Index: /issm/trunk-jpl/src/m/classes/autodiff.m =================================================================== --- /issm/trunk-jpl/src/m/classes/autodiff.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/autodiff.m (revision 10969) @@ -6,7 +6,7 @@ classdef autodiff properties (SetAccess=public) - isautodiff = modelfield('default',false,'marshall',true,'format','Boolean'); - forward = modelfield('default',true,'marshall',true,'format','Boolean'); - reverse = modelfield('default',false,'marshall',true,'format','Boolean'); + isautodiff = false; + forward = true; + reverse = false; end methods @@ -28,10 +28,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -46,4 +40,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','isautodiff','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','forward','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','reverse','format','Boolean'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/balancethickness.m =================================================================== --- /issm/trunk-jpl/src/m/classes/balancethickness.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/balancethickness.m (revision 10969) @@ -6,7 +6,7 @@ classdef balancethickness properties (SetAccess=public) - spcthickness = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - thickening_rate = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - stabilization = modelfield('default',0,'marshall',true,'format','Integer'); + spcthickness = NaN; + thickening_rate = NaN; + stabilization = 0; end methods @@ -27,11 +27,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %Type of stabilization used @@ -55,4 +48,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','spcthickness','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','thickening_rate','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/basalforcings.m =================================================================== --- /issm/trunk-jpl/src/m/classes/basalforcings.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/basalforcings.m (revision 10969) @@ -6,7 +6,7 @@ classdef basalforcings properties (SetAccess=public) - melting_rate = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - melting_rate_correction = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - geothermalflux = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); + melting_rate = NaN; + melting_rate_correction = NaN; + geothermalflux = NaN; end methods @@ -28,10 +28,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -56,4 +50,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','melting_rate','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','melting_rate_correction','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','geothermalflux','format','DoubleMat','mattype',1); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/constants.m =================================================================== --- /issm/trunk-jpl/src/m/classes/constants.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/constants.m (revision 10969) @@ -6,7 +6,7 @@ classdef constants properties (SetAccess=public) - g = modelfield('default',0,'marshall',true,'format','Double'); - yts = modelfield('default',0,'marshall',true,'format','Double'); - referencetemperature = modelfield('default',0,'marshall',true,'format','Double'); + g = 0; + yts = 0; + referencetemperature = 0; end methods @@ -27,11 +27,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %acceleration due to gravity (m/s^2) @@ -60,4 +53,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','g','format','Double'); + WriteData(fid,'object',obj,'fieldname','yts','format','Double'); + WriteData(fid,'object',obj,'fieldname','referencetemperature','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/diagnostic.m =================================================================== --- /issm/trunk-jpl/src/m/classes/diagnostic.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/diagnostic.m (revision 10969) @@ -6,21 +6,21 @@ classdef diagnostic properties (SetAccess=public) - spcvx = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - spcvy = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - spcvz = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - restol = modelfield('default',0,'marshall',true,'format','Double'); - reltol = modelfield('default',0,'marshall',true,'format','Double'); - abstol = modelfield('default',0,'marshall',true,'format','Double'); - stokesreconditioning = modelfield('default',0,'marshall',true,'format','Double'); - viscosity_overshoot = modelfield('default',0,'marshall',true,'format','Double'); - icefront = modelfield('default',NaN,'marshall',true,'preprocess','marshallicefront','format','DoubleMat','mattype',3); - maxiter = modelfield('default',0,'marshall',true,'format','Integer'); - shelf_dampening = modelfield('default',0,'marshall',true,'format','Integer'); - vertex_pairing = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); - penalty_factor = modelfield('default',0,'marshall',true,'format','Double'); - rift_penalty_lock = modelfield('default',0,'marshall',true,'format','Integer'); - rift_penalty_threshold = modelfield('default',0,'marshall',true,'format','Integer'); - referential = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - requested_outputs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); + spcvx = NaN; + spcvy = NaN; + spcvz = NaN; + restol = 0; + reltol = 0; + abstol = 0; + stokesreconditioning = 0; + viscosity_overshoot = 0; + icefront = NaN; + maxiter = 0; + shelf_dampening = 0; + vertex_pairing = NaN; + penalty_factor = NaN; + rift_penalty_lock = NaN; + rift_penalty_threshold = 0; + referential = NaN; + requested_outputs = NaN; end methods @@ -41,11 +41,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %maximum of non-linear iterations. @@ -157,4 +150,29 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','spcvx','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','spcvy','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','spcvz','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','restol','format','Double'); + WriteData(fid,'object',obj,'fieldname','reltol','format','Double'); + WriteData(fid,'object',obj,'fieldname','abstol','format','Double'); + WriteData(fid,'object',obj,'fieldname','stokesreconditioning','format','Double'); + WriteData(fid,'object',obj,'fieldname','viscosity_overshoot','format','Double'); + WriteData(fid,'object',obj,'fieldname','maxiter','format','Integer'); + WriteData(fid,'object',obj,'fieldname','shelf_dampening','format','Integer'); + WriteData(fid,'object',obj,'fieldname','vertex_pairing','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','penalty_factor','format','Double'); + WriteData(fid,'object',obj,'fieldname','rift_penalty_lock','format','Integer'); + WriteData(fid,'object',obj,'fieldname','rift_penalty_threshold','format','Integer'); + WriteData(fid,'object',obj,'fieldname','referential','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3); + + %marshall ice front + data=obj.icefront; + pos=find(data(:,end)==0); data(pos,end)=AirEnum; + pos=find(data(:,end)==1); data(pos,end)=WaterEnum; + pos=find(data(:,end)==2); data(pos,end)=IceEnum; + WriteData(fid,'data',data,'enum',DiagnosticIcefrontEnum,'format','DoubleMat','mattype',3); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/flowequation.m =================================================================== --- /issm/trunk-jpl/src/m/classes/flowequation.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/flowequation.m (revision 10969) @@ -6,12 +6,12 @@ classdef flowequation properties (SetAccess=public) - ismacayealpattyn = modelfield('default',0,'marshall',true,'format','Boolean'); - ishutter = modelfield('default',0,'marshall',true,'format','Boolean'); - isstokes = modelfield('default',0,'marshall',true,'format','Boolean'); - vertex_equation = modelfield('default',NaN,'marshall',true,'preprocess','marshallapproximations','format','DoubleMat','mattype',1); - element_equation = modelfield('default',NaN,'marshall',true,'preprocess','marshallapproximations','format','DoubleMat','mattype',2); - bordermacayeal = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - borderpattyn = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - borderstokes = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); + ismacayealpattyn = 0; + ishutter = 0; + isstokes = 0; + vertex_equation = NaN; + element_equation = NaN; + bordermacayeal = NaN; + borderpattyn = NaN; + borderstokes = NaN; end methods @@ -32,11 +32,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} @@ -82,4 +75,33 