Changeset 9679

Timestamp:

09/08/11 08:07:18 (14 years ago)

Author:

seroussi

Message:

added diagnostic class

Location:

issm/trunk

Files:

• src/c/EnumDefinitions/EnumDefinitions.h (modified) (12 diffs)
• src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp (modified) (1 diff)
• src/c/modules/EnumToStringx/EnumToStringx.cpp (modified) (12 diffs)
• src/c/modules/ModelProcessorx/CreateParameters.cpp (modified) (4 diffs)
• src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp (modified) (2 diffs)
• src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp (modified) (3 diffs)
• src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp (modified) (2 diffs)
• src/c/modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp (modified) (3 diffs)
• src/c/modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp (modified) (3 diffs)
• src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp (modified) (1 diff)
• src/c/modules/RequestedOutputsx/RequestedOutputsx.cpp (modified) (2 diffs)
• src/c/modules/RequestedOutputsx/RequestedOutputsx.h (modified) (1 diff)
• src/c/modules/StringToEnumx/StringToEnumx.cpp (modified) (12 diffs)
• src/c/objects/Elements/Penta.cpp (modified) (18 diffs)
• src/c/objects/Elements/Tria.cpp (modified) (1 diff)
• src/c/objects/Loads/Icefront.cpp (modified) (2 diffs)
• src/c/objects/Loads/Pengrid.cpp (modified) (1 diff)
• src/c/objects/Loads/Penpair.cpp (modified) (2 diffs)
• src/c/objects/Loads/Riftfront.cpp (modified) (2 diffs)
• src/c/solutions/convergence.cpp (modified) (1 diff)
• src/c/solutions/diagnostic_core.cpp (modified) (2 diffs)
• src/c/solutions/steadystate_core.cpp (modified) (2 diffs)
• src/c/solvers/solver_nonlinear.cpp (modified) (1 diff)
• src/c/solvers/solver_stokescoupling_nonlinear.cpp (modified) (1 diff)
• src/m/classes/diagnostic.m (added)
• src/m/classes/model/model.m (modified) (10 diffs)
• src/m/enum/BalancethicknessNumRequestedOutputsEnum.m (added)
• src/m/enum/DiagnosticAbstolEnum.m (added)
• src/m/enum/DiagnosticIcefrontEnum.m (added)
• src/m/enum/DiagnosticMaxiterEnum.m (added)
• src/m/enum/DiagnosticNumRequestedOutputsEnum.m (added)
• src/m/enum/DiagnosticPenaltyFactorEnum.m (added)
• src/m/enum/DiagnosticRefEnum.m (deleted)
• src/m/enum/DiagnosticReferentialEnum.m (added)
• src/m/enum/DiagnosticReltolEnum.m (added)
• src/m/enum/DiagnosticRequestedOutputsEnum.m (added)
• src/m/enum/DiagnosticRestolEnum.m (added)
• src/m/enum/DiagnosticRiftPenaltyLockEnum.m (added)
• src/m/enum/DiagnosticRiftPenaltyThresholdEnum.m (added)
• src/m/enum/DiagnosticShelfDampeningEnum.m (added)
• src/m/enum/DiagnosticSpcvxEnum.m (added)
• src/m/enum/DiagnosticSpcvyEnum.m (added)
• src/m/enum/DiagnosticSpcvzEnum.m (added)
• src/m/enum/DiagnosticStokesreconditioningEnum.m (added)
• src/m/enum/DiagnosticVertexPairingEnum.m (added)
• src/m/enum/DiagnosticViscosityOvershootEnum.m (added)
• src/m/enum/EpsAbsEnum.m (deleted)
• src/m/enum/EpsRelEnum.m (deleted)
• src/m/enum/EpsResEnum.m (deleted)
• src/m/enum/MaxNonlinearIterationsEnum.m (deleted)
• src/m/enum/MinMechanicalConstraintsEnum.m (deleted)
• src/m/enum/NumRequestedOutputsEnum.m (deleted)
• src/m/enum/PenaltiesEnum.m (deleted)
• src/m/enum/PenaltyLockEnum.m (deleted)
• src/m/enum/PenaltyOffsetEnum.m (deleted)
• src/m/enum/PressureloadEnum.m (deleted)
• src/m/enum/PrognosticNumRequestedOutputsEnum.m (added)
• src/m/enum/RequestedOutputsEnum.m (deleted)
• src/m/enum/ShelfDampeningEnum.m (deleted)
• src/m/enum/SpcvxEnum.m (deleted)
• src/m/enum/SpcvyEnum.m (deleted)
• src/m/enum/SpcvzEnum.m (deleted)
• src/m/enum/SteadystateNumRequestedOutputsEnum.m (added)
• src/m/enum/StokesreconditioningEnum.m (deleted)
• src/m/enum/ThermalNumRequestedOutputsEnum.m (added)
• src/m/enum/TransientNumRequestedOutputsEnum.m (added)
• src/m/enum/ViscosityOvershootEnum.m (deleted)
• src/m/model/BasinConstrain.m (modified) (2 diffs)
• src/m/model/BasinConstrainShelf.m (modified) (3 diffs)
• src/m/model/collapse.m (modified) (1 diff)
• src/m/model/contourmassbalance.m (modified) (1 diff)
• src/m/model/display/displaybc.m (modified) (1 diff)
• src/m/model/display/displaydiagnostic.m (deleted)
• src/m/model/extrude.m (modified) (1 diff)
• src/m/model/ismodelselfconsistent.m (modified) (6 diffs)
• src/m/model/marshall.m (modified) (1 diff)
• src/m/model/modelextract.m (modified) (2 diffs)
• src/m/model/plot/plot_BC.m (modified) (1 diff)
• src/m/model/plot/plot_pressureload.m (modified) (1 diff)
• src/m/model/setflowequation.m (modified) (3 diffs)
• src/m/solutions/convergence.m (modified) (5 diffs)
• src/m/solvers/solver_nonlinear.m (modified) (3 diffs)
• src/m/utils/BC/SetIceSheetBC.m (modified) (2 diffs)
• src/m/utils/BC/SetIceShelfBC.m (modified) (2 diffs)
• src/m/utils/BC/SetMarineIceSheetBC.m (modified) (2 diffs)
• template (modified) (1 diff)
• test/Miscellaneous/Bump/Bump.par (modified) (1 diff)
• test/NightlyRun/test1101.m (modified) (2 diffs)
• test/NightlyRun/test1102.m (modified) (2 diffs)
• test/NightlyRun/test1103.m (modified) (2 diffs)
• test/NightlyRun/test1104.m (modified) (2 diffs)
• test/NightlyRun/test1105.m (modified) (2 diffs)
• test/NightlyRun/test1106.m (modified) (1 diff)
• test/NightlyRun/test1107.m (modified) (2 diffs)
• test/NightlyRun/test1108.m (modified) (2 diffs)
• test/NightlyRun/test1109.m (modified) (1 diff)
• test/NightlyRun/test1110.m (modified) (3 diffs)
• test/NightlyRun/test1203.m (modified) (1 diff)
• test/NightlyRun/test1204.m (modified) (1 diff)
• test/NightlyRun/test1205.m (modified) (1 diff)
• test/NightlyRun/test1206.m (modified) (1 diff)
• test/NightlyRun/test1207.m (modified) (1 diff)
• test/NightlyRun/test1208.m (modified) (1 diff)
• test/NightlyRun/test221.m (modified) (1 diff)
• test/NightlyRun/test222.m (modified) (1 diff)
• test/NightlyRun/test232.m (modified) (1 diff)
• test/NightlyRun/test233.m (modified) (2 diffs)
• test/NightlyRun/test234.m (modified) (2 diffs)
• test/NightlyRun/test235.m (modified) (2 diffs)
• test/NightlyRun/test236.m (modified) (2 diffs)
• test/NightlyRun/test423.m (modified) (1 diff)
• test/NightlyRun/test424.m (modified) (1 diff)
• test/NightlyRun/test425.m (modified) (1 diff)
• test/NightlyRun/test426.m (modified) (1 diff)
• test/NightlyRun/test427.m (modified) (2 diffs)
• test/NightlyRun/test428.m (modified) (2 diffs)
• test/NightlyRun/test434.m (modified) (2 diffs)
• test/NightlyRun/test439.m (modified) (1 diff)
• test/NightlyRun/test440.m (modified) (1 diff)
• test/NightlyRun/test443.m (modified) (1 diff)
• test/NightlyRun/test444.m (modified) (1 diff)
• test/Par/79North.par (modified) (2 diffs)
• test/Par/ISMIPF.par (modified) (1 diff)
• test/Par/Pig.par (modified) (2 diffs)
• test/Par/RoundSheetEISMINT.par (modified) (1 diff)
• test/Par/RoundSheetShelf.par (modified) (2 diffs)
• test/Par/RoundSheetStaticEISMINT.par (modified) (1 diff)
• test/Par/SquareSheetConstrained.par (modified) (1 diff)
• test/Par/SquareSheetShelf.par (modified) (1 diff)
• test/Par/SquareShelf.par (modified) (1 diff)
• test/Par/SquareShelfConstrained.par (modified) (1 diff)

