Index: /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h =================================================================== --- /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9690) +++ /issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h (revision 9691) @@ -136,4 +136,9 @@ DiagnosticNumRequestedOutputsEnum, DiagnosticViscosityOvershootEnum, + GeometryHydrostaticRatioEnum, + ThicknessEnum, + BedEnum, + BathymetryEnum, + SurfaceEnum, /*}}}*/ /*Datasets {{{1*/ @@ -281,6 +286,4 @@ AdjointzEnum, AdjointpEnum, - BedEnum, - BathymetryEnum, BedSlopeXEnum, BedSlopeYEnum, @@ -317,5 +320,4 @@ SegmentOnIceShelfEnum, SurfaceAreaEnum, - SurfaceEnum, SurfaceSlopeXEnum, SurfaceSlopeYEnum, @@ -323,6 +325,4 @@ TemperaturePicardEnum, TemperatureOldEnum, - ThicknessEnum, - ThicknessCoeffEnum, TypeEnum, VelEnum, Index: /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp =================================================================== --- /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9690) +++ /issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 9691) @@ -140,4 +140,9 @@ case DiagnosticNumRequestedOutputsEnum : return "DiagnosticNumRequestedOutputs"; case DiagnosticViscosityOvershootEnum : return "DiagnosticViscosityOvershoot"; + case GeometryHydrostaticRatioEnum : return "GeometryHydrostaticRatio"; + case ThicknessEnum : return "Thickness"; + case BedEnum : return "Bed"; + case BathymetryEnum : return "Bathymetry"; + case SurfaceEnum : return "Surface"; case ConstraintsEnum : return "Constraints"; case ElementsEnum : return "Elements"; @@ -248,6 +253,4 @@ case AdjointzEnum : return "Adjointz"; case AdjointpEnum : return "Adjointp"; - case BedEnum : return "Bed"; - case BathymetryEnum : return "Bathymetry"; case BedSlopeXEnum : return "BedSlopeX"; case BedSlopeYEnum : return "BedSlopeY"; @@ -284,5 +287,4 @@ case SegmentOnIceShelfEnum : return "SegmentOnIceShelf"; case SurfaceAreaEnum : return "SurfaceArea"; - case SurfaceEnum : return "Surface"; case SurfaceSlopeXEnum : return "SurfaceSlopeX"; case SurfaceSlopeYEnum : return "SurfaceSlopeY"; @@ -290,6 +292,4 @@ case TemperaturePicardEnum : return "TemperaturePicard"; case TemperatureOldEnum : return "TemperatureOld"; - case ThicknessEnum : return "Thickness"; - case ThicknessCoeffEnum : return "ThicknessCoeff"; case TypeEnum : return "Type"; case VelEnum : return "Vel"; Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 9690) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/UpdateElementsDiagnosticHoriz.cpp (revision 9691) @@ -49,5 +49,5 @@ /*Create inputs: */ iomodel->FetchDataToInput(elements,ThicknessEnum); - iomodel->FetchDataToInput(elements,ThicknessCoeffEnum); + iomodel->FetchDataToInput(elements,GeometryHydrostaticRatioEnum); iomodel->FetchDataToInput(elements,SurfaceEnum); iomodel->FetchDataToInput(elements,BedEnum); Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp (revision 9690) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/UpdateElementsDiagnosticHutter.cpp (revision 9691) @@ -40,5 +40,5 @@ iomodel->FetchDataToInput(elements,ThicknessEnum); - iomodel->FetchDataToInput(elements,ThicknessCoeffEnum); + iomodel->FetchDataToInput(elements,GeometryHydrostaticRatioEnum); /*Free data: */ Index: /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp =================================================================== --- /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp (revision 9690) +++ /issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/UpdateElementsDiagnosticVert.cpp (revision 9691) @@ -40,5 +40,5 @@ iomodel->FetchDataToInput(elements,ThicknessEnum); - iomodel->FetchDataToInput(elements,ThicknessCoeffEnum); + iomodel->FetchDataToInput(elements,GeometryHydrostaticRatioEnum); iomodel->FetchDataToInput(elements,SurfaceEnum); iomodel->FetchDataToInput(elements,BedEnum); Index: /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp =================================================================== --- /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9690) +++ /issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 9691) @@ -138,4 +138,9 @@ else if (strcmp(name,"DiagnosticNumRequestedOutputs")==0) return DiagnosticNumRequestedOutputsEnum; else if (strcmp(name,"DiagnosticViscosityOvershoot")==0) return DiagnosticViscosityOvershootEnum; + else if (strcmp(name,"GeometryHydrostaticRatio")==0) return GeometryHydrostaticRatioEnum; + else if (strcmp(name,"Thickness")==0) return ThicknessEnum; + else if (strcmp(name,"Bed")==0) return BedEnum; + else if (strcmp(name,"Bathymetry")==0) return BathymetryEnum; + else if (strcmp(name,"Surface")==0) return SurfaceEnum; else if (strcmp(name,"Constraints")==0) return ConstraintsEnum; else if (strcmp(name,"Elements")==0) return ElementsEnum; @@ -246,6 +251,4 @@ else if (strcmp(name,"Adjointz")==0) return AdjointzEnum; else if (strcmp(name,"Adjointp")==0) return AdjointpEnum; - else if (strcmp(name,"Bed")==0) return BedEnum; - else if (strcmp(name,"Bathymetry")==0) return BathymetryEnum; else if (strcmp(name,"BedSlopeX")==0) return BedSlopeXEnum; else if (strcmp(name,"BedSlopeY")==0) return BedSlopeYEnum; @@ -282,5 +285,4 @@ else if (strcmp(name,"SegmentOnIceShelf")==0) return SegmentOnIceShelfEnum; else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; - else if (strcmp(name,"Surface")==0) return SurfaceEnum; else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; else if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; @@ -288,6 +290,4 @@ else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; else if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; - else if (strcmp(name,"Thickness")==0) return ThicknessEnum; - else if (strcmp(name,"ThicknessCoeff")==0) return ThicknessCoeffEnum; else if (strcmp(name,"Type")==0) return TypeEnum; else if (strcmp(name,"Vel")==0) return VelEnum; Index: /issm/trunk/src/c/objects/Elements/Penta.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9690) +++ /issm/trunk/src/c/objects/Elements/Penta.cpp (revision 9691) @@ -6485,5 +6485,5 @@ double thickness[6]; double thickness_init[6]; - double thickness_coeff[6]; + double hydrostatic_ratio[6]; double surface[6]; double bed[6]; @@ -6491,5 +6491,5 @@ /*retrieve inputs: */ GetParameterListOnVertices(&thickness_init[0],ThicknessEnum); - GetParameterListOnVertices(&thickness_coeff[0],ThicknessCoeffEnum); + GetParameterListOnVertices(&hydrostatic_ratio[0],GeometryHydrostaticRatioEnum); GetParameterListOnVertices(&bed[0],BedEnum); GetParameterListOnVertices(&surface[0],SurfaceEnum); @@ -6510,6 +6510,6 @@ for (j=0; j<6; j++) { /* for observed/interpolated/hydrostatic thickness, remove scaling from any hydrostatic thickness */ - if (thickness_coeff[j] >= 0.) - thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*thickness_coeff[j]*surface[j]/(1.-di); + if (hydrostatic_ratio[j] >= 0.) + thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*hydrostatic_ratio[j]*surface[j]/(1.-di); /* for minimum thickness, don't scale */ else @@ -6531,5 +6531,5 @@ for (j=0; j<6; j++) { /* for observed thickness, use scaled value */ - if (thickness_coeff[j] >= 0.) + if(hydrostatic_ratio[j] >= 0.) thickness[j]=values[j]; /* for minimum thickness, don't scale */ Index: /issm/trunk/src/c/objects/Elements/Tria.cpp =================================================================== --- /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9690) +++ /issm/trunk/src/c/objects/Elements/Tria.cpp (revision 9691) @@ -3777,5 +3777,5 @@ double thickness[3]; double thickness_init[3]; - double thickness_coeff[3]; + double hydrostatic_ratio[3]; double surface[3]; double bed[3]; @@ -3783,5 +3783,5 @@ /*retrieve inputs: */ GetParameterListOnVertices(&thickness_init[0],ThicknessEnum); - GetParameterListOnVertices(&thickness_coeff[0],ThicknessCoeffEnum); + GetParameterListOnVertices(&hydrostatic_ratio[0],GeometryHydrostaticRatioEnum); GetParameterListOnVertices(&bed[0],BedEnum); GetParameterListOnVertices(&surface[0],SurfaceEnum); @@ -3802,6 +3802,6 @@ for (j=0; j<3; j++) { /* for observed/interpolated/hydrostatic thickness, remove scaling from any hydrostatic thickness */ - if (thickness_coeff[j] >= 0.) - thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*thickness_coeff[j]*surface[j]/(1.