Changeset 13410

Timestamp:

09/20/12 16:39:15 (12 years ago)

Author:

Mathieu Morlighem

Message:

CHG: renaming vertex->dof vertex->pid for consistency (id, sid and pid) and cleaned up some code

Location:

issm/trunk-jpl/src/c

Files:

• Container/Vertices.cpp (modified) (2 diffs)
• Container/Vertices.h (modified) (1 diff)
• classes/objects/Elements/Penta.cpp (modified) (25 diffs)
• classes/objects/Elements/Penta.h (modified) (1 diff)
• classes/objects/Elements/Tria.cpp (modified) (39 diffs)
• classes/objects/Elements/Tria.h (modified) (1 diff)
• classes/objects/Materials/Matdamageice.cpp (modified) (3 diffs)
• classes/objects/Materials/Matice.cpp (modified) (3 diffs)
• classes/objects/Node.cpp (modified) (6 diffs)
• classes/objects/Node.h (modified) (2 diffs)
• classes/objects/Vertex.cpp (modified) (6 diffs)
• classes/objects/Vertex.h (modified) (2 diffs)
• modules/VerticesDofx/VerticesDofx.cpp (modified) (2 diffs)

issm/trunk-jpl/src/c/Container/Vertices.cpp

@@ -38 +38 @@
 
 /*Numerics management*/
-/*FUNCTION Vertices::DistributeDofs{{{*/
-void  Vertices::DistributeDofs(int numberofobjects,int numberofdofsperobject){
+/*FUNCTION Vertices::DistributePids{{{*/
+void  Vertices::DistributePids(int numberofobjects){
 
         extern int num_procs;
@@ -45 +45 @@
 
         int  i;
-        int  dofcount=0;
-        int* alldofcount=NULL;
-        int* truedofs=NULL;
-        int* alltruedofs=NULL;
+        int  pidcount    = 0;
+        int *allpidcount = NULL;
+        int *truepids    = NULL;
+        int *alltruepids = NULL;
 
-        /*Go through objects, and distribute dofs locally, from 0 to numberofdofsperobject*/
+        /*Go through objects, and distribute pids locally, from 0 to numberofpidsperobject*/
         for (i=0;i<this->Size();i++){
                 Vertex* vertex=(Vertex*)this->GetObjectByOffset(i);
-                vertex->DistributeDofs(&dofcount);
+                vertex->DistributePids(&pidcount);
         }
 
-        /* Now every object has distributed dofs, but locally, and with a dof count starting from 
-         * 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*/
-        alldofcount=xNew<int>(num_procs);
+        /* Now every object has distributed pids, but locally, and with a pid count starting from 
+         * 0. This means the pids between all the cpus are not unique. We now offset the pids of each
+         * cpus by the total last pids of the previus cpu, starting from 0.
+         * First: get number of pids for each cpu*/
+        allpidcount=xNew<int>(num_procs);
         #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);
+        MPI_Gather(&pidcount,1,MPI_INT,allpidcount,1,MPI_INT,0,MPI_COMM_WORLD);
+        MPI_Bcast(allpidcount,num_procs,MPI_INT,0,MPI_COMM_WORLD);
         #else
-        alldofcount[0]=dofcount;
+        allpidcount[0]=pidcount;
         #endif
 
-        /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/
-        dofcount=0;
+        /* Every cpu should start its own pid count at the end of the pidcount from cpu-1*/
+        pidcount=0;
         if(my_rank!=0){
                 for(i=0;i<my_rank;i++){
-                        dofcount+=alldofcount[i];
+                        pidcount+=allpidcount[i];
                 }
         }
         for (i=0;i<this->Size();i++){
                 Vertex* vertex=(Vertex*)this->GetObjectByOffset(i);
-                vertex->OffsetDofs(dofcount);
+                vertex->OffsetPids(pidcount);
         }
 
         /* Finally, remember that cpus may have skipped some objects, because they were clones. For every 
-         * object that is not a clone, tell them to show their dofs, so that later on, they can get picked 
+         * object that is not a clone, tell them to show their pids, so that later on, they can get picked 
          * up by their clones: */
-        truedofs   =xNewZeroInit<int>(numberofobjects*numberofdofsperobject);
-        alltruedofs=xNewZeroInit<int>(numberofobjects*numberofdofsperobject);
+        truepids   =xNewZeroInit<int>(numberofobjects);
+        alltruepids=xNewZeroInit<int>(numberofobjects);
         for (i=0;i<this->Size();i++){
                 Vertex* vertex=(Vertex*)this->GetObjectByOffset(i);
-                vertex->ShowTrueDofs(truedofs);
+                vertex->ShowTruePids(truepids);
         }
         #ifdef _HAVE_MPI_
-        MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD);
+        MPI_Allreduce((void*)truepids,(void*)alltruepids,numberofobjects,MPI_INT,MPI_MAX,MPI_COMM_WORLD);
         #else
-        for(i=0;i<numberofobjects*numberofdofsperobject;i++)alltruedofs[i]=truedofs[i];
+        for(i=0;i<numberofobjects;i++)alltruepids[i]=truepids[i];
         #endif
 