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','ismacayealpattyn','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','ishutter','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','isstokes','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','bordermacayeal','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','borderpattyn','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','borderstokes','format','DoubleMat','mattype',1); + %convert approximations to enums + data=obj.vertex_equation; + pos=find(data==0); data(pos,end)=NoneApproximationEnum; + pos=find(data==1); data(pos,end)=HutterApproximationEnum; + pos=find(data==2); data(pos,end)=MacAyealApproximationEnum; + pos=find(data==3); data(pos,end)=PattynApproximationEnum; + pos=find(data==4); data(pos,end)=StokesApproximationEnum; + pos=find(data==5); data(pos,end)=MacAyealPattynApproximationEnum; + pos=find(data==6); data(pos,end)=MacAyealStokesApproximationEnum; + pos=find(data==7); data(pos,end)=PattynStokesApproximationEnum; + WriteData(fid,'data',data,'enum',FlowequationVertexEquationEnum,'format','DoubleMat','mattype',1); + data=obj.element_equation; + pos=find(data==0); data(pos,end)=NoneApproximationEnum; + pos=find(data==1); data(pos,end)=HutterApproximationEnum; + pos=find(data==2); data(pos,end)=MacAyealApproximationEnum; + pos=find(data==3); data(pos,end)=PattynApproximationEnum; + pos=find(data==4); data(pos,end)=StokesApproximationEnum; + pos=find(data==5); data(pos,end)=MacAyealPattynApproximationEnum; + pos=find(data==6); data(pos,end)=MacAyealStokesApproximationEnum; + pos=find(data==7); data(pos,end)=PattynStokesApproximationEnum; + WriteData(fid,'data',data,'enum',FlowequationElementEquationEnum,'format','DoubleMat','mattype',2); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/friction.m =================================================================== --- /issm/trunk-jpl/src/m/classes/friction.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/friction.m (revision 10969) @@ -6,7 +6,7 @@ classdef friction properties (SetAccess=public) - coefficient = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - p = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - q = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); + coefficient = NaN; + p = NaN; + q = NaN; end methods @@ -28,11 +28,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end - end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -51,4 +44,9 @@ fielddisplay(obj,'q','q exponent'); end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','coefficient','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','p','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','q','format','DoubleMat','mattype',2); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/geometry.m =================================================================== --- /issm/trunk-jpl/src/m/classes/geometry.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/geometry.m (revision 10969) @@ -6,9 +6,9 @@ classdef geometry properties (SetAccess=public) - surface = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',SurfaceEnum); - thickness = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',ThicknessEnum); - bed = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',BedEnum); - bathymetry = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',BathymetryEnum); - hydrostatic_ratio = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); + surface = NaN; + thickness = NaN; + bed = NaN; + bathymetry = NaN; + hydrostatic_ratio = NaN; end methods @@ -29,11 +29,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} @@ -57,4 +50,11 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'data',obj.surface,'format','DoubleMat','mattype',1,'enum',SurfaceEnum); + WriteData(fid,'data',obj.thickness,'format','DoubleMat','mattype',1,'enum',ThicknessEnum); + WriteData(fid,'data',obj.bed,'format','DoubleMat','mattype',1,'enum',BedEnum); + WriteData(fid,'data',obj.bathymetry,'format','DoubleMat','mattype',1,'enum',BathymetryEnum); + WriteData(fid,'object',obj,'fieldname','hydrostatic_ratio','format','DoubleMat','mattype',1); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/groundingline.m =================================================================== --- /issm/trunk-jpl/src/m/classes/groundingline.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/groundingline.m (revision 10969) @@ -6,6 +6,6 @@ classdef groundingline properties (SetAccess=public) - migration = modelfield('default','','marshall',true,'preprocess','StringToEnum','format','Integer'); - melting_rate = modelfield('default',NaN,'marshall',true,'format','Double'); + migration = ''; + melting_rate = NaN; end methods @@ -26,11 +26,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %Type of migration @@ -68,4 +61,8 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'data',StringToEnum(obj.migration),'enum',GroundinglineMigrationEnum,'format','Integer'); + WriteData(fid,'object',obj,'fieldname','melting_rate','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/hydrology.m =================================================================== --- /issm/trunk-jpl/src/m/classes/hydrology.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/hydrology.m (revision 10969) @@ -6,11 +6,11 @@ classdef hydrology properties (SetAccess=public) - spcwatercolumn = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - n = modelfield('default',0,'marshall',true,'format','Double'); - CR = modelfield('default',0,'marshall',true,'format','Double'); - p = modelfield('default',0,'marshall',true,'format','Double'); - q = modelfield('default',0,'marshall',true,'format','Double'); - kn = modelfield('default',0,'marshall',true,'format','Double'); - stabilization = modelfield('default',0,'marshall',true,'format','Double'); + spcwatercolumn = NaN; + n = 0; + CR = 0; + p = 0; + q = 0; + kn = 0; + stabilization = 0; end methods @@ -31,11 +31,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %Parameters from Johnson's 2002 thesis, section 3.5.4 @@ -69,4 +62,13 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','spcwatercolumn','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','n','format','Double'); + WriteData(fid,'object',obj,'fieldname','CR','format','Double'); + WriteData(fid,'object',obj,'fieldname','p','format','Double'); + WriteData(fid,'object',obj,'fieldname','q','format','Double'); + WriteData(fid,'object',obj,'fieldname','kn','format','Double'); + WriteData(fid,'object',obj,'fieldname','stabilization','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/initialization.m =================================================================== --- /issm/trunk-jpl/src/m/classes/initialization.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/initialization.m (revision 10969) @@ -6,12 +6,12 @@ classdef initialization properties (SetAccess=public) - vx = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',VxEnum); - vy = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',VyEnum); - vz = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',VzEnum); - vel = modelfield('default',NaN,'marshall',false); - pressure = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',PressureEnum); - temperature = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',TemperatureEnum); - watercolumn = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum); - waterfraction = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum); + vx = NaN; + vy = NaN; + vz = NaN; + vel = NaN; + pressure = NaN; + temperature = NaN; + watercolumn = NaN; + waterfraction = NaN; end methods @@ -32,11 +32,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} @@ -83,4 +76,13 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'data',obj.vx,'format','DoubleMat','mattype',1,'enum',VxEnum); + WriteData(fid,'data',obj.vy,'format','DoubleMat','mattype',1,'enum',VyEnum); + WriteData(fid,'data',obj.vz,'format','DoubleMat','mattype',1,'enum',VzEnum); + WriteData(fid,'data',obj.pressure,'format','DoubleMat','mattype',1,'enum',PressureEnum); + WriteData(fid,'data',obj.temperature,'format','DoubleMat','mattype',1,'enum',TemperatureEnum); + WriteData(fid,'data',obj.watercolumn,'format','DoubleMat','mattype',1,'enum',WatercolumnEnum); + WriteData(fid,'data',obj.waterfraction,'format','DoubleMat','mattype',1,'enum',WaterfractionEnum); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/inversion.m =================================================================== --- /issm/trunk-jpl/src/m/classes/inversion.