issm/trunk/src/c/EnumDefinitions/EnumDefinitions.h

@@ -42 +42 @@
         ThermalPenaltyFactorEnum,
         ThermalRequestedOutputsEnum,
+        ThermalNumRequestedOutputsEnum,
         MiscellaneousNameEnum, //FIXME: only used by qmu, should not be marshalled (already in queueing script)
         TimesteppingTimeStepEnum,
@@ -53 +54 @@
         PrognosticPenaltyFactorEnum,
         PrognosticRequestedOutputsEnum,
+        PrognosticNumRequestedOutputsEnum,
         MaterialsRheologyBEnum,
         MaterialsRheologyBbarEnum,
@@ -83 +85 @@
         BalancethicknessStabilizationEnum,
         BalancethicknessRequestedOutputsEnum,
+        BalancethicknessNumRequestedOutputsEnum,
         FlowequationIshutterEnum,
         FlowequationIsmacayealpattynEnum,
@@ -92 +95 @@
         FlowequationBordermacayealEnum,
         SteadystateRequestedOutputsEnum,
+        SteadystateNumRequestedOutputsEnum,
         SteadystateReltolEnum,
         SteadystateMaxiterEnum,
@@ -99 +103 @@
         TransientIsgroundinglineEnum,
         TransientRequestedOutputsEnum,
+        TransientNumRequestedOutputsEnum,
+        DiagnosticSpcvxEnum,
+        DiagnosticSpcvyEnum,
+        DiagnosticSpcvzEnum,
+        DiagnosticStokesreconditioningEnum,
+        DiagnosticIcefrontEnum,
+        DiagnosticReferentialEnum,
+        DiagnosticVertexPairingEnum,
+        DiagnosticPenaltyFactorEnum,
+        DiagnosticAbstolEnum,
+        DiagnosticReltolEnum,
+        DiagnosticRestolEnum,
+        DiagnosticMaxiterEnum,
+        DiagnosticShelfDampeningEnum,
+        DiagnosticRiftPenaltyLockEnum,
+        DiagnosticRiftPenaltyThresholdEnum,
+        DiagnosticRequestedOutputsEnum,
+        DiagnosticNumRequestedOutputsEnum,
+        DiagnosticViscosityOvershootEnum,
         /*}}}*/
         /*Datasets {{{1*/
@@ -277 +300 @@
         NodeonsurfaceEnum,
         NumberNodeToElementConnectivityEnum,
-        PenaltyOffsetEnum,
         PressureEnum,
         PressurePicardEnum,
@@ -284 +306 @@
         ResetPenaltiesEnum,
         SegmentOnIceShelfEnum,
-        ShelfDampeningEnum,
         SurfaceAreaEnum,
         SurfaceEnum,
@@ -298 +319 @@
         VelEnum,
         VelObsEnum,
-        ViscosityOvershootEnum,
         VxAverageEnum,
         VxEnum,
@@ -387 +407 @@
         ControlSteadyEnum,
         DimEnum,
-        EpsAbsEnum,
         EpsCmEnum,
-        EpsRelEnum,
-        EpsResEnum,
-        MaxNonlinearIterationsEnum,
-        MinMechanicalConstraintsEnum,
         NumberOfElementsEnum,
         NumberOfVerticesEnum,
@@ -446 +461 @@
         NumberOfElements2DEnum,
         NumControlTypeEnum,
-        SpcvyEnum,
         YEnum,
-        PenaltiesEnum,
-        PressureloadEnum,
-        SpcvzEnum,
         NumberOfNodes2DEnum,
         ZEnum,
-        PenaltyLockEnum,
-        SpcvxEnum,
         UpperelementsEnum,
         EdgesEnum,
@@ -462 +471 @@
         ElementconnectivityEnum,
         NumlayersEnum,
-        DiagnosticRefEnum,
-        StokesreconditioningEnum,
         LowerelementsEnum,
         NstepsEnum,
@@ -474 +481 @@
         WaitonlockEnum,
         NumberOfResponsesEnum,
-
-        RequestedOutputsEnum,
-        NumRequestedOutputsEnum,
         BasalFrictionEnum,
         ViscousHeatingEnum,

issm/trunk/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp

@@ -27 +27 @@
 
         /*recover parameters: */
-        parameters->FindParam(&min_mechanical_constraints,MinMechanicalConstraintsEnum);
+        parameters->FindParam(&min_mechanical_constraints,DiagnosticRiftPenaltyThresholdEnum);
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
 

issm/trunk/src/c/modules/EnumToStringx/EnumToStringx.cpp

@@ -46 +46 @@
                 case ThermalPenaltyFactorEnum : return "ThermalPenaltyFactor";
                 case ThermalRequestedOutputsEnum : return "ThermalRequestedOutputs";
+                case ThermalNumRequestedOutputsEnum : return "ThermalNumRequestedOutputs";
                 case MiscellaneousNameEnum : return "MiscellaneousName";
                 case TimesteppingTimeStepEnum : return "TimesteppingTimeStep";
@@ -57 +58 @@
                 case PrognosticPenaltyFactorEnum : return "PrognosticPenaltyFactor";
                 case PrognosticRequestedOutputsEnum : return "PrognosticRequestedOutputs";
+                case PrognosticNumRequestedOutputsEnum : return "PrognosticNumRequestedOutputs";
                 case MaterialsRheologyBEnum : return "MaterialsRheologyB";
                 case MaterialsRheologyBbarEnum : return "MaterialsRheologyBbar";
@@ -87 +89 @@
                 case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization";
                 case BalancethicknessRequestedOutputsEnum : return "BalancethicknessRequestedOutputs";
+                case BalancethicknessNumRequestedOutputsEnum : return "BalancethicknessNumRequestedOutputs";
                 case FlowequationIshutterEnum : return "FlowequationIshutter";
                 case FlowequationIsmacayealpattynEnum : return "FlowequationIsmacayealpattyn";
@@ -96 +99 @@
                 case FlowequationBordermacayealEnum : return "FlowequationBordermacayeal";
                 case SteadystateRequestedOutputsEnum : return "SteadystateRequestedOutputs";
+                case SteadystateNumRequestedOutputsEnum : return "SteadystateNumRequestedOutputs";
                 case SteadystateReltolEnum : return "SteadystateReltol";
                 case SteadystateMaxiterEnum : return "SteadystateMaxiter";
@@ -103 +107 @@
                 case TransientIsgroundinglineEnum : return "TransientIsgroundingline";
                 case TransientRequestedOutputsEnum : return "TransientRequestedOutputs";
+                case TransientNumRequestedOutputsEnum : return "TransientNumRequestedOutputs";
+                case DiagnosticSpcvxEnum : return "DiagnosticSpcvx";
+                case DiagnosticSpcvyEnum : return "DiagnosticSpcvy";
+                case DiagnosticSpcvzEnum : return "DiagnosticSpcvz";
+                case DiagnosticStokesreconditioningEnum : return "DiagnosticStokesreconditioning";
+                case DiagnosticIcefrontEnum : return "DiagnosticIcefront";
+                case DiagnosticReferentialEnum : return "DiagnosticReferential";
+                case DiagnosticVertexPairingEnum : return "DiagnosticVertexPairing";
+                case DiagnosticPenaltyFactorEnum : return "DiagnosticPenaltyFactor";
+                case DiagnosticAbstolEnum : return "DiagnosticAbstol";
+                case DiagnosticReltolEnum : return "DiagnosticReltol";
+                case DiagnosticRestolEnum : return "DiagnosticRestol";
+                case DiagnosticMaxiterEnum : return "DiagnosticMaxiter";
+                case DiagnosticShelfDampeningEnum : return "DiagnosticShelfDampening";
+                case DiagnosticRiftPenaltyLockEnum : return "DiagnosticRiftPenaltyLock";
+                case DiagnosticRiftPenaltyThresholdEnum : return "DiagnosticRiftPenaltyThreshold";
+                case DiagnosticRequestedOutputsEnum : return "DiagnosticRequestedOutputs";
+                case DiagnosticNumRequestedOutputsEnum : return "DiagnosticNumRequestedOutputs";
+                case DiagnosticViscosityOvershootEnum : return "DiagnosticViscosityOvershoot";
                 case ConstraintsEnum : return "Constraints";
                 case ElementsEnum : return "Elements";
@@ -244 +267 @@
                 case NodeonsurfaceEnum : return "Nodeonsurface";
                 case NumberNodeToElementConnectivityEnum : return "NumberNodeToElementConnectivity";
-                case PenaltyOffsetEnum : return "PenaltyOffset";
                 case PressureEnum : return "Pressure";
                 case PressurePicardEnum : return "PressurePicard";
@@ -251 +273 @@
                 case ResetPenaltiesEnum : return "ResetPenalties";
                 case SegmentOnIceShelfEnum : return "SegmentOnIceShelf";
-                case ShelfDampeningEnum : return "ShelfDampening";
                 case SurfaceAreaEnum : return "SurfaceArea";
                 case SurfaceEnum : return "Surface";
@@ -265 +286 @@
                 case VelEnum : return "Vel";
                 case VelObsEnum : return "VelObs";
-                case ViscosityOvershootEnum : return "ViscosityOvershoot";
                 case VxAverageEnum : return "VxAverage";
                 case VxEnum : return "Vx";
@@ -339 +359 @@
                 case ControlSteadyEnum : return "ControlSteady";
                 case DimEnum : return "Dim";
-                case EpsAbsEnum : return "EpsAbs";
                 case EpsCmEnum : return "EpsCm";
-                case EpsRelEnum : return "EpsRel";
-                case EpsResEnum : return "EpsRes";
-                case MaxNonlinearIterationsEnum : return "MaxNonlinearIterations";
-                case MinMechanicalConstraintsEnum : return "MinMechanicalConstraints";
                 case NumberOfElementsEnum : return "NumberOfElements";
                 case NumberOfVerticesEnum : return "NumberOfVertices";
@@ -390 +405 @@
                 case NumberOfElements2DEnum : return "NumberOfElements2D";
                 case NumControlTypeEnum : return "NumControlType";
-                case SpcvyEnum : return "Spcvy";
                 case YEnum : return "Y";
-                case PenaltiesEnum : return "Penalties";
-                case PressureloadEnum : return "Pressureload";
-                case SpcvzEnum : return "Spcvz";
                 case NumberOfNodes2DEnum : return "NumberOfNodes2D";
                 case ZEnum : return "Z";
-                case PenaltyLockEnum : return "PenaltyLock";
-                case SpcvxEnum : return "Spcvx";
                 case UpperelementsEnum : return "Upperelements";
                 case EdgesEnum : return "Edges";
@@ -406 +415 @@
                 case ElementconnectivityEnum : return "Elementconnectivity";
                 case NumlayersEnum : return "Numlayers";
-                case DiagnosticRefEnum : return "DiagnosticRef";
-                case StokesreconditioningEnum : return "Stokesreconditioning";
                 case LowerelementsEnum : return "Lowerelements";
                 case NstepsEnum : return "Nsteps";
@@ -418 +425 @@
                 case WaitonlockEnum : return "Waitonlock";
                 case NumberOfResponsesEnum : return "NumberOfResponses";
-                case RequestedOutputsEnum : return "RequestedOutputs";
-                case NumRequestedOutputsEnum : return "NumRequestedOutputs";
                 case BasalFrictionEnum : return "BasalFriction";
                 case ViscousHeatingEnum : return "ViscousHeating";

issm/trunk/src/c/modules/ModelProcessorx/CreateParameters.cpp

@@ -30 +30 @@
         parameters->AddObject(iomodel->CopyConstantObject(FlowequationIsstokesEnum));
         parameters->AddObject(iomodel->CopyConstantObject(OutputFrequencyEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(EpsResEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(EpsRelEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(EpsAbsEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(MaxNonlinearIterationsEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticRestolEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticReltolEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticAbstolEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticMaxiterEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SteadystateReltolEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SteadystateMaxiterEnum));
@@ -43 +43 @@
         parameters->AddObject(iomodel->CopyConstantObject(PrognosticHydrostaticAdjustmentEnum));
         parameters->AddObject(iomodel->CopyConstantObject(PrognosticStabilizationEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(PenaltyOffsetEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticPenaltyFactorEnum));
         parameters->AddObject(iomodel->CopyConstantObject(ThermalPenaltyFactorEnum));
         parameters->AddObject(iomodel->CopyConstantObject(SettingsLowmemEnum));
@@ -55 +55 @@
         parameters->AddObject(iomodel->CopyConstantObject(ThermalPenaltyThresholdEnum));
         parameters->AddObject(iomodel->CopyConstantObject(ThermalPenaltyLockEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(MinMechanicalConstraintsEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(StokesreconditioningEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(ShelfDampeningEnum));
-        parameters->AddObject(iomodel->CopyConstantObject(ViscosityOvershootEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticRiftPenaltyThresholdEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticStokesreconditioningEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticShelfDampeningEnum));
+        parameters->AddObject(iomodel->CopyConstantObject(DiagnosticViscosityOvershootEnum));
         parameters->AddObject(iomodel->CopyConstantObject(WaitonlockEnum));
         parameters->AddObject(iomodel->CopyConstantObject(NumberOfElementsEnum));
@@ -76 +76 @@
 
