Index: /issm/trunk/src/m/classes/model.m =================================================================== --- /issm/trunk/src/m/classes/model.m (revision 9422) +++ /issm/trunk/src/m/classes/model.m (revision 9423) @@ -16,11 +16,4 @@ runtimename = {'',false}; %name used when running a parallel job counter = {0,false}; - domainoutline = {NaN,false}; - riftoutline = {NaN,false}; - iceshelfoutline = {NaN,false}; - icesheetoutline = {NaN,false}; - wateroutline = {NaN,false}; - parameterfile = {NaN,false}; - runmefile = {NaN,false}; %Mesh @@ -109,5 +102,4 @@ nodeonsurface = {NaN,true,'BooleanMat',1}; minh = {0,false}; - firn_layer = {NaN,false}; %Extraction @@ -118,5 +110,4 @@ rho_ice = {0,true,'Double'}; rho_water = {0,true,'Double'}; - rho_firn = {0,false}; heatcapacity = {0,true,'Double'}; latentheat = {0,true,'Double'}; @@ -154,5 +145,4 @@ bed = {NaN,true,'DoubleMat',1}; bathymetry = {NaN,true,'DoubleMat',1}; - mask = {NaN,false}; %Boundary conditions @@ -171,20 +161,10 @@ vy_obs = {NaN,true,'DoubleMat',1}; vel_obs = {NaN,false}; - vx_obs_raw = {NaN,false}; - vy_obs_raw = {NaN,false}; - vx_bal = {NaN,false}; - vy_bal = {NaN,false}; - vel_bal = {NaN,false}; - vel_obs_raw = {NaN,false}; - surface_accumulation_rate = {NaN,true,'DoubleMat',1}; + surface_accumulation_rate = {NaN,true,'DoubleMat',3}; surface_ablation_rate = {NaN,true,'DoubleMat',1}; surface_mass_balance = {NaN,true,'DoubleMat',1}; dhdt = {NaN,true,'DoubleMat',1}; geothermalflux = {NaN,true,'DoubleMat',1}; - observed_temperature = {NaN,false}; thickness_obs = {NaN,true,'DoubleMat',1}; - - %Forcings - forcings = {struct(),false}; %Statics parameters @@ -207,10 +187,4 @@ artificial_diffusivity = {0,true,'Integer'}; prognostic_DG = {0,true,'Integer'}; - deltaH = {0,false}; - DeltaH = {0,false}; - deltaT = {0,false}; - DeltaT = {0,false}; - timeacc = {0,false}; - timedec = {0,false}; hydrostatic_adjustment = {0,true,'Integer'}; isprognostic = {0,true,'Boolean'}; @@ -237,18 +211,8 @@ %Output requested_outputs = {[],true,'DoubleMat',3}; - viscousheating = {NaN,false}; - pressure_elem = {NaN,false}; - stress = {NaN,false}; - stress_surface = {NaN,false}; - stress_bed = {NaN,false}; - deviatoricstress = {NaN,false}; - strainrate = {NaN,false}; %Debugging verbose = {0,true,'Integer'}; - element_debug = {0,false}; - element_debugid = {NaN,false}; mem_debug = {0,false}; gprof = {0,false}; - memoryleaks = {NaN,false}; %Results fields output_frequency = {0,true,'Integer'}; @@ -282,5 +246,4 @@ outlog = {'',false}; errlog = {'',false}; - alloc_cleanup = {1,false}; waitonlock = {0,true,'Boolean'}; @@ -288,9 +251,4 @@ dummy = {NaN,false}; - %mesh - mesh_domainoutline = {'',false}; - mesh_riftoutline = {'',false}; - mesh_resolution = {NaN,false}; - %PETSc and MATLAB solver string petscoptions = {NaN,false}; @@ -298,7 +256,4 @@ %Analysis solution_type = {'',false}; - - %management of large models - repository = {'',false}; %radar power images @@ -342,7 +297,4 @@ groundingline_migration = {0,true,'Integer'}; - %solution parameters - loadresults = {0,false}; - %partitioner: adjacency = {[],false}; @@ -401,20 +353,12 @@ case 1 - %If single argument of class model, we have a copy constructor. - if (isa(varargin{1},'model')) - md = varargin{1}; - elseif (isa(varargin{1},'char')) - %user gave us the name of the repository, this model is going to be large! - md=model; - md.repository=varargin{1}; - md=activaterepository(md); - elseif (isa(varargin{1},'numeric')) - if varargin{1}==0, + in=varargin{1}; + if (isa(in,'model')) + %If single argument of class model, we have a copy constructor. + md = in; + elseif (isa(in,'numeric') & in==0) %just requesting model, without default parameters, do nothing. - else - error('model constructor