Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 9563) +++ /issm/trunk/src/m/classes/model/model.m (revision 9564) @@ -8,6 +8,10 @@ % {{{1 %Careful here: no other class should be used as default value this is a bug of matlab - %in what follows, any field is defined according to the following convention: - %field={defaultvalue,marshall?,data type,matrix type} + cluster = modelfield('default',0,'marshall',false); + verbose = modelfield('default',0,'marshall',true,'preprocess','marshallverbose','format','Integer'); + results = modelfield('default',0,'marshall',false); + solver = modelfield('default',0,'marshall',false); + + %FIXME: all other fields should belong to other classes %Model general information @@ -195,5 +199,4 @@ requested_outputs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); %Debugging - verbose = modelfield('default',0,'marshall',true,'preprocess','marshallverbose','format','Integer'); mem_debug = modelfield('default',0,'marshall',false); gprof = modelfield('default',0,'marshall',false); @@ -201,5 +204,4 @@ output_frequency = modelfield('default',0,'marshall',true,'format','Integer'); results_on_vertices = modelfield('default',0,'marshall',true,'format','Boolean'); - results = modelfield('default',struct(),'marshall',false); vx = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); vy = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); @@ -223,5 +225,4 @@ %Parallelisation - cluster = modelfield('default',NaN,'marshall',false); outlog = modelfield('default','','marshall',false); errlog = modelfield('default','','marshall',false); @@ -230,7 +231,4 @@ %dummy dummy = modelfield('default',NaN,'marshall',false); - - %PETSc and MATLAB solver string - petscoptions = modelfield('default',NaN,'marshall',false); %Analysis @@ -534,4 +532,11 @@ end + %initialize subclasses + md.cluster=none; + md.solver=solver; + md.solver=addoptions(md.solver,DiagnosticVertAnalysisEnum,mumpsoptions); + md.results=struct(); + + %Materials parameters @@ -712,5 +717,4 @@ %cluster set as none for serial - md.cluster=none; %this option can be activated to load automatically the results @@ -727,7 +731,4 @@ md.hydro_kn=0; - %set petsc options for different analysis - md.petscoptions=petscoptions; - md.petscoptions=addoptions(md.petscoptions,DiagnosticVertAnalysisEnum,mumpsoptions); %Rheology law: what is the temperature dependence of B with T Index: sm/trunk/src/m/classes/petscoptions.m =================================================================== --- /issm/trunk/src/m/classes/petscoptions.m (revision 9563) +++ (revision ) @@ -1,46 +1,0 @@ -%PETSCOPTIONS class definition -% -% Usage: -% options=petscoptions(); - -classdef petscoptions - properties (SetAccess=public) - % {{{1 - options={NoneAnalysisEnum,mumpsoptions}; - %used when marshalling - %}}} - end - methods - function disp(o) % {{{1 - % display the object - disp(sprintf('class ''%s'' object ''%s'' = \n',class(o),inputname(1))); - % display the options - for i=1:size(o.options,1), - analysis=o.options{i,1}; - ioptions=o.options{i,2}; - string=petscoptiontostring(ioptions); - disp(sprintf(' %s -> ''%s''',EnumToString(analysis),string)); - end - disp(sprintf('\n')); - end - %}}} - function o=addoptions(o,analysis,solveroptions) % {{{1 - %first, find out if analysis has already been supplied - found=0; - for i=1:size(o.options,1), - inanalysis=o.options{i,1}; - if inanalysis==analysis, - found=1; - o.options{i,1}=analysis; - o.options{i,2}=solveroptions; - break; - end - end - if ~found, - o.options{end+1,1}=analysis; - o.options{end,2}=solveroptions; - end - end - %}}} - end -end Index: /issm/trunk/src/m/classes/solver.m =================================================================== --- /issm/trunk/src/m/classes/solver.m (revision 9564) +++ /issm/trunk/src/m/classes/solver.m (revision 9564) @@ -0,0 +1,119 @@ +%SOLVER class definition +% +% Usage: +% obj=solver(); + +classdef solver + properties (SetAccess=public) + options={NoneAnalysisEnum,mumpsoptions}; + end + methods + function disp(obj) % {{{1 + % display the object + disp(sprintf('class ''%s'' object ''%s'' = \n',class(o),inputname(1))); + % display the options + for i=1:size(obj.options,1), + analysis=obj.options{i,1}; + ioptions=obj.options{i,2}; + string=PetscString(ioptions); + disp(sprintf(' %s -> ''%s''',EnumToString(analysis),string)); + end + disp(sprintf('\n')); + end + %}}} + function obj=addoptions(obj,analysis,solveroptions) % {{{1 + %first, find out if analysis has already been supplied + found=false; + for i=1:size(obj.options,1), + inanalysis=obj.options{i,1}; + if inanalysis==analysis, + found=true; + obj.options{i,1}=analysis; + obj.options{i,2}=solveroptions; + break; + end + end + if ~found, + obj.options{end+1,1}=analysis; + obj.options{end,2}=solveroptions; + end + end + %}}} + function PetscFile(solver,filename) % {{{ + %PETSCFILE - build petsc file + % + % Build a Petsc compatible options file, from the solver model field + return options string + % + % Usage: PetscFile(solver,filename); + + %open file for writing + fid=fopen(filename,'w'); + if fid==-1, + error(['PetscFile error: could not open ' filename ' for writing']); + end + + %write header + fprintf(fid,'%s%s%s\n','%Petsc options file: ',filename,' written from Matlab solver array'); + + %start writing options + for i=1:size(solver.options,1), + analysis=solver.options{i,1}; + options=solver.options{i,2}; + + %first write analysis: + fprintf(fid,'\n+%s\n',EnumToString(analysis)); %append a + to recognize it's an analysis enum + + %now, write options + for j=1:size(options,2), + option=options{j}; + if isempty(option), + %do nothing + elseif length(option)==1, + %this option has only one argument + fprintf(fid,'-%s\n',option{1}); + elseif length(option)==2, + %option with value. value can be string or scalar + if isscalar(option{2}), + fprintf(fid,'-%s %g\n',option{1},option{2}); + elseif ischar(option{2}), + fprintf(fid,'-%s %s\n',option{1},option{2}); + else + error(['PetscFile error: option #' num2str(j) ' is not well formatted']); + end + else + error(['PetscFile error: option #' num2str(j) ' is not well formatted']); + end + end + end + + fclose(fid); + end %}}} + function string=PetscString(solver) % {{{ + + %initialize string: + string=''; + + %start writing options + for i=1:length(solver), + option=solver{i}; + if isempty(option), + %do nothing + elseif length(option)==1, + %this option has only one argument + string=[string ' -' option{1}]; + elseif length(option)==2, + %option with value. value can be string or scalar + if isscalar(option{2}), + string=[string ' -' option{1} ' ' num2str(option{2})]; + elseif ischar(option{2}), + string=[string ' -' option{1} ' ' option{2}]; + else + error(['PetscString error: option #' num2str(i) ' is not well formatted']); + end + else + error(['PetscString error: option #' num2str(i) ' is not well formatted']); + end + end + end % }}} + end + end Index: sm/trunk/src/m/enum/EpsvelEnum.m =================================================================== --- /issm/trunk/src/m/enum/EpsvelEnum.m (revision 9563) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=EpsvelEnum() -%EPSVELENUM - Enum of Epsvel -% -% 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=EpsvelEnum() - -macro=StringToEnum('Epsvel'); Index: sm/trunk/src/m/enum/MeanvelEnum.m =================================================================== --- /issm/trunk/src/m/enum/MeanvelEnum.m (revision 9563) +++ (revision ) @@ -1,11 +1,0 @@ -function macro=MeanvelEnum() -%MEANVELENUM - Enum of Meanvel -% -% 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=MeanvelEnum() - -macro=StringToEnum('Meanvel'); Index: sm/trunk/src/m/model/PetscOptions2PetscFile.m =================================================================== --- /issm/trunk/src/m/model/PetscOptions2PetscFile.m (revision 9563) +++ (revision ) @@ -1,49 +1,0 @@ -function PetscOptions2PetscFile(petscoptions,filename) -%PETSCOPTIONS2PETSCFILE: build a Petsc