-di); + if (hydrostatic_ratio[j] >= 0.) + thickness[j]=values[j]-(values[j]/thickness_init[j]-1.)*hydrostatic_ratio[j]*surface[j]/(1.-di); /* for minimum thickness, don't scale */ else @@ -3823,5 +3823,5 @@ for (j=0; j<3; j++) { /* for observed thickness, use scaled value */ - if (thickness_coeff[j] >= 0.) + if (hydrostatic_ratio[j] >= 0.) thickness[j]=values[j]; /* for minimum thickness, don't scale */ Index: /issm/trunk/src/m/classes/geometry.m =================================================================== --- /issm/trunk/src/m/classes/geometry.m (revision 9691) +++ /issm/trunk/src/m/classes/geometry.m (revision 9691) @@ -0,0 +1,41 @@ +%GEOMETRY class definition +% +% Usage: +% geometry=geometry(); + +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); + end + methods + function obj = geometry(varargin) % {{{ + switch nargin + case 0 + obj=setdefaultparameters(obj); + case 1 + in=varargin{1}; + if (isa(in,'numeric') & in==0), + % requesting templates do nothing + else + error('constructor not supported'); + end + otherwise + error('constructor not supported'); + end + 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 % }}} + end +end Index: /issm/trunk/src/m/classes/model/model.m =================================================================== --- /issm/trunk/src/m/classes/model/model.m (revision 9690) +++ /issm/trunk/src/m/classes/model/model.m (revision 9691) @@ -38,4 +38,5 @@ diagnostic = modelfield('default',0,'marshall',true); initialization = modelfield('default',0,'marshall',true); + geometry = modelfield('default',0,'marshall',true); %FIXME: all other fields should belong to other classes @@ -86,13 +87,4 @@ extractednodes = modelfield('default',NaN,'marshall',false); extractedelements = modelfield('default',NaN,'marshall',false); - - %Materials parameters - - %Geometrical parameters - surface = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - thickness = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - thickness_coeff = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - bed = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); - bathymetry = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1); %Boundary conditions @@ -351,4 +343,8 @@ if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end + if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end + if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end + if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end + if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end %Field changes @@ -478,6 +474,7 @@ md.inversion = inversion; md.transient = transient; - md.diagnostic =diagnostic; - md.initialization =initialization; + md.diagnostic = diagnostic; + md.initialization = initialization; + md.geometry = geometry; %Solver parameters Index: /issm/trunk/src/m/enum/GeometryHydrostaticRatioEnum.m =================================================================== --- /issm/trunk/src/m/enum/GeometryHydrostaticRatioEnum.m (revision 9691) +++ /issm/trunk/src/m/enum/GeometryHydrostaticRatioEnum.m (revision 9691) @@ -0,0 +1,11 @@ +function macro=GeometryHydrostaticRatioEnum() +%GEOMETRYHYDROSTATICRATIOENUM - Enum of GeometryHydrostaticRatio +% +% WARNING: DO NOT MODIFY THIS FILE +% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +% Please read src/c/EnumDefinitions/README for more information +% +% Usage: +% macro=GeometryHydrostaticRatioEnum() + +macro=StringToEnum('GeometryHydrostaticRatio'); Index: /issm/trunk/src/m/model/DepthAverage.m =================================================================== --- /issm/trunk/src/m/model/DepthAverage.m (revision 9690) +++ /issm/trunk/src/m/model/DepthAverage.m (revision 9691) @@ -19,5 +19,5 @@ vector_average=vector_average+(project2d(md,vector,i)+project2d(md,vector,i+1))/2.*(project2d(md,md.z,i+1)-project2d(md,md.z,i)); end - vector_average=vector_average./project2d(md,md.thickness,1); + vector_average=vector_average./project2d(md,md.geometry.thickness,1); %element data @@ -27,5 +27,5 @@ vector_average=vector_average+project2d(md,vector,i).*(project2d(md,md.z,i+1)-project2d(md,md.z,i)); end - vector_average=vector_average./project2d(md,md.thickness,1); + vector_average=vector_average./project2d(md,md.geometry.thickness,1); else Index: /issm/trunk/src/m/model/SectionValues.m =================================================================== --- /issm/trunk/src/m/model/SectionValues.m (revision 9690) +++ /issm/trunk/src/m/model/SectionValues.m (revision 9691) @@ -94,9 +94,9 @@ %Get bed and surface for each 2d point, offset to make sure that it is inside the glacier system offset=10^-3; - bed=InterpFromMeshToMesh2d(md.elements2d,md.x2d,md.y2d,project2d(md,md.bed,1),X,Y)+offset; - surface=InterpFromMeshToMesh2d(md.elements2d,md.x2d,md.y2d,project2d(md,md.surface,1),X,Y)-offset; + bed=InterpFromMeshToMesh2d(md.elements2d,md.x2d,md.y2d,project2d(md,md.geometry.bed,1),X,Y)+offset; + surface=InterpFromMeshToMesh2d(md.elements2d,md.x2d,md.y2d,project2d(md,md.geometry.surface,1),X,Y)-offset; %Some useful parameters - layers=ceil(mean(md.thickness)/res_v); + layers=ceil(mean(md.geometry.thickness)/res_v); nodesperlayer=numberofnodes; nodestot=nodesperlayer*layers; Index: /issm/trunk/src/m/model/ThicknessCorrection.m =================================================================== --- /issm/trunk/src/m/model/ThicknessCorrection.m (revision 9690) +++ /issm/trunk/src/m/model/ThicknessCorrection.m (revision 9691) @@ -18,7 +18,7 @@ %initialize thickness with the observations, and get hydrostatic thickness from the dem -thickness=md.thickness; -thickness_hydro=md.surface/(1-md.materials.rho_ice/md.materials.rho_water); -thickness_coeff=zeros(size(md.thickness)); +thickness=md.geometry.thickness; +thickness_hydro=md.geometry.surface/(1-md.materials.rho_ice/md.materials.rho_water); +hydrostatic_ratio=zeros(size(md.geometry.thickness)); %get nodes on ice sheet and on ice shelf @@ -53,5 +53,5 @@ %if d > 15km, hydrostatic equilibrium - thickness_coeff(pos_shelf(i))=1; + hydrostatic_ratio(pos_shelf(i))=1; thickness(pos_shelf(i))=thickness_hydro(pos_shelf(i)); @@ -59,6 +59,6 @@ %else: quadratic combination of hydrostatic equilibrium and observations - thickness_coeff(pos_shelf(i))=(d/distance)^2; - thickness(pos_shelf(i))=(1-thickness_coeff(pos_shelf(i)))*thickness(pos_shelf(i))+thickness_coeff(pos_shelf(i))*thickness_hydro(pos_shelf(i)); + hydrostatic_ratio(pos_shelf(i))=(d/distance)^2; + thickness(pos_shelf(i))=(1-hydrostatic_ratio(pos_shelf(i)))*thickness(pos_shelf(i))+hydrostatic_ratio(pos_shelf(i))*thickness_hydro(pos_shelf(i)); end @@ -70,8 +70,8 @@ pos=find(isnan(thickness) | (thickness<=0)); thickness(pos)=minth; -thickness_coeff(pos)=-1; +hydrostatic_ratio(pos)=-1; %change bed to take into account the changes in thickness -md.thickness=thickness; -md.thickness_coeff=thickness_coeff; -md.bed=md.surface-md.thickness; +md.geometry.thickness=thickness; +md.geometry.hydrostatic_ratio=hydrostatic_ratio; +md.geometry.bed=md.geometry.surface-md.geometry.thickness; Index: /issm/trunk/src/m/model/bamg.m =================================================================== --- /issm/trunk/src/m/model/bamg.m (revision 9690) +++ /issm/trunk/src/m/model/bamg.m (revision 9691) @@ -46,5 +46,5 @@ % Examples: % md=bamg(md,'domain','DomainOutline.exp','hmax',3000); -% md=bamg(md,'field',[md.inversion.vel_obs md.thickness],'hmax',20000,'hmin',1000); +% md=bamg(md,'field',[md.inversion.vel_obs md.geometry.thickness],'hmax',20000,'hmin',1000); % md=bamg(md,'metric',A,'hmin',1000,'hmax',20000,'gradation',3,'anisomax',1); Index: /issm/trunk/src/m/model/basalstress.m =================================================================== --- /issm/trunk/src/m/model/basalstress.m (revision 9690) +++ /issm/trunk/src/m/model/basalstress.m (revision 9691) @@ -18,5 +18,5 @@ %compute basal drag -bx=(md.constants.g*(md.materials.rho_ice*md.thickness+md.materials.rho_water*md.bed)).