediaries*/ + int nobs; + int *indices = NULL; + + /*Allocate indices (maximum by default*/ + if(this->NbObs) indices = (int*)xmalloc(this->NbObs*sizeof(int)); + nobs = 0; + + if(this->root) this->root->RangeSearch(indices,&nobs,x,y,range); + + /*Clean-up and return*/ + *pnobs=nobs; + *pindices=indices; + +}/*}}}*/ + +/*QuadtreeBox methos*/ +/*FUNCTION QuadtreeBox::Echo{{{1*/ +void Quadtree::QuadtreeBox::Echo(void){ + + printf("QuadtreeBox:\n"); + printf(" nbitems = %i\n",this->nbitems); + printf(" xcenter = %g\n",this->xcenter); + printf(" ycenter = %g\n",this->ycenter); + printf(" length = %g\n",this->length); + +}/*}}}*/ +/*FUNCTION QuadtreeBox::IsWithinRange{{{1*/ +int Quadtree::QuadtreeBox::IsWithinRange(double x,double y,double range){ + + /*Return 0 if the 2 boxes do not overlap*/ + if(this->xcenter+this->length/2 < x-range) return 0; + if(this->xcenter-this->length/2 > x+range) return 0; + if(this->ycenter+this->length/2 < y-range) return 0; + if(this->ycenter-this->length/2 > y+range) return 0; + + /*Return 2 if the this box is included in the range*/ + if(this->xcenter+this->length/2 <= x+range && + this->ycenter+this->length/2 <= y+range && + this->xcenter-this->length/2 >= x-range && + this->ycenter-this->length/2 >= y-range) return 2; + + /*This is a simple overlap*/ + return 1; + +}/*}}}*/ +/*FUNCTION QuadtreeBox::RangeSearch{{{1*/ +void Quadtree::QuadtreeBox::RangeSearch(int* indices,int *pnobs,double x,double y,double range){ + + /*Intermediaries*/ + int i,nobs; + + /*Recover current number of observations*/ + nobs = *pnobs; + + switch(this->IsWithinRange(x,y,range)){ + case 0: + /*If this box is not within range, return*/ + break; + case 2: + /*This box is included in range*/ + this->WriteObservations(indices,&nobs); + break; + case 1: + /*This box is partly included*/ + if(this->nbitems>0){ + /*If this box has only observations, add indices that are within range*/ + for(i=0;inbitems;i++){ + if(fabs(this->obs[i]->x-x) <= range && fabs(this->obs[i]->y-y) <= range){ + indices[nobs++]=this->obs[i]->index; + } + } + } + else{ + /*This box points toward boxes*/ + if(this->box[0]) this->box[0]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[1]) this->box[1]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[2]) this->box[2]->RangeSearch(indices,&nobs,x,y,range); + if(this->box[3]) this->box[3]->RangeSearch(indices,&nobs,x,y,range); + } + break; + default: + _error_("Case %i not supported",this->IsWithinRange(x,y,range)); + } + + /*Assign output pointers: */ + *pnobs=nobs; +}/*}}}*/ +/*FUNCTION QuadtreeBox::WriteObservations{{{1*/ +void Quadtree::QuadtreeBox::WriteObservations(int* indices,int *pnobs){ + + /*Intermediaries*/ + int i,nobs; + + /*Recover current number of observations*/ + nobs = *pnobs; + + if(this->nbitems>0){ + /*If this box has only observations, add all indices*/ + for(i=0;inbitems;i++){ + indices[nobs++]=this->obs[i]->index; + } + } + else{ + /*This box points toward boxes, */ + if(this->box[0]) this->box[0]->WriteObservations(indices,&nobs); + if(this->box[1]) this->box[1]->WriteObservations(indices,&nobs); + if(this->box[2]) this->box[2]->WriteObservations(indices,&nobs); + if(this->box[3]) this->box[3]->WriteObservations(indices,&nobs); + } + + /*Assign output pointers: */ + *pnobs=nobs; +}/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/Quadtree.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/Quadtree.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/Quadtree.h (revision 12330) @@ -0,0 +1,66 @@ + +#ifndef _QUADTREE_H +#define _QUADTREE_H + +class Observation; + +class Quadtree{ + + private: + /* A quadtree box contains up to 4 points (locations). 4 new quadtree boxes are + * created if a fifth point is added to the same box. A Quadtree box is therefore + * composed of EITHER: + * - up to 4 vertices + * - 4 "sub" quadtree boxes*/ + + class QuadtreeBox: public Object{ + public: + int nbitems; // number of current vertices in the box + double xcenter; // x position of the center (double) + double ycenter; // x position of the center (double) + double length; // width of the box + union{ + QuadtreeBox *box[4]; + Observation *obs[4]; + }; + + /*Object functions (Needed because the Quadtree uses a Container*/ + void Echo(); + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; + int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum(){_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + + /*Methods*/ + int IsWithinRange(double x,double y,double range); + void RangeSearch(int *indices,int *pnobs,double x,double y,double range); + void WriteObservations(int *indices,int *pnobs); + + }; + + /*Quadtree private Fields*/ + DataSet* boxcontainer; + + public: + int MaxDepth; // maximum number of subdivision + QuadtreeBox *root; // main box + long NbQuadtreeBox; // total number of boxes + long NbObs; // number of points + + Quadtree(); + Quadtree(double xmin,double xmax,double ymin,double ymax,int maxdepth_in); + ~Quadtree(); + void Add(Observation *observation); + void AddAndAverage(double x,double y,double value); + void ClosestObs(int *pindex,double x,double y); + void DeepEcho(void); + void Echo(void); + void IntergerCoordinates(int *xi,int *yi,double x,double y); + QuadtreeBox *NewQuadtreeBox(double xcenter,double ycenter,double length); + QuadtreeBox *NewQuadtreeBox(QuadtreeBox* master,int index); + void QuadtreeDepth(int *A,int xi,int yi); + void QuadtreeDepth2(int *A,int xi,int yi); + void RangeSearch(int **pindices,int *pnobs,double x,double y,double range); +}; +#endif //_QUADTREE_H Index: /issm/trunk/src/c/objects/Kriging/SphericalVariogram.cpp =================================================================== --- /issm/trunk/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/SphericalVariogram.cpp (revision 12330) @@ -0,0 +1,98 @@ +/*!\file SphericalVariogram.c + * \brief: implementation of the SphericalVariogram object + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include +#include "../objects.h" +#include "../../EnumDefinitions/EnumDefinitions.h" +#include "../../shared/shared.h" +#include "../../include/include.h" + +/*SphericalVariogram constructors and destructor*/ +/*FUNCTION SphericalVariogram::SphericalVariogram(){{{1*/ +SphericalVariogram::SphericalVariogram(){ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + return; +} +/*}}}*/ +/*FUNCTION SphericalVariogram::SphericalVariogram(Options* options){{{1*/ +SphericalVariogram::SphericalVariogram(Options* options){ + + /*Defaults*/ + this->nugget = 0.2; + this->sill = 1; + this->range = SQRT3; + + /*Overwrite from options*/ + if(options->GetOption("nugget")) options->Get(&this->nugget,"nugget"); + if(options->GetOption("sill")) options->Get(&this->sill,"sill"); + if(options->GetOption("range")) options->Get(&this->range,"range"); + + /*Checks*/ + if(nugget==sill) _error_("nugget and sill cannot be equal (constant semivariogram not allowed)"); +} +/*}}}*/ +/*FUNCTION SphericalVariogram::~SphericalVariogram(){{{1*/ +SphericalVariogram::~SphericalVariogram(){ + return; +} +/*}}}*/ + +/*Object virtual functions definitions:*/ +/*FUNCTION SphericalVariogram::Echo {{{1*/ +void SphericalVariogram::Echo(void){ + printf("SphericalVariogram\n"); + printf(" nugget: %g\n",this->nugget); + printf(" sill : %g\n",this->sill); + printf(" range : %g\n",this->range); +} +/*}}}*/ + +/*Variogram function*/ +/*FUNCTION SphericalVariogram::Covariance{{{1*/ +double SphericalVariogram::Covariance(double deltax,double deltay){ + /*The covariance can be deduced from the variogram from the following + * relationship: + * 2 gamma = C(x,x) + C(y,y) -2 C(x,y) + * so + * C(h) = sill - gamma */ + double h,cova; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return covariance*/ + if(h<=range) + cova = (sill-nugget)*(1 - (3*h)/(2*range) + pow(h,3.)/(2*pow(range,3.)) ); + else + cova = 0.; + + return cova; +} +/*}}}*/ +/*FUNCTION SphericalVariogram::SemiVariogram{{{1*/ +double SphericalVariogram::SemiVariogram(double deltax,double deltay){ + /*http://en.wikipedia.org/wiki/Variogram*/ + double h,gamma; + + /*Calculate length square*/ + h=sqrt(pow(deltax,2.)+pow(deltay,2.)); + + /*return semi-variogram*/ + if(h<=range) + gamma = (sill-nugget)*( (3*h)/(2*range) - pow(h,3.)/(2*pow(range,3.)) ) + nugget; + else + gamma = sill; + + return gamma; +} +/*}}}*/ Index: /issm/trunk/src/c/objects/Kriging/SphericalVariogram.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/SphericalVariogram.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/SphericalVariogram.h (revision 12330) @@ -0,0 +1,35 @@ +/*! \file SphericalVariogram.h + * \brief: header file for triavertexinput object + */ + +#ifndef _SPHERICALVARIOGRAM_H_ +#define _SPHERICALVARIOGRAM_H_ + +/*Headers:*/ +#include "./Variogram.h" + +class SphericalVariogram: public Variogram{ + + public: + double nugget; //The height of the jump of the semivariogram at the discontinuity at the origin + double sill; //Limit of the variogram tending to infinity lag distances + double range; //The distance in which the difference of the variogram from the sill becomes negligible + + /*SphericalVariogram constructors, destructors*/ + SphericalVariogram(); + SphericalVariogram(Options* options); + ~SphericalVariogram(); + + /*Object virtual functions definitions*/ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; + int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + + /*Variogram functions*/ + double SemiVariogram(double deltax,double deltay); + double Covariance(double deltax,double deltay); +}; +#endif /* _SPHERICALVARIOGRAM_H */ Index: /issm/trunk/src/c/objects/Kriging/Variogram.h =================================================================== --- /issm/trunk/src/c/objects/Kriging/Variogram.h (revision 12330) +++ /issm/trunk/src/c/objects/Kriging/Variogram.h (revision 12330) @@ -0,0 +1,18 @@ +/*!\file: Variogram.h + * \brief abstract class for Variogram object + */ + +#ifndef _VARIOGRAM_H_ +#define _VARIOGRAM_H_ + +#include "../Object.h" + +class Variogram: public Object{ + + public: + virtual ~Variogram(){}; + virtual double SemiVariogram(double deltax,double deltay)=0; + virtual double Covariance(double deltax,double deltay)=0; + +}; +#endif Index: /issm/trunk/src/c/objects/Loads/Icefront.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Icefront.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Icefront.cpp (revision 12330) @@ -163,92 +163,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Icefront::Marshall {{{1*/ -void Icefront::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Icefront: */ - enum_type=IcefrontEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Icefront data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION Icefront::MarshallSize {{{1*/ -int Icefront::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +hnodes->MarshallSize() - +helement->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Icefront::Demarshall {{{1*/ -void Icefront::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - element=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Icefront::ObjectEnum{{{1*/ int Icefront::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Loads/Icefront.h =================================================================== --- /issm/trunk/src/c/objects/Loads/Icefront.h (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Icefront.h (revision 12330) @@ -49,9 +49,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Loads/Numericalflux.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Numericalflux.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Numericalflux.cpp (revision 12330) @@ -189,87 +189,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Numericalflux::Marshall {{{1*/ -void Numericalflux::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Numericalflux: */ - enum_type=NumericalfluxEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Numericalflux data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Numericalflux::MarshallSize{{{1*/ -int Numericalflux::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +hnodes->MarshallSize() - +helement->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Numericalflux::Demarshall {{{1*/ -void Numericalflux::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - this->element=NULL; - this->nodes=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Numericalflux::ObjectEnum{{{1*/ int Numericalflux::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Loads/Numericalflux.h =================================================================== --- /issm/trunk/src/c/objects/Loads/Numericalflux.h (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Numericalflux.h (revision 12330) @@ -45,9 +45,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Loads/Pengrid.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Pengrid.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Pengrid.cpp (revision 12330) @@ -132,98 +132,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Pengrid::Marshall {{{1*/ -void Pengrid::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Tria: */ - enum_type=PengridEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Tria data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(marshalled_dataset,&zigzag_counter,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); - - /*Marshall hooks: */ - hnode->Marshall(&marshalled_dataset); - helement->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Pengrid::MarshallSize {{{1*/ -int Pengrid::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +sizeof(active) - +sizeof(zigzag_counter) - +hnode->MarshallSize() - +helement->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Pengrid::Demarshall {{{1*/ -void Pengrid::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(&zigzag_counter,marshalled_dataset,sizeof(zigzag_counter));marshalled_dataset+=sizeof(zigzag_counter); - - /*demarshall hooks: */ - hnode=new Hook(); hnode->Demarshall(&marshalled_dataset); - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - this->node=NULL; - this->element=NULL; - this->matpar=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Pengrid::ObjectEnum{{{1*/ int Pengrid::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Loads/Pengrid.h =================================================================== --- /issm/trunk/src/c/objects/Loads/Pengrid.h (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Pengrid.h (revision 12330) @@ -50,9 +50,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Loads/Penpair.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Penpair.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Penpair.cpp (revision 12330) @@ -85,67 +85,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Penpair::Marshall {{{1*/ -void Penpair::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Penpair: */ - enum_type=PenpairEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Penpair data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*Marshall hooks*/ - hnodes->Marshall(&marshalled_dataset); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION Penpair::MarshallSize {{{1*/ -int Penpair::MarshallSize(){ - - return sizeof(id)+ - +sizeof(analysis_type) - +hnodes->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION Penpair::Demarshall {{{1*/ -void Penpair::Demarshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION Penpair::ObjectEnum{{{1*/ int Penpair::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Loads/Penpair.h =================================================================== --- /issm/trunk/src/c/objects/Loads/Penpair.h (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Penpair.h (revision 12330) @@ -37,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Loads/Riftfront.cpp =================================================================== --- /issm/trunk/src/c/objects/Loads/Riftfront.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Riftfront.cpp (revision 12330) @@ -192,123 +192,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Riftfront::Marshall {{{1*/ -void Riftfront::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Riftfront: */ - enum_type=RiftfrontEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Riftfront data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&active,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(marshalled_dataset,&normal,sizeof(normal));marshalled_dataset+=sizeof(normal); - memcpy(marshalled_dataset,&length,sizeof(length));marshalled_dataset+=sizeof(length); - memcpy(marshalled_dataset,&fraction,sizeof(fraction));marshalled_dataset+=sizeof(fraction); - memcpy(marshalled_dataset,&frozen,sizeof(frozen));marshalled_dataset+=sizeof(frozen); - memcpy(marshalled_dataset,&state,sizeof(state));marshalled_dataset+=sizeof(state); - memcpy(marshalled_dataset,&counter,sizeof(counter));marshalled_dataset+=sizeof(counter); - memcpy(marshalled_dataset,&prestable,sizeof(prestable));marshalled_dataset+=sizeof(prestable); - memcpy(marshalled_dataset,&penalty_lock,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); - memcpy(marshalled_dataset,&material_converged,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); - - /*Marshall hooks: */ - hnodes->Marshall(&marshalled_dataset); - helements->Marshall(&marshalled_dataset); - hmatpar->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - /*parameters: don't do anything about it. parameters are marshalled somewhere else!