-        /* Now every cpu knows the true dofs of everyone else that is not a clone*/
-        for (i=0;i<this->Size();i++){
+        /* Now every cpu knows the true pids of everyone else that is not a clone*/
+        for(i=0;i<this->Size();i++){
                 Vertex* vertex=(Vertex*)this->GetObjectByOffset(i);
-                vertex->UpdateCloneDofs(alltruedofs);
+                vertex->UpdateClonePids(alltruepids);
         }
 
         /* Free ressources: */
-        xDelete<int>(alldofcount);
-        xDelete<int>(truedofs);
-        xDelete<int>(alltruedofs);
+        xDelete<int>(allpidcount);
+        xDelete<int>(truepids);
+        xDelete<int>(alltruepids);
 }
 /*}}}*/

issm/trunk-jpl/src/c/Container/Vertices.h

@@ -19 +19 @@
         public:
 
-                /*constructors, destructors: {{{*/
+                /*constructors, destructors:*/ 
                 Vertices();
                 ~Vertices();
-                /*}}}*/
-                /*numerics: {{{*/
-                void  DistributeDofs(int numberofnodes,int numdofspernode);
+
+                /*numerics:*/
+                void  DistributePids(int numberofnodes);
                 void  FlagClones(int numberofnodes);
                 int   NumberOfVertices(void);
                 void  Ranks(int* ranks);
-                /*}}}*/
-
 };
 

issm/trunk-jpl/src/c/classes/objects/Elements/Penta.cpp

@@ -815 +815 @@
 }
 /*}}}*/
-/*FUNCTION Penta::GetDofList1 {{{*/
-void  Penta::GetDofList1(int* doflist){
+/*FUNCTION Penta::GetVertexPidList {{{*/
+void  Penta::GetVertexPidList(int* doflist){
 
         int i;
-        for(i=0;i<6;i++) doflist[i]=nodes[i]->GetDofList1();
+        for(i=0;i<6;i++) doflist[i]=nodes[i]->GetVertexPid();
+
+}
+/*}}}*/
+/*FUNCTION Penta::GetVertexSidList{{{*/
+void  Penta::GetVertexSidList(int* sidlist){
+
+        int i;
+        for(i=0;i<NUMVERTICES;i++) sidlist[i]=nodes[i]->GetVertexSid();
 
 }
@@ -995 +1003 @@
          *    = 4 * mu * eps_eff ^2*/
         *phi=4*pow(epsilon_eff,2.0)*viscosity;
-}
-/*}}}*/
-/*FUNCTION Penta::GetSidList{{{*/
-void  Penta::GetSidList(int* sidlist){
-
-        int i;
-        for(i=0;i<NUMVERTICES;i++) sidlist[i]=nodes[i]->GetSidList();
-
 }
 /*}}}*/
@@ -1135 +1135 @@
 void  Penta::GetVectorFromInputs(Vector<IssmDouble>* vector,int input_enum){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
 
         /*Get out if this is not an element input*/
@@ -1141 +1141 @@
 
         /*Prepare index list*/
-        this->GetDofList1(&doflist1[0]);
+        this->GetVertexPidList(&vertexpidlist[0]);
 
         /*Get input (either in element or material)*/
@@ -1148 +1148 @@
 
         /*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
-        input->GetVectorFromInputs(vector,&doflist1[0]);
+        input->GetVectorFromInputs(vector,&vertexpidlist[0]);
 }
 /*}}}*/
@@ -1160 +1160 @@
         }  
         if(interp==P1Enum){
-                int doflist1[NUMVERTICES];
+                int vertexpidlist[NUMVERTICES];
                 int connectivity[NUMVERTICES];
-                this->GetSidList(&doflist1[0]);
+                this->GetVertexSidList(&vertexpidlist[0]);
                 this->GetConnectivityList(&connectivity[0]);
-                elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES);
+                elementresult->GetVectorFromResults(vector,&vertexpidlist[0],&connectivity[0],NUMVERTICES);
         }
         else if(interp==P0Enum){
@@ -1960 +1960 @@
                                 /*Get values on the 6 vertices*/
                                 for (int i=0;i<6;i++){
-                                        values[i]=vector[this->nodes[i]->GetVertexDof()];
+                                        values[i]=vector[this->nodes[i]->GetVertexPid()];
                                 }
 
@@ -4463 +4463 @@
 void Penta::ControlInputGetGradient(Vector<IssmDouble>* gradient,int enum_type,int control_index){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
         Input* input=NULL;
 
@@ -4481 +4481 @@
         if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
 
-        GradientIndexing(&doflist1[0],control_index);
-        ((ControlInput*)input)->GetGradient(gradient,&doflist1[0]);
+        GradientIndexing(&vertexpidlist[0],control_index);
+        ((ControlInput*)input)->GetGradient(gradient,&vertexpidlist[0]);
 