         /*Requested output?*/
-        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,RequestedOutputsEnum);
-        parameters->AddObject(new IntParam(NumRequestedOutputsEnum,numoutputs));
-        if(numoutputs)parameters->AddObject(new IntVecParam(RequestedOutputsEnum,requestedoutputs,numoutputs));
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,DiagnosticRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(DiagnosticNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(DiagnosticRequestedOutputsEnum,requestedoutputs,numoutputs));
+        xfree((void**)&requestedoutputs);
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,PrognosticRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(PrognosticNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(PrognosticRequestedOutputsEnum,requestedoutputs,numoutputs));
+        xfree((void**)&requestedoutputs);
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,ThermalRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(ThermalNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(ThermalRequestedOutputsEnum,requestedoutputs,numoutputs));
+        xfree((void**)&requestedoutputs);
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,TransientRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(TransientNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(TransientRequestedOutputsEnum,requestedoutputs,numoutputs));
+        xfree((void**)&requestedoutputs);
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,SteadystateRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(SteadystateNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(SteadystateRequestedOutputsEnum,requestedoutputs,numoutputs));
+        xfree((void**)&requestedoutputs);
+        iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,BalancethicknessRequestedOutputsEnum);
+        parameters->AddObject(new IntParam(BalancethicknessNumRequestedOutputsEnum,numoutputs));
+        if(numoutputs)parameters->AddObject(new IntVecParam(BalancethicknessRequestedOutputsEnum,requestedoutputs,numoutputs));
         xfree((void**)&requestedoutputs);
         

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateConstraintsDiagnosticHoriz.cpp

@@ -44 +44 @@
         iomodel->Constant(&g,ConstantsGEnum);
         iomodel->Constant(&rho_ice,MaterialsRhoIceEnum);
-        iomodel->Constant(&stokesreconditioning,StokesreconditioningEnum);
+        iomodel->Constant(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         iomodel->Constant(&isstokes,FlowequationIsstokesEnum);
         iomodel->Constant(&ismacayealpattyn,FlowequationIsmacayealpattynEnum);
@@ -61 +61 @@
         
         /*Constraints: fetch data: */
-        iomodel->FetchData(&spcvx,NULL,NULL,SpcvxEnum);
-        iomodel->FetchData(&spcvy,NULL,NULL,SpcvyEnum);
-        iomodel->FetchData(&spcvz,NULL,NULL,SpcvzEnum);
+        iomodel->FetchData(&spcvx,NULL,NULL,DiagnosticSpcvxEnum);
+        iomodel->FetchData(&spcvy,NULL,NULL,DiagnosticSpcvyEnum);
+        iomodel->FetchData(&spcvz,NULL,NULL,DiagnosticSpcvzEnum);
         iomodel->FetchData(&nodeonmacayeal,NULL,NULL,FlowequationBordermacayealEnum);
         if(dim==3)iomodel->FetchData(&nodeonpattyn,NULL,NULL,FlowequationBorderpattynEnum);

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateLoadsDiagnosticHoriz.cpp

@@ -60 +60 @@
         /*Create pressure loads as boundary conditions. Pay attention to the partitioning if we are running in parallel (the nodes
          * referenced by a certain load must belong to the cluster node): */
-        iomodel->FetchData(3,PressureloadEnum,ThicknessEnum,BedEnum);
-        iomodel->FetchData(&pressureload,&numberofpressureloads,NULL,PressureloadEnum);
+        iomodel->FetchData(3,DiagnosticIcefrontEnum,ThicknessEnum,BedEnum);
+        iomodel->FetchData(&pressureload,&numberofpressureloads,NULL,DiagnosticIcefrontEnum);
         iomodel->FetchData(&elements_type,NULL,NULL,FlowequationElementEquationEnum);
 
@@ -119 +119 @@
 
         /*Free data: */
-        iomodel->DeleteData(3,PressureloadEnum,ThicknessEnum,BedEnum);
+        iomodel->DeleteData(3,DiagnosticIcefrontEnum,ThicknessEnum,BedEnum);
         xfree((void**)&elements_type);
         xfree((void**)&pressureload);
@@ -149 +149 @@
 
         /*Create Penpair for penalties: */
-        iomodel->FetchData(&penalties,&numpenalties,NULL,PenaltiesEnum);
+        iomodel->FetchData(&penalties,&numpenalties,NULL,DiagnosticVertexPairingEnum);
         
         for(i=0;i<numpenalties;i++){

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHoriz/CreateNodesDiagnosticHoriz.cpp

@@ -46 +46 @@
         /*Create nodes: */
         iomodel->FetchData(9,NodeonbedEnum,NodeonsurfaceEnum,FlowequationBordermacayealEnum,FlowequationBorderstokesEnum,
-                                MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MaskVertexonwaterEnum,FlowequationVertexEquationEnum,DiagnosticRefEnum);
+                                MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MaskVertexonwaterEnum,FlowequationVertexEquationEnum,DiagnosticReferentialEnum);
         
         for (i=0;i<numberofvertices;i++){
@@ -59 +59 @@
         /*Clean fetched data: */
         iomodel->DeleteData(9,NodeonbedEnum,NodeonsurfaceEnum,FlowequationBordermacayealEnum,FlowequationBorderstokesEnum,
-                                MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MaskVertexonwaterEnum,FlowequationVertexEquationEnum,DiagnosticRefEnum);
+                                MaskVertexongroundediceEnum,MaskVertexonfloatingiceEnum,MaskVertexonwaterEnum,FlowequationVertexEquationEnum,DiagnosticReferentialEnum);
 
         /*Assign output pointer: */

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticHutter/CreateConstraintsDiagnosticHutter.cpp

@@ -42 +42 @@
 
         /*Fetch data: */
-        iomodel->FetchData(3,SpcvxEnum,SpcvyEnum,FlowequationVertexEquationEnum);
+        iomodel->FetchData(3,DiagnosticSpcvxEnum,DiagnosticSpcvyEnum,FlowequationVertexEquationEnum);
 
         /*Initialize conunter*/
@@ -60 +60 @@
                         }
                         else{
-                                if (!isnan(iomodel->Data(SpcvxEnum)[i])){
-                                        constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,1,iomodel->Data(SpcvxEnum)[i]/yts,DiagnosticHutterAnalysisEnum)); //add count'th spc, on node i+1, setting dof 1 to vx.
+                                if (!isnan(iomodel->Data(DiagnosticSpcvxEnum)[i])){
+                                        constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,1,iomodel->Data(DiagnosticSpcvxEnum)[i]/yts,DiagnosticHutterAnalysisEnum)); //add count'th spc, on node i+1, setting dof 1 to vx.
                                         count++;
                                 }
 
-                                if (!isnan(iomodel->Data(SpcvyEnum)[i])){
-                                        constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,2,iomodel->Data(SpcvyEnum)[i]/yts,DiagnosticHutterAnalysisEnum)); //add count'th spc, on node i+1, setting dof 2 to vy
+                                if (!isnan(iomodel->Data(DiagnosticSpcvyEnum)[i])){
+                                        constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,2,iomodel->Data(DiagnosticSpcvyEnum)[i]/yts,DiagnosticHutterAnalysisEnum)); //add count'th spc, on node i+1, setting dof 2 to vy
                                         count++;
                                 }
@@ -74 +74 @@
 
         /*Free data: */
-        iomodel->DeleteData(3,SpcvxEnum,SpcvyEnum,FlowequationVertexEquationEnum);
+        iomodel->DeleteData(3,DiagnosticSpcvxEnum,DiagnosticSpcvyEnum,FlowequationVertexEquationEnum);
         
         /*Assign output pointer: */

issm/trunk/src/c/modules/ModelProcessorx/DiagnosticVert/CreateConstraintsDiagnosticVert.cpp

@@ -41 +41 @@
 
         /*Fetch data: */
-        iomodel->FetchData(2,SpcvzEnum,FlowequationBorderstokesEnum);
+        iomodel->FetchData(2,DiagnosticSpcvzEnum,FlowequationBorderstokesEnum);
 
         /*Initialize counter*/
@@ -56 +56 @@
                                 count++;
                         }
-                        else if (!isnan(iomodel->Data(SpcvzEnum)[i])){
+                        else if (!isnan(iomodel->Data(DiagnosticSpcvzEnum)[i])){
                                 constraints->AddObject(new SpcStatic(iomodel->constraintcounter+count+1,iomodel->nodecounter+i+1,1,
-                                                                iomodel->Data(SpcvzEnum)[i]/yts,DiagnosticVertAnalysisEnum)); //add count'th spc, on node i+1, setting dof 1 to vx.
+                                                                iomodel->Data(DiagnosticSpcvzEnum)[i]/yts,DiagnosticVertAnalysisEnum)); //add count'th spc, on node i+1, setting dof 1 to vx.
                                 count++;
 
@@ -66 +66 @@
 
         /*Free data: */
-        iomodel->DeleteData(2,SpcvzEnum,FlowequationBorderstokesEnum);
+        iomodel->DeleteData(2,DiagnosticSpcvzEnum,FlowequationBorderstokesEnum);
 
         cleanup_and_return:

issm/trunk/src/c/modules/ModelProcessorx/ElementsAndVerticesPartitioning.cpp

@@ -130 +130 @@
          * penpair has 2 nodes that are poointing toward 2 vertices.
          * The 2 vertices must be in the same cpu as the penpair*/
-        iomodel->FetchData(&vertex_pairing,&numvertex_pairing,NULL,PenaltiesEnum);
+        iomodel->FetchData(&vertex_pairing,&numvertex_pairing,NULL,DiagnosticVertexPairingEnum);
         for(i=0;i<numvertex_pairing;i++){
                 if(my_vertices[(int)vertex_pairing[2*i+0]-1] && !my_vertices[(int)vertex_pairing[2*i+1]-1]){

issm/trunk/src/c/modules/RequestedOutputsx/RequestedOutputsx.cpp

@@ -9 +9 @@
 #include "../../EnumDefinitions/EnumDefinitions.h"
 