*/ - - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Riftfront::MarshallSize {{{1*/ -int Riftfront::MarshallSize(){ - - return sizeof(id) - +sizeof(analysis_type) - +sizeof(active) - +sizeof(normal) - +sizeof(length) - +sizeof(fraction) - +sizeof(frozen) - +sizeof(state) - +sizeof(counter) - +sizeof(prestable) - +sizeof(penalty_lock) - +sizeof(material_converged) - +hnodes->MarshallSize() - +helements->MarshallSize() - +hmatpar->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Riftfront::Demarshall {{{1*/ -void Riftfront::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&active,marshalled_dataset,sizeof(active));marshalled_dataset+=sizeof(active); - memcpy(&normal,marshalled_dataset,sizeof(normal));marshalled_dataset+=sizeof(normal); - memcpy(&length,marshalled_dataset,sizeof(length));marshalled_dataset+=sizeof(length); - memcpy(&fraction,marshalled_dataset,sizeof(fraction));marshalled_dataset+=sizeof(fraction); - memcpy(&frozen,marshalled_dataset,sizeof(frozen));marshalled_dataset+=sizeof(frozen); - memcpy(&state,marshalled_dataset,sizeof(state));marshalled_dataset+=sizeof(state); - memcpy(&counter,marshalled_dataset,sizeof(counter));marshalled_dataset+=sizeof(counter); - memcpy(&prestable,marshalled_dataset,sizeof(prestable));marshalled_dataset+=sizeof(prestable); - memcpy(&penalty_lock,marshalled_dataset,sizeof(penalty_lock));marshalled_dataset+=sizeof(penalty_lock); - memcpy(&material_converged,marshalled_dataset,sizeof(material_converged));marshalled_dataset+=sizeof(material_converged); - - /*demarshall hooks: */ - hnodes=new Hook(); hnodes->Demarshall(&marshalled_dataset); - helements=new Hook(); helements->Demarshall(&marshalled_dataset); - hmatpar=new Hook(); hmatpar->Demarshall(&marshalled_dataset); - - /*pointers are garbabe, until configuration is carried out: */ - nodes=NULL; - elements=NULL; - matpar=NULL; - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*parameters: may not exist even yet, so let Configure handle it: */ - this->parameters=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION Riftfront::ObjectEnum{{{1*/ int Riftfront::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Loads/Riftfront.h =================================================================== --- /issm/trunk/src/c/objects/Loads/Riftfront.h (revision 12329) +++ /issm/trunk/src/c/objects/Loads/Riftfront.h (revision 12330) @@ -57,9 +57,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Materials/Matice.cpp =================================================================== --- /issm/trunk/src/c/objects/Materials/Matice.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Materials/Matice.cpp (revision 12330) @@ -88,74 +88,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Matice::Marshall {{{1*/ -void Matice::Marshall(char** pmarshalled_dataset){ - - /*Intermediaries*/ - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputs_size; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Matice: */ - enum_type=MaticeEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Matice data: */ - memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); - - /*Marshall hooks: */ - helement->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputs_size=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputs_size*sizeof(char)); - marshalled_dataset+=marshalled_inputs_size; - - *pmarshalled_dataset=marshalled_dataset; - - /*clean up and return*/ - xfree((void**)&marshalled_inputs); -} -/*}}}*/ -/*FUNCTION Matice::MarshallSize{{{1*/ -int Matice::MarshallSize(){ - - return sizeof(mid) - +helement->MarshallSize() - +inputs->MarshallSize() - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Matice::Demarshall {{{1*/ -void Matice::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); - - /*demarshall hooks: */ - helement=new Hook(); helement->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Matice::ObjectEnum{{{1*/ int Matice::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Materials/Matice.h =================================================================== --- /issm/trunk/src/c/objects/Materials/Matice.h (revision 12329) +++ /issm/trunk/src/c/objects/Materials/Matice.h (revision 12330) @@ -35,9 +35,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Materials/Matpar.cpp =================================================================== --- /issm/trunk/src/c/objects/Materials/Matpar.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Materials/Matpar.cpp (revision 12330) @@ -90,92 +90,4 @@ } /*}}}1*/ -#ifdef _SERIAL_ -/*FUNCTION Matpar::Marshall {{{1*/ -void Matpar::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Matpar: */ - enum_type=MatparEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Matpar data: */ - memcpy(marshalled_dataset,&mid,sizeof(mid));marshalled_dataset+=sizeof(mid); - memcpy(marshalled_dataset,&rho_ice,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); - memcpy(marshalled_dataset,&rho_water,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); - memcpy(marshalled_dataset,&rho_freshwater,sizeof(rho_freshwater));marshalled_dataset+=sizeof(rho_freshwater); - memcpy(marshalled_dataset,&mu_water,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); - memcpy(marshalled_dataset,&heatcapacity,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); - memcpy(marshalled_dataset,&thermalconductivity,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); - memcpy(marshalled_dataset,&latentheat,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); - memcpy(marshalled_dataset,&beta,sizeof(beta));marshalled_dataset+=sizeof(beta); - memcpy(marshalled_dataset,&meltingpoint,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); - memcpy(marshalled_dataset,&referencetemperature,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); - memcpy(marshalled_dataset,&mixed_layer_capacity,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); - memcpy(marshalled_dataset,&thermal_exchange_velocity,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); - memcpy(marshalled_dataset,&g,sizeof(g));marshalled_dataset+=sizeof(g); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -/*FUNCTION Matpar::MarshallSize {{{1*/ -int Matpar::MarshallSize(){ - - return sizeof(mid)+ - sizeof(rho_ice)+ - sizeof(rho_water)+ - sizeof(rho_freshwater)+ - sizeof(mu_water)+ - sizeof(heatcapacity)+ - sizeof(thermalconductivity)+ - sizeof(latentheat)+ - sizeof(beta)+ - sizeof(meltingpoint)+ - sizeof(referencetemperature)+ - sizeof(mixed_layer_capacity)+ - sizeof(thermal_exchange_velocity)+ - sizeof(g)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}1*/ -/*FUNCTION Matpar::Demarshall {{{1*/ -void Matpar::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&mid,marshalled_dataset,sizeof(mid));marshalled_dataset+=sizeof(mid); - memcpy(&rho_ice,marshalled_dataset,sizeof(rho_ice));marshalled_dataset+=sizeof(rho_ice); - memcpy(&rho_water,marshalled_dataset,sizeof(rho_water));marshalled_dataset+=sizeof(rho_water); - memcpy(&rho_freshwater,marshalled_dataset,sizeof(rho_freshwater));marshalled_dataset+=sizeof(rho_freshwater); - memcpy(&mu_water,marshalled_dataset,sizeof(mu_water));marshalled_dataset+=sizeof(mu_water); - memcpy(&heatcapacity,marshalled_dataset,sizeof(heatcapacity));marshalled_dataset+=sizeof(heatcapacity); - memcpy(&thermalconductivity,marshalled_dataset,sizeof(thermalconductivity));marshalled_dataset+=sizeof(thermalconductivity); - memcpy(&latentheat,marshalled_dataset,sizeof(latentheat));marshalled_dataset+=sizeof(latentheat); - memcpy(&beta,marshalled_dataset,sizeof(beta));marshalled_dataset+=sizeof(beta); - memcpy(&meltingpoint,marshalled_dataset,sizeof(meltingpoint));marshalled_dataset+=sizeof(meltingpoint); - memcpy(&referencetemperature,marshalled_dataset,sizeof(referencetemperature));marshalled_dataset+=sizeof(referencetemperature); - memcpy(&mixed_layer_capacity,marshalled_dataset,sizeof(mixed_layer_capacity));marshalled_dataset+=sizeof(mixed_layer_capacity); - memcpy(&thermal_exchange_velocity,marshalled_dataset,sizeof(thermal_exchange_velocity));marshalled_dataset+=sizeof(thermal_exchange_velocity); - memcpy(&g,marshalled_dataset,sizeof(g));marshalled_dataset+=sizeof(g); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}1*/ -#endif /*FUNCTION Matpar::ObjectEnum{{{1*/ int Matpar::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Materials/Matpar.h =================================================================== --- /issm/trunk/src/c/objects/Materials/Matpar.h (revision 12329) +++ /issm/trunk/src/c/objects/Materials/Matpar.h (revision 12330) @@ -47,9 +47,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Node.cpp =================================================================== --- /issm/trunk/src/c/objects/Node.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Node.cpp (revision 12330) @@ -193,87 +193,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Node::Marshall{{{1*/ -void Node::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - char* marshalled_inputs=NULL; - int marshalled_inputssize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Node: */ - enum_type=NodeEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Node data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&analysis_type,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(marshalled_dataset,&coord_system,9*sizeof(double));marshalled_dataset+=9*sizeof(double); - - /*marshall objects: */ - indexing.Marshall(&marshalled_dataset); - hvertex->Marshall(&marshalled_dataset); - - /*Marshall inputs: */ - marshalled_inputssize=inputs->MarshallSize(); - marshalled_inputs=inputs->Marshall(); - memcpy(marshalled_dataset,marshalled_inputs,marshalled_inputssize*sizeof(char)); - marshalled_dataset+=marshalled_inputssize; - - /*Free ressources:*/ - xfree((void**)&marshalled_inputs); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Node::MarshallSize{{{1*/ -int Node::MarshallSize(){ - - return sizeof(id)+ - sizeof(sid)+ - indexing.MarshallSize()+ - hvertex->MarshallSize()+ - inputs->MarshallSize()+ - sizeof(analysis_type)+ - 9*sizeof(double)+ - sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Node::Demarshall{{{1*/ -void Node::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&analysis_type,marshalled_dataset,sizeof(analysis_type));marshalled_dataset+=sizeof(analysis_type); - memcpy(&coord_system,marshalled_dataset,9*sizeof(double));marshalled_dataset+=9*sizeof(double); - - /*demarshall objects: */ - indexing.Demarshall(&marshalled_dataset); - hvertex=new Hook(); hvertex->Demarshall(&marshalled_dataset); - - /*demarshall inputs: */ - inputs=(Inputs*)DataSetDemarshallRaw(&marshalled_dataset); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Node::ObjectEnum{{{1*/ int Node::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Node.h =================================================================== --- /issm/trunk/src/c/objects/Node.h (revision 12329) +++ /issm/trunk/src/c/objects/Node.h (revision 12330) @@ -32,5 +32,5 @@ Inputs* inputs; //properties of this node int analysis_type; - double coord_system[3][3]; + IssmDouble coord_system[3][3]; /*Node constructors, destructors {{{1*/ @@ -44,9 +44,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(){_error_("Not implemented yet (similar to Elements)");}; @@ -54,15 +49,15 @@ /*Update virtual functions definitions: {{{1*/ - void InputUpdateFromVector(double* vector, int name, int type); + void InputUpdateFromVector(IssmDouble* vector, int name, int type); void InputUpdateFromVector(int* vector, int name, int type); void InputUpdateFromVector(bool* vector, int name, int type); - void InputUpdateFromMatrixDakota(double* matrix,int nrows, int ncols, int name, int type); - void InputUpdateFromVectorDakota(double* vector, int name, int type); + void InputUpdateFromMatrixDakota(IssmDouble* matrix,int nrows, int ncols, int name, int type); + void InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type); void InputUpdateFromVectorDakota(int* vector, int name, int type); void InputUpdateFromVectorDakota(bool* vector, int name, int type); - void InputUpdateFromConstant(double constant, int name); + void InputUpdateFromConstant(IssmDouble constant, int name); void InputUpdateFromConstant(int constant, int name); void InputUpdateFromConstant(bool constant, int name); - void InputUpdateFromSolution(double* solution){_error_("Not implemented yet!");} + void InputUpdateFromSolution(IssmDouble* solution){_error_("Not implemented yet!");} void InputUpdateFromIoModel(int index, IoModel* iomodel){_error_("Not implemented yet!");} /*}}}*/ @@ -75,5 +70,5 @@ int GetVertexId(void); #ifdef _HAVE_DIAGNOSTIC_ - void GetCoordinateSystem(double* coord_system_out); + void GetCoordinateSystem(IssmDouble* coord_system_out); #endif void SetVertexDof(int in_dof); @@ -82,5 +77,5 @@ int GetNumberOfDofs(int approximation_enum,int setenum); int IsClone(); - void ApplyConstraint(int dof,double value); + void ApplyConstraint(int dof,IssmDouble value); void RelaxConstraint(int dof); void DofInSSet(int dof); @@ -93,8 +88,8 @@ int GetDofList1(void); int GetSidList(void); - double GetX(); - double GetY(); - double GetZ(); - double GetSigma(); + IssmDouble GetX(); + IssmDouble GetY(); + IssmDouble GetZ(); + IssmDouble GetSigma(); int IsOnBed(); int IsOnSurface(); @@ -102,7 +97,7 @@ int IsFloating(); int IsGrounded(); - void UpdateSpcs(double* ys); - void VecMerge(Vector* ug, double* vector_serial,int setenum); - void VecReduce(Vector* vector, double* ug_serial,int setnum); + void UpdateSpcs(IssmDouble* ys); + void VecMerge(Vector* ug, IssmDouble* vector_serial,int setenum); + void VecReduce(Vector* vector, IssmDouble* ug_serial,int setnum); /*}}}*/ Index: /issm/trunk/src/c/objects/Numerics/ElementVector.cpp =================================================================== --- /issm/trunk/src/c/objects/Numerics/ElementVector.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/ElementVector.cpp (revision 12330) @@ -166,4 +166,7 @@ double* localvalues=NULL; + /*In debugging mode, check consistency (no NaN, and values not too big)*/ + this->CheckConsistency(); + if(this->fsize){ /*first, retrieve values that are in the f-set from the g-set values vector: */ @@ -200,4 +203,15 @@ } +} +/*}}}*/ +/*FUNCTION ElementVector::CheckConsistency{{{1*/ +void ElementVector::CheckConsistency(void){ + /*Check element matrix values, only in debugging mode*/ +#ifdef _ISSM_DEBUG_ + for (int i=0;inrows;i++){ + if (isnan(this->values[i])) _error_("NaN found in Element Vector"); + if (fabs( this->values[i])>1.e+50) _error_("Element Vector values exceeds 1.e+50"); + } +#endif } /*}}}*/ Index: /issm/trunk/src/c/objects/Numerics/ElementVector.h =================================================================== --- /issm/trunk/src/c/objects/Numerics/ElementVector.h (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/ElementVector.h (revision 12330) @@ -43,4 +43,5 @@ void InsertIntoGlobal(Vector* pf); void Echo(void); + void CheckConsistency(void); void Init(ElementVector* pe); void SetValue(double scalar); Index: /issm/trunk/src/c/objects/Numerics/Matrix.cpp =================================================================== --- /issm/trunk/src/c/objects/Numerics/Matrix.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/Matrix.cpp (revision 12330) @@ -140,38 +140,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION Matrix::ToMatlabMatrix{{{1*/ -mxArray* Matrix::ToMatlabMatrix(void){ - - mxArray* dataref=NULL; - #ifdef _HAVE_PETSC_ - PetscMatrixToMatlabMatrix(&dataref,this->matrix); - #else - dataref=this->matrix->ToMatlabMatrix(); - #endif - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabMatrixToMatrix{{{1*/ -Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){ - - int dummy; - Matrix* matrix=NULL; - - /*allocate matrix object: */ - matrix=new Matrix(); - - #ifdef _HAVE_PETSC_ - MatlabMatrixToPetscMatrix(&matrix->matrix,NULL,NULL,mxmatrix); - #else - matrix->matrix=MatlabMatrixToSeqMat(mxmatrix); - #endif - - return matrix; -} -/*}}}*/ -#endif /*FUNCTION Matrix::Assemble{{{1*/ void Matrix::Assemble(void){ Index: /issm/trunk/src/c/objects/Numerics/Matrix.h =================================================================== --- /issm/trunk/src/c/objects/Numerics/Matrix.h (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/Matrix.h (revision 12330) @@ -21,7 +21,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif class Vector; @@ -51,7 +48,4 @@ /*Matrix specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabMatrix(void); - #endif void Assemble(void); double Norm(NormMode norm_type); @@ -66,8 +60,4 @@ }; -/*API: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix); -#endif #endif //#ifndef _MATRIX_H_ Index: /issm/trunk/src/c/objects/Numerics/Vector.cpp =================================================================== --- /issm/trunk/src/c/objects/Numerics/Vector.