 }/*}}}*/
@@ -4507 +4507 @@
 void Penta::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){
 
-        int    doflist1[NUMVERTICES];
+        int    vertexpidlist[NUMVERTICES];
         IssmDouble grad_list[NUMVERTICES];
         Input* grad_input=NULL;
@@ -4524 +4524 @@
         if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
 
-        GradientIndexing(&doflist1[0],control_index);
-        for(int i=0;i<NUMVERTICES;i++) grad_list[i]=gradient[doflist1[i]];
+        GradientIndexing(&vertexpidlist[0],control_index);
+        for(int i=0;i<NUMVERTICES;i++) grad_list[i]=gradient[vertexpidlist[i]];
         grad_input=new PentaP1Input(GradientEnum,grad_list);
         ((ControlInput*)input)->SetGradient(grad_input);
@@ -4802 +4802 @@
         /*get gradient indices*/
         for(int i=0;i<NUMVERTICES;i++){
-                indexing[i]=num_controls*this->nodes[i]->GetVertexDof() + control_index;
+                indexing[i]=num_controls*this->nodes[i]->GetVertexPid() + control_index;
         }
 
@@ -4915 +4915 @@
         int        i,j,ig;
         int        analysis_type;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     vx,vy,lambda,mu,alpha_complement,Jdet;
         IssmDouble     bed,thickness,Neff,drag;
@@ -4932 +4932 @@
         /*Retrieve all inputs and parameters*/
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         for(i=0;i<NUMVERTICES2D;i++) for(j=0;j<2;j++) xyz_list_tria[i][j]=xyz_list[i][j];
@@ -4974 +4974 @@
                 }
         }
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -4986 +4986 @@
         int        i,j,ig;
         int        analysis_type;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     bed,thickness,Neff;
         IssmDouble     lambda,mu,xi,Jdet,vx,vy,vz;
@@ -5007 +5007 @@
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         for(i=0;i<NUMVERTICES2D;i++) for(j=0;j<2;j++) xyz_list_tria[i][j]=xyz_list[i][j];
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         Input* drag_input    =inputs->GetInput(FrictionCoefficientEnum); _assert_(drag_input);
         Input* vx_input      =inputs->GetInput(VxEnum);                  _assert_(vx_input);
@@ -5067 +5067 @@
         }
 
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         delete friction;
@@ -5494 +5494 @@
 void  Penta::GetVectorFromControlInputs(Vector<IssmDouble>* vector,int control_enum,int control_index,const char* data){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
 
         /*Get out if this is not an element input*/
@@ -5500 +5500 @@
 
         /*Prepare index list*/
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Get input (either in element or material)*/
@@ -5511 +5511 @@
         }
 
-        ((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data);
+        ((ControlInput*)input)->GetVectorFromInputs(vector,&vertexpidlist[0],data);
 }
 /*}}}*/
@@ -5518 +5518 @@
 
         IssmDouble  values[NUMVERTICES];
-        int     doflist1[NUMVERTICES];
+        int     vertexpidlist[NUMVERTICES];
         Input  *input     = NULL;
         Input  *new_input = NULL;
@@ -5526 +5526 @@
 
         /*Prepare index list*/
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Get values on vertices*/
         for (int i=0;i<NUMVERTICES;i++){
-                values[i]=vector[doflist1[i]];
+                values[i]=vector[vertexpidlist[i]];
         }
         new_input = new PentaP1Input(control_enum,values);
@@ -5569 +5569 @@
                         /*Get values on the 6 vertices*/
                         for (i=0;i<6;i++){
-                                values[i]=vector[this->nodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
+                                values[i]=vector[this->nodes[i]->GetVertexSid()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
                         }
 
@@ -5689 +5689 @@
                                 /*create input values: */
                                 for(i=0;i<6;i++){
-                                        row=this->nodes[i]->GetSidList();
+                                        row=this->nodes[i]->GetVertexSid();
                                         values[i]=(IssmDouble)matrix[ncols*row+t];
                                 }

issm/trunk-jpl/src/c/classes/objects/Elements/Penta.h

@@ -174 +174 @@
                 ElementVector* CreatePVectorSlope(void);
                 void      GetDofList(int** pdoflist,int approximation_enum,int setenum);
-                void      GetDofList1(int* doflist);
-                void    GetSidList(int* sidlist);
+                void      GetVertexPidList(int* doflist);
+                void    GetVertexSidList(int* sidlist);
                 void    GetConnectivityList(int* connectivity);
                 int     GetElementType(void);