-void RequestedOutputsx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters, int step, double time){
-
+void RequestedOutputsx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters, int* requested_outputs, int numoutputs, int step, double time){
 
         int  i,o;
-        int  numoutputs        = 0;
-        int *requested_outputs = NULL;
         int  output_enum;
         Element* element=NULL;
 
         /*retrieve parameters: */
-        parameters->FindParam(&numoutputs,NumRequestedOutputsEnum);
-        if(numoutputs) parameters->FindParam(&requested_outputs,&numoutputs,RequestedOutputsEnum);
-
         if(numoutputs){
                 for(o=0;o<numoutputs;o++){
@@ -32 +26 @@
                 }
         }
-                
-        /*Free ressources:*/
-        xfree((void**)&requested_outputs);
-
 }

issm/trunk/src/c/modules/RequestedOutputsx/RequestedOutputsx.h

@@ -9 +9 @@
 
 /* local prototypes: */
-void RequestedOutputsx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters, int step=1, double time=0);
+void RequestedOutputsx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters, int* requested_outputs, int numoutputs, int step=1, double time=0);
 
 #endif  /* _INPUTTORESULTX_H */

issm/trunk/src/c/modules/StringToEnumx/StringToEnumx.cpp

@@ -44 +44 @@
         else if (strcmp(name,"ThermalPenaltyFactor")==0) return ThermalPenaltyFactorEnum;
         else if (strcmp(name,"ThermalRequestedOutputs")==0) return ThermalRequestedOutputsEnum;
+        else if (strcmp(name,"ThermalNumRequestedOutputs")==0) return ThermalNumRequestedOutputsEnum;
         else if (strcmp(name,"MiscellaneousName")==0) return MiscellaneousNameEnum;
         else if (strcmp(name,"TimesteppingTimeStep")==0) return TimesteppingTimeStepEnum;
@@ -55 +56 @@
         else if (strcmp(name,"PrognosticPenaltyFactor")==0) return PrognosticPenaltyFactorEnum;
         else if (strcmp(name,"PrognosticRequestedOutputs")==0) return PrognosticRequestedOutputsEnum;
+        else if (strcmp(name,"PrognosticNumRequestedOutputs")==0) return PrognosticNumRequestedOutputsEnum;
         else if (strcmp(name,"MaterialsRheologyB")==0) return MaterialsRheologyBEnum;
         else if (strcmp(name,"MaterialsRheologyBbar")==0) return MaterialsRheologyBbarEnum;
@@ -85 +87 @@
         else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum;
         else if (strcmp(name,"BalancethicknessRequestedOutputs")==0) return BalancethicknessRequestedOutputsEnum;
+        else if (strcmp(name,"BalancethicknessNumRequestedOutputs")==0) return BalancethicknessNumRequestedOutputsEnum;
         else if (strcmp(name,"FlowequationIshutter")==0) return FlowequationIshutterEnum;
         else if (strcmp(name,"FlowequationIsmacayealpattyn")==0) return FlowequationIsmacayealpattynEnum;
@@ -94 +97 @@
         else if (strcmp(name,"FlowequationBordermacayeal")==0) return FlowequationBordermacayealEnum;
         else if (strcmp(name,"SteadystateRequestedOutputs")==0) return SteadystateRequestedOutputsEnum;
+        else if (strcmp(name,"SteadystateNumRequestedOutputs")==0) return SteadystateNumRequestedOutputsEnum;
         else if (strcmp(name,"SteadystateReltol")==0) return SteadystateReltolEnum;
         else if (strcmp(name,"SteadystateMaxiter")==0) return SteadystateMaxiterEnum;
@@ -101 +105 @@
         else if (strcmp(name,"TransientIsgroundingline")==0) return TransientIsgroundinglineEnum;
         else if (strcmp(name,"TransientRequestedOutputs")==0) return TransientRequestedOutputsEnum;
+        else if (strcmp(name,"TransientNumRequestedOutputs")==0) return TransientNumRequestedOutputsEnum;
+        else if (strcmp(name,"DiagnosticSpcvx")==0) return DiagnosticSpcvxEnum;
+        else if (strcmp(name,"DiagnosticSpcvy")==0) return DiagnosticSpcvyEnum;
+        else if (strcmp(name,"DiagnosticSpcvz")==0) return DiagnosticSpcvzEnum;
+        else if (strcmp(name,"DiagnosticStokesreconditioning")==0) return DiagnosticStokesreconditioningEnum;
+        else if (strcmp(name,"DiagnosticIcefront")==0) return DiagnosticIcefrontEnum;
+        else if (strcmp(name,"DiagnosticReferential")==0) return DiagnosticReferentialEnum;
+        else if (strcmp(name,"DiagnosticVertexPairing")==0) return DiagnosticVertexPairingEnum;
+        else if (strcmp(name,"DiagnosticPenaltyFactor")==0) return DiagnosticPenaltyFactorEnum;
+        else if (strcmp(name,"DiagnosticAbstol")==0) return DiagnosticAbstolEnum;
+        else if (strcmp(name,"DiagnosticReltol")==0) return DiagnosticReltolEnum;
+        else if (strcmp(name,"DiagnosticRestol")==0) return DiagnosticRestolEnum;
+        else if (strcmp(name,"DiagnosticMaxiter")==0) return DiagnosticMaxiterEnum;
+        else if (strcmp(name,"DiagnosticShelfDampening")==0) return DiagnosticShelfDampeningEnum;
+        else if (strcmp(name,"DiagnosticRiftPenaltyLock")==0) return DiagnosticRiftPenaltyLockEnum;
+        else if (strcmp(name,"DiagnosticRiftPenaltyThreshold")==0) return DiagnosticRiftPenaltyThresholdEnum;
+        else if (strcmp(name,"DiagnosticRequestedOutputs")==0) return DiagnosticRequestedOutputsEnum;
+        else if (strcmp(name,"DiagnosticNumRequestedOutputs")==0) return DiagnosticNumRequestedOutputsEnum;
+        else if (strcmp(name,"DiagnosticViscosityOvershoot")==0) return DiagnosticViscosityOvershootEnum;
         else if (strcmp(name,"Constraints")==0) return ConstraintsEnum;
         else if (strcmp(name,"Elements")==0) return ElementsEnum;
@@ -242 +265 @@
         else if (strcmp(name,"Nodeonsurface")==0) return NodeonsurfaceEnum;
         else if (strcmp(name,"NumberNodeToElementConnectivity")==0) return NumberNodeToElementConnectivityEnum;
-        else if (strcmp(name,"PenaltyOffset")==0) return PenaltyOffsetEnum;
         else if (strcmp(name,"Pressure")==0) return PressureEnum;
         else if (strcmp(name,"PressurePicard")==0) return PressurePicardEnum;
@@ -249 +271 @@
         else if (strcmp(name,"ResetPenalties")==0) return ResetPenaltiesEnum;
         else if (strcmp(name,"SegmentOnIceShelf")==0) return SegmentOnIceShelfEnum;
-        else if (strcmp(name,"ShelfDampening")==0) return ShelfDampeningEnum;
         else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum;
         else if (strcmp(name,"Surface")==0) return SurfaceEnum;
@@ -263 +284 @@
         else if (strcmp(name,"Vel")==0) return VelEnum;
         else if (strcmp(name,"VelObs")==0) return VelObsEnum;
-        else if (strcmp(name,"ViscosityOvershoot")==0) return ViscosityOvershootEnum;
         else if (strcmp(name,"VxAverage")==0) return VxAverageEnum;
         else if (strcmp(name,"Vx")==0) return VxEnum;
@@ -337 +357 @@
         else if (strcmp(name,"ControlSteady")==0) return ControlSteadyEnum;
         else if (strcmp(name,"Dim")==0) return DimEnum;
-        else if (strcmp(name,"EpsAbs")==0) return EpsAbsEnum;
         else if (strcmp(name,"EpsCm")==0) return EpsCmEnum;
-        else if (strcmp(name,"EpsRel")==0) return EpsRelEnum;
-        else if (strcmp(name,"EpsRes")==0) return EpsResEnum;
-        else if (strcmp(name,"MaxNonlinearIterations")==0) return MaxNonlinearIterationsEnum;
-        else if (strcmp(name,"MinMechanicalConstraints")==0) return MinMechanicalConstraintsEnum;
         else if (strcmp(name,"NumberOfElements")==0) return NumberOfElementsEnum;
         else if (strcmp(name,"NumberOfVertices")==0) return NumberOfVerticesEnum;
@@ -388 +403 @@
         else if (strcmp(name,"NumberOfElements2D")==0) return NumberOfElements2DEnum;
         else if (strcmp(name,"NumControlType")==0) return NumControlTypeEnum;
-        else if (strcmp(name,"Spcvy")==0) return SpcvyEnum;
         else if (strcmp(name,"Y")==0) return YEnum;
-        else if (strcmp(name,"Penalties")==0) return PenaltiesEnum;
-        else if (strcmp(name,"Pressureload")==0) return PressureloadEnum;
-        else if (strcmp(name,"Spcvz")==0) return SpcvzEnum;
         else if (strcmp(name,"NumberOfNodes2D")==0) return NumberOfNodes2DEnum;
         else if (strcmp(name,"Z")==0) return ZEnum;
-        else if (strcmp(name,"PenaltyLock")==0) return PenaltyLockEnum;
-        else if (strcmp(name,"Spcvx")==0) return SpcvxEnum;
         else if (strcmp(name,"Upperelements")==0) return UpperelementsEnum;
         else if (strcmp(name,"Edges")==0) return EdgesEnum;
@@ -404 +413 @@
         else if (strcmp(name,"Elementconnectivity")==0) return ElementconnectivityEnum;
         else if (strcmp(name,"Numlayers")==0) return NumlayersEnum;
-        else if (strcmp(name,"DiagnosticRef")==0) return DiagnosticRefEnum;
-        else if (strcmp(name,"Stokesreconditioning")==0) return StokesreconditioningEnum;
         else if (strcmp(name,"Lowerelements")==0) return LowerelementsEnum;
         else if (strcmp(name,"Nsteps")==0) return NstepsEnum;
@@ -416 +423 @@
         else if (strcmp(name,"Waitonlock")==0) return WaitonlockEnum;
         else if (strcmp(name,"NumberOfResponses")==0) return NumberOfResponsesEnum;
-        else if (strcmp(name,"RequestedOutputs")==0) return RequestedOutputsEnum;
-        else if (strcmp(name,"NumRequestedOutputs")==0) return NumRequestedOutputsEnum;
         else if (strcmp(name,"BasalFriction")==0) return BasalFrictionEnum;
         else if (strcmp(name,"ViscousHeating")==0) return ViscousHeatingEnum;