^r.*(md.friction.coefficient).^2.*ubx.^s; -by=(md.constants.g*(md.materials.rho_ice*md.thickness+md.materials.rho_water*md.bed)).^r.*(md.friction.coefficient).^2.*uby.^s; -b=(md.constants.g*(md.materials.rho_ice*md.thickness+md.materials.rho_water*md.bed)).^r.*(md.friction.coefficient).^2.*ub.^s; +bx=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*ubx.^s; +by=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*uby.^s; +b=(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed)).^r.*(md.friction.coefficient).^2.*ub.^s; Index: /issm/trunk/src/m/model/basevert.m =================================================================== --- /issm/trunk/src/m/model/basevert.m (revision 9690) +++ /issm/trunk/src/m/model/basevert.m (revision 9691) @@ -20,6 +20,6 @@ end -hu=md.thickness.*md.initialization.vx; -hv=md.thickness.*md.initialization.vy; +hu=md.geometry.thickness.*md.initialization.vx; +hv=md.geometry.thickness.*md.initialization.vy; summation=[1;1;1]; @@ -30,6 +30,6 @@ velem=md.initialization.vy(md.elements)*summation/3; -dbdx=(md.bed(md.elements).*alpha)*summation; -dbdy=(md.bed(md.elements).*beta)*summation; +dbdx=(md.geometry.bed(md.elements).*alpha)*summation; +dbdy=(md.geometry.bed(md.elements).*beta)*summation; wb=-md.materials.rho_ice/md.materials.rho_water*(hux+hvy)+uelem.*dbdx+velem.*dbdy; Index: /issm/trunk/src/m/model/bedslope.m =================================================================== --- /issm/trunk/src/m/model/bedslope.m (revision 9690) +++ /issm/trunk/src/m/model/bedslope.m (revision 9691) @@ -22,6 +22,6 @@ summation=[1;1;1]; -bx=(md.bed(index).*alpha)*summation; -by=(md.bed(index).*beta)*summation; +bx=(md.geometry.bed(index).*alpha)*summation; +by=(md.geometry.bed(index).*beta)*summation; b=sqrt(bx.^2+by.^2); Index: /issm/trunk/src/m/model/collapse.m =================================================================== --- /issm/trunk/src/m/model/collapse.m (revision 9690) +++ /issm/trunk/src/m/model/collapse.m (revision 9691) @@ -80,7 +80,7 @@ %parameters -md.surface=project2d(md,md.surface,1); -md.thickness=project2d(md,md.thickness,1); -md.bed=project2d(md,md.bed,1); +md.geometry.surface=project2d(md,md.geometry.surface,1); +md.geometry.thickness=project2d(md,md.geometry.thickness,1); +md.geometry.bed=project2d(md,md.geometry.bed,1); md.nodeonboundary=project2d(md,md.nodeonboundary,1); md.mask.elementonfloatingice=project2d(md,md.mask.elementonfloatingice,1); Index: /issm/trunk/src/m/model/contourmassbalance.m =================================================================== --- /issm/trunk/src/m/model/contourmassbalance.m (revision 9690) +++ /issm/trunk/src/m/model/contourmassbalance.m (revision 9691) @@ -30,5 +30,5 @@ vx=mean(md.initialization.vx(segments(:,1:end-1)),2); vy=mean(md.initialization.vy(segments(:,1:end-1)),2); -H=mean(md.thickness(segments(:,1:end-1)),2); +H=mean(md.geometry.thickness(segments(:,1:end-1)),2); nx=cos(atan2((x(segments(:,1))-x(segments(:,2))) , (y(segments(:,2))-y(segments(:,1))))); ny=sin(atan2((x(segments(:,1))-x(segments(:,2))) , (y(segments(:,2))-y(segments(:,1))))); Index: /issm/trunk/src/m/model/drivingstress.m =================================================================== --- /issm/trunk/src/m/model/drivingstress.m (revision 9690) +++ /issm/trunk/src/m/model/drivingstress.m (revision 9691) @@ -12,5 +12,5 @@ %Average thickness over elements -thickness_bar=(md.thickness(md.elements(:,1))+md.thickness(md.elements(:,2))+md.thickness(md.elements(:,3)))/3; +thickness_bar=(md.geometry.thickness(md.elements(:,1))+md.geometry.thickness(md.elements(:,2))+md.geometry.thickness(md.elements(:,3)))/3; px=md.materials.rho_ice*md.constants.g*thickness_bar.*sx; Index: /issm/trunk/src/m/model/effectivepressure.m =================================================================== --- /issm/trunk/src/m/model/effectivepressure.m (revision 9690) +++ /issm/trunk/src/m/model/effectivepressure.m (revision 9691) @@ -8,5 +8,5 @@ % Neff=effectivepressure(md) -Neff=md.materials.rho_ice*md.constants.g*md.thickness+md.materials.rho_ice*md.constants.g*md.bed; +Neff=md.materials.rho_ice*md.constants.g*md.geometry.thickness+md.materials.rho_ice*md.constants.g*md.geometry.bed; pos=find(Neff<0); Neff(pos)=0; Index: /issm/trunk/src/m/model/extrude.m =================================================================== --- /issm/trunk/src/m/model/extrude.m (revision 9690) +++ /issm/trunk/src/m/model/extrude.m (revision 9691) @@ -67,6 +67,6 @@ y3d=[]; z3d=[]; %the lower node is on the bed -thickness3d=md.thickness; %thickness and bed for these nodes -bed3d=md.bed; +thickness3d=md.geometry.thickness; %thickness and bed for these nodes +bed3d=md.geometry.bed; %Create the new layers @@ -197,9 +197,9 @@ %parameters -md.surface=project3d(md,'vector',md.surface,'type','node'); -md.thickness=project3d(md,'vector',md.thickness,'type','node'); -md.thickness_coeff=project3d(md,'vector',md.thickness_coeff,'type','node'); -md.bed=project3d(md,'vector',md.bed,'type','node'); -md.bathymetry=project3d(md,'vector',md.bathymetry,'type','node'); +md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node'); +md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node'); +md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node'); +md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node'); +md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node'); md.nodeonboundary=project3d(md,'vector',md.nodeonboundary,'type','node'); md.mask.elementonfloatingice=project3d(md,'vector',md.mask.elementonfloatingice,'type','element'); @@ -213,5 +213,5 @@ %Put lithostatic pressure is there is an existing pressure if ~isnan(md.initialization.pressure), - md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.surface-md.z); + md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.z); end Index: /issm/trunk/src/m/model/ismodelselfconsistent.m =================================================================== --- /issm/trunk/src/m/model/ismodelselfconsistent.m (revision 9690) +++ /issm/trunk/src/m/model/ismodelselfconsistent.m (revision 9691) @@ -83,5 +83,5 @@ %NO NAN {{{1 fields={'numberofelements','numberofnodes','x','y','z','friction.coefficient','friction.p','friction.q',... - 'materials.rho_ice','materials.rho_water','materials.rheology_B','mask.elementonfloatingice','surface','thickness','bed','constants.g','settings.lowmem','inversion.nsteps','inversion.maxiter_per_step',... + 'materials.rho_ice','materials.rho_water','materials.rheology_B','mask.elementonfloatingice','geometry.surface','geometry.thickness','geometry.bed','constants.g','settings.lowmem','inversion.nsteps','inversion.maxiter_per_step',... 'diagnostic.restol','diagnostic.maxiter','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface','elementconnectivity'}; checknan(md,fields); @@ -89,5 +89,5 @@ %FIELDS >= 0 {{{1 fields={'numberofelements','numberofnodes','elements','friction.coefficient','friction.p','friction.q',... - 'materials.rho_ice','materials.rho_water','materials.rheology_B','mask.elementonfloatingice','thickness','constants.g','diagnostic.restol','diagnostic.maxiter','diagnostic.reltol',... + 'materials.rho_ice','materials.rho_water','materials.rheology_B','mask.elementonfloatingice','geometry.thickness','constants.g','diagnostic.restol','diagnostic.maxiter','diagnostic.reltol',... 'diagnostic.abstol','inversion.nsteps','inversion.maxiter_per_step',... 