issm/trunk-jpl/src/c/classes/objects/Elements/Tria.cpp

@@ -140 +140 @@
 
         /*Figure out the average for this element: */
-        this->GetSidList(&offsetsid[0]);
-        this->GetDofList1(&offsetdof[0]);
+        this->GetVertexSidList(&offsetsid[0]);
+        this->GetVertexPidList(&offsetdof[0]);
         mean=0;
         for(i=0;i<NUMVERTICES;i++){
@@ -1055 +1055 @@
 }
 /*}}}*/
-/*FUNCTION Tria::GetDofList1 {{{*/
-void  Tria::GetDofList1(int* doflist){
-
-        int i;
-        for(i=0;i<3;i++) doflist[i]=nodes[i]->GetDofList1();
-
-}
-/*}}}*/
 /*FUNCTION Tria::GetElementType {{{*/
 int Tria::GetElementType(){
@@ -1180 +1172 @@
 }
 /*}}}*/
-/*FUNCTION Tria::GetSidList {{{*/
-void  Tria::GetSidList(int* sidlist){
-        for(int i=0;i<NUMVERTICES;i++) sidlist[i]=nodes[i]->GetSidList();
+/*FUNCTION Tria::GetVertexPidList {{{*/
+void  Tria::GetVertexPidList(int* doflist){
+
+        int i;
+        for(i=0;i<3;i++) doflist[i]=nodes[i]->GetVertexPid();
+
+}
+/*}}}*/
+/*FUNCTION Tria::GetVertexSidList {{{*/
+void  Tria::GetVertexSidList(int* sidlist){
+        for(int i=0;i<NUMVERTICES;i++) sidlist[i]=nodes[i]->GetVertexSid();
 }
 /*}}}*/
@@ -1243 +1243 @@
 void  Tria::GetVectorFromInputs(Vector<IssmDouble>* vector,int input_enum){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
 
         /*Get out if this is not an element input*/
@@ -1249 +1249 @@
 
         /*Prepare index list*/
-        this->GetDofList1(&doflist1[0]);
+        this->GetVertexPidList(&vertexpidlist[0]);
 
         /*Get input (either in element or material)*/
@@ -1256 +1256 @@
 
         /*We found the enum.  Use its values to fill into the vector, using the vertices ids: */
-        input->GetVectorFromInputs(vector,&doflist1[0]);
+        input->GetVectorFromInputs(vector,&vertexpidlist[0]);
 }
 /*}}}*/
@@ -1268 +1268 @@
         }
         if(interp==P1Enum){
-                int doflist1[NUMVERTICES];
+                int vertexpidlist[NUMVERTICES];
                 int connectivity[NUMVERTICES];
-                this->GetSidList(&doflist1[0]);
+                this->GetVertexSidList(&vertexpidlist[0]);
                 this->GetConnectivityList(&connectivity[0]);
-                elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES);
+                elementresult->GetVectorFromResults(vector,&vertexpidlist[0],&connectivity[0],NUMVERTICES);
         }
         else if(interp==P0Enum){
@@ -1687 +1687 @@
                         /*Get values on the 3 vertices*/
                         for (int i=0;i<3;i++){
-                                values[i]=vector[this->nodes[i]->GetVertexDof()];
+                                values[i]=vector[this->nodes[i]->GetVertexPid()];
                         }
 
@@ -3432 +3432 @@
 void Tria::ControlInputGetGradient(Vector<IssmDouble>* gradient,int enum_type,int control_index){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
         Input* input=NULL;
 
@@ -3444 +3444 @@
         if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
 
-        GradientIndexing(&doflist1[0],control_index);
-        ((ControlInput*)input)->GetGradient(gradient,&doflist1[0]);
+        GradientIndexing(&vertexpidlist[0],control_index);
+        ((ControlInput*)input)->GetGradient(gradient,&vertexpidlist[0]);
 
 }/*}}}*/
@@ -3467 +3467 @@
 void Tria::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){
 
-        int    doflist1[NUMVERTICES];
+        int    vertexpidlist[NUMVERTICES];
         IssmDouble grad_list[NUMVERTICES];
         Input* grad_input=NULL;
@@ -3481 +3481 @@
         if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput");
 
-        GradientIndexing(&doflist1[0],control_index);
-        for(int i=0;i<NUMVERTICES;i++) grad_list[i]=gradient[doflist1[i]];
+        GradientIndexing(&vertexpidlist[0],control_index);
+        for(int i=0;i<NUMVERTICES;i++) grad_list[i]=gradient[vertexpidlist[i]];
         grad_input=new TriaP1Input(GradientEnum,grad_list);
 
@@ -3556 +3556 @@
 
         int        i,ig;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     Jdet,weight;
         IssmDouble     xyz_list[NUMVERTICES][3];
@@ -3566 +3566 @@
         /*Retrieve all inputs we will be needing: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         Input* rheologyb_input=material->inputs->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input);
         Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                _assert_(weights_input);
@@ -3586 +3586 @@
                 for (i=0;i<NUMVERTICES;i++) grade_g[i]+=-weight*Jdet*gauss->weight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]);
         }
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3596 +3596 @@
 
         int        i,ig;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     Jdet,weight;
         IssmDouble     xyz_list[NUMVERTICES][3];
@@ -3606 +3606 @@
         /*Retrieve all inputs we will be needing: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         Input* rheologyz_input=material->inputs->GetInput(MaterialsRheologyZbarEnum); _assert_(rheologyz_input);
         Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                _assert_(weights_input);
@@ -3626 +3626 @@
                 for (i=0;i<NUMVERTICES;i++) grade_g[i]+=-weight*Jdet*gauss->weight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]);
         }
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3751 +3751 @@
         int        i,ig;
         int        analysis_type;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         int        connectivity[NUMVERTICES];
         IssmDouble     vx,vy,lambda,mu,alpha_complement,Jdet;
@@ -3769 +3769 @@
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         this->GetConnectivityList(&connectivity[0]);
 