issm/trunk/src/c/objects/Elements/Penta.cpp

@@ -426 +426 @@
 
         /*retrieve some parameters: */
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         
         if(!IsOnBed()){
@@ -757 +757 @@
         /* Get node coordinates and dof list: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        this->parameters->FindParam(&viscosity_overshoot,ViscosityOvershootEnum);
+        this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
         Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
@@ -939 +939 @@
         /* Get node coordinates and dof list: */
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
@@ -1030 +1030 @@
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-        parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
@@ -1285 +1285 @@
         /*Retrieve all inputs and parameters*/
         GetVerticesCoordinates(&xyz_list[0][0], nodes,NUMVERTICES);
-        this->parameters->FindParam(&viscosity_overshoot,ViscosityOvershootEnum);
+        this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
         Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
@@ -1427 +1427 @@
         inputs->GetParameterValue(&approximation,ApproximationEnum);
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        this->parameters->FindParam(&viscosity_overshoot,ViscosityOvershootEnum);
+        this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
         Input* vx_input=inputs->GetInput(VxEnum);       _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);       _assert_(vy_input);
@@ -1588 +1588 @@
         /*Retrieve all inputs and parameters*/
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
@@ -1657 +1657 @@
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-        parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum); _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum); _assert_(vy_input);
@@ -2484 +2484 @@
         /*Retrieve all inputs and parameters*/
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
@@ -2549 +2549 @@
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
@@ -2629 +2629 @@
         /*Retrieve all inputs and parameters*/
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
@@ -2694 +2694 @@
         GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES);
         parameters->FindParam(&analysis_type,AnalysisTypeEnum);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         Input* vx_input=inputs->GetInput(VxEnum);               _assert_(vx_input);
         Input* vy_input=inputs->GetInput(VyEnum);               _assert_(vy_input);
@@ -3000 +3000 @@
 
         /*Retrieve all inputs and parameters*/
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         rho_ice=matpar->GetRhoIce();
         gravity=matpar->GetG();
@@ -3068 +3068 @@
         if(!IsOnBed() || !IsOnShelf()) return NULL;
         inputs->GetParameterValue(&approximation,ApproximationEnum);
-        this->parameters->FindParam(&shelf_dampening,ShelfDampeningEnum);
+        this->parameters->FindParam(&shelf_dampening,DiagnosticShelfDampeningEnum);
         if(approximation!=StokesApproximationEnum && approximation!=MacAyealStokesApproximationEnum && approximation!=PattynStokesApproximationEnum) return NULL;
         ElementVector* pe=new ElementVector(nodes,NUMVERTICES,this->parameters,StokesApproximationEnum);
@@ -4194 +4194 @@
 
         /*Recondition pressure: */
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
 
         /*Ok, we have vx vy vz and P in values, fill in vx vy vz P arrays: */
@@ -5563 +5563 @@
         penta->GetDofList(&doflistm,MacAyealApproximationEnum,GsetEnum);
         GetDofList(&doflists,StokesApproximationEnum,GsetEnum);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
 
         /*Get node data: */
@@ -5731 +5731 @@
         GetDofList(&doflistp,PattynApproximationEnum,GsetEnum);
         GetDofList(&doflists,StokesApproximationEnum,GsetEnum);
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
 
         /*Get node data: */
@@ -6028 +6028 @@
 
         /*Recondition pressure and compute vel: */
-        this->parameters->FindParam(&stokesreconditioning,StokesreconditioningEnum);
+        this->parameters->FindParam(&stokesreconditioning,DiagnosticStokesreconditioningEnum);
         for(i=0;i<NUMVERTICES;i++) pressure[i]=pressure[i]*stokesreconditioning;
         for(i=0;i<NUMVERTICES;i++) vel[i]=pow( pow(vx[i],2.0) + pow(vy[i],2.0) + pow(vz[i],2.0) , 0.5);

issm/trunk/src/c/objects/Elements/Tria.cpp

@@ -718 +718 @@
         Input* vxold_input=inputs->GetInput(VxPicardEnum);      _assert_(vxold_input);
         Input* vyold_input=inputs->GetInput(VyPicardEnum);      _assert_(vyold_input);
-        this->parameters->FindParam(&viscosity_overshoot,ViscosityOvershootEnum);
+        this->parameters->FindParam(&viscosity_overshoot,DiagnosticViscosityOvershootEnum);
 
         /* Start  looping on the number of gaussian points: */

issm/trunk/src/c/objects/Loads/Icefront.cpp

@@ -64 +64 @@
                 segment_width=6;
         }
-        _assert_(iomodel->Data(PressureloadEnum));
-        element=(int)(*(iomodel->Data(PressureloadEnum)+segment_width*i+segment_width-2)-1); //element is in the penultimate column (node1 node2 ... elem fill)
+        _assert_(iomodel->Data(DiagnosticIcefrontEnum));
+        element=(int)(*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+segment_width-2)-1); //element is in the penultimate column (node1 node2 ... elem fill)
 
         /*Build ids for hook constructors: */
-        icefront_eid=(int) *(iomodel->Data(PressureloadEnum)+segment_width*i+segment_width-2); //matlab indexing
+        icefront_eid=(int) *(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+segment_width-2); //matlab indexing
         icefront_mparid=numberofelements+1; //matlab indexing
 
         if (in_icefront_type==MacAyeal2dIceFrontEnum || in_icefront_type==MacAyeal3dIceFrontEnum){
-                icefront_node_ids[0]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+0);
-                icefront_node_ids[1]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+1);
+                icefront_node_ids[0]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+0);
+                icefront_node_ids[1]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+1);
         }
         else if (in_icefront_type==PattynIceFrontEnum || in_icefront_type==StokesIceFrontEnum){
-                icefront_node_ids[0]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+0);
-                icefront_node_ids[1]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+1);
-                icefront_node_ids[2]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+2);
-                icefront_node_ids[3]=iomodel->nodecounter+(int)*(iomodel->Data(PressureloadEnum)+segment_width*i+3);
+                icefront_node_ids[0]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+0);
+                icefront_node_ids[1]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+1);
+                icefront_node_ids[2]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+2);
+                icefront_node_ids[3]=iomodel->nodecounter+(int)*(iomodel->Data(DiagnosticIcefrontEnum)+segment_width*i+3);
         }
         else _error_("in_icefront_type %s not supported yet!",EnumToStringx(in_icefront_type));
@@ -89 +89 @@
 
         /*Fill*/
-        icefront_fill=(int)iomodel->Data(PressureloadEnum)[segment_width*i+segment_width-1];
+        icefront_fill=(int)iomodel->Data(DiagnosticIcefrontEnum)[segment_width*i+segment_width-1];
         
         /*Ok, we have everything to build the object: */

issm/trunk/src/c/objects/Loads/Pengrid.cpp

@@ -548 +548 @@
 
         /*Retrieve all inputs and parameters*/
-        parameters->FindParam(&penalty_offset,PenaltyOffsetEnum);
+        parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
         penta->GetParameterValue(&slope[0],node,BedSlopeXEnum);
         penta->GetParameterValue(&slope[1],node,BedSlopeYEnum);

issm/trunk/src/c/objects/Loads/Penpair.cpp

@@ -314 +314 @@
 
         /*recover parameters: */
-        parameters->FindParam(&penalty_offset,PenaltyOffsetEnum);
+        parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
 
         //Create elementary matrix: add penalty to 
@@ -341 +341 @@
 
         /*recover parameters: */
-        parameters->FindParam(&penalty_offset,PenaltyOffsetEnum);
+        parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
 
         //Create elementary matrix: add penalty to 

issm/trunk/src/c/objects/Loads/Riftfront.cpp

@@ -57 +57 @@
         /*Fetch parameters: */
         iomodel->Constant(&numberofelements,NumberOfElementsEnum);
-        iomodel->Constant(&penalty_lock,PenaltyLockEnum);
+        iomodel->Constant(&penalty_lock,DiagnosticRiftPenaltyLockEnum);
 
         /*Ok, retrieve all the data needed to add a penalty between the two nodes: */
@@ -523 +523 @@
 
         /*Get some parameters: */
-        this->parameters->FindParam(&penalty_offset,PenaltyOffsetEnum);
+        this->parameters->FindParam(&penalty_offset,DiagnosticPenaltyFactorEnum);
         this->inputs->GetParameterValue(&friction,FrictionEnum);
         tria1->GetParameterValue(&h[0],nodes[0],ThicknessEnum);

issm/trunk/src/c/solutions/convergence.cpp

@@ -38 +38 @@
 
         /*get convergence options*/
-        parameters->FindParam(&eps_res,EpsResEnum);
-        parameters->FindParam(&eps_rel,EpsRelEnum);
-        parameters->FindParam(&eps_abs,EpsAbsEnum);
+        parameters->FindParam(&eps_res,DiagnosticRestolEnum);
+        parameters->FindParam(&eps_rel,DiagnosticReltolEnum);
+        parameters->FindParam(&eps_abs,DiagnosticAbstolEnum);
         parameters->FindParam(&yts,ConstantsYtsEnum);
 

issm/trunk/src/c/solutions/diagnostic_core.cpp

@@ -24 +24 @@
         bool   control_analysis;
         int    solution_type;
+        int    numoutputs         = 0;
+        int    *requested_outputs = NULL;
 
         /* recover parameters:*/
@@ -87 +89 @@
                 InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,PressureEnum);
                 if(dim==3) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,VzEnum);
-                RequestedOutputsx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters);
+                femmodel->parameters->FindParam(&numoutputs,DiagnosticNumRequestedOutputsEnum);
+                if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,DiagnosticRequestedOutputsEnum);
+                RequestedOutputsx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs);
         }
 
+        /*Free ressources:*/
+        xfree((void**)&requested_outputs);
 }

issm/trunk/src/c/solutions/steadystate_core.cpp

@@ -22 +22 @@
         int maxiter;
         bool control_analysis;
+        int  numoutputs         = 0;
+        int  *requested_outputs = NULL;
         
         /* recover parameters:*/
@@ -69 +71 @@
                 InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,TemperatureEnum);
                 InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,BasalforcingsMeltingRateEnum);
-                RequestedOutputsx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters);
+                femmodel->parameters->FindParam(&numoutputs,SteadystateNumRequestedOutputsEnum);
+                if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,SteadystateRequestedOutputsEnum);
+                RequestedOutputsx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs);
         }
 