error message: unknown constructor call'); - end else - error('model constructor error message: copy constructor called on a non ''model'' class object'); + error('model constructor error message: unknown constructor for ''model'' class object'); end @@ -424,39 +368,4 @@ end %}}} - function md = activaterepository(md) % {{{1 - %ACTIVATEREPOSITORY - save the model fields separately - % - % This function is required when a matlab session - % is running low on memory, or when a model is very large. - % By activating a repository (for example, 'repository.model'), - % the model fields will each separately be saved and accessed when - % needed. This will limit the memory use at the maximum; - % - % Usage: - % md=activaterepository(md) - - - %for each field of the model, we create an equivalent variable, with the same name, which we - %save in the repository. - - modelfields=fields(md); - - %then save each of the big fields in their respective files - for i=1:length(modelfields), - field=char(modelfields(i)); - eval([field '=md.' field ';']); - - %anything NaN, will be saved - - if isnumeric(eval(field)), - if isnan(eval(field)), - if exist(['.' md.repository '.' field],'file'); - error(['Repository ' md.repository ' already exists! Delete all files starting with .' md.repository ' in your directory, before activating a new repository']); - end - eval(['save .' md.repository '.' field ' ' field]); - end - end - end - end % }}} function disp(md) % {{{1 disp(sprintf('\n%s = \n',inputname(1))); @@ -492,13 +401,8 @@ end - %repository - if ~isempty(md.repository), - disp(sprintf(' Repository: %s',md.repository)); - end - %diverse - disp(sprintf(' Mesh: %s',md.repository)); + disp(sprintf(' Mesh:'); disp(sprintf('%s%s%s',' Mesh: type ''',inputname(1),'.mesh'' to display')); - disp(sprintf(' Parameters: %s',md.repository)); + disp(sprintf(' Parameters:'); disp(sprintf('%s%s%s',' Boundary conditions: type ''',inputname(1),'.bc'' to display')); disp(sprintf('%s%s%s',' Observations: type ''',inputname(1),'.obs'' to display')); @@ -506,5 +410,5 @@ disp(sprintf('%s%s%s',' Parameters: type ''',inputname(1),'.par'' to display')); disp(sprintf('%s%s%s',' ExpPar: type ''',inputname(1),'.exppar'' to display')); - disp(sprintf(' Solution parameters: %s',md.repository)); + disp(sprintf(' Solution parameters: %s'); disp(sprintf('%s%s%s',' Qmu: type ''',inputname(1),'.qmu'' to display')); disp(sprintf('%s%s%s',' FLAIM: type ''',inputname(1),'.flaim'' to display')); @@ -624,7 +528,4 @@ md.rho_water=1023; - %firn density (kg/m^3) - md.rho_firn=830; - %ice heat capacity cp (J/kg/K) md.heatcapacity=2093; @@ -757,26 +658,4 @@ md.prognostic_DG=0; - %minimum thickness change between 2 time steps (m) - md.deltaH=10^-2; - - %maximum thickness change between 2 time steps (m) - md.DeltaH=50; - - %minimum temperature change between 2 time steps (K) - md.deltaT=10^-2; - - %maximum temperature change between 2 time steps (K) - md.DeltaT=1; - - %When the previous criteria are fulfilled, if the time steps - %can be accelerated as follows - %dt = timeacc * dt - md.timeacc=2; - - %When the previous criteria are fulfilled, if the time steps - %can be reduced as follows - %dt = timedec * dt - md.timedec=.5; - %Solution activated for transient runs. By default we do a %full analysis: Diagnostic, Prognostic and Thermal @@ -847,7 +726,4 @@ md.waitonlock=Inf; - %prerun allocation cleanup - md.alloc_cleanup=1; - %hydrology: from Johnson's 2002 thesis, section 3.5.4 md.hydro_n=.02; @@ -869,27 +745,4 @@ end %}}} - function md = subsasgn(md,index,val) % {{{1 - - if ~isempty(md.repository), - field=index(1).subs; - if exist(['.' md.repository '.' field],'file'), - if length(index)==1, - %save val in corresponding