'settings.lowmem','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface'}; @@ -96,5 +96,5 @@ %FIELDS > 0 {{{1 fields={'numberofelements','numberofnodes','elements','friction.p',... - 'materials.rho_ice','materials.rho_water','materials.rheology_B','thickness','constants.g','diagnostic.maxiter','diagnostic.restol','diagnostic.reltol','diagnostic.abstol','inversion.maxiter_per_step'}; + 'materials.rho_ice','materials.rho_water','materials.rheology_B','geometry.thickness','constants.g','diagnostic.maxiter','diagnostic.restol','diagnostic.reltol','diagnostic.abstol','inversion.maxiter_per_step'}; checkgreaterstrict(md,fields,0); %}}} @@ -104,5 +104,5 @@ %}}} %SIZE NUMBEROFNODES {{{1 -fields={'x','y','z','materials.rheology_B','friction.coefficient','basalforcings.melting_rate','surface','thickness','bed','nodeonbed','nodeonsurface'}; +fields={'x','y','z','materials.rheology_B','friction.coefficient','basalforcings.melting_rate','geometry.surface','geometry.thickness','geometry.bed','nodeonbed','nodeonsurface'}; checksize(md,fields,[md.numberofnodes 1]); %}}} @@ -117,5 +117,5 @@ %}}} %THICKNESS = SURFACE - BED {{{1 -if any((md.thickness-md.surface+md.bed)>tolerance), +if any((md.geometry.thickness-md.geometry.surface+md.geometry.bed)>tolerance), message(['model not consistent: model ' md.miscellaneous.name ' violates the equality thickness=surface-bed!']); end @@ -128,13 +128,13 @@ message(['model ' md.miscellaneous.name ' requesting grounding line migration, but grounding line module only implemented for 2d models and parallel runs!']); end - if isnan(md.bathymetry), + if isnan(md.geometry.bathymetry), message(['model not consistent: model ' md.miscellaneous.name ' requesting grounding line migration, but bathymetry is absent!']); end pos=find(md.mask.vertexongroundedice); - if any(md.bed(pos)-md.bathymetry(pos)), + if any(md.geometry.bed(pos)-md.geometry.bathymetry(pos)), message(['model not consistent: model ' md.miscellaneous.name ' bathymetry not equal to bed on grounded ice !']); end pos=find(md.mask.vertexonfloatingice); - if any(md.bathymetry(pos)-md.bed(pos)>tolerance), + if any(md.geometry.bathymetry(pos)-md.geometry.bed(pos)>tolerance), message(['model not consistent: model ' md.miscellaneous.name ' bathymetry superior to bed on floating ice !']); end @@ -244,6 +244,6 @@ %DIRICHLET IF THICKNESS <= 0 - if any(md.thickness<=0), - pos=find(md.thickness<=0); + if any(md.geometry.thickness<=0), + pos=find(md.geometry.thickness<=0); if any(isnan(md.balancethickness.spcthickness(pos))), message(['model not consistent: model ' md.miscellaneous.name ' has some nodes with 0 thickness']); @@ -468,6 +468,6 @@ %DIRICHLET IF THICKNESS <= 0 %Check the size of prognostic.spcthickness - if any(md.thickness<=0), - pos=find(md.thickness<=0); + if any(md.geometry.thickness<=0), + pos=find(md.geometry.thickness<=0); if any(isnan(md.prognostic.spcthickness(pos))), message(['model not consistent: model ' md.miscellaneous.name ' has some nodes with 0 thickness']); Index: /issm/trunk/src/m/model/plot/plot_basaldrag.m =================================================================== --- /issm/trunk/src/m/model/plot/plot_basaldrag.m (revision 9690) +++ /issm/trunk/src/m/model/plot/plot_basaldrag.m (revision 9691) @@ -30,5 +30,5 @@ %compute basal drag -drag=(max(md.constants.g*(md.materials.rho_ice*md.thickness+md.materials.rho_water*md.bed),0)).^r.*(md.friction.coefficient).^2.*ub.^s/1000; +drag=(max(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed),0)).^r.*(md.friction.coefficient).^2.*ub.^s/1000; %Figure out if this is a Section plot Index: /issm/trunk/src/m/model/sia.m =================================================================== --- /issm/trunk/src/m/model/sia.m (revision 9690) +++ /issm/trunk/src/m/model/sia.m (revision 9691) @@ -17,5 +17,5 @@ %Average thickness and B over all elements. summer=[1;1;1]; -hel=md.thickness(md.elements)*summer/3; +hel=md.geometry.thickness(md.elements)*summer/3; Bel=md.B(md.elements)*summer/3; Index: /issm/trunk/src/m/model/slope.m =================================================================== --- /issm/trunk/src/m/model/slope.m (revision 9690) +++ /issm/trunk/src/m/model/slope.m (revision 9691) @@ -22,6 +22,6 @@ summation=[1;1;1]; -sx=(md.surface(index).*alpha)*summation; -sy=(md.surface(index).*beta)*summation; +sx=(md.geometry.surface(index).*alpha)*summation; +sy=(md.geometry.surface(index).*beta)*summation; s=sqrt(sx.^2+sy.^2); Index: /issm/trunk/src/m/model/thicknessevolution.m =================================================================== --- /issm/trunk/src/m/model/thicknessevolution.m (revision 9690) +++ /issm/trunk/src/m/model/thicknessevolution.m (revision 9691) @@ -14,5 +14,5 @@ %load some variables -H=md.thickness; +H=md.geometry.thickness; vx=md.initialization.vx; vy=md.initialization.vy; Index: /issm/trunk/src/m/utils/Interp/FillHole.m =================================================================== --- /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9690) +++ /issm/trunk/src/m/utils/Interp/FillHole.m (revision 9691) @@ -6,5 +6,5 @@ % % Example: -% md.surface=FillHole(md.elements,x,md.y,md.surface) +% md.geometry.surface=FillHole(md.elements,x,md.y,md.geometry.surface) % Index: /issm/trunk/src/m/utils/Interp/InterpFromFile.m =================================================================== --- /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 9690) +++ /issm/trunk/src/m/utils/Interp/InterpFromFile.m (revision 9691) @@ -19,5 +19,5 @@ % % Example: -% md.surface=InterpFromFile(md.x,md.y,'surfacefile.mat',0); +% md.geometry.surface=InterpFromFile(md.x,md.y,'surfacefile.mat',0); % % See also: PLUGVELOCITIES, INTERPFROMGRID, INTERPFROMMESH2D, INTERPFROMMESH3D Index: /issm/trunk/template =================================================================== --- /issm/trunk/template (revision 9690) +++ /issm/trunk/template (revision 9691) @@ -43,22 +43,4 @@ extractedelements }}} -geometry {{{ - surface - thickness - bed - bathymetry - - thickness_coeff -> rename hydrostatic_ratio (change ThicknessCorrection.m accordingly) -}}} -initialization{{{ - vx - vy - vz - vel - pressure - temperature - watercolumn - waterfraction -}}} %To be completed Index: /issm/trunk/test/Miscellaneous/Bump/Bump.par =================================================================== --- /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9690) +++ /issm/trunk/test/Miscellaneous/Bump/Bump.par (revision 9691) @@ -7,9 +7,9 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness+10; -md.surface=md.bed+md.thickness; -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness+height*exp(-((md.x-50000).^2+(md.y-50000).^2)/(4000)^2)+10; -md.thickness=md.surface-md.bed; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+10; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+height*exp(-((md.x-50000).^2+(md.y-50000).^2)/(4000)^2)+10; +md.geometry.thickness=md.geometry.surface-md.geometry.bed; md.drag_type=2; %0 none 1 plastic 2 viscous Index: /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par =================================================================== --- /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9690) +++ /issm/trunk/test/Miscellaneous/GJM_test1/SquareShelf.par (revision 9691) @@ -6,7 +6,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Materials Index: /issm/trunk/test/Miscellaneous/connectivity/Square.par =================================================================== --- /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9690) +++ /issm/trunk/test/Miscellaneous/connectivity/Square.par (revision 9691) @@ -11,7 +11,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; md.drag_type=2; %0 none 1 plastic 2 viscous Index: /issm/trunk/test/NightlyRun/test111.m =================================================================== --- /issm/trunk/test/NightlyRun/test111.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test111.m (revision 9691) @@ -6,5 +6,5 @@ md.cluster=none; md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test1110.m =================================================================== --- /issm/trunk/test/NightlyRun/test1110.