+        /*Free ressources:*/
+        xfree((void**)&requested_outputs);
 }

issm/trunk/src/c/solvers/solver_nonlinear.cpp

@@ -32 +32 @@
 
         /*Recover parameters: */
-        femmodel->parameters->FindParam(&min_mechanical_constraints,MinMechanicalConstraintsEnum);
-        femmodel->parameters->FindParam(&max_nonlinear_iterations,MaxNonlinearIterationsEnum);
+        femmodel->parameters->FindParam(&min_mechanical_constraints,DiagnosticRiftPenaltyThresholdEnum);
+        femmodel->parameters->FindParam(&max_nonlinear_iterations,DiagnosticMaxiterEnum);
         femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum);
         UpdateConstraintsx(femmodel->nodes,femmodel->constraints,femmodel->parameters);

issm/trunk/src/c/solvers/solver_stokescoupling_nonlinear.cpp

@@ -33 +33 @@
 
         /*Recover parameters: */
-        femmodel->parameters->FindParam(&min_mechanical_constraints,MinMechanicalConstraintsEnum);
-        femmodel->parameters->FindParam(&max_nonlinear_iterations,MaxNonlinearIterationsEnum);
+        femmodel->parameters->FindParam(&min_mechanical_constraints,DiagnosticRiftPenaltyThresholdEnum);
+        femmodel->parameters->FindParam(&max_nonlinear_iterations,DiagnosticMaxiterEnum);
         UpdateConstraintsx(femmodel->nodes,femmodel->constraints,femmodel->parameters);
         

issm/trunk/src/m/classes/model/model.m

@@ -35 +35 @@
                  steadystate = modelfield('default',0,'marshall',true);
                  transient = modelfield('default',0,'marshall',true);
+                 diagnostic = modelfield('default',0,'marshall',true);
 
                  %FIXME: all other fields should belong to other classes
@@ -62 +63 @@
                  hemisphere = modelfield('default',NaN,'marshall',false);
 
-                 %Stokes
-                 stokesreconditioning = modelfield('default',0,'marshall',true,'format','Double');
-                 shelf_dampening      = modelfield('default',0,'marshall',true,'format','Integer');
-
                  %Penalties
-                 penalties            = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
-                 penalty_offset       = modelfield('default',0,'marshall',true,'format','Double');
-                 penalty_lock         = modelfield('default',0,'marshall',true,'format','Integer');
                  segments             = modelfield('default',NaN,'marshall',false);
                  segmentmarkers       = modelfield('default',NaN,'marshall',false);
@@ -93 +87 @@
                  %Materials parameters
 
-                 min_mechanical_constraints = modelfield('default',0,'marshall',true,'format','Integer');
-
                  %Geometrical parameters
                  surface           = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1);
@@ -104 +96 @@
                  %Boundary conditions
                  nodeonboundary = modelfield('default',NaN,'marshall',false);
-                 pressureload   = modelfield('default',NaN,'marshall',true,'preprocess','marshallpressureload','format','DoubleMat','mattype',3);
-                 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);
-                 diagnostic_ref = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',1);
 
                  %Observations 
@@ -118 +105 @@
 
                  %Statics parameters
-                 eps_res                  = modelfield('default',0,'marshall',true,'format','Double');
-                 eps_rel                  = modelfield('default',0,'marshall',true,'format','Double');
-                 eps_abs                  = modelfield('default',0,'marshall',true,'format','Double');
-                 max_nonlinear_iterations = modelfield('default',0,'marshall',true,'format','Integer');
                  connectivity             = modelfield('default',0,'marshall',true,'format','Integer');
-                 viscosity_overshoot      = modelfield('default',0,'marshall',true,'format','Double');
 
                  %Control
@@ -140 +122 @@
                  num_control_type               = modelfield('default',0,'marshall',true,'format','Integer');
                  num_cm_responses               = modelfield('default',0,'marshall',true,'format','Integer');
-                 %Output
-                 requested_outputs               = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
+
                  %Results fields
                  output_frequency               = modelfield('default',0,'marshall',true,'format','Integer');
@@ -507 +488 @@
                          md.steadystate=steadystate;
                          md.transient=transient;
+                         md.diagnostic=diagnostic;
 
                          %Solver parameters
 
-                         %mechanical residue convergence criterion norm(K(uold)uold - F)/norm(F)
-                         md.eps_res=10^-4; %from test233 in nightly runs
-
-                         %relative convergence criterion ((vel(n-1)-vel(n))/vel(n))
-                         md.eps_rel=0.01;
-
-                         %absolute convergence criterion (max(vel(n-1)-vel(n)) (m/year)
-                         md.eps_abs=10;
-
-                         %maximum of non-linear iterations.
-                         md.max_nonlinear_iterations=100;
-                         
                          %the connectivity is the avergaded number of nodes linked to a
                          %given node through an edge. This connectivity is used to initially
@@ -529 +499 @@
                          md.connectivity=25;
 
-                         %coefficient to update the viscosity between each iteration of
-                         %a diagnostic according to the following formula
-                         %viscosity(n)=viscosity(n)+viscosity_overshoot(viscosity(n)-viscosity(n-1))
-                         md.viscosity_overshoot=0;
 
                          %parameter used to print temporary results (convergence criterion,
@@ -538 +504 @@
                          md.verbose=verbose('solution',true,'qmu',true,'control',true);
 
-                         %Stokes
-                         md.stokesreconditioning=10^13;
-                         md.shelf_dampening=0;
-
-                         %Penalties
-
-                         %the penalty offset is the power used to compute the value
-                         %of the penalty as follows
-                         %kappa=max(stiffness matrix)*10^penalty_offset
-                         md.penalty_offset=3;
-
-                         %in some solutions, it might be needed to stop a run when only
-                         %a few constraints remain unstable. For thermal computation, this
-                         %parameter is often used.
-                         md.penalty_lock=10;
-
                          %minimum thickness to avoid stiffness singularity, used in
                          %the parameter file
                          md.minh=1;
-
-                         %in some cases, it might be needed to stop a run when only
-                         %a few constraints remain unstable. For thermal computation, this
-                         %parameter is often used.
-                         md.min_mechanical_constraints=0;
 
                          %Control
@@ -624 +569 @@
                                  if(strcmp(index1.subs,'res')), displayresults(md);return; end
                                  if(strcmp(index1.subs,'obs')), displayobservations(md);return; end
-                                 if(strcmp(index1.subs,'diagnostic')), displaydiagnostic(md);return; end
                                  if(strcmp(index1.subs,'control')), displaycontrol(md);return; end
                                  if(strcmp(index1.subs,'parallel')), displayparallel(md);return; end

issm/trunk/src/m/model/BasinConstrain.m

@@ -48 +48 @@
 
 %all elements outside the constraint domain are equivalent to water. all nodes outside are spc'd.
-md.spcvx(vertexnotondomain)=md.vx_obs(vertexnotondomain);
-md.spcvy(vertexnotondomain)=md.vy_obs(vertexnotondomain);
+md.diagnostic.spcvx(vertexnotondomain)=md.vx_obs(vertexnotondomain);
+md.diagnostic.spcvy(vertexnotondomain)=md.vy_obs(vertexnotondomain);
 md.mask.elementonwater(elementnotondomain)=1;
 
@@ -56 +56 @@
 numpos=unique(md.elements(pos,:));
 nodes=setdiff(1:1:md.numberofnodes,numpos);
-md.spcvx(nodes)=md.vx_obs(nodes);
-md.spcvy(nodes)=md.vy_obs(nodes);
+md.diagnostic.spcvx(nodes)=md.vx_obs(nodes);
+md.diagnostic.spcvy(nodes)=md.vy_obs(nodes);
 
 %make sure icefronts that are completely spc'd are taken out:
-free_segments=find((~isnan(md.spcvx(md.pressureload(:,1:2))) + ~isnan(md.spcvy(md.pressureload(:,1:2))))~=2);
-md.pressureload=md.pressureload(free_segments,:);
+free_segments=find((~isnan(md.diagnostic.spcvx(md.diagnostic.icefront(:,1:2))) + ~isnan(md.diagnostic.spcvy(md.diagnostic.icefront(:,1:2))))~=2);
+md.diagnostic.icefront=md.diagnostic.icefront(free_segments,:);

issm/trunk/src/m/model/BasinConstrainShelf.m

@@ -48 +48 @@
 
 %all elements outside the constraint domain are equivalent to water. all nodes outside are spc'd.
-md.spcvx(vertexnotondomain)=md.vx_obs(vertexnotondomain);
-md.spcvy(vertexnotondomain)=md.vy_obs(vertexnotondomain);
+md.diagnostic.spcvx(vertexnotondomain)=md.vx_obs(vertexnotondomain);
+md.diagnostic.spcvy(vertexnotondomain)=md.vy_obs(vertexnotondomain);
 md.mask.elementonwater(elementnotondomain)=1;
 
@@ -56 +56 @@
 numpos=unique(md.elements(pos,:));
 nodes=setdiff(1:1:md.numberofnodes,numpos);
-md.spcvx(nodes)=md.vx_obs(nodes);
-md.spcvy(nodes)=md.vy_obs(nodes);
+md.diagnostic.spcvx(nodes)=md.vx_obs(nodes);
+md.diagnostic.spcvy(nodes)=md.vy_obs(nodes);
 
 
@@ -63 +63 @@
 %we spc to the smoothed value, so that control methods don't go berserk trying to figure out what reaction force to apply for the spc to stand.
 pos=find(isnan(md.vel_obs_raw));
-md.spcvx(pos)=md.vx_obs(pos); 
-md.spcvy(pos)=md.vy_obs(pos); 
+md.diagnostic.spcvx(pos)=md.vx_obs(pos); 
+md.diagnostic.spcvy(pos)=md.vy_obs(pos); 
 
 %iceshelves: any vertex on floating ice is spc'd
 pos=find(md.mask.vertexongroundedice);
-md.spcvx(pos)=md.vx_obs(pos); 
-md.spcvy(pos)=md.vy_obs(pos); 
+md.diagnostic.spcvx(pos)=md.vx_obs(pos); 
+md.diagnostic.spcvy(pos)=md.vy_obs(pos); 
 