repository - eval([field '=val;']); - eval(['save .' md.repository '.' field ' ' field]); - else - %load field from file - load(['.' md.repository '.' field],'-mat'); - fieldval=eval(field); - eval([field '=builtin(''subsasgn'',fieldval,index(2),val);']); - eval(['save .' md.repository '.' field ' ' field]); - end - else - md=builtin('subsasgn',md,index,val); - end - else - md=builtin('subsasgn',md,index,val); - end - end %}}} function result = subsref(md,index) % {{{1 @@ -911,33 +764,8 @@ if(strcmp(index1.subs,'control')), displaycontrol(md);return; end if(strcmp(index1.subs,'parallel')), displayparallel(md);return; end - - if ~isempty(md.repository), - %load variable needed, if necessary - if exist(['.' md.repository '.' index1.subs],'file'), - structure=load(['.' md.repository '.' index1.subs],'-mat'); - eval(['result=structure.' index1.subs ';']); - else - %the file does not exist, just return built in value - result=builtin('subsref',md,index); - end - else - %return built in value - result=builtin('subsref',md,index); - end - else - if ~isempty(md.repository), - if exist(['.' md.repository '.' index(1).subs],'file'), - %load variable needed - variable=load(['.' md.repository '.' index(1).subs],'-mat'); - - %use temporary structure. - result=builtin('subsref',variable,index); - else - result=builtin('subsref',md,index); - end - else - result=builtin('subsref',md,index); - end - end + end + + %return built in value + result=builtin('subsref',md,index); end %}}} end Index: /issm/trunk/src/m/classes/organizer.m =================================================================== --- /issm/trunk/src/m/classes/organizer.m (revision 9422) +++ /issm/trunk/src/m/classes/organizer.m (revision 9423) @@ -142,11 +142,4 @@ if (org.currentstep>length(org.steps)), error(['organizer error message: element with id ' num2str(org.currentstep) ' not found']); end - %before saving model, try and find a runme.m file, and save it. - A=dbstack; - if length(A)>=2, - runmefilename=A(2).file; - md.runmefile=char(textread(runmefilename,'%s','delimiter','\n')); - end - %save model save(name,'md','-v7.3'); Index: sm/trunk/src/m/classes/runsteps.m =================================================================== --- /issm/trunk/src/m/classes/runsteps.m (revision 9422) +++ (revision ) @@ -1,193 +1,0 @@ -%RUNSTEPS class definition -% -% Usage: -% rs = runsteps(varargin) -% -% Examples: -% rs = runsteps; %build an empty runsteps object -% rs = runsteps('../Models/'); %build an empty runsteps object with a given repository -% rs = runsteps('../Models/','models.AGU.'); %build an empty runsteps object with a given repository and a prefix -% rs = runsteps('../Models/','models.AGU.','model.init'); %repository, prefix, and initial trunk prefix - -classdef runsteps - properties (SetAccess=public) - % {{{1 - repository ='./'; - prefix ='model.'; - trunkprefix =''; - steps =[]; - %}}} - end - methods - function rs=runsteps(varargin) % {{{1 - if nargin>3, - help runsteps - error('runsteps constructor error message: bad usage'); - end - if nargin>2, - trunkprefix=varargin{3}; - if ~ischar(trunkprefix), error('trunkprefix is not a string'); end - if ~strcmp(regexprep(trunkprefix,'\s+',''),trunkprefix), error('trunkprefix should not have any white space'); end - rs.trunkprefix=trunkprefix; - end - if nargin>1, - prefix=varargin{2}; - if ~ischar(prefix), error('prefix is not a string'); end - if ~strcmp(regexprep(prefix,'\s+',''),prefix), error('prefix should not have any white space'); end - rs.prefix=prefix; - end - if nargin>0, - repository=varargin{1}; - if ~ischar(repository), error('repository is not a string'); end - if exist(repository,'dir')~=7, error(['Directory ' repository ' not found']), end - rs.repository=repository; - end - end - %}}} - function disp(rs) % {{{1 - disp(sprintf(' Repository: ''%s''',rs.repository)); - disp(sprintf(' Prefix: ''%s''',rs.prefix)); - if isempty(rs.steps) - disp(' no step'); - else - for i=1:length(rs.steps), - disp(sprintf(' step #%2i: ''%s''',rs.steps(i).id,rs.steps(i).string)); - end - end - end - %}}} - function rs = addstep(rs,string),% {{{1 - - %check string - if ~ischar(string), error('Step provided should be a string'); end - if ~strcmp(regexprep(string,'\s+',''),string), error('Step provided should not have any white space'); end - - rs.steps(end+1).id=length(rs.steps)+1; - rs.steps(end).string=string; - end% }}} - function bool=echo(rs,steps,varargin)% {{{1 - disp('WARNING: obsolete function. Use PerformStep instead (see issm/projetcs/scripts/runme.m)'); - if length(steps)==0, - error('steps is empty'), - elseif (length(steps)==1 & steps==0) - if isempty(rs.steps) - disp(' no step'); - else - for i=1:length(rs.steps), - disp(sprintf(' step #%2i : %s',rs.steps(i).id,rs.steps(i).string)); - end - end - bool=true; - return; - else - bool=false; - return; - end - end%}}} - function id=GetId(rs,string) % {{{1 - %GetId - get step id from string - % - % Usage: - % GetId(rs,num) - - for i=1:length(rs.steps), - if strcmp(rs.steps(i).string,string), - id=i; - return; - end - end - error(['No step of flag ' string ' has been found']); - - end%}}} - function md=loadmodel(rs,string),% {{{1 - - %Get model path - if ~ischar(string), error('argument provided is not a string'); end - path=[rs.repository '/' rs.prefix string]; - - %figure out if the model is there, otherwise, we have to use the default path supplied by user. - if exist(path,'file'), - md=loadmodel(path); - return; - end - - %If we are here, the model has not been found. Try trunk prefix if provided - if ~isempty(rs.trunkprefix), - path2=[rs.repository '/' rs.trunkprefix string]; - if ~exist(path2,'file'), - error(['Could neither find ' path ', nor ' path2]); - else - disp(['--> Branching ' rs.prefix ' from trunk ' rs.trunkprefix]); - md=loadmodel(path2); - return; - end - else - error(['Could not find ' path ]); - end - end%}}} - function message(rs,num) % {{{1 - %MESSAGE - display string of rs with id =num - % - % Usage: - % string(rs,num) - - %Some checks - if (abs(floor(num))~=num), - error(['runsteps error message: the number provided is not a positive integer']); - end - if (num>length(rs.steps)), - error(['runsteps error message: element with id ' num2str(num) ' not found']); - end - - %Print string - disp('WARNING: obsolete function. Use PerformStep instead (see issm/projetcs/scripts/runme.m'); - disp(sprintf('\n step #%i -> %s\n',rs.steps(num).id,rs.steps(num).string)); - end%}}} - function bool=PerformStep(rs,steps,num) % {{{1 - - %Some checks - if (abs(floor(num))~=num), - error(['runsteps error message: the number provided is not a positive integer']); - end - if (num>length(rs.steps)), - error(['runsteps error message: element with id ' num2str(num) ' not found']); - end - - bool=false; - - %if steps = 0, print all steps in rs - if any(steps==0), - if num==1, - disp(sprintf(' prefix: %s',rs.prefix(1:end-6))); - for i=1:length(rs.steps), - disp(sprintf(' step #%2i : %s',rs.steps(i).id,rs.steps(i).string)); - end - end - end - - %Ok, now if num is a member of steps, return true - if ismember(num,steps), - disp(sprintf('\n step #%i : %s\n',rs.steps(num).id,rs.steps(num).string)); - bool=true; - end - end%}}} - function savemodel(rs,num,md) % {{{1 - - %check that md is a model - if ~isa(md,'model'), error('savemodel error message: third argument is not a model'); end - if (num>length(rs.steps)), error(['runsteps error message: element with id ' num2str(num) ' not