@@ -3827 +3827 @@
         /*End Analytical gradient*/
 
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3838 +3838 @@
 
         int        i,ig;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     Jdet,weight;
         IssmDouble     xyz_list[NUMVERTICES][3];
@@ -3849 +3849 @@
         if(IsFloating())return;
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         Input* dragcoefficient_input=inputs->GetInput(FrictionCoefficientEnum); _assert_(dragcoefficient_input);
         Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum);                 _assert_(weights_input);
@@ -3872 +3872 @@
                 }
         }
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3882 +3882 @@
 
         /*Intermediaries*/
-        int    doflist1[NUMVERTICES];
+        int    vertexpidlist[NUMVERTICES];
         IssmDouble lambda[NUMVERTICES];
         IssmDouble gradient_g[NUMVERTICES];
 
         /*Compute Gradient*/
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
         GetInputListOnVertices(&lambda[0],AdjointEnum);
         for(int i=0;i<NUMVERTICES;i++) gradient_g[i]=-lambda[i];
 
-        gradient->SetValues(NUMVERTICES,doflist1,gradient_g,INS_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,gradient_g,INS_VAL);
 }
 /*}}}*/
@@ -3899 +3899 @@
         /*Intermediaries*/
         int        i,ig;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     thickness,Jdet;
         IssmDouble     basis[3];
@@ -3909 +3909 @@
         /* Get node coordinates and dof list: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Retrieve all inputs we will be needing: */
@@ -3931 +3931 @@
         }
 
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3942 +3942 @@
         /*Intermediaries*/
         int        i,ig;
-        int        doflist1[NUMVERTICES];
+        int        vertexpidlist[NUMVERTICES];
         IssmDouble     thickness,Jdet;
         IssmDouble     basis[3];
@@ -3952 +3952 @@
         /* Get node coordinates and dof list: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Retrieve all inputs we will be needing: */
@@ -3973 +3973 @@
                 for(i=0;i<NUMVERTICES;i++) grade_g[i]+=thickness*Dlambda[1]*Jdet*gauss->weight*basis[i];
         }
-        gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL);
+        gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL);
 
         /*Clean up and return*/
@@ -3988 +3988 @@
         /*get gradient indices*/
         for(int i=0;i<NUMVERTICES;i++){
-                indexing[i]=num_controls*this->nodes[i]->GetVertexDof() + control_index;
+                indexing[i]=num_controls*this->nodes[i]->GetVertexPid() + control_index;
         }
 
@@ -5205 +5205 @@
 void  Tria::GetVectorFromControlInputs(Vector<IssmDouble>* vector,int control_enum,int control_index,const char* data){
 
-        int doflist1[NUMVERTICES];
+        int vertexpidlist[NUMVERTICES];
         Input *input=NULL;
 
@@ -5212 +5212 @@
 
         /*Prepare index list*/
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Get input (either in element or material)*/
@@ -5227 +5227 @@
         }
 
-        ((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data);
+        ((ControlInput*)input)->GetVectorFromInputs(vector,&vertexpidlist[0],data);
 }
 /*}}}*/
@@ -5234 +5234 @@
 
         IssmDouble  values[NUMVERTICES];
-        int     doflist1[NUMVERTICES];
+        int     vertexpidlist[NUMVERTICES];
         Input  *input     = NULL;
         Input  *new_input = NULL;
@@ -5242 +5242 @@
 
         /*Prepare index list*/
-        GradientIndexing(&doflist1[0],control_index);
+        GradientIndexing(&vertexpidlist[0],control_index);
 
         /*Get values on vertices*/
         for (int i=0;i<NUMVERTICES;i++){
-                values[i]=vector[doflist1[i]];
+                values[i]=vector[vertexpidlist[i]];
         }
         new_input = new TriaP1Input(control_enum,values);
@@ -5556 +5556 @@
                         /*Get values on the 3 vertices*/
                         for (i=0;i<3;i++){
-                                values[i]=vector[this->nodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
+                                values[i]=vector[this->nodes[i]->GetVertexSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!)
                         }
 