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/Vector.cpp (revision 12330) @@ -85,5 +85,5 @@ /*}}}*/ #endif -#ifdef _HAVE_GSL_ +#if defined(_HAVE_GSL_) && !defined(_HAVE_PETSC_) /*FUNCTION Vector::Vector(SeqVec* seq_vec){{{1*/ Vector::Vector(SeqVec* seq_vec){ @@ -132,38 +132,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION Vector::ToMatlabVector{{{1*/ -mxArray* Vector::ToMatlabVector(void){ - - mxArray* dataref=NULL; - #ifdef _HAVE_PETSC_ - PetscVectorToMatlabVector(&dataref,this->vector); - #else - dataref=this->vector->ToMatlabVector(); - #endif - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabVectorToVector{{{1*/ -Vector* MatlabVectorToVector(const mxArray* mxvector){ - - int dummy; - Vector* vector=NULL; - - /*allocate vector object: */ - vector=new Vector(); - - #ifdef _HAVE_PETSC_ - MatlabVectorToPetscVector(&vector->vector,&dummy,mxvector); - #else - vector->vector=MatlabVectorToSeqVec(mxvector); - #endif - - return vector; -} -/*}}}*/ -#endif /*FUNCTION Vector::Assemble{{{1*/ void Vector::Assemble(void){ Index: /issm/trunk/src/c/objects/Numerics/Vector.h =================================================================== --- /issm/trunk/src/c/objects/Numerics/Vector.h (revision 12329) +++ /issm/trunk/src/c/objects/Numerics/Vector.h (revision 12330) @@ -21,8 +21,4 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif - /*}}}*/ @@ -47,5 +43,5 @@ Vector(Vec petsc_vec); #endif - #ifdef _HAVE_GSL_ + #if defined(_HAVE_GSL_) && !defined(_HAVE_PETSC_) Vector(SeqVec* seq_vec); #endif @@ -54,7 +50,4 @@ /*Vector specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabVector(void); - #endif void AXPY(Vector *X, double a); void AYPX(Vector *X, double a); @@ -77,8 +70,4 @@ }; -/*API: */ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -Vector* MatlabVectorToVector(const mxArray* mxvector); -#endif #endif //#ifndef _VECTOR_H_ Index: /issm/trunk/src/c/objects/Object.h =================================================================== --- /issm/trunk/src/c/objects/Object.h (revision 12329) +++ /issm/trunk/src/c/objects/Object.h (revision 12330) @@ -21,9 +21,4 @@ virtual int Id()=0; virtual int MyRank()=0; - #ifdef _SERIAL_ - virtual void Marshall(char** pmarshalled_dataset)=0; - virtual int MarshallSize()=0; - virtual void Demarshall(char** pmarshalled_dataset)=0; - #endif virtual int ObjectEnum()=0; virtual Object* copy()=0; Index: /issm/trunk/src/c/objects/OptArgs.h =================================================================== --- /issm/trunk/src/c/objects/OptArgs.h (revision 12329) +++ /issm/trunk/src/c/objects/OptArgs.h (revision 12330) @@ -6,19 +6,8 @@ #define _OPTARGS_H_ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -#include "mex.h" -struct OptArgs{ - char* function_name; - mxArray* femmodel; -}; - -#else - class Model; struct OptArgs{ FemModel* femmodel; }; -#endif #endif Index: /issm/trunk/src/c/objects/OptPars.h =================================================================== --- /issm/trunk/src/c/objects/OptPars.h (revision 12329) +++ /issm/trunk/src/c/objects/OptPars.h (revision 12330) @@ -8,7 +8,7 @@ struct OptPars{ - double xmin; - double xmax; - double cm_jump; + IssmDouble xmin; + IssmDouble xmax; + IssmDouble cm_jump; int maxiter; Index: /issm/trunk/src/c/objects/Options/Option.h =================================================================== --- /issm/trunk/src/c/objects/Options/Option.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/Option.h (revision 12330) @@ -33,9 +33,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -47,4 +42,5 @@ virtual int NDims()=0; virtual int* Size()=0; + virtual void Get(int* pvalue)=0; virtual void Get(double* pvalue)=0; virtual void Get(bool* pvalue)=0; Index: /issm/trunk/src/c/objects/Options/OptionCell.h =================================================================== --- /issm/trunk/src/c/objects/Options/OptionCell.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionCell.h (revision 12330) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionCellEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -44,4 +39,5 @@ int NDims(); int* Size(); + void Get(int* pvalue){_error_("An OptionCell object cannot return a int");}; void Get(double* pvalue){_error_("An OptionCell object cannot return a double");}; void Get(bool* pvalue){ _error_("An OptionCell object cannot return a bool");}; Index: /issm/trunk/src/c/objects/Options/OptionChar.h =================================================================== --- /issm/trunk/src/c/objects/Options/OptionChar.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionChar.h (revision 12330) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionCharEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -44,4 +39,5 @@ int NDims(); int* Size(); + void Get(int* pvalue){_error_("An OptionChar object cannot return a int");}; void Get(double* pvalue){_error_("An OptionChar object cannot return a double");}; void Get(bool* pvalue){ _error_("An OptionChar object cannot return a bool");}; Index: /issm/trunk/src/c/objects/Options/OptionDouble.cpp =================================================================== --- /issm/trunk/src/c/objects/Options/OptionDouble.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionDouble.cpp (revision 12330) @@ -120,4 +120,16 @@ } /*}}}*/ +/*FUNCTION OptionDouble::Get(int* pvalue) {{{1*/ +void OptionDouble::Get(int* pvalue){ + + /*We should first check that the size is one*/ + if(this->NumEl()!=1){ + _error_("option \"%s\" has %i elements and cannot return a single int",this->name,this->NumEl()); + } + + /*Assign output pointer*/ + *pvalue=(int)this->values[0]; +} +/*}}}*/ /*FUNCTION OptionDouble::Get(double* pvalue) {{{1*/ void OptionDouble::Get(double* pvalue){ Index: /issm/trunk/src/c/objects/Options/OptionDouble.h =================================================================== --- /issm/trunk/src/c/objects/Options/OptionDouble.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionDouble.h (revision 12330) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionDoubleEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -44,4 +39,5 @@ int NDims(); int* Size(); + void Get(int* pvalue); void Get(double* pvalue); void Get(bool* pvalue){ _error_("An OptionDouble object cannot return a bool");}; Index: /issm/trunk/src/c/objects/Options/OptionLogical.h =================================================================== --- /issm/trunk/src/c/objects/Options/OptionLogical.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionLogical.h (revision 12330) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionLogicalEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -44,4 +39,5 @@ int NDims(); int* Size(); + void Get(int* pvalue){_error_("An OptionLogical object cannot return a int");}; void Get(double* pvalue){_error_("An OptionLogical object cannot return a double");}; void Get(bool* pvalue); Index: /issm/trunk/src/c/objects/Options/OptionStruct.h =================================================================== --- /issm/trunk/src/c/objects/Options/OptionStruct.h (revision 12329) +++ /issm/trunk/src/c/objects/Options/OptionStruct.h (revision 12330) @@ -30,9 +30,4 @@ int Id(){_error_("Not implemented yet");}; int MyRank(){_error_("Not implemented yet");}; - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - int MarshallSize(){_error_("Not implemented yet");}; - void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet");}; - #endif int ObjectEnum(){return OptionStructEnum;}; Object* copy(){_error_("Not implemented yet");}; @@ -44,4 +39,5 @@ int NDims(); int* Size(); + void Get(int* pvalue){_error_("An OptionStruct object cannot return a int");}; void Get(double* pvalue){_error_("An OptionStruct object cannot return a double");}; void Get(bool* pvalue){ _error_("An OptionStruct object cannot return a bool");}; Index: /issm/trunk/src/c/objects/Params/BoolParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/BoolParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/BoolParam.cpp (revision 12330) @@ -62,55 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION BoolParam::Marshall{{{1*/ -void BoolParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of BoolParam: */ - enum_value=BoolParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall BoolParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION BoolParam::MarshallSize{{{1*/ -int BoolParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION BoolParam::Demarshall{{{1*/ -void BoolParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION BoolParam::ObjectEnum{{{1*/ int BoolParam::ObjectEnum(void){ @@ -134,13 +83,4 @@ } /*}}}*/ -/*FUNCTION BoolParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void BoolParam::SetMatlabField(mxArray* dataref){ - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); -} -#endif -/*}}}*/ /*FUNCTION BoolParam::UnitConversion{{{1*/ void BoolParam::UnitConversion(int direction_enum){ Index: /issm/trunk/src/c/objects/Params/BoolParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/BoolParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/BoolParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -41,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -81,7 +72,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.cpp (revision 12330) @@ -127,111 +127,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatArrayParam::Marshall{{{1*/ -void DoubleMatArrayParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatArrayParam: */ - enum_value=DoubleMatArrayParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatArrayParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - memcpy(marshalled_dataset,mdim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - memcpy(marshalled_dataset,ndim_array,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - for(i=0;iarray[i]; - int m=this->mdim_array[i]; - int n=this->ndim_array[i]; - memcpy(marshalled_dataset,&m,sizeof(m));marshalled_dataset+=sizeof(m); - memcpy(marshalled_dataset,&n,sizeof(n));marshalled_dataset+=sizeof(n); - if(m*n)memcpy(marshalled_dataset,matrix,m*n*sizeof(double));marshalled_dataset+=m*n*sizeof(double); - } - } - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatArrayParam::MarshallSize{{{1*/ -int DoubleMatArrayParam::MarshallSize(){ - - int size=0; - int i; - - size+=sizeof(enum_type)+ - sizeof(M)+ - M*sizeof(int)+ - M*sizeof(int); - - for(i=0;imdim_array[i]; - int n=this->ndim_array[i]; - size+=sizeof(m)+sizeof(n)+m*n*sizeof(double); - } - size+=sizeof(int); //sizeof(int) for enum value - - return size; -} -/*}}}*/ -/*FUNCTION DoubleMatArrayParam::Demarshall{{{1*/ -void DoubleMatArrayParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - double* matrix=NULL; - int m,n; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum value, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - /*data: */ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - this->mdim_array=(int*)xmalloc(M*sizeof(int)); - this->ndim_array=(int*)xmalloc(M*sizeof(int)); - memcpy(this->mdim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - memcpy(this->ndim_array,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - - this->array=(double**)xmalloc(M*sizeof(double*)); - for(i=0;iarray[i]=matrix; - } - } - else{ - this->array=NULL; - this->mdim_array=NULL; - this->ndim_array=NULL; - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatArrayParam::ObjectEnum{{{1*/ int DoubleMatArrayParam::ObjectEnum(void){ @@ -307,44 +200,4 @@ EnumToStringx(pname,this->enum_type); } -/*}}}*/ -/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatArrayParam::SetMatlabField(mxArray* dataref){ - - int i,m,n; - double* matrix=NULL; - double* outmatrix=NULL; - char* name=NULL; - mwSize dims[2]={0}; - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - mxArray* pfield3=NULL; - - this->GetParameterName(&name); - dims[0]=this->M; - dims[1]=1; - pfield=mxCreateCellArray(2,dims); - - for(i=0;iM;i++){ - matrix=this->array[i]; - m=this->mdim_array[i]; - n=this->ndim_array[i]; - outmatrix=(double*)xmalloc(m*n*sizeof(double)); - memcpy(outmatrix,matrix,m*n*sizeof(double)); - - pfield2=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield2,n); - mxSetN(pfield2,m); - mxSetPr(pfield2,outmatrix); - - //transpose the outmatrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&pfield3, 1, &pfield2, "transpose"); - - mxSetCell(pfield,i,pfield3); - } - - mxSetField( dataref, 0, name,pfield); -} -#endif /*}}}*/ /*FUNCTION DoubleMatArrayParam::SetValue(double** array, int M, int* mdim_array, int* ndim_array){{{1*/ Index: /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleMatArrayParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -44,9 +40,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/DoubleMatParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleMatParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleMatParam.cpp (revision 12330) @@ -78,64 +78,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleMatParam::Marshall{{{1*/ -void DoubleMatParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleMatParam: */ - enum_value=DoubleMatParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleMatParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,value,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleMatParam::MarshallSize{{{1*/ -int DoubleMatParam::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleMatParam::Demarshall{{{1*/ -void DoubleMatParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - value=(double*)xmalloc(M*N*sizeof(double)); - memcpy(value,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=M*N*sizeof(double); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleMatParam::ObjectEnum{{{1*/ int DoubleMatParam::ObjectEnum(void){ @@ -169,18 +109,5 @@ /*FUNCTION DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/ void DoubleMatParam::GetParameterValue(int** pintarray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - int i; - - output=(int*)xmalloc((int)(M*N*sizeof(int))); - for(i=0;ienum_type); } -/*}}}*/ -/*FUNCTION DoubleMatParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleMatParam::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - mxArray* pfield2=NULL; - double* doublemat=NULL; - char* name=NULL; - - this->GetParameterName(&name); - this->GetParameterValue(&doublemat,NULL,NULL); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,N); - mxSetN(pfield,M); - mxSetPr(pfield,doublemat); - - //transpose the matrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&pfield2, 1, &pfield, "transpose"); - mxSetField( dataref, 0, name,pfield2); -} -#endif /*}}}*/ /*FUNCTION DoubleMatParam::SetValue{{{1*/ Index: /issm/trunk/src/c/objects/Params/DoubleMatParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleMatParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleMatParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/DoubleParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleParam.cpp (revision 12330) @@ -59,55 +59,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleParam::Marshall{{{1*/ -void DoubleParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleParam: */ - enum_value=DoubleParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleParam::MarshallSize{{{1*/ -int DoubleParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleParam::Demarshall{{{1*/ -void DoubleParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleParam::ObjectEnum{{{1*/ int DoubleParam::ObjectEnum(void){ @@ -133,99 +82,31 @@ /*FUNCTION DoubleParam::GetParameterValue(int* pinteger){{{1*/ void DoubleParam::GetParameterValue(int* pinteger){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - *pinteger=(int)value; -#else _error_("Double param of enum %i (%s) cannot return an integer",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(bool* pbool){{{1*/ void DoubleParam::GetParameterValue(bool* pbool){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - /*If debugging mode, cheeck that the double is 0 or 1*/ - _assert_(value==0 || value==1); - *pbool=(bool)value; - -#else _error_("Double param of enum %i (%s) cannot return an bool",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM){{{1*/ void DoubleParam::GetParameterValue(int** pintarray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - - output=(int*)xmalloc(1*sizeof(int)); - *output=(int)value; - - /*Assign output pointers:*/ - if(pM) *pM=1; - *pintarray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){{{1*/ void DoubleParam::GetParameterValue(int** pintarray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - - output=(int*)xmalloc(1*sizeof(int)); - *output=(int)value; - - /*Assign output pointers:*/ - if(pM) *pM=1; - if(pN) *pN=1; - *pintarray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of integers",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM){{{1*/ void DoubleParam::GetParameterValue(double** pdoublearray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - double* output=NULL; - - output=(double*)xmalloc(1*sizeof(double)); - *output=(double)value; - - /*Assign output podoubleers:*/ - if(pM) *pM=1; - *pdoublearray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type)); -#endif } /*}}}*/ /*FUNCTION DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){{{1*/ void DoubleParam::GetParameterValue(double** pdoublearray,int* pM,int* pN){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - double* output=NULL; - - output=(double*)xmalloc(1*sizeof(double)); - *output=(double)value; - - /*Assign output podoubleers:*/ - if(pM) *pM=1; - if(pN) *pN=1; - *pdoublearray=output; -#else _error_("Double param of enum %i (%s) cannot return an array of double",enum_type,EnumToStringx(enum_type)); -#endif } -/*}}}*/ -/*FUNCTION DoubleParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar(value)); -} -#endif /*}}}*/ /*FUNCTION DoubleParam::UnitConversion{{{1*/ Index: /issm/trunk/src/c/objects/Params/DoubleParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/DoubleTransientMatParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleTransientMatParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleTransientMatParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif Index: /issm/trunk/src/c/objects/Params/DoubleVecParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleVecParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleVecParam.cpp (revision 12330) @@ -75,61 +75,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION DoubleVecParam::Marshall{{{1*/ -void DoubleVecParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of DoubleVecParam: */ - enum_value=DoubleVecParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall DoubleVecParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,values,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION DoubleVecParam::MarshallSize{{{1*/ -int DoubleVecParam::MarshallSize(){ - - return sizeof(M) - +M*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION DoubleVecParam::Demarshall{{{1*/ -void DoubleVecParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - values=(double*)xmalloc(M*sizeof(double)); - memcpy(values,marshalled_dataset,M*sizeof(double));marshalled_dataset+=M*sizeof(double); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION DoubleVecParam::ObjectEnum{{{1*/ int DoubleVecParam::ObjectEnum(void){ @@ -181,18 +124,5 @@ /*FUNCTION DoubleVecParam::GetParameterValue(int** pintarray,int* pM){{{1*/ void DoubleVecParam::GetParameterValue(int** pintarray,int* pM){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - int* output=NULL; - int i; - - /*Cast values into integers*/ - output=(int*)xmalloc(M*sizeof(int)); - for(i=0;ienum_type); } -/*}}}*/ -/*FUNCTION DoubleVecParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void DoubleVecParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - double* doublevec=NULL; - mxArray* pfield=NULL; - - this->GetParameterValue(&doublevec,NULL); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, 0, name, pfield); -} -#endif /*}}}*/ /*FUNCTION DoubleVecParam::SetValue{{{1*/ Index: /issm/trunk/src/c/objects/Params/DoubleVecParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/DoubleVecParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/DoubleVecParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/trunk/src/c/objects/Params/FileParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/FileParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/FileParam.cpp (revision 12330) @@ -62,22 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION FileParam::Marshall{{{1*/ -void FileParam::Marshall(char** pmarshalled_dataset){ - - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -/*FUNCTION FileParam::MarshallSize{{{1*/ -int FileParam::MarshallSize(){ - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -/*FUNCTION FileParam::Demarshall{{{1*/ -void FileParam::Demarshall(char** pmarshalled_dataset){ - _error_("FileParam is a pointer and cannot be marshalled"); -} -/*}}}*/ -#endif /*FUNCTION FileParam::ObjectEnum{{{1*/ int FileParam::ObjectEnum(void){ @@ -101,12 +83,4 @@ } /*}}}*/ -/*FUNCTION FileParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void FileParam::SetMatlabField(mxArray* dataref){ - - _error_("FileParam is a pointer and cannot be converted into a matlab object"); -} -#endif -/*}}}*/ /*FUNCTION FileParam::UnitConversion{{{1*/ void FileParam::UnitConversion(int direction_enum){ Index: /issm/trunk/src/c/objects/Params/FileParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/FileParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/FileParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -41,9 +37,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -81,7 +72,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/IntMatParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/IntMatParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/IntMatParam.cpp (revision 12330) @@ -78,64 +78,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntMatParam::Marshall{{{1*/ -void IntMatParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntMatParam: */ - enum_value=IntMatParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntMatParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,value,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntMatParam::MarshallSize{{{1*/ -int IntMatParam::MarshallSize(){ - - return sizeof(M) - +sizeof(N) - +M*N*sizeof(int) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntMatParam::Demarshall{{{1*/ -void IntMatParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - value=(int*)xmalloc(M*N*sizeof(int)); - memcpy(value,marshalled_dataset,M*N*sizeof(int));marshalled_dataset+=M*N*sizeof(int); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntMatParam::ObjectEnum{{{1*/ int IntMatParam::ObjectEnum(void){ @@ -172,33 +112,4 @@ } /*}}}*/ -/*FUNCTION IntMatParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntMatParam::SetMatlabField(mxArray* dataref){ - - char *name = NULL; - double *doublearray = NULL; - int *intarray = NULL; - mxArray *pfield = NULL; - mxArray *pfield2 = NULL; - - this->GetParameterValue(&intarray,NULL,NULL); - this->GetParameterName(&name); - - /*cast intarray into doublearray for Matlab*/ - doublearray=(double*)xmalloc(M*N*sizeof(double)); - for(int i=0;i #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -83,7 +74,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/IntParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/IntParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/IntParam.cpp (revision 12330) @@ -62,55 +62,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntParam::Marshall{{{1*/ -void IntParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntParam: */ - enum_value=IntParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&value,sizeof(value));marshalled_dataset+=sizeof(value); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntParam::MarshallSize{{{1*/ -int IntParam::MarshallSize(){ - - return sizeof(value)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntParam::Demarshall{{{1*/ -void IntParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(&value,marshalled_dataset,sizeof(value));marshalled_dataset+=sizeof(value); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntParam::ObjectEnum{{{1*/ int IntParam::ObjectEnum(void){ @@ -134,14 +83,4 @@ } /*}}}*/ -/*FUNCTION IntParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - this->GetParameterName(&name); - mxSetField( dataref, 0, name,mxCreateDoubleScalar((double)value)); -} -#endif -/*}}}*/ /*FUNCTION IntParam::UnitConversion{{{1*/ void IntParam::UnitConversion(int direction_enum){ Index: /issm/trunk/src/c/objects/Params/IntParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/IntParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/IntParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/IntVecParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/IntVecParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/IntVecParam.cpp (revision 12330) @@ -91,63 +91,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION IntVecParam::Marshall{{{1*/ -void IntVecParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of IntVecParam: */ - enum_value=IntVecParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall IntVecParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - if(M)memcpy(marshalled_dataset,values,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION IntVecParam::MarshallSize{{{1*/ -int IntVecParam::MarshallSize(){ - - return sizeof(M)+ - +M*sizeof(int) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION IntVecParam::Demarshall{{{1*/ -void IntVecParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M) { - values=(int*)xmalloc(M*sizeof(int)); - memcpy(values,marshalled_dataset,M*sizeof(int));marshalled_dataset+=M*sizeof(int); - } - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION IntVecParam::ObjectEnum{{{1*/ int IntVecParam::ObjectEnum(void){ @@ -185,33 +126,4 @@ } /*}}}*/ -/*FUNCTION IntVecParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void IntVecParam::SetMatlabField(mxArray* dataref){ - - char *name = NULL; - double *doublevec = NULL; - int *intvec = NULL; - mxArray *pfield = NULL; - - this->GetParameterValue(&intvec,NULL); - this->GetParameterName(&name); - - /*cast intvec into doublevec for Matlab*/ - if(M){ - doublevec=(double*)xmalloc(M*sizeof(double)); - for(int i=0;i #endif @@ -43,9 +39,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -83,7 +74,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/trunk/src/c/objects/Params/MatrixParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/MatrixParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/MatrixParam.cpp (revision 12330) @@ -70,93 +70,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION MatrixParam::Marshall{{{1*/ -void MatrixParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M,N; - double* serial_mat=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of MatrixParam: */ - enum_value=MatrixParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall MatrixParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - value->GetSize(&M,&N); - serial_mat=value->ToSerial(); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - memcpy(marshalled_dataset,serial_mat,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - } - else{ - M=0; - N=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,&N,sizeof(N));marshalled_dataset+=sizeof(N); - } - - /*Free ressources:*/ - xfree((void**)&serial_mat); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION MatrixParam::MarshallSize{{{1*/ -int MatrixParam::MarshallSize(){ - - int M=0; - int N=0; - if(value)value->GetSize(&M,&N); - - return sizeof(M)+ - sizeof(N)+ - M*N*sizeof(double)+ - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION MatrixParam::Demarshall{{{1*/ -void MatrixParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int M,N; - double* serial_mat=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(&N,marshalled_dataset,sizeof(N));marshalled_dataset+=sizeof(N); - if(M!=0 && N!=0){ - serial_mat=(double*)xmalloc(M*N*sizeof(double)); - memcpy(serial_mat,marshalled_dataset,M*N*sizeof(double));marshalled_dataset+=(M*N*sizeof(double)); - value=new Matrix(serial_mat,M,N,.001); - } - else{ - value=NULL; - } - - /*Free ressources:*/ - xfree((void**)&serial_mat); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION MatrixParam::ObjectEnum{{{1*/ int MatrixParam::ObjectEnum(void){ @@ -190,25 +101,4 @@ } /*}}}*/ -/*FUNCTION MatrixParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void MatrixParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - int M,N; - double* doublemat=NULL; - mxArray* pfield=NULL; - - doublemat=value->ToSerial(); - value->GetSize(&M,&N); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,N); - mxSetPr(pfield,doublemat); - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ /*FUNCTION MatrixParam::SetValue{{{1*/ void MatrixParam::SetValue(Matrix* matrix){ Index: /issm/trunk/src/c/objects/Params/MatrixParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/MatrixParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/MatrixParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/Param.h =================================================================== --- /issm/trunk/src/c/objects/Params/Param.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/Param.h (revision 12330) @@ -14,8 +14,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -60,7 +56,4 @@ virtual void UnitConversion(int direction_enum)=0; virtual void GetParameterName(char**pname)=0; - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - virtual void SetMatlabField(mxArray* dataref)=0; - #endif }; #endif Index: /issm/trunk/src/c/objects/Params/StringArrayParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/StringArrayParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/StringArrayParam.cpp (revision 12330) @@ -92,96 +92,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringArrayParam::Marshall{{{1*/ -void StringArrayParam::Marshall(char** pmarshalled_dataset){ - - int i; - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - char* string=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringArrayParam: */ - enum_value=StringArrayParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - memcpy(marshalled_dataset,&numstrings,sizeof(numstrings));marshalled_dataset+=sizeof(numstrings); - for(i=0;ivalue[i]; - stringsize=strlen(string)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,string,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - } - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringArrayParam::MarshallSize{{{1*/ -int StringArrayParam::MarshallSize(){ - - int i; - int marshallsize=0; - int stringsize; - char* string=NULL; - - marshallsize+=sizeof(numstrings); - - for(i=0;ivalue[i]; - stringsize=strlen(string)+1; - marshallsize+=sizeof(stringsize); - marshallsize+=stringsize*sizeof(char); - } - - marshallsize+=sizeof(enum_type); - marshallsize+=sizeof(int); //sizeof(int) for enum value - - return marshallsize; -} -/*}}}*/ -/*FUNCTION StringArrayParam::Demarshall{{{1*/ -void StringArrayParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - char* string=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&numstrings,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - if(numstrings){ - this->value=(char**)xmalloc(numstrings*sizeof(char*)); - - for(i=0;ivalue[i]=string; - } - } - else this->value=NULL; - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringArrayParam::ObjectEnum{{{1*/ int StringArrayParam::ObjectEnum(void){ @@ -236,26 +144,4 @@ } /*}}}*/ -/*FUNCTION StringArrayParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringArrayParam::SetMatlabField(mxArray* dataref){ - - int i; - char* name=NULL; - mwSize dims[2]={0}; - mxArray* pfield=NULL; - - this->GetParameterName(&name); - - dims[0]=this->numstrings; - dims[1]=1; - pfield=mxCreateCellArray(2,dims); - for(i=0;inumstrings;i++){ - char* string=value[i]; - mxSetCell(pfield,i,mxCreateString(string)); - } - mxSetField( dataref, 0, name,pfield); -} -#endif -/*}}}*/ /*FUNCTION StringArrayParam::SetValue{{{1*/ void StringArrayParam::SetValue(char** stringarray,int M){ Index: /issm/trunk/src/c/objects/Params/StringArrayParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/StringArrayParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/StringArrayParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -44,9 +40,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -84,7 +75,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ }; Index: /issm/trunk/src/c/objects/Params/StringParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/StringParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/StringParam.cpp (revision 12330) @@ -64,68 +64,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION StringParam::Marshall{{{1*/ -void StringParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of StringParam: */ - enum_value=StringParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - stringsize=strlen(this->value)+1; - - memcpy(marshalled_dataset,&stringsize,sizeof(stringsize));marshalled_dataset+=sizeof(stringsize); - memcpy(marshalled_dataset,this->value,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION StringParam::MarshallSize{{{1*/ -int StringParam::MarshallSize(){ - - int stringsize; - stringsize=strlen(this->value)+1; - - return sizeof(int)+ - stringsize*sizeof(char)+ - sizeof(enum_type)+ - sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION StringParam::Demarshall{{{1*/ -void StringParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - int stringsize; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - memcpy(&stringsize,marshalled_dataset,sizeof(int));marshalled_dataset+=sizeof(int); - - this->value=(char*)xmalloc(stringsize*sizeof(char)); - memcpy(this->value,marshalled_dataset,stringsize*sizeof(char));marshalled_dataset+=stringsize*sizeof(char); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION StringParam::ObjectEnum{{{1*/ int StringParam::ObjectEnum(void){ @@ -164,15 +100,4 @@ } /*}}}*/ -/*FUNCTION StringParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void StringParam::SetMatlabField(mxArray* dataref){ - - char* name=NULL; - - this->GetParameterName(&name); - mxSetField( dataref, 0, name, mxCreateString(value)); -} -#endif -/*}}}*/ /*FUNCTION StringParam::SetValue{{{1*/ void StringParam::SetValue(char* string){ Index: /issm/trunk/src/c/objects/Params/StringParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/StringParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/StringParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Params/VectorParam.cpp =================================================================== --- /issm/trunk/src/c/objects/Params/VectorParam.