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/inversion.m (revision 10969) @@ -18,6 +18,4 @@ step_threshold = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); gradient_only = modelfield('default',0,'marshall',true,'format','Boolean'); - num_control_parameters = modelfield('default',0,'marshall',true,'format','Integer'); - num_cost_functions = modelfield('default',0,'marshall',true,'format','Integer'); vx_obs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); vy_obs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); @@ -126,6 +124,4 @@ fielddisplay(obj,'max_parameters','absolute maximum acceptable value of the inversed parameter on each vertex'); fielddisplay(obj,'gradient_only','stop control method solution at gradient'); - %fielddisplay(obj,'num_control_parameters','number of control_parameters'); - %fielddisplay(obj,'num_cost_functions','number of cost_functions'); fielddisplay(obj,'vx_obs','observed velocity x component [m/a]'); fielddisplay(obj,'vy_obs','observed velocity y component [m/a]'); @@ -143,4 +139,46 @@ disp(' 503: ThicknessAbsGradient'); end % }}} + function marshall(obj,fid) % {{{ + + WriteData(fid,'object',obj,'fieldname','iscontrol','format','Boolean'); + if ~obj.iscontrol, return; end + WriteData(fid,'object',obj,'fieldname','nsteps','format','Integer'); + WriteData(fid,'object',obj,'fieldname','maxiter_per_step','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','cost_functions_coefficients','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','gradient_scaling','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','cost_function_threshold','format','Double'); + WriteData(fid,'object',obj,'fieldname','min_parameters','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','max_parameters','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','step_threshold','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','gradient_only','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','vx_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','vy_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','vz_obs','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','thickness_obs','format','DoubleMat','mattype',1); + + %process control parameters + num_control_parameters=numel(obj.control_parameters); + data=zeros(1,num_control_parameters); + for i=1:num_control_parameters, + data(i)=StringToEnum(obj.control_parameters{i}); + end + WriteData(fid,'data',data,'enum',InversionControlParametersEnum,'format','DoubleMat','mattype',3); + WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum,'format','Integer'); + + %process cost functions + num_cost_functions=size(obj.cost_functions,2); + data=obj.cost_functions; + pos=find(data==101); data(pos)=SurfaceAbsVelMisfitEnum; + pos=find(data==102); data(pos)=SurfaceRelVelMisfitEnum; + pos=find(data==103); data(pos)=SurfaceLogVelMisfitEnum; + pos=find(data==104); data(pos)=SurfaceLogVxVyMisfitEnum; + pos=find(data==105); data(pos)=SurfaceAverageVelMisfitEnum; + pos=find(data==201); data(pos)=ThicknessAbsMisfitEnum; + pos=find(data==501); data(pos)=DragCoefficientAbsGradientEnum; + pos=find(data==502); data(pos)=RheologyBbarAbsGradientEnum; + pos=find(data==503); data(pos)=ThicknessAbsGradientEnum; + WriteData(fid,'data',data,'enum',InversionCostFunctionsEnum,'format','DoubleMat','mattype',3); + WriteData(fid,'data',num_cost_functions,'enum',InversionNumCostFunctionsEnum,'format','Integer'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/mask.m =================================================================== --- /issm/trunk-jpl/src/m/classes/mask.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/mask.m (revision 10969) @@ -6,10 +6,10 @@ classdef mask properties (SetAccess=public) - elementonfloatingice = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2); - elementongroundedice = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2); - elementonwater = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2); - vertexonfloatingice = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - vertexongroundedice = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - vertexonwater = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); + elementonfloatingice = NaN; + elementongroundedice = NaN; + elementonwater = NaN; + vertexonfloatingice = NaN; + vertexongroundedice = NaN; + vertexonwater = NaN; end methods @@ -31,11 +31,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end - end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -49,5 +42,4 @@ end % }}} function disp(obj) % {{{ - fielddisplay(obj,'elementonfloatingice','element on floating ice flags list'); fielddisplay(obj,'vertexonfloatingice','vertex on floating ice flags list'); @@ -57,4 +49,12 @@ fielddisplay(obj,'vertexonwater','vertex on water flags list'); end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','elementonfloatingice','format','BooleanMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','elementongroundedice','format','BooleanMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','elementonwater','format','BooleanMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','vertexonfloatingice','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','vertexongroundedice','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','vertexonwater','format','DoubleMat','mattype',1); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/materials.m =================================================================== --- /issm/trunk-jpl/src/m/classes/materials.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/materials.m (revision 10969) @@ -6,17 +6,17 @@ classdef materials properties (SetAccess=public) - rho_ice = modelfield('default',0,'marshall',true,'format','Double'); - rho_water = modelfield('default',0,'marshall',true,'format','Double'); - mu_water = modelfield('default',0,'marshall',true,'format','Double'); - heatcapacity = modelfield('default',0,'marshall',true,'format','Double'); - latentheat = modelfield('default',0,'marshall',true,'format','Double'); - thermalconductivity = modelfield('default',0,'marshall',true,'format','Double'); - meltingpoint = modelfield('default',0,'marshall',true,'format','Double'); - beta = modelfield('default',0,'marshall',true,'format','Double'); - mixed_layer_capacity = modelfield('default',0,'marshall',true,'format','Double'); - thermal_exchange_velocity = modelfield('default',0,'marshall',true,'format','Double'); - rheology_B = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - rheology_n = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - rheology_law = modelfield('default','','marshall',true,'preprocess','StringToEnum','format','Integer'); + rho_ice = 0; + rho_water = 0; + mu_water = 0; + heatcapacity = 0; + latentheat = 0; + thermalconductivity = 0; + meltingpoint = 0; + beta = 0; + mixed_layer_capacity = 0; + thermal_exchange_velocity = 0; + rheology_B = NaN; + rheology_n = NaN; + rheology_law = ''; end methods @@ -37,11 +37,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %ice density (kg/m^3) @@ -104,4 +97,19 @@ fielddisplay(obj,'rheology_law','law for the temperature dependance of the rheology: ''None'', ''Paterson'' or ''Arrhenius'''); end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','rho_ice','format','Double'); + WriteData(fid,'object',obj,'fieldname','rho_water','format','Double'); + WriteData(fid,'object',obj,'fieldname','mu_water','format','Double'); + WriteData(fid,'object',obj,'fieldname','heatcapacity','format','Double'); + WriteData(fid,'object',obj,'fieldname','latentheat','format','Double'); + WriteData(fid,'object',obj,'fieldname','thermalconductivity','format','Double'); + WriteData(fid,'object',obj,'fieldname','meltingpoint','format','Double'); + WriteData(fid,'object',obj,'fieldname','beta','format','Double'); + WriteData(fid,'object',obj,'fieldname','mixed_layer_capacity','format','Double'); + WriteData(fid,'object',obj,'fieldname','thermal_exchange_velocity','format','Double'); + WriteData(fid,'object',obj,'fieldname','rheology_B','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','rheology_n','format','DoubleMat','mattype',2); + WriteData(fid,'data',StringToEnum(obj.rheology_law),'enum',MaterialsRheologyLawEnum,'format','Integer'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/mesh.m =================================================================== --- /issm/trunk-jpl/src/m/classes/mesh.