@@ -5662 +5662 @@
                                 /*create input values: */
                                 for(i=0;i<3;i++){
-                                        row=this->nodes[i]->GetSidList();
+                                        row=this->nodes[i]->GetVertexSidList();
                                         values[i]=(IssmDouble)matrix[ncols*row+t];
                                 }

issm/trunk-jpl/src/c/classes/objects/Elements/Tria.h

@@ -190 +190 @@
                 int            GetElementType(void);
                 void             GetDofList(int** pdoflist,int approximation_enum,int setenum);
-                void             GetDofList1(int* doflist);
-                void           GetSidList(int* sidlist);
+                void             GetVertexPidList(int* doflist);
+                void           GetVertexSidList(int* sidlist);
                 void           GetConnectivityList(int* connectivity);
                 void           GetInputListOnVertices(IssmDouble* pvalue,int enumtype);

issm/trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp

@@ -210 +210 @@
                         /*Prepare index list*/
                         int doflist1[3];
-                        for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof();
+                        for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexPid();
 
                         /*Get input (either in element or material)*/
@@ -640 +640 @@
                                 case TriaEnum: {
                                         IssmDouble values[3];
-                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()];
+                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexPid()];
                                         this->inputs->AddInput(new TriaP1Input(name,values));
                                         return;
@@ -682 +682 @@
                                 case TriaEnum: {
                                         IssmDouble values[3];
-                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector 
+                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexSid()]; //use sid list, to index into serial oriented vector 
                                         this->inputs->AddInput(new TriaP1Input(name,values));
                                         /*Special case for rheology B in 2D: Pourave land for this solution{{{*/

issm/trunk-jpl/src/c/classes/objects/Materials/Matice.cpp

@@ -190 +190 @@
                         /*Prepare index list*/
                         int doflist1[3];
-                        for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof();
+                        for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexPid();
 
                         /*Get input (either in element or material)*/
@@ -560 +560 @@
                                 case TriaEnum: {
                                         IssmDouble values[3];
-                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()];
+                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexPid()];
                                         this->inputs->AddInput(new TriaP1Input(name,values));
                                         return;
@@ -602 +602 @@
                                 case TriaEnum: {
                                         IssmDouble values[3];
-                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector 
+                                        for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexSid()]; //index into serial oriented vector 
                                         this->inputs->AddInput(new TriaP1Input(name,values));
                                         /*Special case for rheology B in 2D: Pourave land for this solution{{{*/

issm/trunk-jpl/src/c/classes/objects/Node.cpp

@@ -234 +234 @@
 
 } /*}}}*/
-/*FUNCTION Node::GetDofList1{{{*/
-int  Node::GetDofList1(void){
-
-        Vertex* vertex=NULL;
-
-        vertex=(Vertex*)this->hvertex->delivers();
-
-        return vertex->dof;
-}
-/*}}}*/
 /*FUNCTION Node::GetDofList{{{*/
 void  Node::GetDofList(int* outdoflist,int approximation_enum,int setenum){
@@ -304 +294 @@
                 else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!");
         }
-}
-/*}}}*/
-/*FUNCTION Node::GetSidList{{{*/
-int  Node::GetSidList(void){
-
-        Vertex* vertex=NULL;
-
-        vertex=(Vertex*)this->hvertex->delivers();
-
-        return vertex->sid;
 }
 /*}}}*/
@@ -427 +407 @@
 }
 /*}}}*/
-/*FUNCTION Node::GetVertexDof {{{*/
-int   Node::GetVertexDof(void){
+/*FUNCTION Node::GetVertexPid{{{*/
+int   Node::GetVertexPid(void){
 
         Vertex*  vertex=NULL;
 
         vertex=(Vertex*)hvertex->delivers();
-        return vertex->dof;
+        return vertex->pid;
+}
+/*}}}*/
+/*FUNCTION Node::GetVertexSid{{{*/
+int  Node::GetVertexSid(void){
+
+        Vertex* vertex=NULL;
+
+        vertex=(Vertex*)this->hvertex->delivers();
+
+        return vertex->sid;
 }
 /*}}}*/
@@ -446 +436 @@
 /*}}}*/
 #endif
-/*FUNCTION Node::SetVertexDof {{{*/
-void   Node::SetVertexDof(int in_dof){
-
-        Vertex*  vertex=NULL;
-
-        vertex=(Vertex*)hvertex->delivers();
-        vertex->dof=in_dof;
-
-}
-/*}}}*/
 /*FUNCTION Node::InAnalysis{{{*/
 bool Node::InAnalysis(int in_analysis_type){
@@ -887 +867 @@
 /*}}}*/
 
-/* DofObject routines:*/
+/* indexing routines:*/
 /*FUNCTION Node::DistributeDofs{{{*/
 void  Node::DistributeDofs(int* pdofcount,int setenum){
@@ -935 +915 @@
 }
 /*}}}*/
-/*FUNCTION Node::Off_setDofs{{{*/
+/*FUNCTION Node::OffsetDofs{{{*/
 void  Node::OffsetDofs(int dofcount,int setenum){
         