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Params/VectorParam.cpp (revision 12330) @@ -72,88 +72,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION VectorParam::Marshall{{{1*/ -void VectorParam::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_value=0; - int M; - double* serial_value=NULL; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum value of VectorParam: */ - enum_value=VectorParamEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_value,sizeof(enum_value));marshalled_dataset+=sizeof(enum_value); - - /*marshall VectorParam data: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - if(value){ - value->GetSize(&M); - serial_value=value->ToMPISerial(); - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - memcpy(marshalled_dataset,serial_value,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - } - else{ - M=0; - memcpy(marshalled_dataset,&M,sizeof(M));marshalled_dataset+=sizeof(M); - } - /*Free ressources:*/ - xfree((void**)&serial_value); - - /*return:*/ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -/*FUNCTION VectorParam::MarshallSize{{{1*/ -int VectorParam::MarshallSize(){ - - int M=0; - if(value)value->GetSize(&M); - - return sizeof(M)+M*sizeof(double) - +sizeof(enum_type)+ - +sizeof(int); //sizeof(int) for enum value -} -/*}}}*/ -/*FUNCTION VectorParam::Demarshall{{{1*/ -void VectorParam::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - double* serial_vec=NULL; - int M; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - memcpy(&enum_type,marshalled_dataset,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*data: */ - - memcpy(&M,marshalled_dataset,sizeof(M));marshalled_dataset+=sizeof(M); - if(M){ - serial_vec=(double*)xmalloc(M*sizeof(double)); - memcpy(serial_vec,marshalled_dataset,M*sizeof(double));marshalled_dataset+=(M*sizeof(double)); - - value=new Vector(serial_vec,M); - } - else{ - value=NULL; - } - - /*Free ressources:*/ - xfree((void**)&serial_vec); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; -} -/*}}}*/ -#endif /*FUNCTION VectorParam::ObjectEnum{{{1*/ int VectorParam::ObjectEnum(void){ @@ -188,26 +104,4 @@ } /*}}}*/ -/*FUNCTION VectorParam::SetMatlabField{{{1*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -void VectorParam::SetMatlabField(mxArray* dataref){ - - mxArray* pfield=NULL; - char* name=NULL; - double* doublevec=NULL; - int M; - - doublevec=value->ToMPISerial(); - value->GetSize(&M); - this->GetParameterName(&name); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,M); - mxSetN(pfield,1); - mxSetPr(pfield,doublevec); - - mxSetField( dataref, 0, name, pfield); -} -#endif -/*}}}*/ /*FUNCTION VectorParam::SetValue{{{1*/ void VectorParam::SetValue(Vector* vector){ Index: /issm/trunk/src/c/objects/Params/VectorParam.h =================================================================== --- /issm/trunk/src/c/objects/Params/VectorParam.h (revision 12329) +++ /issm/trunk/src/c/objects/Params/VectorParam.h (revision 12330) @@ -13,8 +13,4 @@ #else #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include #endif @@ -42,9 +38,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -82,7 +73,4 @@ void GetParameterName(char**pname); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - void SetMatlabField(mxArray* dataref); - #endif /*}}}*/ Index: /issm/trunk/src/c/objects/Patch.cpp =================================================================== --- /issm/trunk/src/c/objects/Patch.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Patch.cpp (revision 12330) @@ -120,13 +120,15 @@ int node_numrows; double *total_values = NULL; + #ifdef _HAVE_MPI_ MPI_Status status; + #endif - #ifdef _SERIAL_ - return; //nothing to be done - #endif - /*First, figure out total number of rows combining all the cpus: */ + #ifdef _HAVE_MPI_ MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD); + #else + total_numrows=this->numrows; + #endif /*return if patch empty*/ @@ -144,4 +146,5 @@ /*Now, ask other nodes to send their values: */ + #ifdef _HAVE_MPI_ for (i=1;inumcols. Update the fields in the patch, to reflect this new @@ -163,7 +167,9 @@ this->values=total_values; } + #ifdef _HAVE_MPI_ else{ this->numrows=0; xfree((void**)&this->values); } + #endif }/*}}}*/ Index: /issm/trunk/src/c/objects/Patch.h =================================================================== --- /issm/trunk/src/c/objects/Patch.h (revision 12329) +++ /issm/trunk/src/c/objects/Patch.h (revision 12330) @@ -34,5 +34,5 @@ int maxnodes; // maxnodes corresponds to the largest amout of nodes on a given element, determined by the interpolation type. - double* values; //result values + IssmDouble* values; //result values Patch(); @@ -40,5 +40,5 @@ ~Patch(); void fillelementinfo(int row, int element_id, int* vertices_ids, int num_vertices); - void fillresultinfo(int row,int enum_type,int step, double time, int interpolation, double* nodal_values, int num_nodes); + void fillresultinfo(int row,int enum_type,int step, IssmDouble time, int interpolation, IssmDouble* nodal_values, int num_nodes); void Gather(void); Index: /issm/trunk/src/c/objects/Segment.cpp =================================================================== --- /issm/trunk/src/c/objects/Segment.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Segment.cpp (revision 12330) @@ -71,22 +71,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Segment::Marshall{{{1*/ -void Segment::Marshall(char** pmarshalled_dataset){ - - _error_(" not supported yet!"); -} -/*}}}*/ -/*FUNCTION Segment::MarshallSize{{{1*/ -int Segment::MarshallSize(){ - _error_(" not supported yet!"); -} -/*}}}*/ -/*FUNCTION Segment::Demarshall{{{1*/ -void Segment::Demarshall(char** pmarshalled_dataset){ - _error_(" not supported yet!"); -} -/*}}}*/ -#endif /*FUNCTION Segment::ObjectEnum{{{1*/ int Segment::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Segment.h =================================================================== --- /issm/trunk/src/c/objects/Segment.h (revision 12329) +++ /issm/trunk/src/c/objects/Segment.h (revision 12330) @@ -15,12 +15,12 @@ public: int eid; - double x1; - double y1; - double x2; - double y2; + IssmDouble x1; + IssmDouble y1; + IssmDouble x2; + IssmDouble y2; /*Segment constructors, destructors {{{1*/ Segment(); - Segment(int eid,double x1,double y1, double x2, double y2); + Segment(int eid,IssmDouble x1,IssmDouble y1, IssmDouble x2, IssmDouble y2); ~Segment(); /*}}}*/ @@ -30,9 +30,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); Index: /issm/trunk/src/c/objects/Update.h =================================================================== --- /issm/trunk/src/c/objects/Update.h (revision 12329) +++ /issm/trunk/src/c/objects/Update.h (revision 12330) @@ -15,17 +15,17 @@ public: - virtual void InputUpdateFromVector(double* vector, int name, int type)=0; + virtual void InputUpdateFromVector(IssmDouble* vector, int name, int type)=0; virtual void InputUpdateFromVector(int* vector, int name, int type)=0; virtual void InputUpdateFromVector(bool* vector, int name, int type)=0; #ifdef _HAVE_DAKOTA_ - virtual void InputUpdateFromMatrixDakota(double* matrix, int rows, int ncols, int name, int type)=0; - virtual void InputUpdateFromVectorDakota(double* vector, int name, int type)=0; + virtual void InputUpdateFromMatrixDakota(IssmDouble* matrix, int rows, int ncols, int name, int type)=0; + virtual void InputUpdateFromVectorDakota(IssmDouble* vector, int name, int type)=0; virtual void InputUpdateFromVectorDakota(int* vector, int name, int type)=0; virtual void InputUpdateFromVectorDakota(bool* vector, int name, int type)=0; #endif - virtual void InputUpdateFromConstant(double constant, int name)=0; + virtual void InputUpdateFromConstant(IssmDouble constant, int name)=0; virtual void InputUpdateFromConstant(int constant, int name)=0; virtual void InputUpdateFromConstant(bool constant, int name)=0; - virtual void InputUpdateFromSolution(double* solution)=0; + virtual void InputUpdateFromSolution(IssmDouble* solution)=0; virtual void InputUpdateFromIoModel(int index, IoModel* iomodel)=0; Index: /issm/trunk/src/c/objects/Vertex.cpp =================================================================== --- /issm/trunk/src/c/objects/Vertex.cpp (revision 12329) +++ /issm/trunk/src/c/objects/Vertex.cpp (revision 12330) @@ -92,78 +92,4 @@ } /*}}}*/ -#ifdef _SERIAL_ -/*FUNCTION Vertex::Marshall {{{1*/ -void Vertex::Marshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int enum_type=0; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*get enum type of Vertex: */ - enum_type=VertexEnum; - - /*marshall enum: */ - memcpy(marshalled_dataset,&enum_type,sizeof(enum_type));marshalled_dataset+=sizeof(enum_type); - - /*marshall Vertex data: */ - memcpy(marshalled_dataset,&id,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(marshalled_dataset,&sid,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(marshalled_dataset,&x,sizeof(x));marshalled_dataset+=sizeof(x); - memcpy(marshalled_dataset,&y,sizeof(y));marshalled_dataset+=sizeof(y); - memcpy(marshalled_dataset,&z,sizeof(z));marshalled_dataset+=sizeof(z); - memcpy(marshalled_dataset,&sigma,sizeof(sigma));marshalled_dataset+=sizeof(sigma); - memcpy(marshalled_dataset,&connectivity,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); - memcpy(marshalled_dataset,&dof,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(marshalled_dataset,&clone,sizeof(clone));marshalled_dataset+=sizeof(clone); - - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -/*FUNCTION Vertex::MarshallSize {{{1*/ -int Vertex::MarshallSize(){ - - return sizeof(id)+ - sizeof(sid)+ - sizeof(x)+ - sizeof(y)+ - sizeof(z)+ - sizeof(sigma)+ - sizeof(connectivity)+ - sizeof(dof)+ - sizeof(clone)+ - +sizeof(int); //sizeof(int) for enum type -} -/*}}}*/ -/*FUNCTION Vertex::Demarshall {{{1*/ -void Vertex::Demarshall(char** pmarshalled_dataset){ - - char* marshalled_dataset=NULL; - int i; - - /*recover marshalled_dataset: */ - marshalled_dataset=*pmarshalled_dataset; - - /*this time, no need to get enum type, the pointer directly points to the beginning of the - *object data (thanks to DataSet::Demarshall):*/ - - memcpy(&id,marshalled_dataset,sizeof(id));marshalled_dataset+=sizeof(id); - memcpy(&sid,marshalled_dataset,sizeof(sid));marshalled_dataset+=sizeof(sid); - memcpy(&x,marshalled_dataset,sizeof(x));marshalled_dataset+=sizeof(x); - memcpy(&y,marshalled_dataset,sizeof(y));marshalled_dataset+=sizeof(y); - memcpy(&z,marshalled_dataset,sizeof(z));marshalled_dataset+=sizeof(z); - memcpy(&sigma,marshalled_dataset,sizeof(sigma));marshalled_dataset+=sizeof(sigma); - memcpy(&connectivity,marshalled_dataset,sizeof(connectivity));marshalled_dataset+=sizeof(connectivity); - memcpy(&dof,marshalled_dataset,sizeof(dof));marshalled_dataset+=sizeof(dof); - memcpy(&clone,marshalled_dataset,sizeof(clone));marshalled_dataset+=sizeof(clone); - - /*return: */ - *pmarshalled_dataset=marshalled_dataset; - return; -} -/*}}}*/ -#endif /*FUNCTION Vertex::ObjectEnum{{{1*/ int Vertex::ObjectEnum(void){ Index: /issm/trunk/src/c/objects/Vertex.h =================================================================== --- /issm/trunk/src/c/objects/Vertex.h (revision 12329) +++ /issm/trunk/src/c/objects/Vertex.h (revision 12330) @@ -25,8 +25,8 @@ int id; int sid; //sid for "serial" id, ie the rank of this vertex in the vertices dataset, if the dataset was serial on 1 cpu. - double x; - double y; - double z; - double sigma; //sigma coordinate: (z-bed)/thickness + IssmDouble x; + IssmDouble y; + IssmDouble z; + IssmDouble sigma; //sigma coordinate: (z-bed)/thickness int connectivity; //number of vertices connected to this vertex @@ -37,6 +37,6 @@ /*Vertex constructors, destructors {{{1*/ Vertex(); - Vertex(int id, int sid,double x, double y, double z, double sigma, int connectivity); - void Init(int id, int sid, double x, double y, double z, double sigma,int connectivity); + Vertex(int id, int sid,IssmDouble x, IssmDouble y, IssmDouble z, IssmDouble sigma, int connectivity); + void Init(int id, int sid, IssmDouble x, IssmDouble y, IssmDouble z, IssmDouble sigma,int connectivity); Vertex(int id, int sid, int i, IoModel* iomodel); ~Vertex(); @@ -47,9 +47,4 @@ int Id(); int MyRank(); - #ifdef _SERIAL_ - void Marshall(char** pmarshalled_dataset); - int MarshallSize(); - void Demarshall(char** pmarshalled_dataset); - #endif int ObjectEnum(); Object* copy(); @@ -65,5 +60,5 @@ int Sid(void); int Connectivity(void); - void UpdatePosition(Vector* vz,Parameters* parameters,double* thickness,double* bed); + void UpdatePosition(Vector* vz,Parameters* parameters,IssmDouble* thickness,IssmDouble* bed); /*}}}*/ }; Index: /issm/trunk/src/c/objects/objects.h =================================================================== --- /issm/trunk/src/c/objects/objects.h (revision 12329) +++ /issm/trunk/src/c/objects/objects.h (revision 12330) @@ -170,6 +170,15 @@ #include "./Bamg/Mesh.h" #include "./Bamg/Geometry.h" -#include "./Bamg/QuadTree.h" +#include "./Bamg/BamgQuadtree.h" #include "./Bamg/SetOfE4.h" +/*Kriging*/ +#include "./Kriging/Variogram.h" +#include "./Kriging/GaussianVariogram.h" +#include "./Kriging/ExponentialVariogram.h" +#include "./Kriging/SphericalVariogram.h" +#include "./Kriging/PowerVariogram.h" +#include "./Kriging/Quadtree.h" +#include "./Kriging/Observation.h" + #endif Index: /issm/trunk/src/c/python/include/python_macros.h =================================================================== --- /issm/trunk/src/c/python/include/python_macros.h (revision 12330) +++ /issm/trunk/src/c/python/include/python_macros.h (revision 12330) @@ -0,0 +1,82 @@ +/* \file python_macros.h + * \brief: macros used for the python bindings + */ + +#ifndef _PYTHON_MACROS_H_ +#define _PYTHON_MACROS_H_ + +/*Header {{{1*/ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif +/*}}}*/ + +#ifdef _HAVE_PYTHON_ +/* MODULEBOOT/MODULEEND {{{1*/ + +/*The following macros hide the error exception handling in a matlab module. Just put + * MODULEBOOT(); and MODULEEND(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +#define MODULEBOOT(); ModuleBoot(); \ + PyObject* output = PyTuple_New(NLHS); if (!output) return NULL;\ + int nrhs = (int)PyTuple_Size(args); + +#define MODULEEND(); ModuleEnd(); \ + return output; +//}}} +#if _PYTHON_MAJOR_ >=3 +/* WRAPPER 3.2 {{{1*/ +#define WRAPPER(modulename,...) \ +\ +static PyObject* modulename(PyObject* self,PyObject* args);\ +static PyMethodDef modulename##_funcs[] = {\ + {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ + {NULL,NULL,0,NULL}\ +};\ +\ +static struct PyModuleDef modulename##module= {\ + PyModuleDef_HEAD_INIT,\ + #modulename, /* name of module */\ + NULL, /* module documentation, may be NULL */\ + -1, /* size of per-interpreter state of the module,\ + or -1 if the module keeps state in global variables. */\ + modulename##_funcs\ +};\ +\ +PyMODINIT_FUNC PyInit_##modulename(void){\ +\ + import_array();\ + return PyModule_Create(&modulename##module);\ +}\ +\ +static PyObject* modulename(PyObject* self,PyObject* args) +/*}}}*/ +#else +/* WRAPPER 2.7 {{{1*/ +#define WRAPPER(modulename,...) \ +\ +static PyObject* modulename(PyObject* self,PyObject* args);\ +static PyMethodDef modulename##_funcs[] = {\ + {#modulename, (PyCFunction)modulename, METH_VARARGS, ""},\ + {NULL,NULL,0,NULL}\ +};\ +\ +PyMODINIT_FUNC init##modulename(void){\ +\ + import_array();\ + (void) Py_InitModule(#modulename, modulename##_funcs);\ +}\ +\ +static PyObject* modulename(PyObject* self,PyObject* args) +/*}}}*/ +#endif +/* CHECKARGUMENTS {{{1*/ +#define CHECKARGUMENTS(NLHS,NRHS,functionpointer) CheckNumPythonArguments(args, NRHS,functionpointer) +/*}}}*/ +#endif + +#endif Index: /issm/trunk/src/c/python/io/CheckNumPythonArguments.cpp =================================================================== --- /issm/trunk/src/c/python/io/CheckNumPythonArguments.cpp (revision 12330) +++ /issm/trunk/src/c/python/io/CheckNumPythonArguments.cpp (revision 12330) @@ -0,0 +1,36 @@ +/*!\file CheckNumPythonArguments.cpp: + * \brief: check number of arguments and report an usage error message. + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../shared/Exceptions/exceptions.h" +#include "../../include/include.h" + +int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )){ + + Py_ssize_t size=0; + + /*figure out size of tuple in input: */ + size=PyTuple_Size(inputs); + + /*check on requested size: */ + if (size==0){ + function(); + _error_("usage: see above"); + } + else if (size!