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/mesh.m (revision 10969) @@ -6,43 +6,43 @@ classdef mesh properties (SetAccess=public) - x = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - y = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - z = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - elements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - dimension = modelfield('default',0,'marshall',true,'format','Integer'); - numberoflayers = modelfield('default',0,'marshall',true,'format','Integer'); - numberofelements = modelfield('default',0,'marshall',true,'format','Integer'); - numberofvertices = modelfield('default',0,'marshall',true,'format','Integer'); - numberofedges = modelfield('default',0,'marshall',true,'format','Integer'); + x = NaN; + y = NaN; + z = NaN + elements = NaN + dimension = 0; + numberoflayers = 0; + numberofelements = 0; + numberofvertices = 0; + numberofedges = 0; - lat = modelfield('default',NaN,'marshall',false); - long = modelfield('default',NaN,'marshall',false); - hemisphere = modelfield('default',NaN,'marshall',false); - - elementonbed = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2); - elementonsurface = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2); - vertexonbed = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1); - vertexonsurface = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1); - lowerelements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - lowervertex = modelfield('default',NaN,'marshall',false); - upperelements = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - uppervertex = modelfield('default',NaN,'marshall',false); - vertexonboundary = modelfield('default',NaN,'marshall',false); - - edges = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); - segments = modelfield('default',NaN,'marshall',false); - segmentmarkers = modelfield('default',NaN,'marshall',false); - vertexconnectivity = modelfield('default',NaN,'marshall',false); - elementconnectivity = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); - average_vertex_connectivity = modelfield('default',0,'marshall',true,'format','Integer'); - - x2d = modelfield('default',NaN,'marshall',false); - y2d = modelfield('default',NaN,'marshall',false); - elements2d = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); - numberofvertices2d = modelfield('default',0,'marshall',true,'format','Integer'); - numberofelements2d = modelfield('default',0,'marshall',true,'format','Integer'); - - extractedvertices = modelfield('default',NaN,'marshall',false); - extractedelements = modelfield('default',NaN,'marshall',false); + lat = NaN + long = NaN + hemisphere = NaN + + elementonbed = NaN + elementonsurface = NaN + vertexonbed = NaN + vertexonsurface = NaN + lowerelements = NaN + lowervertex = NaN + upperelements = NaN + uppervertex = NaN + vertexonboundary = NaN + + edges = NaN + segments = NaN + segmentmarkers = NaN + vertexconnectivity = NaN + elementconnectivity = NaN + average_vertex_connectivity = 0; + + x2d = NaN + y2d = NaN + elements2d = NaN + numberofvertices2d = 0; + numberofelements2d = 0; + + extractedvertices = NaN + extractedelements = NaN end methods @@ -63,11 +63,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %the connectivity is the avergaded number of nodes linked to a @@ -183,4 +176,27 @@ fielddisplay(obj,'hemisphere','Indicate hemisphere ''n'' or ''s'' '); end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','x','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','y','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','z','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','elements','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','dimension','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberoflayers','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofelements','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofvertices','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofedges','format','Integer'); + WriteData(fid,'object',obj,'fieldname','elementonbed','format','BooleanMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','elementonsurface','format','BooleanMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','vertexonbed','format','BooleanMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','vertexonsurface','format','BooleanMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','lowerelements','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','upperelements','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','edges','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','elementconnectivity','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','average_vertex_connectivity','format','Integer'); + WriteData(fid,'object',obj,'fieldname','elements2d','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','numberofvertices2d','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofelements2d','format','Integer'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/miscellaneous.m =================================================================== --- /issm/trunk-jpl/src/m/classes/miscellaneous.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/miscellaneous.m (revision 10969) @@ -6,7 +6,7 @@ classdef miscellaneous properties (SetAccess=public) - notes = modelfield('default','','marshall',false); - name = modelfield('default','','marshall',true,'format','String'); - dummy = modelfield('default',NaN,'marshall',false); + notes = ''; + name = ''; + dummy = struct(); end methods @@ -33,10 +33,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} function disp(obj) % {{{ @@ -48,4 +42,7 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','name','format','String'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/model/model.m =================================================================== --- /issm/trunk-jpl/src/m/classes/model/model.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/model/model.m (revision 10969) @@ -8,42 +8,42 @@ % {{{1 %Careful here: no other class should be used as default value this is a bug of matlab - mesh = modelfield('default',0,'marshall',true); - mask = modelfield('default',0,'marshall',true); - - geometry = modelfield('default',0,'marshall',true); - constants = modelfield('default',0,'marshall',true); - surfaceforcings = modelfield('default',0,'marshall',true); - basalforcings = modelfield('default',0,'marshall',true); - materials = modelfield('default',0,'marshall',true); - friction = modelfield('default',0,'marshall',true); - flowequation = modelfield('default',0,'marshall',true); - timestepping = modelfield('default',0,'marshall',true); - initialization = modelfield('default',0,'marshall',true); - rifts = modelfield('default',0,'marshall',true); - - debug = modelfield('default',0,'marshall',false); - verbose = modelfield('default',0,'marshall',true,'preprocess','marshallverbose','format','Integer'); - settings = modelfield('default',0,'marshall',true); - solver = modelfield('default',0,'marshall',false); - cluster = modelfield('default',0,'marshall',false); - - balancethickness = modelfield('default',0,'marshall',true); - diagnostic = modelfield('default',0,'marshall',true); - groundingline = modelfield('default',0,'marshall',true); - hydrology = modelfield('default',0,'marshall',true); - prognostic = modelfield('default',0,'marshall',true); - thermal = modelfield('default',0,'marshall',true); - steadystate = modelfield('default',0,'marshall',true); - transient = modelfield('default',0,'marshall',true); - - autodiff = modelfield('default',0,'marshall',true); - flaim = modelfield('default',0,'marshall',false); - inversion = modelfield('default',0,'marshall',true); - qmu = modelfield('default',0,'marshall',true); - - results = modelfield('default',0,'marshall',false); - radaroverlay = modelfield('default',0,'marshall',false); - miscellaneous = modelfield('default',0,'marshall',true); - private = modelfield('default',0,'marshall',false); + mesh = 0; + mask = 0; + + geometry = 0; + constants = 0; + surfaceforcings = 0; + basalforcings = 0; + materials = 0; + friction = 0; + flowequation = 0; + timestepping = 0; + initialization = 0; + rifts = 0; + + debug = 0; + verbose = 0; + settings = 0; + solver = 0; + cluster = 0; + + balancethickness = 0; + diagnostic = 0; + groundingline = 0; + hydrology = 0; + prognostic = 0; + thermal = 0; + steadystate = 0; + transient = 0; + + autodiff = 0; + flaim = 0; + inversion = 0; + qmu = 0; + + results = 0; + radaroverlay = 0; + miscellaneous = 0; + private = 0; %}}} @@ -388,46 +388,39 @@ function md = setdefaultparameters(md) % {{{1 - %first, use the defaults provided by the properties definition above. - fieldnames=fields(md); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - md.(fieldname)=md.