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1110.m (revision 9691) @@ -85,5 +85,5 @@ end - plotmodel(md,'data',PatchToVec(md.results.TransientSolution(end).Surface)-md.surface,'layer',md.numlayers,'sectionvalue','../Exp/ISMIP100000.exp','title','','xlabel','','ylabel','Surface (m)','linewidth',3,'grid','on','unit','km','ylim',[-30 50]) + plotmodel(md,'data',PatchToVec(md.results.TransientSolution(end).Surface)-md.geometry.surface,'layer',md.numlayers,'sectionvalue','../Exp/ISMIP100000.exp','title','','xlabel','','ylabel','Surface (m)','linewidth',3,'grid','on','unit','km','ylim',[-30 50]) if printingflag, set(gcf,'Color','w') @@ -124,5 +124,5 @@ PatchToVec(result.Vy),... PatchToVec(result.Vz),... - PatchToVec(result.Surface)-md.surface,... + PatchToVec(result.Surface)-md.geometry.surface,... }; end Index: /issm/trunk/test/NightlyRun/test112.m =================================================================== --- /issm/trunk/test/NightlyRun/test112.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test112.m (revision 9691) @@ -6,5 +6,5 @@ md.cluster=generic('name',oshostname(),'np',3); md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test1205.m =================================================================== --- /issm/trunk/test/NightlyRun/test1205.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1205.m (revision 9691) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.thickness).^-1; -vy_obs=constant/2*md.y.*(md.thickness).^-1; +vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); Index: /issm/trunk/test/NightlyRun/test1206.m =================================================================== --- /issm/trunk/test/NightlyRun/test1206.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1206.m (revision 9691) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.thickness).^-1; -vy_obs=constant/2*md.y.*(md.thickness).^-1; +vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); Index: /issm/trunk/test/NightlyRun/test1207.m =================================================================== --- /issm/trunk/test/NightlyRun/test1207.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1207.m (revision 9691) @@ -13,6 +13,6 @@ %Calculation of the analytical 2d velocity field constant=0.3; -vx_obs=constant/2*md.x.*(md.thickness).^-1; -vy_obs=constant/2*md.y.*(md.thickness).^-1; +vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; +vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); Index: /issm/trunk/test/NightlyRun/test1303.m =================================================================== --- /issm/trunk/test/NightlyRun/test1303.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1303.m (revision 9691) @@ -18,5 +18,5 @@ %d2T/dz2=0 T(bed)=10 T(surface)=0 => T=0*(z-bed)/thickness+10*(surface-z)/thickness %each layer of the 3d mesh must have a constant value -md.initialization.temperature=10*(md.surface-md.z)./md.thickness; +md.initialization.temperature=10*(md.geometry.surface-md.z)./md.geometry.thickness; %modeled results Index: /issm/trunk/test/NightlyRun/test1304.m =================================================================== --- /issm/trunk/test/NightlyRun/test1304.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1304.m (revision 9691) @@ -19,5 +19,5 @@ %the result is linear with depth and is equal to 0 on the upper surface (See BC) %d2T/dz2=0 -k*dT/dz(bed)=G T(surface)=0 => T=-G/k*(z-surface) -md.initialization.temperature=-0.1/md.thermalconductivity*(md.z-md.surface); %G=0.1 W/m2 +md.initialization.temperature=-0.1/md.thermalconductivity*(md.z-md.geometry.surface); %G=0.1 W/m2 %modeled results Index: /issm/trunk/test/NightlyRun/test131.m =================================================================== --- /issm/trunk/test/NightlyRun/test131.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test131.m (revision 9691) @@ -4,5 +4,5 @@ %Add boundary conditions on thickness on the border pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); md=setflowequation(md,'macayeal','all'); md.cluster=none; Index: /issm/trunk/test/NightlyRun/test132.m =================================================================== --- /issm/trunk/test/NightlyRun/test132.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test132.m (revision 9691) @@ -4,5 +4,5 @@ %Add boundary conditions on thickness on the border pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); md=setflowequation(md,'macayeal','all'); md.cluster=generic('name',oshostname(),'np',3); Index: /issm/trunk/test/NightlyRun/test133.m =================================================================== --- /issm/trunk/test/NightlyRun/test133.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test133.m (revision 9691) @@ -5,5 +5,5 @@ %Add boundary conditions on thickness on the border pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); md=setflowequation(md,'macayeal','all'); md.cluster=none; Index: /issm/trunk/test/NightlyRun/test134.m =================================================================== --- /issm/trunk/test/NightlyRun/test134.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test134.m (revision 9691) @@ -5,5 +5,5 @@ %Add boundary conditions on thickness on the border pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); md=setflowequation(md,'macayeal','all'); md.cluster=generic('name',oshostname(),'np',3); Index: /issm/trunk/test/NightlyRun/test1501.m =================================================================== --- /issm/trunk/test/NightlyRun/test1501.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1501.m (revision 9691) @@ -21,5 +21,5 @@ for i=1:10 md=solve(md,PrognosticSolutionEnum); - md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (PatchToVec(md.results.PrognosticSolution.Thickness)-md.thickness); + md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (PatchToVec(md.results.PrognosticSolution.Thickness)-md.geometry.thickness); end Index: /issm/trunk/test/NightlyRun/test1502.m =================================================================== --- /issm/trunk/test/NightlyRun/test1502.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test1502.m (revision 9691) @@ -22,5 +22,5 @@ for i=1:10 md=solve(md,PrognosticSolutionEnum); - md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (PatchToVec(md.results.PrognosticSolution.Thickness)-md.thickness); + md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (PatchToVec(md.results.PrognosticSolution.Thickness)-md.geometry.thickness); end Index: /issm/trunk/test/NightlyRun/test233.m =================================================================== --- /issm/trunk/test/NightlyRun/test233.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test233.m (revision 9691) @@ -21,7 +21,7 @@ h=1000; -md.thickness=h*ones(md.numberofnodes,1); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=h*ones(md.numberofnodes,1); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity and pressure @@ -61,5 +61,5 @@ %create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. -%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.thickness./(4*md.materials.rheology_B)).^3; +%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; %vy_c=ey_c.*md.y*md.constants.yts; Index: /issm/trunk/test/NightlyRun/test234.m =================================================================== --- /issm/trunk/test/NightlyRun/test234.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test234.m (revision 9691) @@ -21,7 +21,7 @@ h=1000; -md.thickness=h*ones(md.numberofnodes,1); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=h*ones(md.numberofnodes,1); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity and pressure @@ -61,5 +61,5 @@ %create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. -%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.thickness./(4*md.materials.rheology_B)).^3; +%ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; %vy_c=ey_c.*md.y*md.constants.yts; Index: /issm/trunk/test/NightlyRun/test235.m =================================================================== --- /issm/trunk/test/NightlyRun/test235.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test235.m (revision 9691) @@ -18,7 +18,7 @@ h=1000; -md.thickness=h*ones(md.numberofnodes,1); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=h*ones(md.numberofnodes,1); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity and pressure Index: /issm/trunk/test/NightlyRun/test236.m =================================================================== --- /issm/trunk/test/NightlyRun/test236.