found']); end - - %before saving model, try and find a runme.m file, and save it. - A=dbstack; - if length(A)>=2, - runmefilename=A(2).file; - md.runmefile=char(textread(runmefilename,'%s','delimiter','\n')); - end - - %save model - name=[rs.repository '/' rs.prefix rs.steps(num).string ]; - save(name,'md','-v7.3'); - disp(['model saved as: ' name]); - end%}}} - end -end Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 9422) +++ /issm/trunk/src/m/model/collapse.m (revision 9423) @@ -31,5 +31,4 @@ if ~isnan(md.surface_mass_balance), md.surface_mass_balance=project2d(md,md.surface_mass_balance,md.numlayers); end; if ~isnan(md.dhdt), md.dhdt=project2d(md,md.dhdt,md.numlayers); end; -if ~isnan(md.firn_layer), md.firn_layer=project2d(md,md.firn_layer,md.numlayers); end; %results @@ -79,5 +78,4 @@ %special for thermal modeling: md.basal_melting_rate=project2d(md,md.basal_melting_rate,1); -md.observed_temperature=DepthAverage(md,md.observed_temperature); md.geothermalflux=project2d(md,md.geothermalflux,1); %bedrock only gets geothermal flux Index: sm/trunk/src/m/model/deepcopy.m =================================================================== --- /issm/trunk/src/m/model/deepcopy.m (revision 9422) +++ (revision ) @@ -1,30 +1,0 @@ -function md2=deepcopy(md) -%DEEPCOPY - copies a model -% -% This routine will copy md into md2. If md is being held in an out of core -% repository, user will be prompted for a different repository name, and a -% copy of the repository, with the new name, will be done. -% -% Usage: -% md2=deepcopy(md) - -if isempty(md.repository), - md2=md; -else - %New repository name? - new_repository=input([' input model is held in repository: ' md.repository '. you need a new name for the model copy: ']); - md2=model(new_repository); - - structfields=fields(md); - for i=1:length(structfields), - field=structfields(i);field=field{1}; - if strcmpi(field,'repository'), - %we don't want to clobber md2.repository! - continue; - end - fieldval=getfield(md,field); - if isfield(struct(md2),field), - eval(['md2.' field '=fieldval;']); - end - end -end Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 9422) +++ /issm/trunk/src/m/model/extrude.m (revision 9423) @@ -154,5 +154,4 @@ md.surface_ablation_rate=project3d(md,'vector',md.surface_ablation_rate,'type','node'); md.dhdt=project3d(md,'vector',md.dhdt,'type','node'); -md.firn_layer=project3d(md,'vector',md.firn_layer,'type','node','layer',md.numlayers); %results @@ -243,11 +242,7 @@ %special for thermal modeling: md.basal_melting_rate=project3d(md,'vector',md.basal_melting_rate,'type','node','layer',1); -md.observed_temperature=project3d(md,'vector',md.observed_temperature,'type','node'); if ~isnan(md.geothermalflux) md.geothermalflux=project3d(md,'vector',md.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux end - -%mask: -md.mask=project3d(md,'vector',md.mask,'type','node'); %increase connectivity if less than 25: Index: /issm/trunk/src/m/model/geography.m =================================================================== --- /issm/trunk/src/m/model/geography.m (revision 9422) +++ /issm/trunk/src/m/model/geography.m (revision 9423) @@ -59,18 +59,2 @@ md.nodeonwater=zeros(md.numberofnodes,1); md.elementonwater=zeros(md.numberofelements,1); - -%Keep track of input files -if (strcmp(iceshelfname,'') | strcmp(iceshelfname,'all')), - md.iceshelfoutline=iceshelfname; -elseif ischar(iceshelfname), - md.iceshelfoutline=char(textread(iceshelfname,'%s','delimiter','\n')); -else - md.iceshelfoutline=iceshelfname; -end -if (strcmp(icesheetname,'') | strcmp(icesheetname,'all')), - md.icesheetoutline=icesheetname; -elseif ischar(icesheetname), - md.icesheetoutline=char(textread(icesheetname,'%s','delimiter','\n')); -else - md.icesheetoutline=icesheetname; -end Index: /issm/trunk/src/m/model/mechanicalproperties.m =================================================================== --- /issm/trunk/src/m/model/mechanicalproperties.m (revision 9422) +++ /issm/trunk/src/m/model/mechanicalproperties.m (revision 9423) @@ -4,5 +4,5 @@ % this routine computes the components of the stress tensor % strain rate tensor and their respective principal directions. -% the results are in the model md: md.stress and md.strainrate +% the results are in the model md: md.results % % Usage: @@ -94,5 +94,5 @@ stress.principalaxis1=directionsstress(:,3:4); stress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2); -md.stress=stress; +md.results.stress=stress; strainrate=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]); @@ -105,5 +105,5 @@ strainrate.principalaxis1=directionsstrain(:,3:4); strainrate.effectivevalue=1/sqrt(2)*sqrt(strainrate.xx.^2+strainrate.yy.^2+2*strainrate.xy.^2); -md.strainrate=strainrate; +md.results.strainrate=strainrate; deviatoricstress=struct('xx',[],'yy',[],'xy',[],'principalvalue1',[],'principalaxis1',[],'principalvalue2',[],'principalaxis2',[],'effectivevalue',[]); @@ -116,3 +116,3 @@ deviatoricstress.principalaxis1=directionsstress(:,3:4); deviatoricstress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2); -md.deviatoricstress=deviatoricstress; +md.results.deviatoricstress=deviatoricstress; Index: /issm/trunk/src/m/model/mesh/mesh.m =================================================================== --- /issm/trunk/src/m/model/mesh/mesh.m (revision 9422) +++ /issm/trunk/src/m/model/mesh/mesh.m (revision 9423) @@ -82,12 +82,4 @@ md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); -%outline names -md.domainoutline=char(textread(domainname,'%s','delimiter','\n')); -if strcmp(riftname,''), - md.riftoutline=''; -else - md.riftoutline=readfile(riftname); -end - %type of model md.dim=2; Index: /issm/trunk/src/m/model/mesh/meshnodensity.m =================================================================== --- /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9422) +++ /issm/trunk/src/m/model/mesh/meshnodensity.m (revision 9423) @@ -68,12 +68,4 @@ md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity); -%outline names -md.domainoutline=char(textread(domainname,'%s','delimiter','\n')); -if strcmp(riftname,''), - md.riftoutline=''; -else - md.riftoutline=readfile(riftname); -end - %type of model md.dim=2; Index: sm/trunk/src/m/model/model2ocmodel.m =================================================================== --- /issm/trunk/src/m/model/model2ocmodel.m (revision 9422) +++ (revision ) @@ -1,26 +1,0 @@ -function md2=model2ocmodel(md,repository) -%MODEL2OCMODEL - create an out of core model -% -% This routine will take an input model, running in core (ie: md.repository=''), -% and copy all its fields to an output model which will run out of core on 'repository'. -% -% Usage: -% md2=model2ocmodel(md,repository); -% -% Example: -% md2=model2ocmodel(md,'PineIsland'); - -md2=model(repository); - -structfields=fields(md); -for i=1:length(structfields), - field=structfields(i);field=field{1}; - if strcmpi(field,'repository'), - %we don't want to clobber md2.repository! - continue; - end - fieldval=getfield(md,field); - if isfield(struct(md2),field), - eval(['md2.' field '=fieldval;']); - end -end Index: /issm/trunk/src/m/model/parameterization/parameterize.m =================================================================== --- /issm/trunk/src/m/model/parameterization/parameterize.m (revision 9422) +++ /issm/trunk/src/m/model/parameterization/parameterize.m (revision 9423) @@ -68,7 +68,4 @@ end -%Keep track of parameter file -md.parameterfile=char(textread(parametername,'%s','delimiter','\n')); - %Name and notes if isempty(md.name), Index: /issm/trunk/src/m/model/plot/plot_tensor.