(fieldname).default; - end - %initialize subclasses - md.cluster = none; - md.solver = solver; + md.mesh = mesh(); + md.mask = mask(); + md.constants = constants(); + md.geometry = geometry(); + md.initialization = initialization(); + md.surfaceforcings = surfaceforcings(); + md.basalforcings = basalforcings(); + md.friction = friction(); + md.rifts = rifts(); + md.timestepping = timestepping(); + md.groundingline = groundingline(); + md.materials = materials(); + md.flowequation = flowequation(); + md.debug = debug(); + md.verbose = verbose('solution',true,'qmu',true,'control',true); + md.settings = settings(); + md.solver = solver(); md.solver = addoptions(md.solver,DiagnosticVertAnalysisEnum,mumpsoptions); + md.cluster = none(); + md.balancethickness = balancethickness(); + md.diagnostic = diagnostic(); + md.hydrology = hydrology(); + md.prognostic = prognostic(); + md.thermal = thermal(); + md.steadystate = steadystate(); + md.transient = transient(); + md.autodiff = autodiff(); + md.flaim = flaim(); + md.inversion = inversion(); + md.qmu = qmu(); + md.radaroverlay = radaroverlay(); md.results = struct(); - md.debug = debug; - md.constants = constants; - md.flaim = flaim; - md.surfaceforcings = surfaceforcings; - md.basalforcings = basalforcings; - md.friction = friction; - md.private = private; - md.rifts = rifts; - md.hydrology = hydrology; - md.settings = settings; - md.radaroverlay = radaroverlay; - md.thermal = thermal; - md.miscellaneous = miscellaneous; - md.timestepping = timestepping; - md.groundingline = groundingline; - md.prognostic = prognostic; - md.materials = materials; - md.mask = mask; - md.qmu = qmu; - md.balancethickness = balancethickness; - md.flowequation = flowequation; - md.steadystate = steadystate; - md.inversion = inversion; - md.transient = transient; - md.diagnostic = diagnostic; - md.initialization = initialization; - md.geometry = geometry; - md.verbose = verbose('solution',true,'qmu',true,'control',true); - md.autodiff = autodiff; - md.mesh = mesh; + md.miscellaneous = miscellaneous(); + md.private = private(); end %}}} Index: /issm/trunk-jpl/src/m/classes/private.m =================================================================== --- /issm/trunk-jpl/src/m/classes/private.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/private.m (revision 10969) @@ -6,7 +6,7 @@ classdef private properties (SetAccess=public) - runtimename = modelfield('default','','marshall',false); - bamg = modelfield('default',0,'marshall',false); - solution = modelfield('default','','marshall',false); + runtimename = ''; + bamg = struct(); + solution = ''; end methods @@ -28,11 +28,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end - end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ Index: /issm/trunk-jpl/src/m/classes/prognostic.m =================================================================== --- /issm/trunk-jpl/src/m/classes/prognostic.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/prognostic.m (revision 10969) @@ -6,9 +6,9 @@ classdef prognostic properties (SetAccess=public) - spcthickness = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - hydrostatic_adjustment = modelfield('default',0,'marshall',true,'preprocess','StringToEnum','format','Integer'); - stabilization = modelfield('default',0,'marshall',true,'format','Integer'); - vertex_pairing = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); - penalty_factor = modelfield('default',0,'marshall',true,'format','Double'); + spcthickness = NaN; + hydrostatic_adjustment = 0; + stabilization = 0; + vertex_pairing = NaN; + penalty_factor = 0; end methods @@ -29,11 +29,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %Type of stabilization to use 0:nothing 1:artificial_diffusivity 3:Discontinuous Galerkin @@ -67,4 +60,11 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','spcthickness','format','DoubleMat','mattype',1); + WriteData(fid,'data',StringToEnum(obj.hydrostatic_adjustment),'format','Integer','enum',PrognosticHydrostaticAdjustmentEnum); + WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer'); + WriteData(fid,'object',obj,'fieldname','vertex_pairing','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','penalty_factor','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/qmu.m =================================================================== --- /issm/trunk-jpl/src/m/classes/qmu.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/qmu.m (revision 10969) @@ -6,20 +6,20 @@ classdef qmu properties (SetAccess=public) - isdakota = modelfield('default',0,'marshall',true,'format','Boolean'); - variables = modelfield('default',struct(),'marshall',false); - responses = modelfield('default',struct(),'marshall',false); - method = modelfield('default',struct(),'marshall',false); - params = modelfield('default',struct(),'marshall',false); - results = modelfield('default',struct(),'marshall',false); - partition = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2); - numberofpartitions = modelfield('default',0,'marshall',true,'format','Integer'); - numberofresponses = modelfield('default',0,'marshall',true,'format','Integer'); - variabledescriptors = modelfield('default',{},'marshall',true,'format','StringArray'); - responsedescriptors = modelfield('default',{},'marshall',true,'format','StringArray'); - mass_flux_profile_directory = modelfield('default',NaN,'marshall',false); - mass_flux_profiles = modelfield('default',NaN,'marshall',false); - mass_flux_segments = modelfield('default',{},'marshall',true,'format','MatArray'); - adjacency = modelfield('default',NaN,'marshall',false); - vertex_weight = modelfield('default',NaN,'marshall',false); + isdakota = 0; + variables = struct(); + responses = struct(); + method = struct(); + params = struct(); + results = struct(); + partition = NaN; + numberofpartitions = 0; + numberofresponses = 0; + variabledescriptors = {}; + responsedescriptors = {}; + mass_flux_profile_directory = NaN; + mass_flux_profiles = NaN; + mass_flux_segments = {}; + adjacency = NaN; + vertex_weight = NaN; end methods @@ -40,11 +40,5 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end + end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -165,4 +159,14 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','isdakota','format','Boolean'); + if ~obj.isdakota, return; end + WriteData(fid,'object',obj,'fieldname','partition','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','numberofpartitions','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofresponses','format','Integer'); + WriteData(fid,'object',obj,'fieldname','variabledescriptors','format','StringArray'); + WriteData(fid,'object',obj,'fieldname','responsedescriptors','format','StringArray'); + WriteData(fid,'object',obj,'fieldname','mass_flux_segments','format','MatArray'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/rifts.m =================================================================== --- /issm/trunk-jpl/src/m/classes/rifts.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/rifts.m (revision 10969) @@ -6,7 +6,6 @@ classdef rifts properties (SetAccess=public) - riftstruct = modelfield('default',NaN,'marshall',true,'preprocess','marshallrifts','format','DoubleMat','mattype',3); - riftproperties = modelfield('default',NaN,'marshall',false); - numrifts = modelfield('default',0,'marshall',true,'format','Integer'); + riftstruct = NaN; + riftproperties = NaN; end methods @@ -28,13 +27,12 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ - if obj.numrifts, + if isempty(obj.riftstruct) | isnans(obj.riftstruct), + numrifts=0; + else + numrifts=numel(obj.riftstruct); + end + if numrifts, if ~(md.mesh.dimension==2), checkmessage(['model not consistent: models with rifts are only supported in 2d for now!']); @@ -50,5 +48,5 @@ else if ~isnans(obj.riftstruct), - checkmessage(['riftstruct shoud be NaN since obj.numrifts is 0!']); + checkmessage(['riftstruct shoud be NaN since numrifts is 0!']); end end @@ -62,4 +60,34 @@ end % }}} + function marshall(obj,fid) % {{{ + + %Process rift info + if isempty(obj.riftstruct) | isnans(obj.riftstruct), + numrifts=0; + else + numrifts=numel(obj.riftstruct); + end + numpairs=0; + for i=1:numrifts, + numpairs=numpairs+size(obj.riftstruct(i).penaltypairs,1); + end + + % 2 for nodes + 2 for elements+ 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. + data=zeros(numpairs,12); + count=1; + for i=1:numrifts, + numpairsforthisrift=size(obj.riftstruct(i).penaltypairs,1); + data(count:count+numpairsforthisrift-1,1:7)=obj.riftstruct(i).penaltypairs; + data(count:count+numpairsforthisrift-1,8)=obj.riftstruct(i).fill; + data(count:count+numpairsforthisrift-1,9)=obj.riftstruct(i).friction; + data(count:count+numpairsforthisrift-1,10)=obj.riftstruct(i).fraction; + data(count:count+numpairsforthisrift-1,11)=obj.riftstruct(i).fractionincrement; + data(count:count+numpairsforthisrift-1,12)=obj.riftstruct(i).state; + count=count+numpairsforthisrift; + end + + WriteData(fid,'data',numrifts,'enum',RiftsNumriftsEnum,'format','Integer'); + WriteData(fid,'data',data,'enum',RiftsRiftstructEnum,'format','DoubleMat','mattype',3); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/settings.m =================================================================== --- /issm/trunk-jpl/src/m/classes/settings.