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test236.m (revision 9691) @@ -18,7 +18,7 @@ h=1000; -md.thickness=h*ones(md.numberofnodes,1); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=h*ones(md.numberofnodes,1); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity and pressure Index: /issm/trunk/test/NightlyRun/test245.m =================================================================== --- /issm/trunk/test/NightlyRun/test245.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test245.m (revision 9691) @@ -3,5 +3,5 @@ md=parameterize(md,'../Par/SquareShelf.par'); md=setflowequation(md,'macayeal','all'); -md.bed=md.bed+50; md.surface=md.surface+50; +md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; md.cluster=none; md.prognostic.hydrostatic_adjustment='Incremental'; Index: /issm/trunk/test/NightlyRun/test246.m =================================================================== --- /issm/trunk/test/NightlyRun/test246.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test246.m (revision 9691) @@ -3,5 +3,5 @@ md=parameterize(md,'../Par/SquareShelf.par'); md=setflowequation(md,'macayeal','all'); -md.bed=md.bed+50; md.surface=md.surface+50; +md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; md.cluster=generic('name',oshostname(),'np',3); md.prognostic.hydrostatic_adjustment='Incremental'; Index: /issm/trunk/test/NightlyRun/test249.m =================================================================== --- /issm/trunk/test/NightlyRun/test249.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test249.m (revision 9691) @@ -4,5 +4,5 @@ md=extrude(md,3,1); md=setflowequation(md,'pattyn','all'); -md.bed=md.bed+50; md.surface=md.surface+50; +md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; md.cluster=none; md.prognostic.hydrostatic_adjustment='Incremental'; Index: /issm/trunk/test/NightlyRun/test250.m =================================================================== --- /issm/trunk/test/NightlyRun/test250.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test250.m (revision 9691) @@ -4,5 +4,5 @@ md=extrude(md,3,1); md=setflowequation(md,'pattyn','all'); -md.bed=md.bed+50; md.surface=md.surface+50; +md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; md.cluster=generic('name',oshostname(),'np',3); md.prognostic.hydrostatic_adjustment='Incremental'; Index: /issm/trunk/test/NightlyRun/test319.m =================================================================== --- /issm/trunk/test/NightlyRun/test319.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test319.m (revision 9691) @@ -5,5 +5,5 @@ md=setflowequation(md,'macayeal','all'); md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md.cluster=none; md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test320.m =================================================================== --- /issm/trunk/test/NightlyRun/test320.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test320.m (revision 9691) @@ -5,5 +5,5 @@ md=setflowequation(md,'macayeal','all'); md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md.cluster=generic('name',oshostname(),'np',3); md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test427.m =================================================================== --- /issm/trunk/test/NightlyRun/test427.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test427.m (revision 9691) @@ -5,5 +5,5 @@ md.cluster=none; md.materials.rho_ice=10^7; %involved in the mass flux, make it easy -md.thickness(:)=1; %make it easy +md.geometry.thickness(:)=1; %make it easy %constrain all velocities to 1 m/yr, in the y-direction Index: /issm/trunk/test/NightlyRun/test428.m =================================================================== --- /issm/trunk/test/NightlyRun/test428.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test428.m (revision 9691) @@ -5,5 +5,5 @@ md.cluster=generic('name',oshostname(),'np',3); md.materials.rho_ice=10^7; %involved in the mass flux, make it easy -md.thickness(:)=1; %make it easy +md.geometry.thickness(:)=1; %make it easy %constrain all velocities to 1 m/yr, in the y-direction Index: /issm/trunk/test/NightlyRun/test434.m =================================================================== --- /issm/trunk/test/NightlyRun/test434.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test434.m (revision 9691) @@ -5,5 +5,5 @@ md.cluster=generic('name',oshostname(),'np',3); md.materials.rho_ice=10^7; %involved in the mass flux, make it easy -md.thickness(:)=1; %make it easy +md.geometry.thickness(:)=1; %make it easy %constrain all velocities to 1 m/yr, in the y-direction Index: /issm/trunk/test/NightlyRun/test446.m =================================================================== --- /issm/trunk/test/NightlyRun/test446.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test446.m (revision 9691) @@ -26,17 +26,17 @@ rad=sqrt((md.x).*md.x+(md.y).*md.y); pos=find(rad<200000); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); pos=find(md.x<.2*1e6 & md.x>-.2*1e6 & md.y>0); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); pos=find(md.x<.1*1e6 & md.x>-.1*1e6 & md.y<-.5*1e6 & md.y>-.6*1e6); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); %}}} Index: /issm/trunk/test/NightlyRun/test521.m =================================================================== --- /issm/trunk/test/NightlyRun/test521.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test521.m (revision 9691) @@ -4,6 +4,6 @@ %impose hydrostatic equilibrium (required by Stokes) -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; md=extrude(md,3,1); md=setflowequation(md,'stokes','all'); Index: /issm/trunk/test/NightlyRun/test522.m =================================================================== --- /issm/trunk/test/NightlyRun/test522.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test522.m (revision 9691) @@ -4,6 +4,6 @@ %impose hydrostatic equilibrium (required by Stokes) -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; md=extrude(md,3,1); md=setflowequation(md,'stokes','all'); Index: /issm/trunk/test/NightlyRun/test527.m =================================================================== --- /issm/trunk/test/NightlyRun/test527.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test527.m (revision 9691) @@ -39,5 +39,5 @@ %refine existing mesh 5 -md2=bamg(md,'field',[md.inversion.vy_obs md.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); +md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); x7=md2.x; y7=md2.y; Index: /issm/trunk/test/NightlyRun/test603.m =================================================================== --- /issm/trunk/test/NightlyRun/test603.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test603.m (revision 9691) @@ -5,5 +5,5 @@ md=setflowequation(md,'macayeal','all'); md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md.cluster=none; md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test604.m =================================================================== --- /issm/trunk/test/NightlyRun/test604.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test604.m (revision 9691) @@ -5,5 +5,5 @@ md=setflowequation(md,'macayeal','all'); md.prognostic.stabilization=3; -md.prognostic.spcthickness=md.thickness; +md.prognostic.spcthickness=md.geometry.thickness; md.cluster=generic('name',oshostname(),'np',3); md=solve(md,PrognosticSolutionEnum); Index: /issm/trunk/test/NightlyRun/test621.m =================================================================== --- /issm/trunk/test/NightlyRun/test621.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test621.m (revision 9691) @@ -9,5 +9,5 @@ md.inversion.iscontrol=1; md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.min_parameters=-50*ones(md.numberofnodes,1); md.inversion.max_parameters=50*ones(md.numberofnodes,1); Index: /issm/trunk/test/NightlyRun/test622.m =================================================================== --- /issm/trunk/test/NightlyRun/test622.