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_tensor.m (revision 9422) +++ /issm/trunk/src/m/model/plot/plot_tensor.m (revision 9423) @@ -15,4 +15,5 @@ %Figure out tensor type: +%FIXME does not work anymore if strncmpi(type,'strain',6), tensor=md.strainrate; Index: /issm/trunk/src/m/model/process_solve_options.m =================================================================== --- /issm/trunk/src/m/model/process_solve_options.m (revision 9422) +++ /issm/trunk/src/m/model/process_solve_options.m (revision 9423) @@ -9,5 +9,4 @@ %solution_type: check on this option, error out otherwise solution_type=getfieldvalue(options,'solution_type'); -if ischar(solution_type), error(['only Enums are supported as ''solution_type''. For example: md=solve(md,''solution_type'',DiagnosticSolutionEnum); ']); end if ~ismember(solution_type,[DiagnosticSolutionEnum,PrognosticSolutionEnum,ThermalSolutionEnum,... SteadystateSolutionEnum,ParametersSolutionEnum,TransientSolutionEnum,EnthalpySolutionEnum,... @@ -19,4 +18,5 @@ outoptions.upload=getfieldvalue(options,'upload','off'); outoptions.batch=getfieldvalue(options,'batch','no'); +outoptions.loadonly=getfieldvalue(options,'loadonly','no'); outoptions.directory=getfieldvalue(options,'directory',''); Index: /issm/trunk/src/m/model/solveparallel.m =================================================================== --- /issm/trunk/src/m/model/solveparallel.m (revision 9422) +++ /issm/trunk/src/m/model/solveparallel.m (revision 9423) @@ -8,5 +8,7 @@ cluster=md.cluster; -if ~md.loadresults, +if options.loadonly, + md=loadresultsfromcluster(md); +else %First, build a runtime name that is unique, that we will use to create @@ -45,6 +47,4 @@ error('solveparallel done uploading test decks'); end -else - %just load results - md=loadresultsfromcluster(md); + end Index: /issm/trunk/src/m/utils/BC/SetIceSheetBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceSheetBC.m (revision 9422) +++ /issm/trunk/src/m/utils/BC/SetIceSheetBC.m (revision 9423) @@ -36,15 +36,12 @@ if isnan(md.surface_accumulation_rate), md.surface_accumulation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_accumulation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_accumulation_rate specified: values set as zero'); end if isnan(md.surface_ablation_rate), md.surface_ablation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_ablation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_ablation_rate specified: values set as zero'); end if isnan(md.surface_mass_balance), md.surface_mass_balance=zeros(md.numberofnodes,1); - md.forcings.surface_mass_balance=zeros(md.numberofnodes+1,1); disp(' no surface_mass_balance specified: values set as zero'); end @@ -60,7 +57,7 @@ md.spcthickness=NaN*ones(md.numberofnodes,1); -if (length(md.observed_temperature)==md.numberofnodes), +if (length(md.temperature)==md.numberofnodes), md.spctemperature=NaN*ones(md.numberofnodes,1); - pos=find(md.nodeonsurface); md.spctemperature(pos)=md.observed_temperature(pos); %impose observed temperature on surface + pos=find(md.nodeonsurface); md.spctemperature(pos)=md.temperature(pos); %impose observed temperature on surface if (length(md.geothermalflux)~=md.numberofnodes), md.geothermalflux=50*10^-3*ones(md.numberofnodes,1); %50 mW/m^2 Index: /issm/trunk/src/m/utils/BC/SetIceShelfBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9422) +++ /issm/trunk/src/m/utils/BC/SetIceShelfBC.m (revision 9423) @@ -68,15 +68,12 @@ if isnan(md.surface_accumulation_rate), md.surface_accumulation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_accumulation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_accumulation_rate