 %make sure icefronts that are completely spc'd are taken out:
-free_segments=find((~isnan(md.spcvx(md.pressureload(:,1:2))) + ~isnan(md.spcvy(md.pressureload(:,1:2))) )~=2);
-md.pressureload=md.pressureload(free_segments,:);
+free_segments=find((~isnan(md.diagnostic.spcvx(md.diagnostic.icefront(:,1:2))) + ~isnan(md.diagnostic.spcvy(md.diagnostic.icefront(:,1:2))) )~=2);
+md.diagnostic.icefront=md.diagnostic.icefront(free_segments,:);

issm/trunk/src/m/model/collapse.m

@@ -52 +52 @@
 
 %boundary conditions
-md.spcvx=project2d(md,md.spcvx,md.numlayers);
-md.spcvy=project2d(md,md.spcvy,md.numlayers);
-md.spcvz=project2d(md,md.spcvz,md.numlayers);
+md.diagnostic.spcvx=project2d(md,md.diagnostic.spcvx,md.numlayers);
+md.diagnostic.spcvy=project2d(md,md.diagnostic.spcvy,md.numlayers);
+md.diagnostic.spcvz=project2d(md,md.diagnostic.spcvz,md.numlayers);
 md.prognostic.spcthickness=project2d(md,md.prognostic.spcthickness,md.numlayers);
 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.numlayers);
 
 %Extrusion of Neumann BC
-if ~isnan(md.pressureload),
-        numberofneumann2d=size(md.pressureload,1)/md.numlayers;
-        md.pressureload=[md.pressureload(1:numberofneumann2d,1:2) md.pressureload(1:numberofneumann2d,5:6)]; %Add two columns on the first layer 
+if ~isnan(md.diagnostic.icefront),
+        numberofneumann2d=size(md.diagnostic.icefront,1)/md.numlayers;
+        md.diagnostic.icefront=[md.diagnostic.icefront(1:numberofneumann2d,1:2) md.diagnostic.icefront(1:numberofneumann2d,5:6)]; %Add two columns on the first layer 
 end
 

issm/trunk/src/m/model/contourmassbalance.m

@@ -19 +19 @@
 %Get segments enveloping contour
 segments=contourenvelope(md,file);
-%md.pressureload=segments; plotmodel(md,'data','pressureload','expdisp',file);
+%md.diagnostic.icefront=segments; plotmodel(md,'data','pressureload','expdisp',file);
 
 %get flag list of elements and nodes inside the contour

issm/trunk/src/m/model/display/displaybc.m

@@ -12 +12 @@
 
 disp(sprintf('\n      diagnostic:'));
-fielddisplay(md,'spcvx','x-axis velocity constraint (NaN means no constraint)');
-fielddisplay(md,'spcvy','y-axis velocity constraint (NaN means no constraint)');
-fielddisplay(md,'spcvz','z-axis velocity constraint (NaN means no constraint)');
+fielddisplay(md,'diagnostic.spcvx','x-axis velocity constraint (NaN means no constraint)');
+fielddisplay(md,'diagnostic.spcvy','y-axis velocity constraint (NaN means no constraint)');
+fielddisplay(md,'diagnostic.spcvz','z-axis velocity constraint (NaN means no constraint)');
 fielddisplay(md,'pressureload','segments on ice front list (0:Air 1:Water 2:Ice)');
 

issm/trunk/src/m/model/extrude.m

@@ -168 +168 @@
 
 %boundary conditions
-md.spcvx=project3d(md,'vector',md.spcvx,'type','node');
-md.spcvy=project3d(md,'vector',md.spcvy,'type','node');
-md.spcvz=project3d(md,'vector',md.spcvz,'type','node');
+md.diagnostic.spcvx=project3d(md,'vector',md.diagnostic.spcvx,'type','node');
+md.diagnostic.spcvy=project3d(md,'vector',md.diagnostic.spcvy,'type','node');
+md.diagnostic.spcvz=project3d(md,'vector',md.diagnostic.spcvz,'type','node');
 md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.numlayers,'padding',NaN);
 md.prognostic.spcthickness=project3d(md,'vector',md.prognostic.spcthickness,'type','node');
-md.diagnostic_ref=project3d(md,'vector',md.diagnostic_ref,'type','node');
+md.diagnostic.referential=project3d(md,'vector',md.diagnostic.referential,'type','node');
 
 %in 3d, pressureload: [node1 node2 node3 node4 element]
-pressureload_layer1=[md.pressureload(:,1:2)  md.pressureload(:,2)+md.numberofnodes2d  md.pressureload(:,1)+md.numberofnodes2d  md.pressureload(:,3:4)]; %Add two columns on the first layer 
+pressureload_layer1=[md.diagnostic.icefront(:,1:2)  md.diagnostic.icefront(:,2)+md.numberofnodes2d  md.diagnostic.icefront(:,1)+md.numberofnodes2d  md.diagnostic.icefront(:,3:4)]; %Add two columns on the first layer 
 pressureload=[];
 for i=1:numlayers-1,
         pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.numberofnodes2d pressureload_layer1(:,5)+(i-1)*md.numberofelements2d pressureload_layer1(:,6)];
 end
-md.pressureload=pressureload;
+md.diagnostic.icefront=pressureload;
 
 %connectivity

issm/trunk/src/m/model/ismodelselfconsistent.m

@@ -71 +71 @@
 %PRESSURELOAD{{{1
 if (md.dim==2),
-        fields={'pressureload'};
+        fields={'diagnostic.icefront'};
         checksize(md,fields,[NaN 4]);
 elseif md.dim==3,
-        fields={'pressureload'};
+        fields={'diagnostic.icefront'};
         checksize(md,fields,[NaN 6]);
 else
         message('dim should be either 2 3');
 end
-checkvalues(md,{'pressureload(:,end)'},[0 1 2]);
+checkvalues(md,{'diagnostic.icefront(:,end)'},[0 1 2]);
 %}}}
 %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','nsteps','maxiter',...
-        'eps_res','max_nonlinear_iterations','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface','elementconnectivity'};
+        'diagnostic.restol','diagnostic.maxiter','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface','elementconnectivity'};
 checknan(md,fields);
 %}}}}
 %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','eps_res','max_nonlinear_iterations','eps_rel','eps_abs','nsteps','maxiter',...
-        'settings.lowmem','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface'};
+        'materials.rho_ice','materials.rho_water','materials.rheology_B','mask.elementonfloatingice','thickness','constants.g','diagnostic.restol','diagnostic.maxiter','diagnostic.reltol',...
+        'diagnostic.abstol','nsteps','maxiter','settings.lowmem','materials.rheology_n','nodeonbed','nodeonsurface','elementonbed','elementonsurface'};
 checkgreater(md,fields,0);
 %}}}
 %FIELDS > 0 {{{1
 fields={'numberofelements','numberofnodes','elements','friction.p',...
-        'materials.rho_ice','materials.rho_water','materials.rheology_B','thickness','constants.g','max_nonlinear_iterations','eps_res','eps_rel','eps_abs','maxiter'};
+        'materials.rho_ice','materials.rho_water','materials.rheology_B','thickness','constants.g','diagnostic.maxiter','diagnostic.restol','diagnostic.reltol','diagnostic.abstol','maxiter'};
 checkgreaterstrict(md,fields,0);
 %}}}
@@ -107 +107 @@
 %}}}
 %OTHER SIZES {{{1
-fields={'diagnostic_ref'};
+fields={'diagnostic.referential'};
 checksize(md,fields,[md.numberofnodes 6]);
-if ~isempty(md.requested_outputs),
-        if(size(md.requested_outputs,2)~=1),
+if ~isempty(md.diagnostic.requested_outputs),
+        if(size(md.diagnostic.requested_outputs,2)~=1),
                 message(['model ' md.miscellaneous.name ' requested outputs should be a column vector']);
         end
@@ -326 +326 @@
 
         %eps: 
-        if isnan(md.eps_rel),
-                message(['model not consistent: for a steadystate computation, eps_rel (relative convergence criterion) must be defined!']);
+        if isnan(md.diagnostic.reltol),
+                message(['model not consistent: for a steadystate computation, diagnostic.reltol (relative convergence criterion) must be defined!']);
         end
 end
@@ -370 +370 @@
                         % {{{2
                         %SINGULAR
-                        if ~any((~isnan(md.spcvx)+~isnan(md.spcvy))==2),
+                        if ~any((~isnan(md.diagnostic.spcvx)+~isnan(md.diagnostic.spcvy))==2),
                                 message(['model not consistent: model ' md.miscellaneous.name ' is not well posed (singular). You need at least one node with fixed velocity!'])
                         end
@@ -376 +376 @@
                         %ROTATED SPC
                         %CHECK THAT EACH LINES CONTAINS ONLY NAN VALUES OR NO NAN VALUES
-                        if any(sum(isnan(md.diagnostic_ref),2)~=0 & sum(isnan(md.diagnostic_ref),2)~=6),
-                                message(['model not consistent: model ' md.miscellaneous.name ' has problem with rotated spc. Each line of diagnostic_ref should contain either only NaN values or no NaN values']);
+                        if any(sum(isnan(md.diagnostic.referential),2)~=0 & sum(isnan(md.diagnostic.referential),2)~=6),
+                                message(['model not consistent: model ' md.miscellaneous.name ' has problem with rotated spc. Each line of diagnostic.referential should contain either only NaN values or no NaN values']);
                         end
                         %CHECK THAT THE TWO VECTORS PROVIDED ARE ORTHOGONAL
-                        if any(sum(isnan(md.diagnostic_ref),2)==0),
-                                pos=find(sum(isnan(md.diagnostic_ref),2)==0);
-                                if any(dot(md.diagnostic_ref(pos,1:3),md.diagnostic_ref(pos,4:6))),
-                                        dot(md.diagnostic_ref(pos,1:3),md.diagnostic_ref(pos,4:6))
-                                        message(['model not consistent: model ' md.miscellaneous.name ' has problem with rotated spc. Vectors in diagnostic_ref (colums 1 to 3 and 4 to 6) must be orthogonal']);
+                        if any(sum(isnan(md.diagnostic.referential),2)==0),
+                                pos=find(sum(isnan(md.diagnostic.referential),2)==0);
+                                if any(dot(md.diagnostic.referential(pos,1:3),md.diagnostic.referential(pos,4:6))),
+                                        dot(md.diagnostic.referential(pos,1:3),md.diagnostic.referential(pos,4:6))
+                                        message(['model not consistent: model ' md.miscellaneous.name ' has problem with rotated spc. Vectors in diagnostic.referential (colums 1 to 3 and 4 to 6) must be orthogonal']);
                                 end
 