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/settings.m (revision 10969) @@ -6,9 +6,9 @@ classdef settings properties (SetAccess=public) - io_gather = modelfield('default',0,'marshall',true,'format','Boolean'); - lowmem = modelfield('default',0,'marshall',true,'format','Boolean'); - results_on_vertices = modelfield('default',0,'marshall',true,'format','Boolean'); - output_frequency = modelfield('default',0,'marshall',true,'format','Integer'); - waitonlock = modelfield('default',0,'marshall',true,'format','Boolean'); + io_gather = 0; + lowmem = 0; + results_on_vertices = 0; + output_frequency = 0; + waitonlock = 0; end methods @@ -29,11 +29,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %are we short in memory ? (0 faster but requires more memory) @@ -71,4 +64,11 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','io_gather','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','lowmem','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','results_on_vertices','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','output_frequency','format','Integer'); + WriteData(fid,'object',obj,'fieldname','waitonlock','format','Boolean'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/steadystate.m =================================================================== --- /issm/trunk-jpl/src/m/classes/steadystate.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/steadystate.m (revision 10969) @@ -6,7 +6,7 @@ classdef steadystate properties (SetAccess=public) - reltol = modelfield('default',0,'marshall',true,'format','Double'); - maxiter = modelfield('default',0,'marshall',true,'format','Integer'); - requested_outputs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); + reltol = 0; + maxiter = 0; + requested_outputs = NaN; end methods @@ -27,12 +27,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end - %maximum of steady state iterations obj.maxiter=100; @@ -62,4 +54,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','reltol','format','Double'); + WriteData(fid,'object',obj,'fieldname','maxiter','format','Integer'); + WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/surfaceforcings.m =================================================================== --- /issm/trunk-jpl/src/m/classes/surfaceforcings.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/surfaceforcings.m (revision 10969) @@ -6,7 +6,7 @@ classdef surfaceforcings properties (SetAccess=public) - accumulation_rate = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - ablation_rate = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - mass_balance = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); + accumulation_rate = NaN; + ablation_rate = NaN; + mass_balance = NaN; end methods @@ -28,10 +28,4 @@ function obj = setdefaultparameters(obj) % {{{ - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end end % }}} function checkconsistency(obj,md,solution,analyses) % {{{ @@ -52,4 +46,9 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','accumulation_rate','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','ablation_rate','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','mass_balance','format','DoubleMat','mattype',1); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/thermal.m =================================================================== --- /issm/trunk-jpl/src/m/classes/thermal.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/thermal.m (revision 10969) @@ -6,10 +6,10 @@ classdef thermal properties (SetAccess=public) - spctemperature = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - penalty_threshold = modelfield('default',0,'marshall',true,'format','Integer'); - stabilization = modelfield('default',0,'marshall',true,'format','Integer'); - maxiter = modelfield('default',0,'marshall',true,'format','Integer'); - penalty_lock = modelfield('default',0,'marshall',true,'format','Integer'); - penalty_factor = modelfield('default',0,'marshall',true,'format','Double'); + spctemperature = NaN; + penalty_threshold = 0; + stabilization = 0; + maxiter = 0; + penalty_lock = 0; + penalty_factor = 0; end methods @@ -30,11 +30,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %Number of unstable constraints acceptable @@ -68,4 +61,12 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','spctemperature','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','penalty_threshold','format','Integer'); + WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer'); + WriteData(fid,'object',obj,'fieldname','maxiter','format','Integer'); + WriteData(fid,'object',obj,'fieldname','penalty_lock','format','Integer'); + WriteData(fid,'object',obj,'fieldname','penalty_factor','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/timestepping.m =================================================================== --- /issm/trunk-jpl/src/m/classes/timestepping.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/timestepping.m (revision 10969) @@ -6,8 +6,8 @@ classdef timestepping properties (SetAccess=public) - time_step = modelfield('default',0,'marshall',true,'format','Double'); - final_time = modelfield('default',0,'marshall',true,'format','Double'); - time_adapt = modelfield('default',0,'marshall',true,'format','Boolean'); - cfl_coefficient = modelfield('default',0,'marshall',true,'format','Double'); + time_step = 0; + final_time = 0; + time_adapt = 0; + cfl_coefficient = 0; end methods @@ -28,11 +28,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %time between 2 time steps @@ -60,4 +53,10 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','time_step','format','Double'); + WriteData(fid,'object',obj,'fieldname','final_time','format','Double'); + WriteData(fid,'object',obj,'fieldname','time_adapt','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','cfl_coefficient','format','Double'); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/transient.m =================================================================== --- /issm/trunk-jpl/src/m/classes/transient.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/transient.m (revision 10969) @@ -6,9 +6,9 @@ classdef transient properties (SetAccess=public) - isprognostic = modelfield('default',0,'marshall',true,'format','Boolean'); - isdiagnostic = modelfield('default',0,'marshall',true,'format','Boolean'); - isthermal = modelfield('default',0,'marshall',true,'format','Boolean'); - isgroundingline = modelfield('default',0,'marshall',true,'format','Boolean'); - requested_outputs = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3); + isprognostic = 0; + isdiagnostic = 0; + isthermal = 0; + isgroundingline = 0; + requested_outputs = NaN; end methods @@ -29,11 +29,4 @@ end % }}} function obj = setdefaultparameters(obj) % {{{ - - %first, use the defaults provided by the properties definition above. - fieldnames=fields(obj); - for i=1:length(fieldnames), - fieldname=fieldnames{i}; - obj.(fieldname)=obj.(fieldname).default; - end %full analysis: Diagnostic, Prognostic and Thermal but no groundingline migration for now @@ -65,4 +58,11 @@ end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','isprognostic','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','isdiagnostic','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','isthermal','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','isgroundingline','format','Boolean'); + WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3); + end % }}} end end Index: /issm/trunk-jpl/src/m/classes/verbose.m =================================================================== --- /issm/trunk-jpl/src/m/classes/verbose.m (revision 10968) +++ /issm/trunk-jpl/src/m/classes/verbose.m (revision 10969) @@ -23,11 +23,11 @@ % {{{1 %BEGINFIELDS - mprocessor=false; - module=false; - solution=false; - solver=false; - convergence=false; - control=false; - qmu=false; + mprocessor = false; + module = false; + solution = false; + solver = false; + convergence = false; + control = false; + qmu = false; %ENDFIELDS % }}} @@ -117,4 +117,7 @@ end %}}} + function marshall(obj,fid) % {{{ + WriteData(fid,'data',VerboseToBinary(obj),'enum',VerboseEnum,'format','Integer'); + end % }}} end end Index: /issm/trunk-jpl/src/m/model/WriteData.m =================================================================== --- /issm/trunk-jpl/src/m/model/WriteData.m (revision 10969) +++ /issm/trunk-jpl/src/m/model/WriteData.m (revision 10969) @@ -0,0 +1,260 @@ +function WriteData(fid,varargin) +%WRITEDATA - write model field in binary file +% +% Usage: +% WriteData(fid,varargin); + +%process options +options=pairoptions(varargin{:}); + +%Get data properties +if exist(options,'object'); + %This is a object field, construct enum and data + obj = getfieldvalue(options,'object'); + fieldname = getfieldvalue(options,'fieldname'); + classname = class(obj); + + enum = BuildEnum([classname '_' fieldname]); + data = obj.