=NRHS ) { + function(); + _error_("usage error."); + } + return 1; +} Index: /issm/trunk/src/c/python/io/FetchPythonData.cpp =================================================================== --- /issm/trunk/src/c/python/io/FetchPythonData.cpp (revision 12330) +++ /issm/trunk/src/c/python/io/FetchPythonData.cpp (revision 12330) @@ -0,0 +1,137 @@ +/*\file FetchData.cpp: + * \brief: general I/O interface to fetch data in python + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../include/include.h" +#include "../../shared/shared.h" + +/*Primitive data types*/ +/*FUNCTION FetchData(double* pscalar,PyObject* py_float){{{1*/ +void FetchData(double* pscalar,PyObject* py_float){ + + double scalar; + + /*return internal value: */ + scalar=PyFloat_AsDouble(py_float); + + /*output: */ + *pscalar=scalar; +} +/*}}}*/ +/*FUNCTION FetchData(int* pinteger,PyObject* py_long){{{1*/ +void FetchData(int* pinteger, PyObject* py_long){ + + int integer; + + /*return internal value: */ + integer=(int)PyLong_AsLong(py_long); + + /*output: */ + *pinteger=integer; +} +/*}}}*/ +/*FUNCTION FetchData(bool* pboolean,PyObject* py_boolean){{{1*/ +void FetchData(bool* pboolean,PyObject* py_boolean){ + + bool boolean; + + /*check this is indeed a subtype of long type: */ + if(!PyBool_Check(py_boolean))_error_("expecting a boolean in input!"); + + /*extract boolean: */ + boolean=(bool)PyLong_AsLong(py_boolean); + + /*simple copy: */ + *pboolean=boolean; + +} +/*}}}*/ +/*FUNCTION FetchData(double** pmatrix,int* pM, int* pN, PyObject* py_matrix){{{1*/ +void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_matrix){ + + /*output: */ + double* matrix=NULL; + int M,N; + int ndim; + npy_intp* dims=NULL; + + /*retrive dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_matrix); + if(ndim!=2)_error_("expecting an MxN matrix in input!"); + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=dims[1]; + + /*retrieve internal value: */ + matrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); + + /*output: */ + if(pM)*pM=M; + if(pN)*pN=N; + if(pmatrix)*pmatrix=matrix; +} +/*}}}*/ +/*FUNCTION FetchData(double** pvector,int* pM, PyObject* py_vector){{{1*/ +void FetchData(double** pvector,int* pM,PyObject* py_vector){ + + /*output: */ + double* vector=NULL; + int M; + int ndim; + npy_intp* dims=NULL; + + /*retrive dimensions: */ + ndim=PyArray_NDIM((const PyArrayObject*)py_vector); + if(ndim!=1)_error_("expecting an Mx1 vector in input!"); + dims=PyArray_DIMS((PyArrayObject*)py_vector); + M=dims[0]; + + /*retrieve internal value: */ + vector=(double*)PyArray_DATA((PyArrayObject*)py_vector); + + /*output: */ + if(pM)*pM=M; + if(pvector)*pvector=vector; +} +/*}}}*/ + +/*Python version dependent: */ +#if _PYTHON_MAJOR_ >= 3 +/*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{1*/ +void FetchData(char** pstring,PyObject* py_unicode){ + + PyObject* py_bytes; + char* string=NULL; + + + /*convert to bytes format: */ + PyUnicode_FSConverter(py_unicode,&py_bytes); + + /*convert from bytes to string: */ + string=PyBytes_AS_STRING(py_bytes); + + *pstring=string; +} +/*}}}*/ +#else +/*FUNCTION FetchData(char** pstring,PyObject* py_string){{{1*/ +void FetchData(char** pstring,PyObject* py_string){ + + char* string=NULL; + + /*extract internal string: */ + string=PyString_AsString(py_string); + + *pstring=string; +} +/*}}}*/ +#endif Index: /issm/trunk/src/c/python/io/WritePythonData.cpp =================================================================== --- /issm/trunk/src/c/python/io/WritePythonData.cpp (revision 12330) +++ /issm/trunk/src/c/python/io/WritePythonData.cpp (revision 12330) @@ -0,0 +1,78 @@ +/* \file WriteData.c: + * \brief: general interface for writing data + */ + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#define PY_ARRAY_UNIQUE_SYMBOL PythonIOSymbol +#define NO_IMPORT + +#include "../../toolkits/toolkits.h" +#include "../../include/include.h" +#include "../../modules/modules.h" +#include "../../Container/Container.h" +#include "../../shared/shared.h" +#include "../../io/io.h" +#include "../../EnumDefinitions/EnumDefinitions.h" + + +/*FUNCTION WriteData(PyObject* py_tuple,int index,char* string){{{1*/ +void WriteData(PyObject* py_tuple, int index, char* string){ + + PyTuple_SetItem(py_tuple, index, PyUnicode_FromString(string)); + +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* tuple,int index,Matrix* matrix){{{1*/ +void WriteData(PyObject* tuple,int index,Matrix* matrix){ + + int M,N; + double* buffer=NULL; + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + buffer=matrix->ToSerial(); + matrix->GetSize(&M,&N); + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,buffer); + + PyTuple_SetItem(tuple, index, array); + + +} +/*FUNCTION WriteData(PyObject* py_tuple,int index,Vector* vector){{{1*/ +void WriteData(PyObject* tuple,int index,Vector* vector){ + + int M; + double* buffer=NULL; + npy_intp dim=10; + PyObject* array=NULL; + + buffer=vector->ToMPISerial(); + vector->GetSize(&M); + dim=(npy_intp)M; + array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer); + + PyTuple_SetItem(tuple, index, array); + + +} +/*}}}*/ +/*FUNCTION WriteData(PyObject* py_tuple,int index, double* matrix, int M, int N){{{1*/ +void WriteData(PyObject* tuple, int index, double* matrix, int M,int N){ + + npy_intp dims[2]={0,0}; + PyObject* array=NULL; + + dims[0]=(npy_intp)M; + dims[1]=(npy_intp)N; + array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix); + + PyTuple_SetItem(tuple, index, array); + +} Index: /issm/trunk/src/c/python/io/pythonio.h =================================================================== --- /issm/trunk/src/c/python/io/pythonio.h (revision 12330) +++ /issm/trunk/src/c/python/io/pythonio.h (revision 12330) @@ -0,0 +1,56 @@ +/*\file pythonio.h + *\brief: I/O for ISSM in python mode + */ + +#ifndef _PYTHON_IO_H_ +#define _PYTHON_IO_H_ + +#ifdef HAVE_CONFIG_H +#include +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + + +#include "../../objects/objects.h" +#include "../../Container/Container.h" +#include "../../include/include.h" + +class DataSet; +class Parameters; + +//void WriteData(PyObject* py_tuple,DataSet* dataset); +//void WriteData(PyObject* py_tuple,int* matrix, int M,int N); +//void WriteData(PyObject* py_tuple,double* vector, int M); +//void WriteData(PyObject* py_tuple,int integer); +//void WriteData(PyObject* py_tuple,bool boolean); +//void WriteData(PyObject* py_tuple,double scalar); +//void WriteData(DataHandle* py_tuple,Parameters* parameters); +void WriteData(PyObject* py_tuple, int index, double* matrix, int M,int N); +void WriteData(PyObject* py_tuple, int index, char* string); +void WriteData(PyObject* py_tuple, int index, Matrix* matrix); +void WriteData(PyObject* py_tuple, int index, Vector* vector); + + +//void FetchData(DataSet** pdataset,PyObject* py_ref); +//void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(int** pmatrix,int* pM,int *pN,PyObject* py_ref); +//void FetchData(bool** pmatrix,int* pM,int *pN,PyObject* py_ref); +//void FetchData(bool** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(Matrix** pmatrix,PyObject* py_ref); +//void FetchData(int** pvector,int* pM,PyObject* py_ref); +//void FetchData(float** pvector,int* pM,PyObject* py_ref); +//void FetchData(bool** pvector,int* pM,PyObject* py_ref); +//void FetchData(Vector** pvector,PyObject* py_ref); +//void FetchData(char** pmatrix,int* pnumel,int* pndims,int** psize,PyObject* py_ref); +//void FetchData(Parameters** pparameters, DataHandle py_ref); +void FetchData(double** pvector,int* pM,PyObject* py_ref); +void FetchData(double** pmatrix,int* pM,int *pN,PyObject* py_array); +void FetchData(char** pstring,PyObject* py_unicode); +void FetchData(double* pscalar,PyObject* py_float); +void FetchData(int* pinteger,PyObject* py_long); +void FetchData(bool* pbool,PyObject* py_boolean); + +int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )); + +#endif /* _IO_H_ */ Index: /issm/trunk/src/c/python/python-binding.h =================================================================== --- /issm/trunk/src/c/python/python-binding.h (revision 12330) +++ /issm/trunk/src/c/python/python-binding.h (revision 12330) @@ -0,0 +1,7 @@ +#ifndef _PYTHON_BINDING_H_ +#define _PYTHON_BINDING_H_ + +#include "./io/pythonio.h" +#include "./include/python_macros.h" + +#endif Index: /issm/trunk/src/c/shared/Alloc/alloc.cpp =================================================================== --- /issm/trunk/src/c/shared/Alloc/alloc.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Alloc/alloc.cpp (revision 12330) @@ -19,8 +19,4 @@ #endif -#if defined(_SERIAL_) && defined(_HAVE_MATLAB_) -#include "mex.h" -#endif - #include #include @@ -37,11 +33,6 @@ if(!size)_error_(" attempting to 0 size allocation!"); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - /* Use the matlab api to do the allocation: */ - memptr=mxMalloc(size); - #else /* Use the c library to do the allocation: */ memptr=malloc(size); - #endif if(!memptr) _error_("memory allocation failed!"); @@ -55,11 +46,6 @@ if(!size)_error_("attempting to 0 size allocation!"); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - /* Use the matlab api to do the allocation: */ - memptr=mxCalloc(n,size); - #else /* Use the c library to do the allocation: */ memptr=calloc(n,size); - #endif if(!memptr) _error_("memory allocation failed!"); @@ -70,9 +56,5 @@ if (pv && *pv){ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxFree(*pv); - #else - free(*pv); - #endif + free(*pv); *pv=NULL; @@ -83,16 +65,8 @@ if (pv && *pv){ - #ifdef _PARALLEL_ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we * don't actually free memory in Matlab, we let the memory manager do that. We only * free in parallel: */ delete *pv; - #else - /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ - * correctly: */ - #ifdef _HAVE_PETSC_ - MatFree(&(*pv)->matrix); - #endif - #endif *pv=NULL; } @@ -102,16 +76,8 @@ if (pv && *pv){ - #ifdef _PARALLEL_ /*There is no mxDelete in the Matlab API -> using delete trips up Matlab. So we * don't actually free memory in Matlab, we let the memory manager do that. We only * free in parallel: */ delete *pv; - #else - /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ - * correctly: */ - #ifdef _HAVE_PETSC_ - VecFree(&(*pv)->vector); - #endif - #endif *pv=NULL; } @@ -124,10 +90,5 @@ if(!size)_error_("attempting to realloc to zero"); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - value = (void*)mxRealloc(pv,size); - #else value = (void*)realloc(pv,size); - #endif if (value == NULL) { Index: /issm/trunk/src/c/shared/Alloc/alloc_module.cpp =================================================================== --- /issm/trunk/src/c/shared/Alloc/alloc_module.cpp (revision 12330) +++ /issm/trunk/src/c/shared/Alloc/alloc_module.cpp (revision 12330) @@ -0,0 +1,41 @@ +/* \file alloc_module.h + */ + + +#ifdef HAVE_CONFIG_H + #include +#else +#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include +#include + +#include "./alloc_module.h" +#include "../Exceptions/exceptions.h" +#include "../../include/include.h" +#include "../../objects/objects.h" + +void xdelete_module(Matrix** pv){ + + if (pv && *pv){ + /*Actually, still get rid of internal Petsc matrix. Quick fix until Matlab handles C++ + * correctly: */ + #ifdef _HAVE_PETSC_ + MatFree(&(*pv)->matrix); + #endif + *pv=NULL; + } +} + +void xdelete_module(Vector** pv){ + + if (pv && *pv){ + /*Actually, still get rid of internal Petsc vector. Quick fix until Matlab handles C++ + * correctly: */ + #ifdef _HAVE_PETSC_ + VecFree(&(*pv)->vector); + #endif + *pv=NULL; + } +} Index: /issm/trunk/src/c/shared/Alloc/alloc_module.h =================================================================== --- /issm/trunk/src/c/shared/Alloc/alloc_module.h (revision 12330) +++ /issm/trunk/src/c/shared/Alloc/alloc_module.h (revision 12330) @@ -0,0 +1,11 @@ +/* \file alloc.h + */ + +#ifndef _ALLOC_MODULE_H_ +#define _ALLOC_MODULE_H_ +class Matrix; +class Vector; +void xdelete_module(Matrix** pvptr); +void xdelete_module(Vector** pvptr); + +#endif Index: /issm/trunk/src/c/shared/Alloc/xNewDelete.h =================================================================== --- /issm/trunk/src/c/shared/Alloc/xNewDelete.h (revision 12330) +++ /issm/trunk/src/c/shared/Alloc/xNewDelete.h (revision 12330) @@ -0,0 +1,25 @@ +/* \file xNewDelete.h + * \brief: header file for templated new/delete checking for non-null pointers + */ + +#ifndef _XNEWDELETE_H_ +#define _XNEWDELETE_H_ + +#include + +template +T* xNew(unsigned int size) { + T* aT_p=new T[size]; + assert(aT_p); + return aT_p; +}; + +template +void xDelete(T*& aT_p) { + if (aT_p) + delete []aT_p; + aT_p=0; +}; + +#endif + Index: /issm/trunk/src/c/shared/Elements/elements.h =================================================================== --- /issm/trunk/src/c/shared/Elements/elements.h (revision 12329) +++ /issm/trunk/src/c/shared/Elements/elements.h (revision 12330) @@ -47,4 +47,15 @@ printf("\n"); } +inline void printbinary(int n) { + unsigned int i=1L<<(sizeof(n)*8-1); + + while (i>0) { + if (n&i) + printf("1"); + else + printf("0"); + i>>=1; + } +} #endif //ifndef _SHARED_ELEMENTS_H_ Index: /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp =================================================================== --- /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Exceptions/Exceptions.cpp (revision 12330) @@ -11,7 +11,4 @@ #include "../shared.h" #include "../../include/include.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif ErrorException::ErrorException(const string &what_arg){ @@ -32,4 +29,8 @@ ErrorException::~ErrorException() throw(){ + extern int num_procs; + /*We want the report only for matlab modules, otherwise we get twice the report + * We assume that if num_procs==1, it is a module (FIXME)*/ + if(num_procs==1) this->Report(); } @@ -40,4 +41,5 @@ void ErrorException::Report(){ extern int my_rank; + extern int num_procs; if (function_name=="" || file_line==0){ //WINDOWS @@ -45,11 +47,12 @@ } else{ - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mexErrMsgTxt(exprintf("\n??? Error using ==> %s at %i\n%s error message: %s\n", - file_name.c_str(),file_line,function_name.c_str(),what())); - #else + if(num_procs==1){ + printf("\n??? Error using ==> %s:%i\n",file_name.c_str(),file_line); + printf("%s error message: %s\n\n",function_name.c_str(),what()); + } + else{ printf("\n[%i] ??? Error using ==> %s:%i\n",my_rank,file_name.c_str(),file_line); printf("[%i] %s error message: %s\n\n",my_rank,function_name.c_str(),what()); - #endif + } } return; Index: /issm/trunk/src/c/shared/Exceptions/exceptions.h =================================================================== --- /issm/trunk/src/c/shared/Exceptions/exceptions.h (revision 12329) +++ /issm/trunk/src/c/shared/Exceptions/exceptions.h (revision 12330) @@ -23,11 +23,8 @@ public: - ErrorException(const string &what_arg); //for windows ErrorException(string what_file,string what_function,int what_line,string what_arg);//UNIX ~ErrorException() throw(); - virtual const char *what() const throw(); - void Report(); Index: /issm/trunk/src/c/shared/Exp/DomainOutlineRead.cpp =================================================================== --- /issm/trunk/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Exp/DomainOutlineRead.cpp (revision 12330) @@ -13,6 +13,5 @@ #include "../../Container/DataSet.h" -int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole=true){ - +int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname){ /*indexing: */ @@ -102,7 +101,4 @@ if((x[0]==x[n-1]) && (y[0]==y[n-1])){ cl=true; - if (!whole) { - n=n-1; - } } @@ -126,30 +122,30 @@ } -DataSet* DomainOutlineRead(char* domainname,bool whole=true){ - - /*indexing: */ - int i; +DataSet* DomainOutlineRead(char* domainname){ /*intermediary: */ - int nprof; - int* profnvertices=NULL; - double** pprofx=NULL; - double** pprofy=NULL; - - Contour* contour=NULL; + int nprof; + int *profnvertices = NULL; + double **pprofx = NULL; + double **pprofy = NULL; + Contour *contour = NULL; /*output: */ DataSet* domain=NULL; - /*get domain outline from intermediary function:*/ - DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname,whole); + /*If domainname is an empty string, return empty dataset*/ + if (strcmp(domainname,"")==0){ + nprof=0; + } + else{ + DomainOutlineRead(&nprof,&profnvertices,&pprofx, &pprofy, NULL,domainname); + } /*now create dataset of contours: */ domain=new DataSet(0); - for(i=0;iAddObject(new Contour(i,profnvertices[i],pprofx[i],pprofy[i],1)); } - return domain; } Index: /issm/trunk/src/c/shared/Exp/DomainOutlineWrite.cpp =================================================================== --- /issm/trunk/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Exp/DomainOutlineWrite.cpp (revision 12330) @@ -11,5 +11,5 @@ #include "../Exceptions/exceptions.h" -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole=true){ +int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname){ @@ -20,11 +20,4 @@ /*I/O: */ FILE* fid=NULL; - - /*input: */ -// int nprof; //number of profiles in the domainname file -// int* profnvertices=NULL; //array holding the number of vertices for the nprof profiles -// double** pprofx=NULL; //array of profiles x coordinates -// double** pprofy=NULL; //array of profiles y coordinates -// bool* closed=NULL; //array holding closed flags for the nprof profiles /*open domain outline file for writing: */ @@ -43,8 +36,5 @@ /*Write number of profile vertices: */ - if(closed[counter] && !whole) - fprintf(fid,"%u %s\n",profnvertices[counter]+1,"1."); - else - fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); + fprintf(fid,"%u %s\n",profnvertices[counter] ,"1."); /*Write next line: */ @@ -55,8 +45,4 @@ fprintf(fid,"%lf\t%lf\n",pprofx[counter][i],pprofy[counter][i]); } - - /*Now check that we are dealing with open contours: */ - if(closed[counter] && !whole) - fprintf(fid,"%lf\t%lf\n",pprofx[counter][0],pprofy[counter][0]); /*Write blank line: */ Index: /issm/trunk/src/c/shared/Exp/exp.h =================================================================== --- /issm/trunk/src/c/shared/Exp/exp.h (revision 12329) +++ /issm/trunk/src/c/shared/Exp/exp.h (revision 12330) @@ -13,9 +13,9 @@ int IsOutsidePoly(Vector* in,double* xc,double* yc,int numvertices,double* x,double* y,int i0,int i1, int edgevalue); int IsInPolySerial(double* in,double* xc,double* yc,int numvertices,double* x,double* y,int nods, int edgevalue); -int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname,bool whole); +int DomainOutlineWrite(int nprof,int* profnvertices,double** pprofx,double** pprofy,bool* closed,char* domainname); int pnpoly(int npol, double *xp, double *yp, double x, double y, int edgevalue); -int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname,bool whole); -DataSet* DomainOutlineRead(char* domainname,bool whole); +int DomainOutlineRead(int* pnprof,int** pprofnvertices,double*** ppprofx,double*** ppprofy,bool** pclosed,char* domainname); +DataSet* DomainOutlineRead(char* domainname); Index: sm/trunk/src/c/shared/Numerics/OptFunc.