specified: values set as zero'); end if isnan(md.surface_ablation_rate), md.surface_ablation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_ablation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_ablation_rate specified: values set as zero'); end if isnan(md.surface_mass_balance), md.surface_mass_balance=zeros(md.numberofnodes,1); - md.forcings.surface_mass_balance=zeros(md.numberofnodes+1,1); disp(' no surface_mass_balance specified: values set as zero'); end @@ -92,7 +89,7 @@ md.spcthickness=NaN*ones(md.numberofnodes,1); -if (length(md.observed_temperature)==md.numberofnodes), +if (length(md.temperature)==md.numberofnodes), md.spctemperature=NaN*ones(md.numberofnodes,1); - pos=find(md.nodeonsurface); md.spctemperature(pos)=md.observed_temperature(pos); %impose observed temperature on surface + pos=find(md.nodeonsurface); md.spctemperature(pos)=md.temperature(pos); %impose observed temperature on surface if (length(md.geothermalflux)~=md.numberofnodes), md.geothermalflux=zeros(md.numberofnodes,1); Index: /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m =================================================================== --- /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 9422) +++ /issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m (revision 9423) @@ -79,15 +79,12 @@ if isnan(md.surface_accumulation_rate), md.surface_accumulation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_accumulation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_accumulation_rate specified: values set as zero'); end if isnan(md.surface_ablation_rate), md.surface_ablation_rate=zeros(md.numberofnodes,1); - md.forcings.surface_ablation_rate=zeros(md.numberofnodes+1,1); disp(' no surface_ablation_rate specified: values set as zero'); end if isnan(md.surface_mass_balance), md.surface_mass_balance=zeros(md.numberofnodes,1); - md.forcings.surface_mass_balance=zeros(md.numberofnodes+1,1); disp(' no surface_mass_balance specified: values set as zero'); end @@ -103,7 +100,7 @@ md.spcthickness=NaN*ones(md.numberofnodes,1); -if (length(md.observed_temperature)==md.numberofnodes), +if (length(md.temperature)==md.numberofnodes), md.spctemperature=NaN*ones(md.numberofnodes,1); - pos=find(md.nodeonsurface); md.spctemperature(pos)=md.observed_temperature(pos); %impose observed temperature on surface + pos=find(md.nodeonsurface); md.spctemperature(pos)=md.temperature(pos); %impose observed temperature on surface if (length(md.geothermalflux)~=md.numberofnodes), md.geothermalflux=zeros(md.numberofnodes,1); Index: /issm/trunk/src/m/utils/Interp/PatchToVec.m =================================================================== --- /issm/trunk/src/m/utils/Interp/PatchToVec.m (revision 9422) +++ /issm/trunk/src/m/utils/Interp/PatchToVec.m (revision 9423) @@ -4,4 +4,9 @@ % Usage: % vec=PatchToVec(Patch) + +connectivity=sparse(Patch.index(:),1,1); +value =sparse(Patch.index(:),1,Patch.value(:)); +vec=full(value./connectivity); +return; %if the patch is P0: we have element values, return an element vector Index: /issm/trunk/src/m/utils/Mesh/argusmesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9422) +++ /issm/trunk/src/m/utils/Mesh/argusmesh.m (revision 9423) @@ -89,6 +89,4 @@ md.counter=1; md.dim=2; -md.riftoutline=''; -md.domainoutline=['' infile '']; md=addnote(md,notes); Index: /issm/trunk/src/m/utils/Mesh/squaremesh.m =================================================================== --- /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9422) +++ /issm/trunk/src/m/utils/Mesh/squaremesh.m (revision 9423) @@ -79,4 +79,2 @@ md.dim=2; md.counter=1; -md.riftoutline=''; -md.domainoutline='Square';