compatible options file, from the petscoptions model field + return options string -% -% Usage: PetscOptions2PetscFile(petscoptions,filename); -% -% Example: PetscOptions2PetscFile(md.petscoptions,'petsc.rc'); -% - -%open file for writing -fid=fopen(filename,'w'); -if fid==-1, - error(['PetscOptions2PetscFile error: could not open ' filename ' for writing']); -end - -%write header -fprintf(fid,'%s%s%s\n','%Petsc options file: ',filename,' written from Matlab petscoptions array'); - -%start writing options -for i=1:size(petscoptions.options,1), - analysis=petscoptions.options{i,1}; - options=petscoptions.options{i,2}; - - %first write analysis: - fprintf(fid,'\n+%s\n',EnumToString(analysis)); %append a + to recognize it's an analysis enum - - %now, write options - for j=1:size(options,2), - option=options{j}; - if isempty(option), - %do nothing - elseif length(option)==1, - %this option has only one argument - fprintf(fid,'-%s\n',option{1}); - elseif length(option)==2, - %option with value. value can be string or scalar - if isscalar(option{2}), - fprintf(fid,'-%s %g\n',option{1},option{2}); - elseif ischar(option{2}), - fprintf(fid,'-%s %s\n',option{1},option{2}); - else - error(['PetscOptions2PetscFile error: option #' num2str(j) ' is not well formatted']); - end - else - error(['PetscOptions2PetscFile error: option #' num2str(j) ' is not well formatted']); - end - end -end - -fclose(fid); Index: /issm/trunk/src/m/model/display/displayparallel.m =================================================================== --- /issm/trunk/src/m/model/display/displayparallel.m (revision 9563) +++ /issm/trunk/src/m/model/display/displayparallel.m (revision 9564) @@ -14,4 +14,2 @@ fielddisplay(md,'alloc_cleanup','allocation cleanup before starting a job, default 1'); fielddisplay(md,'waitonlock','maximum number of minutes to wait for batch results, or return 0'); -disp('petsc options:'); -disp(md.petscoptions) Index: sm/trunk/src/m/model/petscoptiontostring.m =================================================================== --- /issm/trunk/src/m/model/petscoptiontostring.m (revision 9563) +++ (revision ) @@ -1,30 +1,0 @@ -function petscstring=petscoptiontostring(petscoptions) -%PETSCOPTIONTOSTRING: build a Petsc compatible options string -% -% Usage: petscstring=PetscOptions2PetscRc(petscoptions); -% - -%initialize petscstring: -petscstring=''; - -%start writing options -for i=1:length(petscoptions), - option=petscoptions{i}; - if isempty(option), - %do nothing - elseif length(option)==1, - %this option has only one argument - petscstring=[petscstring ' -' option{1}]; - elseif length(option)==2, - %option with value. value can be string or scalar - if isscalar(option{2}), - petscstring=[petscstring ' -' option{1} ' ' num2str(option{2})]; - elseif ischar(option{2}), - petscstring=[petscstring ' -' option{1} ' ' option{2}]; - else - error(['PetscOptions2PetscRc error: option #' num2str(i) ' is not well formatted']); - end - else - error(['PetscOptions2PetscRc error: option #' num2str(i) ' is not well formatted']); - end -end Index: /issm/trunk/src/m/model/solve.m =================================================================== --- /issm/trunk/src/m/model/solve.m (revision 9563) +++ /issm/trunk/src/m/model/solve.m (revision 9564) @@ -61,5 +61,5 @@ %write a template file for issm to use, in parallel -PetscOptions2PetscFile(md.petscoptions,[md.name '.petsc']); +PetscFile(md.solver,[md.name '.petsc']); %If running in parallel, we have a different way of launching the solution Index: sm/trunk/src/m/model/solvers/solversettosor.m =================================================================== --- /issm/trunk/src/m/model/solvers/solversettosor.m (revision 9563) +++ (revision ) @@ -1,7 +1,0 @@ -function md=solversettosor(md) -%SOLVERSETTOSOR - associate solver sor to the model -% -% Usage: -% md=solversettosor(md) - -md.petscoptions={{'mat_type','aij'},{'ksp_type','cg'},{'pc_type','sor'},{'pc_sor_omega',1.1},{pc_sor_its',2}};