(fieldname); +else + %No processing required + data = getfieldvalue(options,'data'); + enum = getfieldvalue(options,'enum'); +end +format = getfieldvalue(options,'format'); +mattype = getfieldvalue(options,'mattype',0); %only required for matrices + +%Process sparse matrices +if issparse(data), + data=full(data); +end + +%Step 1: write the enum to identify this record uniquely +fwrite(fid,enum,'int'); + +%Step 2: write the data itself. +if strcmpi(format,'Boolean'),% {{{ + if(numel(data)~=1), error(['field ' field ' cannot be marshalled as it has more than one element!']); end + + %first write length of record + fwrite(fid,4+4,'int'); %1 bool (disguised as an int)+code + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %now write integer + fwrite(fid,data,'int'); %send an int, not easy to send a bool + % }}} +elseif strcmpi(format,'Integer'), % {{{ + if(numel(data)~=1), error(['field ' EnumToString(enum) ' cannot be marshalled as it has more than one element!']); end + + %first write length of record + fwrite(fid,4+4,'int'); %1 integer + code + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %now write integer + fwrite(fid,data,'int'); + % }}} +elseif strcmpi(format,'Double'), % {{{ + if(numel(data)~=1), error(['field ' field ' cannot be marshalled as it has more than one element!']); end + + %first write length of record + fwrite(fid,8+4,'int'); %1 double+code + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %now write double + fwrite(fid,data,'double'); + % }}} +elseif strcmpi(format,'String'), % {{{ + %first write length of record + fwrite(fid,length(data)+4+4,'int'); %string + string size + code + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %now write string + fwrite(fid,length(data),'int'); + fwrite(fid,data,'char'); + % }}} +elseif strcmpi(format,'BooleanMat'), % {{{ + + %Get size + s=size(data); + %if matrix = NaN, then do not write anything + if (s(1)==1 & s(2)==1 & isnan(data)), + s(1)=0; s(2)=0; + end + + %first write length of record + fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type + + %write data code and matrix type: + fwrite(fid,FormatToCode(format),'int'); + fwrite(fid,mattype,'int'); + + %now write matrix + fwrite(fid,s(1),'int'); + fwrite(fid,s(2),'int'); + if s(1)*s(2), + fwrite(fid,data','double'); %get to the "c" convention, hence the transpose + end + % }}} +elseif strcmpi(format,'IntMat'), % {{{ + + %Get size + s=size(data); + %if matrix = NaN, then do not write anything + if (s(1)==1 & s(2)==1 & isnan(data)), + s(1)=0; s(2)=0; + end + + %first write length of record + fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type + + %write data code and matrix type: + fwrite(fid,FormatToCode(format),'int'); + fwrite(fid,mattype,'int'); + + %now write matrix + fwrite(fid,s(1),'int'); + fwrite(fid,s(2),'int'); + if s(1)*s(2), + fwrite(fid,data','double'); %get to the "c" convention, hence the transpose + end + % }}} +elseif strcmpi(format,'DoubleMat'), % {{{ + + %Get size + s=size(data); + %if matrix = NaN, then do not write anything + if (s(1)==1 & s(2)==1 & isnan(data)), + s(1)=0; s(2)=0; + end + + %first write length of record + fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type + + %write data code and matrix type: + fwrite(fid,FormatToCode(format),'int'); + fwrite(fid,mattype,'int'); + + %now write matrix + fwrite(fid,s(1),'int'); + fwrite(fid,s(2),'int'); + if s(1)*s(2), + fwrite(fid,data','double'); %get to the "c" convention, hence the transpose + end + % }}} +elseif strcmpi(format,'MatArray'), % {{{ + + numrecords=numel(data); + + %first get length of record + recordlength=4+4; %number of records + code + for i=1:numrecords, + matrix=data{i}; + s=size(matrix); + recordlength=recordlength+4*2+... %row and col of matrix + s(1)*s(2)*8; %matrix of doubles + end + + %write length of record + fwrite(fid,recordlength,'int'); + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %write data, first number of records + fwrite(fid,numrecords,'int'); + + %write each matrix: + for i=1:numrecords, + matrix=data{i}; + s=size(matrix); + fwrite(fid,s(1),'int'); + fwrite(fid,s(2),'int'); + fwrite(fid,matrix','double'); + end + % }}} +elseif strcmpi(format,'StringArray'), % {{{ + + %first get length of string array: + num=numel(data); + %now get length of record: + recordlength=4+4; %for length of array + code + for i=1:num, + string=data{i}; + recordlength=recordlength+4+length(string); %for each string + end + + %write length of record + fwrite(fid,recordlength,'int'); + + %write data code: + fwrite(fid,FormatToCode(format),'int'); + + %now write length of string array + fwrite(fid,num,'int'); + + %now write the strings + for i=1:num, + string=data{i}; + fwrite(fid,length(string),'int'); + fwrite(fid,string,'char'); + end + % }}} +else % {{{ + error(['WriteData error message: data type: ' num2str(format) ' not supported yet! (' EnumToString(enum) ')']); +end % }}} +end + +function enum=BuildEnum(string) % {{{ +%BUILDENUM - build enum out of string +% +% Usage: +% enum=BuildEnum(string) + + if findstr(string,'_'), + indices=findstr(string,'_'); + for i=1:length(indices), + string(indices(i)+1)=upper(string(indices(i)+1)); + end + string(indices)=[]; + end + + %take first letter of string and make it uppercase: + string(1)=upper(string(1)); + + %Get Enum + enum=eval([string 'Enum();']); +end % }}} +function code=FormatToCode(format) % {{{1 +%This routine takes the format string, and hardcodes it into an integer, which +%is passed along the record, in order to identify the nature of the dataset being +%sent. + if strcmpi(format,'Boolean'), + code=1; + elseif strcmpi(format,'Integer'), + code=2; + elseif strcmpi(format,'Double'), + code=3; + elseif strcmpi(format,'String'), + code=4; + elseif strcmpi(format,'BooleanMat'), + code=5; + elseif strcmpi(format,'IntMat'), + code=6; + elseif strcmpi(format,'DoubleMat'), + code=7; + elseif strcmpi(format,'MatArray'), + code=8; + elseif strcmpi(format,'StringArray'), + code=9; + else + error('FormatToCode error message: data type not supported yet!'); + end +end% }}} Index: /issm/trunk-jpl/src/m/model/marshall.m =================================================================== --- /issm/trunk-jpl/src/m/model/marshall.m (revision 10968) +++ /issm/trunk-jpl/src/m/model/marshall.m (revision 10969) @@ -1,6 +1,6 @@ function marshall(md) -%MARSHALL - output JPL-package compatible binary file from @model md, for certain solution type. +%MARSHALL - output compatible binary file from @model md, for certain solution type. % -% The routine creates a JPL-package compatible binary file from @model md +% The routine creates a compatible binary file from @model md % This binary file will be used for parallel runs in JPL-package % @@ -16,7 +16,23 @@ end -%automatically marshall model md, using template information available from an empty model class. -template=model.template(); -MarshallObject(fid,template,md,''); +%Go through al model field check that it is a class and call checkconsistency +fields=properties(md); +for i=1:length(fields), + field=fields{i}; + + %Some properties do not need to be marshalled + if ismember(field,{'results' 'debug' 'radaroverlay' 'solver' 'cluster' 'flaim' 'private'}), + continue; + end + + %Check that current field is an object + if ~isobject(md.(field)) + checkmessage(['field ''' char(field) ''' is not an object']); + end + + %Marshall current object + %disp(['marshalling ' field '...']); + md.(field).marshall(fid); +end %close file @@ -25,346 +41,2 @@ error(['marshall error message: could not close file ' [md.miscellaneous.name '.bin']]); end - -function MarshallObject(fid,template,object,prefix) % {{{ -fields=fieldnames(template); -for i=1:length(fields), - fieldname=fields{i}; - if ~isa(template.(fieldname),'modelfield'), - %Recursive call - MarshallObject(fid,template.(fieldname),object.(fieldname),[prefix fieldname]) - elseif template.(fieldname).marshall, - if ~isempty(template.(fieldname).preprocess), - eval(['fieldvalue=' template.(fieldname).preprocess '(object.(fieldname));']); - else - fieldvalue=object.(fieldname); - end - - %Capitalize for enums - fieldnamecap=fieldname; - fieldnamecap(1)=upper(fieldname(1)); - prefixcap=prefix; - if ~isempty(prefix), prefixcap(1)=upper(prefix(1)); end - - %Write Data - WriteData(fid,[prefixcap fieldnamecap],fieldvalue,template.