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test622.m (revision 9691) @@ -9,5 +9,5 @@ md.inversion.iscontrol=1; md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.min_parameters=-50*ones(md.numberofnodes,1); md.inversion.max_parameters=50*ones(md.numberofnodes,1); Index: /issm/trunk/test/NightlyRun/test623.m =================================================================== --- /issm/trunk/test/NightlyRun/test623.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test623.m (revision 9691) @@ -10,5 +10,5 @@ md.inversion.iscontrol=1; md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.min_parameters=-50*ones(md.numberofnodes,1); md.inversion.max_parameters=50*ones(md.numberofnodes,1); Index: /issm/trunk/test/NightlyRun/test624.m =================================================================== --- /issm/trunk/test/NightlyRun/test624.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test624.m (revision 9691) @@ -10,5 +10,5 @@ md.inversion.iscontrol=1; md.inversion.control_parameters={'BalancethicknessThickeningRate'}; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.min_parameters=-50*ones(md.numberofnodes,1); md.inversion.max_parameters=50*ones(md.numberofnodes,1); Index: /issm/trunk/test/NightlyRun/test625.m =================================================================== --- /issm/trunk/test/NightlyRun/test625.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test625.m (revision 9691) @@ -8,10 +8,10 @@ md=modelextract(md,md.mask.elementongroundedice); pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); %control parameters -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.iscontrol=1; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.nsteps=2; md.inversion.control_parameters={'Vx' 'Vy'}; Index: /issm/trunk/test/NightlyRun/test626.m =================================================================== --- /issm/trunk/test/NightlyRun/test626.m (revision 9690) +++ /issm/trunk/test/NightlyRun/test626.m (revision 9691) @@ -8,10 +8,10 @@ md=modelextract(md,md.mask.elementongroundedice); pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); %control parameters -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.iscontrol=1; -md.inversion.thickness_obs=md.thickness; +md.inversion.thickness_obs=md.geometry.thickness; md.inversion.nsteps=2; md.inversion.control_parameters={'Vx' 'Vy'}; Index: /issm/trunk/test/Par/79North.par =================================================================== --- /issm/trunk/test/Par/79North.par (revision 9690) +++ /issm/trunk/test/Par/79North.par (revision 9691) @@ -5,7 +5,7 @@ md.initialization.vx =InterpFromMeshToMesh2d(index,x,y,vx,md.x,md.y); md.initialization.vy =InterpFromMeshToMesh2d(index,x,y,vy,md.x,md.y); -md.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); -md.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); -md.bed=md.surface-md.thickness; +md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); +md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); +md.geometry.bed=md.geometry.surface-md.geometry.thickness; clear surface thickness vx vy x y index; @@ -45,6 +45,6 @@ md=SetMarineIceSheetBC(md); pos=find(md.nodeonboundary); -md.balancethickness.spcthickness(pos)=md.thickness(pos); -md.prognostic.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); +md.prognostic.spcthickness(pos)=md.geometry.thickness(pos); %Change name so that no test have the same name Index: /issm/trunk/test/Par/ISMIPA.par =================================================================== --- /issm/trunk/test/Par/ISMIPA.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPA.par (revision 9691) @@ -2,7 +2,7 @@ disp(' creating thickness'); -md.surface=-md.x*tan(0.5*pi/180); -md.bed=md.surface-1000+500*sin(md.x*2*pi/max(md.x)).*sin(md.y*2*pi/max(md.x)); -md.thickness=md.surface-md.bed; +md.geometry.surface=-md.x*tan(0.5*pi/180); +md.geometry.bed=md.geometry.surface-1000+500*sin(md.x*2*pi/max(md.x)).*sin(md.y*2*pi/max(md.x)); +md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); Index: /issm/trunk/test/Par/ISMIPB.par =================================================================== --- /issm/trunk/test/Par/ISMIPB.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPB.par (revision 9691) @@ -2,7 +2,7 @@ disp(' creating thickness'); -md.surface=-md.x*tan(0.5*pi/180); -md.bed=md.surface-1000+500*sin(md.x*2*pi/max(md.x)); -md.thickness=md.surface-md.bed; +md.geometry.surface=-md.x*tan(0.5*pi/180); +md.geometry.bed=md.geometry.surface-1000+500*sin(md.x*2*pi/max(md.x)); +md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); Index: /issm/trunk/test/Par/ISMIPC.par =================================================================== --- /issm/trunk/test/Par/ISMIPC.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPC.par (revision 9691) @@ -2,10 +2,10 @@ disp(' creating thickness'); -md.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 -md.bed=md.surface-1000; -md.thickness=md.surface-md.bed; +md.geometry.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 +md.geometry.bed=md.geometry.surface-1000; +md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); -%md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x/2)).*sin(md.y*2*pi/max(md.x/2)))./(md.constants.g*(md.materials.rho_ice*md.thickness+md.materials.rho_water*md.bed))); +%md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x/2)).*sin(md.y*2*pi/max(md.x/2)))./(md.constants.g*(md.materials.rho_ice*md.geometry.thickness+md.materials.rho_water*md.geometry.bed))); md.friction.coefficient=sqrt(md.constants.yts.*(1000+1000*sin(md.x*2*pi/max(md.x)).*sin(md.y*2*pi/max(md.x)))); %Take care of iceshelves: no basal drag Index: /issm/trunk/test/Par/ISMIPD.par =================================================================== --- /issm/trunk/test/Par/ISMIPD.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPD.par (revision 9691) @@ -2,7 +2,7 @@ disp(' creating thickness'); -md.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 -md.bed=md.surface-1000; -md.thickness=md.surface-md.bed; +md.geometry.surface=2000-md.x*tan(0.1*pi/180); %to have z>0 +md.geometry.bed=md.geometry.surface-1000; +md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); Index: /issm/trunk/test/Par/ISMIPE.par =================================================================== --- /issm/trunk/test/Par/ISMIPE.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPE.par (revision 9691) @@ -4,6 +4,6 @@ data=load('../Data/ISMIPE.data','-mat'); data=data.data; -md.surface=zeros(md.numberofnodes,1); -md.bed=zeros(md.numberofnodes,1); +md.geometry.surface=zeros(md.numberofnodes,1); +md.geometry.bed=zeros(md.numberofnodes,1); for i=1:md.numberofnodes y=md.y(i); @@ -11,10 +11,10 @@ point2=min(point1+1,51); coeff=(y-(point1-1)*100)/100; - md.bed(i)=(1-coeff)*data(point1,2)+coeff*data(point2,2); - md.surface(i)=(1-coeff)*data(point1,3)+coeff*data(point2,3); + md.geometry.bed(i)=(1-coeff)*data(point1,2)+coeff*data(point2,2); + md.geometry.surface(i)=(1-coeff)*data(point1,3)+coeff*data(point2,3); end -md.thickness=md.surface-md.bed; -md.thickness(find(~md.thickness))=0.01; -md.bed=md.surface-md.thickness; +md.geometry.thickness=md.geometry.surface-md.geometry.bed; +md.geometry.thickness(find(~md.geometry.thickness))=0.01; +md.geometry.bed=md.geometry.surface-md.geometry.thickness; disp(' creating drag'); Index: /issm/trunk/test/Par/ISMIPF.par =================================================================== --- /issm/trunk/test/Par/ISMIPF.par (revision 9690) +++ /issm/trunk/test/Par/ISMIPF.par (revision 9691) @@ -3,8 +3,8 @@ disp(' creating thickness'); -md.surface=-md.x*tan(3*pi/180); -%md.bed=md.surface-1000; -md.bed=md.surface-1000+100*exp(-((md.x-max(md.x)/2).^2+(md.y-max(md.y)/2).^2)/(10000^2)); -md.thickness=md.surface-md.bed; +md.geometry.surface=-md.x*tan(3*pi/180); +%md.geometry.bed=md.geometry.surface-1000; +md.geometry.bed=md.geometry.surface-1000+100*exp(-((md.x-max(md.x)/2).^2+(md.y-max(md.y)/2).