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/OptFunc.cpp (revision 12329) +++ (revision ) @@ -1,41 +1,0 @@ -/*!\file: OptFunc.cpp - * \brief: "C" code wrapper to matlab objectivefunctionC call - */ - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -#include "../../objects/objects.h" -#include "../../shared/shared.h" -#include "../../include/include.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -double OptFunc(double scalar, OptArgs* optargs){ - - /*output: */ - double J; - - mxArray* inputs[2]; - mxArray* psearch_scalar=NULL; - mxArray* mxJ=NULL; - - psearch_scalar=mxCreateDoubleScalar(scalar); - inputs[0]=psearch_scalar; - inputs[1]=optargs->femmodel; - - mexCallMATLAB(1,&mxJ,2,(mxArray**)inputs, optargs->function_name); - - /*extract misfit from mxArray*/ - J=mxGetScalar(mxJ); - - return J; -} -#else -double OptFunc(double scalar, OptArgs* optargs){ - _error_(" not implemented yet"); -} -#endif Index: /issm/trunk/src/c/shared/Numerics/OptionsFromAnalysis.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Numerics/OptionsFromAnalysis.cpp (revision 12330) @@ -8,4 +8,6 @@ #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" #endif + +#include #include "../../objects/objects.h" @@ -30,11 +32,5 @@ parameters->FindParam(&strings,&numanalyses,PetscOptionsStringsEnum); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) //do not take this away, because ISSM loads analyses as a Double Param instead of a DoubleVec Param when running with only 1 analysis - if(numanalyses==1){ analyses=(double*)xmalloc(1*sizeof(double)); parameters->FindParam(analyses,PetscOptionsAnalysesEnum); - } - else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #else parameters->FindParam(&analyses,&dummy,PetscOptionsAnalysesEnum); - #endif if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. Index: /issm/trunk/src/c/shared/Numerics/Synchronize.sh =================================================================== --- /issm/trunk/src/c/shared/Numerics/Synchronize.sh (revision 12329) +++ /issm/trunk/src/c/shared/Numerics/Synchronize.sh (revision 12330) @@ -2,5 +2,5 @@ #Synchronize Verbosity #first remove existing files -rm $ISSM_TIER/src/m/shared/Verb*.m +rm $ISSM_DIR/src/m/shared/Verb*.m echo "Synchronizing Verbosity levels..." @@ -29,7 +29,4 @@ #include "../../include/macros.h" #include "../Exceptions/exceptions.h" -#ifdef _SERIAL_ -#include -#endif /*}}}*/ @@ -54,5 +51,5 @@ #Add Verbosity Matlab file{{{ - cat < $ISSM_TIER"/src/m/shared/"$(echo $FILENAME".m") + cat < $ISSM_DIR"/src/m/shared/"$(echo $FILENAME".m") function bool=$(echo $FILENAME)() %$(echo $FILENAME | awk {'print toupper($1)'}) - Return true if $(echo $LEVELNAME | awk {'print tolower($1)'}) level is activated @@ -140,42 +137,16 @@ if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); -#ifdef _SERIAL_ - - mxArray* output=NULL; - mxArray* input=NULL; - input=mxCreateDoubleScalar((double)level); - - mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); -#else - verbositylevel = level; -#endif }/*}}}*/ /*FUNCTION GetVerbosityLevel {{{*/ int GetVerbosityLevel(void){ -#ifdef _SERIAL_ - - mxArray* output=NULL; - mxArray* input=NULL; - double level; - - mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); - level=mxGetScalar(output); - - verbositylevel = (int)level; - return verbositylevel; - -#else - _assert_(verbositylevel>=0); return verbositylevel; - -#endif }/*}}}*/ END #}}} #Complete verbose.m {{{1 -VERBOSEPATH="$ISSM_TIER/src/m/classes/verbose.m" +VERBOSEPATH="$ISSM_DIR/src/m/classes/verbose.m" cat $VERBOSEPATH | sed "/%BEGINFIELDS/,$ d" > temp_begin cat $VERBOSEPATH | sed "1,/%ENDFIELDS/d" > temp_end Index: /issm/trunk/src/c/shared/Numerics/Verbosity.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/Verbosity.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Numerics/Verbosity.cpp (revision 12330) @@ -18,7 +18,4 @@ #include "../../include/macros.h" #include "../Exceptions/exceptions.h" -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include -#endif /*}}}*/ @@ -39,36 +36,12 @@ if(level<0) _error_("vebosity level should be a positive integer (user provided %i)",level); -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - mxArray* output=NULL; - mxArray* input=NULL; - input=mxCreateDoubleScalar((double)level); - - mexCallMATLAB(0,&output,1,&input,"SetVerbosityLevel"); -#else - verbositylevel = level; -#endif }/*}}}*/ /*FUNCTION GetVerbosityLevel {{{*/ int GetVerbosityLevel(void){ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - - mxArray* output=NULL; - mxArray* input=NULL; - double level; - - mexCallMATLAB(1,&output,0,&input,"GetVerbosityLevel"); - level=mxGetScalar(output); - - verbositylevel = (int)level; - return verbositylevel; - -#else _assert_(verbositylevel>=0); return verbositylevel; -#endif }/*}}}*/ Index: /issm/trunk/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp =================================================================== --- /issm/trunk/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Numerics/XZvectorsToCoordinateSystem.cpp (revision 12330) @@ -1,6 +1,6 @@ -#include "../../io/Matlab/matlabio.h" #include "../Alloc/alloc.h" #include "../../include/include.h" #include "../Exceptions/exceptions.h" +#include "./isnan.h" #include Index: sm/trunk/src/c/shared/Sorting/Quicksort.c =================================================================== --- /issm/trunk/src/c/shared/Sorting/Quicksort.c (revision 12329) +++ (revision ) @@ -1,19 +1,0 @@ -void swap(int *a, int *b) { - int t=*a; *a=*b; *b=t; -} -void sort(int arr[], int beg, int end) { - - if (end > beg + 1) { - int piv = arr[beg], l = beg + 1, r = end; - while (l < r) - { - if (arr[l] <= piv) - l++; - else - swap(&arr[l], &arr[--r]); - } - swap(&arr[--l], &arr[beg]); - sort(arr, beg, l); - sort(arr, r, end); - } -} Index: /issm/trunk/src/c/shared/Sorting/binary_search.cpp =================================================================== --- /issm/trunk/src/c/shared/Sorting/binary_search.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Sorting/binary_search.cpp (revision 12330) @@ -11,9 +11,9 @@ #include -int binary_search(int* poffset,int target, int* sorted_integers,int num_integers){ +int binary_search(int* poffset,int target,int* sorted_integers,int num_integers){ /*output: */ int offset; //offset, if found - int found=0; //found=0 if target is not found, 1 otherwise. + int found=0; //found=0 if target is not found, 1 otherwise. /*intermediary: */ @@ -64,3 +64,2 @@ return found; } - Index: /issm/trunk/src/c/shared/Sorting/sorting.h =================================================================== --- /issm/trunk/src/c/shared/Sorting/sorting.h (revision 12329) +++ /issm/trunk/src/c/shared/Sorting/sorting.h (revision 12330) @@ -6,7 +6,5 @@ #define _SORTING_H_ -int binary_search(int* poffset,int target, int* sorted_integers,int num_integers); - +int binary_search(int* poffset,int target,int* sorted_integers,int num_integers); #endif //ifndef _SORTING_H_ - Index: /issm/trunk/src/c/shared/Threads/LaunchThread.cpp =================================================================== --- /issm/trunk/src/c/shared/Threads/LaunchThread.cpp (revision 12329) +++ /issm/trunk/src/c/shared/Threads/LaunchThread.cpp (revision 12330) @@ -67,4 +67,3 @@ function((void*)&handle); #endif - } Index: /issm/trunk/src/c/shared/TriMesh/SplitMeshForRifts.cpp =================================================================== --- /issm/trunk/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12329) +++ /issm/trunk/src/c/shared/TriMesh/SplitMeshForRifts.cpp (revision 12330) @@ -47,8 +47,7 @@ segmentmarkerlist=*psegmentmarkerlist; - /*Establish list of segments that belong to a rift: */ - RiftSegmentsFromSegments(&nriftsegs,&riftsegments,nel,index,nsegs,segments); /*riftsegments of size nriftsegsx4 (4 for first element on segment,second element, - first node and second snode)*/ + /*riftsegments of size nriftsegsx4 (4 for first element on segment,second element,first node and second snode)*/ + RiftSegmentsFromSegments(&nriftsegs,&riftsegments,nel,index,nsegs,segments); /*Go through all nodes of the rift segments, and start splitting the mesh: */ @@ -57,5 +56,5 @@ for (j=0;j<2;j++){ - node=*(riftsegments+4*i+j+2); + node=riftsegments[4*i+j+2]; if(flags[node-1]){ /*This node was already split, skip:*/ @@ -70,7 +69,11 @@ DetermineGridElementListOnOneSideOfRift(&NumGridElementListOnOneSideOfRift,&GridElementListOnOneSideOfRift,i,nriftsegs,riftsegments,node,index,nel); - /*Summary: we have for node, a list of elements (GridElementListOnOneSideOfRift, of size NumGridElementListOnOneSideOfRift) that all contain node - *and that are on the same side of the rift. For all these elements, we clone node into another node, and we swap all instances of node in the triangulation - *for those elements, to the new node.*/ + /*Summary: we have for node, a list of elements + * (GridElementListOnOneSideOfRift, of size + * NumGridElementListOnOneSideOfRift) that all contain node + *and that are on the same side of the rift. For all these + elements, we clone node into another node, and we swap all + instances of node in the triangulation *for those elements, to the + new node.*/ //augment number of nodes @@ -94,5 +97,5 @@ /*update segments: they got modified completely by adding new nodes.*/ - UpdateSegments(&segments,&segmentmarkerlist, &nsegs,index,x,y,riftsegments,nriftsegs); + UpdateSegments(&segments,&segmentmarkerlist, &nsegs,index,x,y,riftsegments,nriftsegs,nods,nel); /*Assign output pointers: */ Index: /issm/trunk/src/c/shared/TriMesh/TriMeshUtils.cpp =================================================================== --- /issm/trunk/src/c/shared/TriMesh/TriMeshUtils.cpp (revision 12329) +++ /issm/trunk/src/c/shared/TriMesh/TriMeshUtils.cpp (revision 12330) @@ -11,4 +11,5 @@ #define RIFTPENALTYPAIRSWIDTH 8 +/*FUNCTION IsGridOnRift{{{*/ int IsGridOnRift(int* riftsegments, int nriftsegs, int node){ @@ -32,7 +33,6 @@ return 0; } -} - - +}/*}}}*/ +/*FUNCTION GridElementsList{{{*/ int GridElementsList(int** pGridElements, int* pNumGridElements,int node,double * index,int nel){ @@ -87,7 +87,6 @@ *pNumGridElements=NumGridElements; return noerr; -} - - +}/*}}}*/ +/*FUNCTION IsNeighbor{{{*/ int IsNeighbor(int el1,int el2,double* index){ /*From a triangulation held in index, figure out if elements 1 and 2 have two nodes in common: */ @@ -105,7 +104,6 @@ return 0; } -} - - +}/*}}}*/ +/*FUNCTION IsOnRift{{{*/ int IsOnRift(int el,int nriftsegs,int* riftsegments){ /*From a list of elements segments, figure out if el belongs to it: */ @@ -117,11 +115,6 @@ } return 0; -} - - -/****************************************************************************************************************************** - RiftSegmentsFromSegments -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION RiftSegmentsFromSegments{{{*/ void RiftSegmentsFromSegments(int* pnriftsegs, int** priftsegments, int nel, double* index, int nsegs,double* segments){ @@ -189,10 +182,6 @@ *priftsegments=riftsegments; *pnriftsegs=nriftsegs; -} - -/****************************************************************************************************************************** - DetermineGridElementListOnOneSideOfRift -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION DetermineGridElementListOnOneSideOfRift{{{*/ int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel){ @@ -257,11 +246,7 @@ *pGridElementListOnOneSideOfRift=GridElementListOnOneSideOfRift; return noerr; -} - -/****************************************************************************************************************************** - UpdateSegments -******************************************************************************************************************************/ - -int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs){ +}/*}}}*/ +/*FUNCTION UpdateSegments{{{*/ +int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel){ int noerr=1; @@ -284,8 +269,8 @@ /*First, update the existing segments to the new nodes :*/ for (i=0;i0 && node4>0); + if ((x[node1-1]==x[node4-1]) && (y[node1-1]==y[node4-1])){ /*Swap node3 and node4:*/ temp_node=node3; @@ -943,10 +874,6 @@ *priftstips=riftstips; return noerr; -} - -/****************************************************************************************************************************** - PenaltyPairs -******************************************************************************************************************************/ - +}/*}}}*/ +/*FUNCTION PenaltyPairs{{{*/ int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, int* riftsnumsegs,double** riftspairs,double* riftstips,double* x,double* y){ Index: /issm/trunk/src/c/shared/TriMesh/trimesh.h =================================================================== --- /issm/trunk/src/c/shared/TriMesh/trimesh.h (revision 12329) +++ /issm/trunk/src/c/shared/TriMesh/trimesh.h (revision 12330) @@ -6,20 +6,13 @@ #define _SHARED_TRIMESH_H - #include #include - - //#define REAL double //took it out because it may conflict with stdlib.h defines. put back if necessary - int AssociateSegmentToElement(double** psegments,int nseg, double* index,int nel); int OrderSegments(double** psegments,int nseg, double* index,int nel); - int GridInsideHole(double* px0,double* py0,int n,double* x,double* y); int FindElement(double A,double B,double* index,int nel); - int SplitMeshForRifts(int* pnel,double** pindex,int* pnods,double** px,double** py,int* pnsegs,double** psegments,double** psegmentmarkerlist); - int IsGridOnRift(int* riftsegments, int nriftsegs, int node); int GridElementsList(int** pGridElements, int* pNumGridElements,int node,double * index,int nel); @@ -28,17 +21,15 @@ void RiftSegmentsFromSegments(int* pnriftsegs, int** priftsegments, int nel, double* index, int nsegs,double* segments); int DetermineGridElementListOnOneSideOfRift(int* pNumGridElementListOnOneSideOfRift, int** pGridElementListOnOneSideOfRift, int segmentnumber, int nriftsegs, int* riftsegments, int node,double* index,int nel); -int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs); +int UpdateSegments(double** psegments,double** psegmentmarkerlist, int* pnsegs, double* index, double* x,double* y,int* riftsegments,int nriftsegs,int nods,int nel); int pnpoly(int npol, double *xp, double *yp, double x, double y); int FindElement(double A,double B,double* index,int nel); int RemoveRifts(double** pindex,double** px,double** py,int* pnods,double** psegments,int* pnumsegs,int numrifts1,int* rifts1numsegs,double** rifts1segments,double** rifts1pairs,int nel); int IsRiftPresent(int* priftflag,int* pnumrifts, double* segmentmarkerlist,int nsegs); -int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts); -int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y); +int SplitRiftSegments(double** psegments,double** psegmentmarkerlist, int* pnumsegs, int* pnumrifts,int** priftsnumsegs,double*** priftssegments,int numrifts,int nods,int nels); +int OrderRifts(double** priftstips, double** riftssegments,double** riftspairs,int numrifts,int* riftsnumsegments,double* x,double* y,int nods,int nels); int PenaltyPairs(double*** priftspenaltypairs,int** priftsnumpenaltypairs,int numrifts,double** riftssegments, int* riftsnumsegments,double** riftspairs,double* riftstips,double* x,double* y); - int