(fieldname)); - end -end - % }}} -function WriteData(fid,fieldname,fieldvalue,fieldprop) % {{{ -%WRITEDATA - write model field in binary file -% -% Usage: -% WriteData(fid,fieldname,fieldvalue,fieldprop) -% - -%first recover data, enum of the data and type of data -data=fieldvalue; -if fieldprop.enum==NoneEnum, - enum=BuildEnum(fieldname); -else - %Field enum overloaded - enum=fieldprop.enum; -end -data_type=fieldprop.format; - -if issparse(data), - data=full(data); -end - -%Ok! write the enum (name) to identify this record uniquely -fwrite(fid,enum,'int'); - -%Now, write the data itself. -if strcmpi(data_type,'Boolean'),% {{{ - if(numel(data)~=1), error(['field ' field ' cannot be marshalled as it has more than one element!']); end - - %first write length of record - fwrite(fid,4+4,'int'); %1 bool (disguised as an int)+code - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %now write integer - fwrite(fid,data,'int'); %send an int, not easy to send a bool - % }}} -elseif strcmpi(data_type,'Integer'), % {{{ - if(numel(data)~=1), error(['field ' field ' cannot be marshalled as it has more than one element!']); end - - %first write length of record - fwrite(fid,4+4,'int'); %1 integer + code - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %now write integer - fwrite(fid,data,'int'); - % }}} -elseif strcmpi(data_type,'Double'), % {{{ - if(numel(data)~=1), error(['field ' field ' cannot be marshalled as it has more than one element!']); end - - %first write length of record - fwrite(fid,8+4,'int'); %1 double+code - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %now write double - fwrite(fid,data,'double'); - % }}} -elseif strcmpi(data_type,'String'), % {{{ - %first write length of record - fwrite(fid,length(data)+4+4,'int'); %string + string size + code - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %now write string - fwrite(fid,length(data),'int'); - fwrite(fid,data,'char'); - % }}} -elseif strcmpi(data_type,'BooleanMat'), % {{{ - - %matrix type: - mattype=fieldprop.mattype; - - %Get size - s=size(data); - %if matrix = NaN, then do not write anything - if (s(1)==1 & s(2)==1 & isnan(data)), - s(1)=0; s(2)=0; - end - - %first write length of record - fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type - - %write data code and matrix type: - fwrite(fid,TypeToCode(data_type),'int'); - fwrite(fid,mattype,'int'); - - %now write matrix - fwrite(fid,s(1),'int'); - fwrite(fid,s(2),'int'); - if s(1)*s(2), - fwrite(fid,data','double'); %get to the "c" convention, hence the transpose - end - % }}} -elseif strcmpi(data_type,'IntMat'), % {{{ - - %matrix type: - mattype=fieldtype{2}; - - %Get size - s=size(data); - %if matrix = NaN, then do not write anything - if (s(1)==1 & s(2)==1 & isnan(data)), - s(1)=0; s(2)=0; - end - - %first write length of record - fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type - - %write data code and matrix type: - fwrite(fid,TypeToCode(data_type),'int'); - fwrite(fid,mattype,'int'); - - %now write matrix - fwrite(fid,s(1),'int'); - fwrite(fid,s(2),'int'); - if s(1)*s(2), - fwrite(fid,data','double'); %get to the "c" convention, hence the transpose - end - % }}} -elseif strcmpi(data_type,'DoubleMat'), % {{{ - - %matrix type: - mattype=fieldprop.mattype; - - %Get size - s=size(data); - %if matrix = NaN, then do not write anything - if (s(1)==1 & s(2)==1 & isnan(data)), - s(1)=0; s(2)=0; - end - - %first write length of record - fwrite(fid,4+4+8*s(1)*s(2)+4+4,'int'); %2 integers (32 bits) + the double matrix + code + matrix type - - %write data code and matrix type: - fwrite(fid,TypeToCode(data_type),'int'); - fwrite(fid,mattype,'int'); - - %now write matrix - fwrite(fid,s(1),'int'); - fwrite(fid,s(2),'int'); - if s(1)*s(2), - fwrite(fid,data','double'); %get to the "c" convention, hence the transpose - end - % }}} -elseif strcmpi(data_type,'MatArray'), % {{{ - - numrecords=numel(data); - - %first get length of record - recordlength=4+4; %number of records + code - for i=1:numrecords, - matrix=data{i}; - s=size(matrix); - recordlength=recordlength+4*2+... %row and col of matrix - s(1)*s(2)*8; %matrix of doubles - end - - %write length of record - fwrite(fid,recordlength,'int'); - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %write data, first number of records - fwrite(fid,numrecords,'int'); - - %write each matrix: - for i=1:numrecords, - matrix=data{i}; - s=size(matrix); - fwrite(fid,s(1),'int'); - fwrite(fid,s(2),'int'); - fwrite(fid,matrix','double'); - end - % }}} -elseif strcmpi(data_type,'StringArray'), % {{{ - - %first get length of string array: - num=numel(data); - %now get length of record: - recordlength=4+4; %for length of array + code - for i=1:num, - string=data{i}; - recordlength=recordlength+4+length(string); %for each string - end - - %write length of record - fwrite(fid,recordlength,'int'); - - %write data code: - fwrite(fid,TypeToCode(data_type),'int'); - - %now write length of string array - fwrite(fid,num,'int'); - - %now write the strings - for i=1:num, - string=data{i}; - fwrite(fid,length(string),'int'); - fwrite(fid,string,'char'); - end - % }}} -else - error(['WriteData error message: data type: ' num2str(data_type) ' not supported yet! (' EnumToString(enum) ')']); -end -% }}} -function enum=BuildEnum(string) % {{{ -%BUILDENUM - build enum out of string -% -% Usage: -% enum=BuildEnum(string) - -if findstr(string,'_'), - indices=findstr(string,'_'); - for i=1:length(indices), - string(indices(i)+1)=upper(string(indices(i)+1)); - end - string(indices)=[]; -end - -%take first letter of string and make it uppercase: -string(1)=upper(string(1)); - -%Get Enum -enum=eval([string 'Enum']); -% }}} -function code=TypeToCode(data_type) % {{{1 -%This routine takes the data_type string, and hardcodes it into an integer, which -%is passed along the record, in order to identify the nature of the dataset being -%sent. -if strcmpi(data_type,'Boolean'), - code=1; -elseif strcmpi(data_type,'Integer'), - code=2; -elseif strcmpi(data_type,'Double'), - code=3; -elseif strcmpi(data_type,'String'), - code=4; -elseif strcmpi(data_type,'BooleanMat'), - code=5; -elseif strcmpi(data_type,'IntMat'), - code=6; -elseif strcmpi(data_type,'DoubleMat'), - code=7; -elseif strcmpi(data_type,'MatArray'), - code=8; -elseif strcmpi(data_type,'StringArray'), - code=9; -else - error('TypeToCode error message: data type not supported yet!'); -end% }}} - -%FIXME Some processing, should be moved to the corresponding classes in the future -function out=marshallverbose(in) - out = VerboseToBinary(in); -function out=marshallicefront(in) - out=in; - pos=find(in(:,end)==0); out(pos,end)=AirEnum; - pos=find(in(:,end)==1); out(pos,end)=WaterEnum; - pos=find(in(:,end)==2); out(pos,end)=IceEnum; - -function out=marshallrifts(in) - if isempty(in) | isnans(in), - numrifts=0; - else - numrifts=numel(in); - end - numpairs=0; - for i=1:numrifts, - numpairs=numpairs+size(in(i).penaltypairs,1); - end - - out=zeros(numpairs,12); % 2 for nodes + 2 for elements+ 2 for normals + 1 for length + 1 for fill + 1 for friction + 1 for fraction + 1 for fractionincrement + 1 for state. - - count=1; - for i=1:numrifts, - numpairsforthisrift=size(in(i).penaltypairs,1); - out(count:count+numpairsforthisrift-1,1:7)=in(i).penaltypairs; - out(count:count+numpairsforthisrift-1,8)=in(i).fill; - out(count:count+numpairsforthisrift-1,9)=in(i).friction; - out(count:count+numpairsforthisrift-1,10)=in(i).fraction; - out(count:count+numpairsforthisrift-1,11)=in(i).fractionincrement; - out(count:count+numpairsforthisrift-1,12)=in(i).state; - count=count+numpairsforthisrift; - end -function out=marshallapproximations(in), - out=in; - pos=find(in==0); out(pos,end)=NoneApproximationEnum; - pos=find(in==1); out(pos,end)=HutterApproximationEnum; - pos=find(in==2); out(pos,end)=MacAyealApproximationEnum; - pos=find(in==3); out(pos,end)=PattynApproximationEnum; - pos=find(in==4); out(pos,end)=StokesApproximationEnum; - pos=find(in==5); out(pos,end)=MacAyealPattynApproximationEnum; - pos=find(in==6); out(pos,end)=MacAyealStokesApproximationEnum; - pos=find(in==7); out(pos,end)=PattynStokesApproximationEnum; - -function out=marshallcontroltype(in) - out=zeros(1,numel(in)); - for i=1:numel(in), - out(i)=StringToEnum(in{i}); - end -function out=marshallcmresponses(in), - out=in; - pos=find(in==101); out(pos)=SurfaceAbsVelMisfitEnum; - pos=find(in==102); out(pos)=SurfaceRelVelMisfitEnum; - pos=find(in==103); out(pos)=SurfaceLogVelMisfitEnum; - pos=find(in==104); out(pos)=SurfaceLogVxVyMisfitEnum; - pos=find(in==105); out(pos)=SurfaceAverageVelMisfitEnum; - pos=find(in==201); out(pos)=ThicknessAbsMisfitEnum; - pos=find(in==501); out(pos)=DragCoefficientAbsGradientEnum; - pos=find(in==502); out(pos)=RheologyBbarAbsGradientEnum; - pos=find(in==503); out(pos)=ThicknessAbsGradientEnum; Index: sm/trunk-jpl/src/m/model/presolve.m =================================================================== --- /issm/trunk-jpl/src/m/model/presolve.m (revision 10968) +++ (revision ) @@ -1,16 +1,0 @@ -function md=presolve(md) -%PRESOLVE - pre-solve phase operations. -% -% Usage: -% md=presolve(md) - -%deal with rifts. -if isempty(md.rifts.riftstruct) | isnans(md.rifts.riftstruct), - md.rifts.numrifts=0; -else - md.rifts.numrifts=numel(md.rifts.riftstruct); -end - -%Control methods -md.inversion.num_control_parameters=numel(md.inversion.control_parameters); -md.inversion.num_cost_functions=size(md.inversion.cost_functions,2); Index: /issm/trunk-jpl/src/m/model/solve.m =================================================================== --- /issm/trunk-jpl/src/m/model/solve.m (revision 10968) +++ /issm/trunk-jpl/src/m/model/solve.m (revision 10969) @@ -52,7 +52,4 @@ end -%preprocesses model before solving -md=presolve(md); - %Save model as is (in case of a crash) assignin('base',inputname(1),md);