issm/trunk-jpl/src/c/classes/objects/Node.h

@@ -67 +67 @@
                 void   SetCurrentConfiguration(DataSet* nodes,Vertices* vertices);
                 int    Sid(void); 
-                int    GetVertexDof(void);
-                int    GetVertexId(void);
 #ifdef _HAVE_DIAGNOSTIC_
                 void   GetCoordinateSystem(IssmDouble* coord_system_out);
 #endif
-                void   SetVertexDof(int in_dof);
                 bool   InAnalysis(int analysis_type);
                 int    GetApproximation();
@@ -86 +83 @@
                 void   GetDofList(int* poutdoflist,int approximation_enum,int setenum);
                 void   GetLocalDofList(int* poutdoflist,int approximation_enum,int setenum);
-                int    GetDofList1(void);
-                int    GetSidList(void);
+                int    GetVertexId(void);
+                int    GetVertexPid(void);
+                int    GetVertexSid(void);
                 IssmDouble GetX();
                 IssmDouble GetY();

issm/trunk-jpl/src/c/classes/objects/Vertex.cpp

@@ -49 +49 @@
         this->id=vertex_id;
         this->sid=vertex_sid;
+        this->pid=UNDEF;
         this->x=vertex_x;
         this->y=vertex_y;
@@ -54 +55 @@
         this->sigma=vertex_sigma;
         this->connectivity=vertex_connectivity;
-        this->dof=UNDEF;
 
         return;
@@ -67 +67 @@
         _printLine_("   id: " << id);
         _printLine_("   sid: " << sid);
+        _printLine_("   pid: " << pid);
         _printLine_("   x: " << x);
         _printLine_("   y: " << y);
@@ -72 +73 @@
         _printLine_("   sigma: " << sigma);
         _printLine_("   connectivity: " << connectivity);
-        _printLine_("   dof: " << dof);
         _printLine_("   clone: " << clone);
 
@@ -107 +107 @@
 /*}}}*/
 
-/* DofObject routines: */
-/*FUNCTION Vertex::DistributeDofs{{{*/
-void  Vertex::DistributeDofs(int* pdofcount){
-
-        int i;
-        extern int my_rank;
-        int dofcount;
-
-        dofcount=*pdofcount;
-        
-        if(this->clone){
-                /*This vertex is a clone! Don't distribute dofs, it will get them from another cpu!*/
-                return;
-        }
-
-        /*This vertex should distribute his dof, go ahead: */
-        this->dof=dofcount;
-        dofcount++;
-
-        /*Assign output pointers: */
-        *pdofcount=dofcount;
-
-}
-/*}}}*/
-/*FUNCTION Vertex::OffsetDofs{{{*/
-void  Vertex::OffsetDofs(int dofcount){
-        
-        int i;
-        extern int my_rank;
-        
-        if(this->clone){
-                /*This vertex is a clone, don't offset the dofs!: */
-                return;
-        }
-
-        /*This vertex should offset his dof, go ahead: */
-        this->dof+=dofcount;
-}
-/*}}}*/
-/*FUNCTION Vertex::ShowTrueDofs{{{*/
-void  Vertex::ShowTrueDofs(int* truedofs){
-
-        int j;
-        extern int my_rank;
-        
-        /*Are we a clone? : */
-        if(this->clone)return;
-
-        /*Ok, we are not a clone, just plug our dof into truedofs: */
-        truedofs[this->id-1]=this->dof;
-
-}
-/*}}}*/
-/*FUNCTION Vertex::UpdateCloneDofs{{{*/
-void  Vertex::UpdateCloneDofs(int* alltruedofs){
-
-        int j;
-        extern int my_rank;
-        
-        /*If we are not a clone, don't update, we already have dofs!: */
-        if(this->clone==0)return;
-
-        /*Ok, we are a clone node, but we did not create the dof for this vertex 
-         * Therefore, our dof is garbage right now. Go pick it up in the alltruedofs: */
-        this->dof=alltruedofs[id-1];
-}
-/*}}}*/
-/*FUNCTION Vertex::SetClone {{{*/
-void  Vertex::SetClone(int* minranks){
-
-        extern int my_rank;
-
-        if (minranks[id-1]==my_rank){
-                this->clone=0;
-        }
-        else{
-                /*!there is a cpu with lower rank that has the same vertex, 
-                therefore, I am a clone*/
-                this->clone=1;  
-        }
-
-}
-/*}}}*/
-
 /*Vertex management: */
 /*FUNCTION Vertex::Connectivity{{{*/
@@ -209 +125 @@
         /*sigma remains constant. z=bed+sigma*thickness*/
         oldz = this->z;
-        newz = bed[this->dof]+sigma*thickness[this->dof];
+        newz = bed[this->pid]+sigma*thickness[this->pid];
         velz = (newz-oldz)/dt;
         this->z = newz;
 