^2)/(10000^2)); +md.geometry.thickness=md.geometry.surface-md.geometry.bed; disp(' creating drag'); @@ -30,7 +30,7 @@ pos=find(md.x==min(md.x) | md.x==max(md.x) | md.y==min(md.y) | md.y==max(md.y)); md.balancethickness.spcthickness=NaN*ones(md.numberofnodes,1); -md.balancethickness.spcthickness(pos)=md.thickness(pos); +md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos); md.prognostic.spcthickness=NaN*ones(md.numberofnodes,1); -md.prognostic.spcthickness(pos)=md.thickness(pos); +md.prognostic.spcthickness(pos)=md.geometry.thickness(pos); md.thermal.spctemperature=255*ones(md.numberofnodes,1); md.basalforcings.geothermalflux=0.4*ones(md.numberofnodes,1); Index: /issm/trunk/test/Par/Pig.par =================================================================== --- /issm/trunk/test/Par/Pig.par (revision 9690) +++ /issm/trunk/test/Par/Pig.par (revision 9691) @@ -5,7 +5,7 @@ md.inversion.vx_obs =InterpFromMeshToMesh2d(index,x,y,vx_obs,md.x,md.y); md.inversion.vy_obs =InterpFromMeshToMesh2d(index,x,y,vy_obs,md.x,md.y); -md.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); -md.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); -md.bed=md.surface-md.thickness; +md.geometry.surface =InterpFromMeshToMesh2d(index,x,y,surface,md.x,md.y); +md.geometry.thickness=InterpFromMeshToMesh2d(index,x,y,thickness,md.x,md.y); +md.geometry.bed=md.geometry.surface-md.geometry.thickness; clear surface thickness vx_obs vy_obs x y index; md.initialization.vx=md.inversion.vx_obs; Index: /issm/trunk/test/Par/RoundSheetEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 9690) +++ /issm/trunk/test/Par/RoundSheetEISMINT.par (revision 9691) @@ -1,7 +1,7 @@ %Ok, start defining model parameters here disp(' creating thickness'); -md.thickness=10*ones(md.numberofnodes,1); -md.bed=zeros(md.numberofnodes,1); -md.surface=md.bed+md.thickness; +md.geometry.thickness=10*ones(md.numberofnodes,1); +md.geometry.bed=zeros(md.numberofnodes,1); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); @@ -29,6 +29,6 @@ disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.x.*(md.thickness).^-1; -md.inversion.vy_obs=constant/2*md.y.*(md.thickness).^-1; +md.inversion.vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); md.initialization.vx=zeros(md.numberofnodes,1); Index: /issm/trunk/test/Par/RoundSheetShelf.par =================================================================== --- /issm/trunk/test/Par/RoundSheetShelf.par (revision 9690) +++ /issm/trunk/test/Par/RoundSheetShelf.par (revision 9691) @@ -10,26 +10,26 @@ ymin=min(radius); ymax=max(radius); -md.thickness=hmax+(hmin-hmax)*(radius-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(radius-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; pos=find(md.mask.vertexongroundedice); -md.bed(pos)=md.bed(pos)-300*(radius(pos)-(rad-shelfextent))/(rad-shelfextent); -md.surface=md.bed+md.thickness; +md.geometry.bed(pos)=md.geometry.bed(pos)-300*(radius(pos)-(rad-shelfextent))/(rad-shelfextent); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; pos=find(radius<200000); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); pos=find(md.x<.2*1e6 & md.x>-.2*1e6 & md.y>0); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); pos=find(md.x<.1*1e6 & md.x>-.1*1e6 & md.y<-.5*1e6 & md.y>-.6*1e6); -md.thickness(pos)=100; -md.bed(pos)=-di*md.thickness(pos)-20; -md.surface(pos)=md.bed(pos)+md.thickness(pos); +md.geometry.thickness(pos)=100; +md.geometry.bed(pos)=-di*md.geometry.thickness(pos)-20; +md.geometry.surface(pos)=md.geometry.bed(pos)+md.geometry.thickness(pos); %Initial velocity @@ -71,6 +71,6 @@ %bathymetry and grounding line migration: md.groundingline.migration='AgressiveMigration'; -md.bathymetry=md.bed; -pos=find(md.mask.vertexonfloatingice); md.bathymetry(pos)=md.bed(pos)-900; +md.geometry.bathymetry=md.geometry.bed; +pos=find(md.mask.vertexonfloatingice); md.geometry.bathymetry(pos)=md.geometry.bed(pos)-900; %Deal with boundary conditions: Index: /issm/trunk/test/Par/RoundSheetStaticEISMINT.par =================================================================== --- /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9690) +++ /issm/trunk/test/Par/RoundSheetStaticEISMINT.par (revision 9691) @@ -4,7 +4,7 @@ radius=(sqrt((md.x).^2+(md.y).^2)); radiusmax=max(radius); -md.thickness=hmin*ones(size(md.x,1),1)+hmax*(4*((1/2)^(4/3)*ones(size(md.x,1),1)-((radius)./(2*radiusmax)).^(4/3))).^(3/8); -md.bed=0*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmin*ones(size(md.x,1),1)+hmax*(4*((1/2)^(4/3)*ones(size(md.x,1),1)-((radius)./(2*radiusmax)).^(4/3))).^(3/8); +md.geometry.bed=0*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); @@ -34,6 +34,6 @@ disp(' creating velocities'); constant=0.3; -md.inversion.vx_obs=constant/2*md.x.*(md.thickness).^-1; -md.inversion.vy_obs=constant/2*md.y.*(md.thickness).^-1; +md.inversion.vx_obs=constant/2*md.x.*(md.geometry.thickness).^-1; +md.inversion.vy_obs=constant/2*md.y.*(md.geometry.thickness).^-1; md.inversion.vel_obs=(sqrt((md.inversion.vx_obs).^2+(md.inversion.vy_obs).^2)); md.initialization.vx=zeros(md.numberofnodes,1); Index: /issm/trunk/test/Par/SquareEISMINT.par =================================================================== --- /issm/trunk/test/Par/SquareEISMINT.par (revision 9690) +++ /issm/trunk/test/Par/SquareEISMINT.par (revision 9691) @@ -4,7 +4,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=500*ones(md.numberofnodes,1); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=500*ones(md.numberofnodes,1); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating drag'); Index: /issm/trunk/test/Par/SquareSheetConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9690) +++ /issm/trunk/test/Par/SquareSheetConstrained.par (revision 9691) @@ -6,7 +6,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness+20; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness+20; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity Index: /issm/trunk/test/Par/SquareSheetShelf.par =================================================================== --- /issm/trunk/test/Par/SquareSheetShelf.par (revision 9690) +++ /issm/trunk/test/Par/SquareSheetShelf.par (revision 9691) @@ -6,10 +6,10 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; bed_sheet=-md.materials.rho_ice/md.materials.rho_water*(hmax+(hmin-hmax)*(ymax/2-ymin)/(ymax-ymin)); pos=find(md.y<=ymax/2); -md.bed(pos)=bed_sheet; -md.surface=md.bed+md.thickness; +md.geometry.bed(pos)=bed_sheet; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity Index: /issm/trunk/test/Par/SquareShelf.par =================================================================== --- /issm/trunk/test/Par/SquareShelf.par (revision 9690) +++ /issm/trunk/test/Par/SquareShelf.par (revision 9691) @@ -6,7 +6,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity and pressure Index: /issm/trunk/test/Par/SquareShelfConstrained.par =================================================================== --- /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9690) +++ /issm/trunk/test/Par/SquareShelfConstrained.par (revision 9691) @@ -6,7 +6,7 @@ ymin=min(md.y); ymax=max(md.y); -md.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); -md.bed=-md.materials.rho_ice/md.materials.rho_water*md.thickness; -md.surface=md.bed+md.thickness; +md.geometry.thickness=hmax+(hmin-hmax)*(md.y-ymin)/(ymax-ymin); +md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; +md.geometry.surface=md.geometry.bed+md.geometry.thickness; %Initial velocity Index: /issm/trunk/test/Par/SquareThermal.par =================================================================== --- /issm/trunk/test/Par/SquareThermal.par (revision 9690) +++ /issm/trunk/test/Par/SquareThermal.par (revision 9691) @@ -5,7 +5,7 @@ disp(' creating thickness'); h=1000; -md.thickness=h*ones(md.numberofnodes,1); -md.bed=-1000*ones(md.numberofnodes,1); -md.surface=md.bed+md.thickness; +md.geometry.thickness=h*ones(md.numberofnodes,1); +md.geometry.bed=-1000*ones(md.numberofnodes,1); +md.geometry.surface=md.geometry.bed+md.geometry.thickness; disp(' creating velocities');