RemoveCornersFromRifts(double** pindex,int* pnel,double** px,double** py,int* pnods, double* segments,double* segmentmarkers,int num_seg); int PairRiftElements(int** priftsnumpairs, double*** priftspairs,int numrifts,int* riftsnumsegments, double** riftssegments,double* x,double* y); - #endif /* _SHARED_TRIMESH_H */ Index: /issm/trunk/src/c/shared/Wrapper/wrappershared.h =================================================================== --- /issm/trunk/src/c/shared/Wrapper/wrappershared.h (revision 12329) +++ /issm/trunk/src/c/shared/Wrapper/wrappershared.h (revision 12330) @@ -8,8 +8,6 @@ #include "../../objects/objects.h" -#ifdef _SERIAL_ int ModuleBoot(void); int ModuleEnd(void); -#endif #endif Index: /issm/trunk/src/c/shared/shared.h =================================================================== --- /issm/trunk/src/c/shared/shared.h (revision 12329) +++ /issm/trunk/src/c/shared/shared.h (revision 12330) @@ -8,4 +8,5 @@ #include "Alloc/alloc.h" +#include "Alloc/alloc_module.h" #include "Exceptions/exceptions.h" #include "Exp/exp.h" Index: /issm/trunk/src/c/solutions/ProcessArguments.cpp =================================================================== --- /issm/trunk/src/c/solutions/ProcessArguments.cpp (revision 12329) +++ /issm/trunk/src/c/solutions/ProcessArguments.cpp (revision 12330) @@ -4,4 +4,6 @@ #include +#include + #include "../shared/shared.h" #include "../include/include.h" Index: /issm/trunk/src/c/solutions/issm.cpp =================================================================== --- /issm/trunk/src/c/solutions/issm.cpp (revision 12329) +++ /issm/trunk/src/c/solutions/issm.cpp (revision 12330) @@ -35,9 +35,5 @@ int ierr; - MODULEBOOT(); - - #ifndef _PARALLEL_ - _error_(" parallel executable was compiled without support of parallel libraries!"); - #endif + ISSMBOOT(); /*Initialize environments: Petsc, MPI, etc...: */ @@ -46,12 +42,20 @@ if(ierr) _error_("Could not initialize Petsc"); #else + #ifdef _HAVE_MPI_ MPI_Init(&argc,&argv); #endif + #endif + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); + #else + start=(double)clock(); + #endif /*Size and rank: */ + #ifdef _HAVE_MPI_ MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); MPI_Comm_size(MPI_COMM_WORLD,&num_procs); + #endif /*First process inputs*/ @@ -66,5 +70,9 @@ /*Create femmodel, using input file: */ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); + #else + start_init=(double)clock(); + #endif femmodel=new FemModel(binfilename,outbinfilename,solution_type,analyses,numanalyses); @@ -86,8 +94,17 @@ femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime(); + #else + finish_init=(double)clock(); + #endif _printf_(true,"call computational core:\n"); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( ); + #else + start_core=(double)clock(); + #endif + if(dakota_analysis){ #ifdef _HAVE_DAKOTA_ @@ -110,6 +127,10 @@ solutioncore(femmodel); } + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( ); - + #else + finish_core=(double)clock(); + #endif + _printf_(true,"write results to disk:\n"); OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); @@ -131,21 +152,31 @@ /*Get finish time and close*/ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish = MPI_Wtime( ); _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",finish_init-start_init); _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); + #else + finish=(double)clock(); + _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",(finish_init-start_init)/CLOCKS_PER_SEC); + _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",(finish_core-start_core)/CLOCKS_PER_SEC); + _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600/CLOCKS_PER_SEC),int(int((finish-start)/CLOCKS_PER_SEC)%3600/60),(int(finish-start)/CLOCKS_PER_SEC)%60); + #endif + + #ifdef _HAVE_PETSC_ _printf_(true,"closing MPI and Petsc\n"); - #ifdef _HAVE_PETSC_ PetscFinalize(); #else + #ifdef _HAVE_MPI_ + _printf_(true,"closing MPI and Petsc\n"); MPI_Finalize(); + #endif #endif /*end module: */ - MODULEEND(); + ISSMEND(); return 0; //unix success return; } - Index: /issm/trunk/src/c/solvers/solver_newton.cpp =================================================================== --- /issm/trunk/src/c/solvers/solver_newton.cpp (revision 12329) +++ /issm/trunk/src/c/solvers/solver_newton.cpp (revision 12330) @@ -67,7 +67,17 @@ convergence(&converged,Kff,pf,uf,old_uf,femmodel->parameters); xdelete(&Kff); xdelete(&pf); - if(converged==true) break; + if(converged==true){ + bool max_iteration_state=false; + int tempStep=1; + double tempTime=1.0; + femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); + break; + } if(count>=max_nonlinear_iterations){ - _printf_(true," maximum number of iterations (%i) exceeded\n",max_nonlinear_iterations); + _printf_(true," maximum number of Newton iterations (%i) exceeded\n",max_nonlinear_iterations); + bool max_iteration_state=true; + int tempStep=1; + double tempTime=1.0; + femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); break; } Index: /issm/trunk/src/c/solvers/solver_nonlinear.cpp =================================================================== --- /issm/trunk/src/c/solvers/solver_nonlinear.cpp (revision 12329) +++ /issm/trunk/src/c/solvers/solver_nonlinear.cpp (revision 12330) @@ -85,10 +85,20 @@ /*Increase count: */ count++; - if(converged==true)break; + if(converged==true){ + bool max_iteration_state=false; + int tempStep=1; + double tempTime=1.0; + femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); + break; + } if(count>=max_nonlinear_iterations){ - _printf_(true," maximum number of iterations (%i) exceeded\n",max_nonlinear_iterations); + _printf_(true," maximum number of nonlinear iterations (%i) exceeded\n",max_nonlinear_iterations); converged=true; - InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); - InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); + InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); + bool max_iteration_state=true; + int tempStep=1; + double tempTime=1.0; + femmodel->results->AddObject(new BoolExternalResult(femmodel->results->Size()+1, MaxIterationConvergenceFlagEnum, max_iteration_state, tempStep, tempTime)); break; } Index: /issm/trunk/src/c/toolkits/issm/SeqMat.cpp =================================================================== --- /issm/trunk/src/c/toolkits/issm/SeqMat.cpp (revision 12329) +++ /issm/trunk/src/c/toolkits/issm/SeqMat.cpp (revision 12330) @@ -92,52 +92,4 @@ } /*}}}*/ - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION SeqMat::ToMatlabMatrix{{{1*/ -mxArray* SeqMat::ToMatlabMatrix(void){ - - /*Intermediary: */ - double* buffer=NULL; - mxArray* pfield=NULL; - - /*output: */ - mxArray* dataref=NULL; - - /*copy vector into a new buffer: */ - if(this->M*this->N){ - buffer=(double*)xmalloc(this->M*this->N*sizeof(double)); - memcpy(buffer,this->matrix,M*N*sizeof(double)); - - pfield=mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(pfield,this->N); - mxSetN(pfield,this->M); - mxSetPr(pfield,buffer); - - //transpose the matrix, written directly to matlab! from C to matlab. - mexCallMATLAB(1,&dataref, 1, &pfield, "transpose"); - } - else dataref=mxCreateDoubleMatrix(0,0,mxREAL); - - /*do not erase buffer!: */ - return dataref; - -} - - - - -/*}}}*/ -/*FUNCTION MatlabMatrixToSeqMat{{{1*/ -SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){ - - SeqMat* output=NULL; - - output=new SeqMat(); - MatlabMatrixToDoubleMatrix(&output->matrix,&output->M,&output->N,dataref); - return output; - -} -/*}}}*/ -#endif /*FUNCTION SeqMat::Assemble{{{1*/ void SeqMat::Assemble(void){ Index: /issm/trunk/src/c/toolkits/issm/SeqMat.h =================================================================== --- /issm/trunk/src/c/toolkits/issm/SeqMat.h (revision 12329) +++ /issm/trunk/src/c/toolkits/issm/SeqMat.h (revision 12330) @@ -15,8 +15,4 @@ #include "../toolkitsenums.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif /*}}}*/ @@ -40,7 +36,4 @@ /*SeqMat specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabMatrix(void); - #endif void Assemble(void); double Norm(NormMode norm_type); @@ -56,8 +49,3 @@ }; -/*API :*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref); -#endif - #endif //#ifndef _SEQMAT_H_ Index: /issm/trunk/src/c/toolkits/issm/SeqVec.cpp =================================================================== --- /issm/trunk/src/c/toolkits/issm/SeqVec.cpp (revision 12329) +++ /issm/trunk/src/c/toolkits/issm/SeqVec.cpp (revision 12330) @@ -66,42 +66,4 @@ /*}}}*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -/*FUNCTION SeqVec::ToMatlabVector{{{1*/ -mxArray* SeqVec::ToMatlabVector(void){ - - double* buffer=NULL; - - mxArray* dataref=NULL; - - /*copy vector into a new buffer: */ - if(this->M){ - buffer=(double*)xmalloc(this->M*sizeof(double)); - memcpy(buffer,vector,M*sizeof(double)); - - dataref = mxCreateDoubleMatrix(0,0,mxREAL); - mxSetM(dataref,this->M); - mxSetN(dataref,1); - mxSetPr(dataref,buffer); - } - else dataref = mxCreateDoubleMatrix(0,0,mxREAL); - - - /*do not erase buffer!: */ - return dataref; - -} -/*}}}*/ -/*FUNCTION MatlabVectorToSeqVec{{{1*/ -SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){ - - SeqVec* output=NULL; - - output=new SeqVec(); - MatlabVectorToDoubleVector(&output->vector,&output->M,dataref); - return output; - -} -/*}}}*/ -#endif /*FUNCTION SeqVec::Assemble{{{1*/ void SeqVec::Assemble(void){ Index: /issm/trunk/src/c/toolkits/issm/SeqVec.h =================================================================== --- /issm/trunk/src/c/toolkits/issm/SeqVec.h (revision 12329) +++ /issm/trunk/src/c/toolkits/issm/SeqVec.h (revision 12330) @@ -15,8 +15,4 @@ #include "../toolkitsenums.h" - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "mex.h" -#endif /*}}}*/ @@ -37,7 +33,4 @@ /*SeqVec specific routines {{{1*/ void Echo(void); - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - mxArray* ToMatlabVector(void); - #endif void Assemble(void); void SetValues(int ssize, int* list, double* values, InsMode mode); @@ -59,9 +52,3 @@ }; - -/*API :*/ -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); -#endif - #endif //#ifndef _SEQVEC_H_ Index: /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12329) +++ /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 12330) @@ -55,10 +55,6 @@ MatAssemblyBegin(inv,MAT_FINAL_ASSEMBLY); MatAssemblyEnd(inv,MAT_FINAL_ASSEMBLY); - - #if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - MatConvert(inv, MATSEQAIJ,MAT_REUSE_MATRIX,&inv); - #else - MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); - #endif + + MatConvert(inv, MATMPIAIJ,MAT_REUSE_MATRIX,&inv); /*Free ressources:*/ Index: sm/trunk/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 12329) +++ (revision ) @@ -1,123 +1,0 @@ -/* \file MatlabMatrixToPetscMatrix.cpp - * \brief: convert a sparse or dense matlab matrix to a serial Petsc matrix: - */ - - -#ifdef HAVE_CONFIG_H - #include -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){ - - int rows, cols; - double* mxmatrix_ptr=NULL; - double* tmatrix=NULL; - int ierr; - int i,j; - - /*output: */ - Mat matrix=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; - - /*petsc indices: */ - int* idxm=NULL; - int* idxn=NULL; - - /*Ok, first check if we are dealing with a sparse or full matrix: */ - if (mxIsSparse(mxmatrix)){ - - /*Dealing with sparse matrix: recover size first: */ - mxmatrix_ptr=(double*)mxGetPr(mxmatrix); - rows=mxGetM(mxmatrix); - cols=mxGetN(mxmatrix); - nnz=mxGetNzmax(mxmatrix); - if(rows){ - nz=(int)((double)nnz/(double)rows); - } - else{ - nz=0; - } - - ierr=MatCreateSeqAIJ(PETSC_COMM_SELF,rows,cols,nz,PETSC_NULL,&matrix);CHKERRQ(ierr); - - /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxmatrix); - ir=mxGetIr(mxmatrix); - jc=mxGetJc(mxmatrix); - - /*Now, start inserting data into sparse matrix: */ - count=0; - for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Matlab includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" - -int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){ - - int rows, cols; - double* mxvector_ptr=NULL; - int ierr; - int i,j; - - /*output: */ - Vec vector=NULL; - - /*matlab indices: */ - mwIndex* ir=NULL; - mwIndex* jc=NULL; - double* pr=NULL; - int count; - int nnz; - int nz; - - /*petsc indices: */ - int* idxm=NULL; - - /*Ok, first check if we are dealing with a sparse or full vector: */ - if (mxIsSparse(mxvector)){ - - /*Dealing with sparse vector: recover size first: */ - mxvector_ptr=(double*)mxGetPr(mxvector); - rows=mxGetM(mxvector); - cols=mxGetN(mxvector); - nnz=mxGetNzmax(mxvector); - nz=(int)((double)nnz/(double)rows); - - ierr=VecCreateSeq(PETSC_COMM_SELF,rows,&vector);CHKERRQ(ierr); - - /*Now, get ir,jc and pr: */ - pr=mxGetPr(mxvector); - ir=mxGetIr(mxvector); - jc=mxGetJc(mxvector); - - /*Now, start inserting data into sparse vector: */ - count=0; - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +/*Petsc includes: */ +#include "../../../shared/shared.h" + + +void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ + + int i,j,k; + + /*output: */ + double* matrix=NULL; + int rows,cols; + + /*intermediary: */ + int* idxm=NULL; + int* idxn=NULL; + + /*Some needed information: */ + MatGetSize(petsc_matrix,&rows,&cols); + + idxm=(int*)xmalloc(rows*sizeof(int)); + idxn=(int*)xmalloc(cols*sizeof(int)); + + for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Petsc includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" -#include - - -int PetscMatrixToMatlabMatrix(mxArray** pdataref,Mat tmatrix){ - - int i,j,k; - - /*output: */ - mxArray* dataref=NULL; - int rows,cols; - - int ncols; - int nnz=0; - int nzmax=0; - const int* columns=NULL; - const double* column_values=NULL; - double* matrix_ptr=NULL; - - /*compress row format: */ - double* val=NULL; - mwIndex* col_ind=NULL; - mwIndex* row_ptr=NULL; - - /*petsc type: */ - const char* type=NULL; - int* idxm=NULL; - int* idxn=NULL; - Mat matrix=NULL; - - - /*First off, we need to transpose the matrix using the Petsc API. We tried using the transpose operation from - * Matlab, but this ends up creating issues with lost pointers and references: */ - MatTranspose(tmatrix,MAT_INITIAL_MATRIX,&matrix); - - /*Some needed information: */ - MatGetType(matrix,&type); - MatGetSize(matrix,&rows,&cols); - - if (strcmp(type,MATSEQAIJ)==0){ - - /*Dealing with a sparse sequential matrix: build ir, jc and val, as though it was a row comvalessed - *format, instead of a column comvalessed format. We'll transpose later.*/ - - /*First get nnz: */ - nnz=0; - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#include + +/*Petsc includes: */ +#include "petscmat.h" +#include "petscvec.h" +#include "petscksp.h" + +#include "../../../shared/shared.h" + +void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ + + int i; + int rows; + int *idxm = NULL; + double *vector = NULL; + + /*Get size of vector: */ + if(petsc_vector){ + VecGetSize(petsc_vector,&rows); + if(rows){ + idxm=(int*)xmalloc(rows*sizeof(int)); + vector=(double*)xmalloc(rows*sizeof(double)); + for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Petsc includes: */ -#include "mex.h" - -#include "../../../shared/shared.h" -#include - - -int PetscVectorToMatlabVector(mxArray** pdataref,Vec vector){ - - int i; - int rows; - int *idxm = NULL; - double *values = NULL; - - /*output: */ - mxArray* dataref=NULL; - - /*Get size of vector: */ - if(vector){ - VecGetSize(vector,&rows); - if(rows){ - idxm=(int*)xmalloc(rows*sizeof(int)); - values=(double*)xmalloc(rows*sizeof(double)); - for(i=0;i +#else +#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +#endif + +#if _PYTHON_MAJOR_ == 2 +#undef NPY_NO_DEPRECATED_API +#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION +#else +#define NPY_NO_DEPRECATED_API +#endif + #include "Python.h" #include "arrayobject.h" - - #ifdef _HAVE_BOOST_ Index: /issm/trunk/src/c/toolkits/toolkits.h =================================================================== --- /issm/trunk/src/c/toolkits/toolkits.h (revision 12329) +++ /issm/trunk/src/c/toolkits/toolkits.h (revision 12330) @@ -12,5 +12,5 @@ #endif -#if defined(_HAVE_PYTHON_) && defined(_SERIAL_) +#ifdef _HAVE_PYTHON_ #include "./python/pythonincludes.h" #endif @@ -20,13 +20,13 @@ #endif -#if defined(_HAVE_MATLAB_) && defined(_SERIAL_) -#include "./matlab/matlabincludes.h" +#ifdef _HAVE_MPI_ +#include "./mpi/mpiincludes.h" #endif +#ifdef _HAVE_METIS_ +#include "./metis/metisincludes.h" +#endif -#include "./mpi/mpiincludes.h" -#include "./metis/metisincludes.h" #include "./triangle/triangleincludes.h" -#include "./double/double.h" #include "./toolkitsenums.h" #include "./issm/issmtoolkit.h" Index: /issm/trunk/src/c/toolkits/triangle/triangleincludes.h =================================================================== --- /issm/trunk/src/c/toolkits/triangle/triangleincludes.h (revision 12329) +++ /issm/trunk/src/c/toolkits/triangle/triangleincludes.h (revision 12330) @@ -6,6 +6,4 @@ #define _TRIANGLE_INCLUDES_H_ -#ifdef _SERIAL_ - #ifdef _C_ //only valid for iso C, not C++ /*Triangle includes: */ @@ -13,6 +11,4 @@ #endif //#ifdef _C_ -#endif //ifdef _SERIAL_ - #endif