         /*put vz in vector*/
-        vz->SetValue(this->dof,velz,INS_VAL);
+        vz->SetValue(this->pid,velz,INS_VAL);
 }
 /*}}}*/
+/*FUNCTION Vertex::DistributePids{{{*/
+void  Vertex::DistributePids(int* ppidcount){
+
+        /*retrieve current pid*/
+        int pidcount=*ppidcount;
+        
+        /*This vertex is a clone! Don't distribute pids, it will get them from another cpu!*/
+        if(this->clone) return;
+
+        /*This vertex should distribute its pid*/
+        this->pid=pidcount;
+        pidcount++;
+
+        /*Assign output pointers: */
+        *ppidcount=pidcount;
+}
+/*}}}*/
+/*FUNCTION Vertex::OffsetPids{{{*/
+void  Vertex::OffsetPids(int pidcount){
+        
+        /*This vertex is a clone, don't offset the pids*/
+        if(this->clone) return;
+
+        /*This vertex should offset his pid, go ahead: */
+        this->pid+=pidcount;
+}
+/*}}}*/
+/*FUNCTION Vertex::ShowTruePids{{{*/
+void  Vertex::ShowTruePids(int* truepids){
+
+        /*Are we a clone? : */
+        if(this->clone)return;
+
+        /*Ok, we are not a clone, just plug our pid into truepids: */
+        truepids[this->sid]=this->pid;
+}
+/*}}}*/
+/*FUNCTION Vertex::UpdateClonePids{{{*/
+void  Vertex::UpdateClonePids(int* alltruepids){
+
+        /*If we are not a clone, don't update, we already have pids: */
+        if(!this->clone)return;
+
+        /*Ok, we are a clone node, but we did not create the pid for this vertex 
+         * Therefore, our pid is garbage right now. Go pick it up in the alltruepids: */
+        this->pid=alltruepids[this->pid];
+}
+/*}}}*/
+/*FUNCTION Vertex::SetClone {{{*/
+void  Vertex::SetClone(int* minranks){
+
+        extern int my_rank;
+
+        if (minranks[this->sid]==my_rank){
+                this->clone=false;
+        }
+        else{
+                /*!there is a cpu with lower rank that has the same vertex, 
+                therefore, I am a clone*/
+                this->clone=true;
+        }
+
+}
+/*}}}*/
+

issm/trunk-jpl/src/c/classes/objects/Vertex.h

@@ -22 +22 @@
 
         public: 
-
-                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.
+                bool       clone;
+                int        id;           // random index
+                int        sid;          // "serial" id (rank of this vertex if the dataset was on 1 cpu)
+                int        pid;          // "parallel" id
                 IssmDouble x;
                 IssmDouble y;
                 IssmDouble z;
-                IssmDouble sigma;          //sigma coordinate: (z-bed)/thickness
-                int    connectivity;   //number of vertices connected to this vertex
-
-                /*dof management: */
-                int    clone;
-                int    dof; //dof to recover values in a vertex indexed vector
+                IssmDouble sigma;        //sigma coordinate: (z-bed)/thickness
+                int        connectivity; //number of vertices connected to this vertex
 
                 /*Vertex constructors, destructors {{{*/
@@ -50 +47 @@
                 Object* copy();
                 /*}}}*/
-                /*DofObject routines {{{*/
-                void  DistributeDofs(int* pdofcount);
-                void  OffsetDofs(int dofcount);
-                void  ShowTrueDofs(int* borderdofs);
-                void  UpdateCloneDofs(int* allborderdofs);
-                void  SetClone(int* minranks);
-                /*}}}*/
-                /*Vertex management: {{{*/
+                /*Vertex management:*/ 
                 int   Sid(void); 
                 int   Connectivity(void); 
                 void  UpdatePosition(Vector<IssmDouble>* vz,Parameters* parameters,IssmDouble* thickness,IssmDouble* bed);
-                /*}}}*/
+                void  DistributePids(int* ppidcount);
+                void  OffsetPids(int pidcount);
+                void  ShowTruePids(int* borderpids);
+                void  UpdateClonePids(int* allborderpids);
+                void  SetClone(int* minranks);
 };
 #endif  /* _VERTEX_H */

issm/trunk-jpl/src/c/modules/VerticesDofx/VerticesDofx.cpp

@@ -11 +11 @@
 void VerticesDofx( Vertices* vertices, Parameters* parameters) {
 
-        int i;
-
-        int  found=0;
-        extern int num_procs;
-        extern int my_rank;
-        
         /*intermediary: */
         int  numberofvertices;
@@ -23 +17 @@
         numberofvertices=vertices->NumberOfVertices();
 
-        /*Ensure that only for each cpu, the partition border vertices only will be taken into account once 
-         * across the cluster. To do so, we flag all the clone vertices: */
+        /*Ensure that only for each cpu, the partition border vertices only will be
+         * taken into account once across the cluster. To do so, we flag all the
+         * clone vertices: */
         vertices->FlagClones(numberofvertices);
 
-        /*Go through all vertices and distribute 1 dof at a time. When a  vertex has already been distributed his dof on a cpu, 
-         * all other cpus with the same vertex cannot distribute it anymore. Use clone field to be sure of that: */
-        vertices->DistributeDofs(numberofvertices,1); //only 1 dof per vertex.
+        /*Go through all vertices and distribute pids*/
+        vertices->DistributePids(numberofvertices); 
 
 }