@@ -390 +390 @@
                         %CHECK THAT ROTATION IS IN THE (X,Y) PLANE FOR 2D MODELS
                         if md.dim==2,
-                                pos=find(sum(isnan(md.diagnostic_ref),2)==0  & md.flowequation.vertex_equation==2);
-                                if any(md.diagnostic_ref(pos,3:5)~=0);
+                                pos=find(sum(isnan(md.diagnostic.referential),2)==0  & md.flowequation.vertex_equation==2);
+                                if any(md.diagnostic.referential(pos,3:5)~=0);
                                         message(['model not consistent: model ' md.miscellaneous.name ' has problem with rotated spc. The rotation should be in the (x,y) plane for 2D diagnostic models (nodeonmacayeal)']);
                                 end

issm/trunk/src/m/model/marshall.m

@@ -334 +334 @@
 function out=marshallverbose(in)
         out = VerboseToBinary(in);
-function out=marshallpressureload(in)
+function out=marshallicefront(in)
         out=in;
         pos=find(in(:,end)==0); out(pos,end)=AirEnum;

issm/trunk/src/m/model/modelextract.m

@@ -216 +216 @@
         nodestoflag1=intersect(orphans_node,pos_node);
         nodestoflag2=Pnode(nodestoflag1);
-        if numel(md1.spcvx)>1 & numel(md1.spcvy)>2 & numel(md1.spcvz)>2,
+        if numel(md1.diagnostic.spcvx)>1 & numel(md1.diagnostic.spcvy)>2 & numel(md1.diagnostic.spcvz)>2,
                 if numel(md1.vx_obs)>1 & numel(md1.vy_obs)>1
-                        md2.spcvx(nodestoflag2)=md2.vx_obs(nodestoflag2); 
-                        md2.spcvy(nodestoflag2)=md2.vy_obs(nodestoflag2);
+                        md2.diagnostic.spcvx(nodestoflag2)=md2.vx_obs(nodestoflag2); 
+                        md2.diagnostic.spcvy(nodestoflag2)=md2.vy_obs(nodestoflag2);
                 else
-                        md2.spcvx(nodestoflag2)=NaN;
-                        md2.spcvy(nodestoflag2)=NaN;
+                        md2.diagnostic.spcvx(nodestoflag2)=NaN;
+                        md2.diagnostic.spcvy(nodestoflag2)=NaN;
                         disp(' ')
                         disp('!! modelextract warning: spc values should be checked !!')
@@ -228 +228 @@
                 end
                 %put 0 for vz
-                md2.spcvz(nodestoflag2)=0;
+                md2.diagnostic.spcvz(nodestoflag2)=0;
         end
         if ~isnan(md1.thermal.spctemperature),

issm/trunk/src/m/model/plot/plot_BC.m

@@ -7 +7 @@
 
 %plot dirichlets
-h1=plot(md.x(find(~isnan(md.spcvx))),md.y(find(~isnan(md.spcvx))),'ro','MarkerSize',14,'MarkerFaceColor','r');
-h2=plot(md.x(find(~isnan(md.spcvy))),md.y(find(~isnan(md.spcvy))),'bo','MarkerSize',10,'MarkerFaceColor','b');
-h3=plot(md.x(find(~isnan(md.spcvz))),md.y(find(~isnan(md.spcvz))),'yo','MarkerSize',6 ,'MarkerFaceColor','y');
+h1=plot(md.x(find(~isnan(md.diagnostic.spcvx))),md.y(find(~isnan(md.diagnostic.spcvx))),'ro','MarkerSize',14,'MarkerFaceColor','r');
+h2=plot(md.x(find(~isnan(md.diagnostic.spcvy))),md.y(find(~isnan(md.diagnostic.spcvy))),'bo','MarkerSize',10,'MarkerFaceColor','b');
+h3=plot(md.x(find(~isnan(md.diagnostic.spcvz))),md.y(find(~isnan(md.diagnostic.spcvz))),'yo','MarkerSize',6 ,'MarkerFaceColor','y');
 
 %update legend

issm/trunk/src/m/model/plot/plot_pressureload.m

@@ -12 +12 @@
 %process mesh and data
 [x y z elements is2d isplanet]=processmesh(md,[],options);
-pressureload=md.pressureload;
+pressureload=md.diagnostic.icefront;
 
 if (md.dim==2),

issm/trunk/src/m/model/setflowequation.m

@@ -92 +92 @@
         nodeonstokes=zeros(md.numberofnodes,1);
         nodeonstokes(md.elements(find(stokesflag),:))=1;
-        fullspcnodes=double((~isnan(md.spcvx)+~isnan(md.spcvy)+~isnan(md.spcvz))==3 | (nodeonpattyn & nodeonstokes));         %find all the nodes on the boundary of the domain without icefront
+        fullspcnodes=double((~isnan(md.diagnostic.spcvx)+~isnan(md.diagnostic.spcvy)+~isnan(md.diagnostic.spcvz))==3 | (nodeonpattyn & nodeonstokes));         %find all the nodes on the boundary of the domain without icefront
         fullspcelems=double(sum(fullspcnodes(md.elements),2)==6);         %find all the nodes on the boundary of the domain without icefront
         stokesflag(find(fullspcelems))=0;
@@ -120 +120 @@
 
 %Now take care of the coupling between MacAyeal and Pattyn
-md.penalties=[];
+md.diagnostic.vertex_pairing=[];
 nodeonmacayealpattyn=zeros(md.numberofnodes,1);
 nodeonpattynstokes=zeros(md.numberofnodes,1);
@@ -136 +136 @@
                         penalties=[penalties; [bordernodes2d bordernodes2d+md.numberofnodes2d*(i)]];
                 end
-                md.penalties=penalties;
+                md.diagnostic.vertex_pairing=penalties;
         end
 elseif strcmpi(coupling_method,'tiling'),

issm/trunk/src/m/solutions/convergence.m

@@ -6 +6 @@
 %Get convergence options
 yts=parameters.ConstantsYts;
-eps_res=parameters.EpsRes;
-eps_rel=parameters.EpsRel;
-eps_abs=parameters.EpsAbs;
+restol=parameters.DiagnosticRestol;
+reltol=parameters.DiagnosticReltol;
+abstol=parameters.DiagnosticAbstol;
 
 %initialization
@@ -25 +25 @@
         error('convergence error message: mechanical equilibrium convergence criterion is NaN!'); 
 end
-if (res<=eps_res),
-        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      mechanical equilibrium convergence criterion',res*100,' < ',eps_res*100,' %');
+if (res<=restol),
+        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      mechanical equilibrium convergence criterion',res*100,' < ',restol*100,' %');
         converged=true;
 else
-        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      mechanical equilibrium convergence criterion',res*100,' > ',eps_res*100,' %');
+        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      mechanical equilibrium convergence criterion',res*100,' > ',restol*100,' %');
         converged=false;
 end
 
 %Relative criterion (optional)
-if ((~isnan(eps_rel)) | (VerboseConvergence())),
+if ((~isnan(reltol)) | (VerboseConvergence())),
 
         %compute ndu/nu
@@ -45 +45 @@
 
         %print criterion
-        if ~isnan(eps_rel),
+        if ~isnan(reltol),
                 if nu, %avoid "dividing by zero" warning
-                        if (ndu/nu<=eps_rel),
-                                issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      relative convergence criterion: norm(du)/norm(u)',ndu/nu*100,' < ',eps_rel*100,' %');
+                        if (ndu/nu<=reltol),
+                                issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      relative convergence criterion: norm(du)/norm(u)',ndu/nu*100,' < ',reltol*100,' %');
                         else
-                                issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      relative convergence criterion: norm(du)/norm(u)',ndu/nu*100,' > ',eps_rel*100,' %');
+                                issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      relative convergence criterion: norm(du)/norm(u)',ndu/nu*100,' > ',reltol*100,' %');
                                 converged=false;
                         end
@@ -65 +65 @@
 
 %Absolute criterion (optional)
-if ((~isnan(eps_abs)) | VerboseConvergence()),
+if ((~isnan(abstol)) | VerboseConvergence()),
 
         %compute max(du)
@@ -75 +75 @@
 
         %print criterion
-        if ~isnan(eps_abs),
-                if (nduinf<=eps_abs),
-                        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      absolute convergence criterion: max(du)',nduinf,' < ',eps_abs,' m/yr');
+        if ~isnan(abstol),
+                if (nduinf<=abstol),
+                        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      absolute convergence criterion: max(du)',nduinf,' < ',abstol,' m/yr');
                 else
-                        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      absolute convergence criterion: max(du)',nduinf,' > ',eps_abs,' m/yr');
+                        issmprintf(VerboseConvergence(),'%-60s%g%s%g%s','      absolute convergence criterion: max(du)',nduinf,' > ',abstol,' m/yr');
                         converged=false;
                 end

issm/trunk/src/m/solvers/solver_nonlinear.m

@@ -6 +6 @@
 
         %Branch on partitioning schema requested
-        min_mechanical_constraints=femmodel.parameters.MinMechanicalConstraints;
-        max_nonlinear_iterations=femmodel.parameters.MaxNonlinearIterations;
+        rift_penalty_threshold=femmodel.parameters.DiagnosticRiftPenaltyThreshold;
+        maxiter=femmodel.parameters.DiagnosticMaxiter;
         configuration_type=femmodel.parameters.ConfigurationType;
         [femmodel.nodes]=UpdateConstraints(femmodel.nodes,femmodel.constraints,femmodel.parameters);
@@ -51 +51 @@
                 if ~constraints_converged,
                         if converged,
-                                if num_unstable_constraints <= min_mechanical_constraints,
+                                if num_unstable_constraints <= rift_penalty_threshold,
                                         converged=1;
                                 else 
@@ -62 +62 @@
                 count=count+1;
                 if(converged==1) break; end
-                if(count>max_nonlinear_iterations),
-                        issmprintf(true,'%s%i%s','      maximum number of iterations ',max_nonlinear_iterations,' exceeded');
+                if(count>maxiter),
+                        issmprintf(true,'%s%i%s','      maximum number of iterations ',maxiter,' exceeded');
                         break;
                 end

issm/trunk/src/m/utils/BC/SetIceSheetBC.m

@@ -9 +9 @@
 %node on Dirichlet
 pos=find(md.nodeonboundary);
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
-md.diagnostic_ref=NaN*ones(md.numberofnodes,6);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
+md.diagnostic.referential=NaN*ones(md.numberofnodes,6);
 
 %Dirichlet Values
 if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes)
         disp('      boundary conditions for diagnostic model: spc set as observed velocities');
-        md.spcvx(pos)=md.vx_obs(pos);
-        md.spcvy(pos)=md.vy_obs(pos);
+        md.diagnostic.spcvx(pos)=md.vx_obs(pos);
+        md.diagnostic.spcvy(pos)=md.vy_obs(pos);
 else
         disp('      boundary conditions for diagnostic model: spc set as zero');
@@ -28 +28 @@
 %segment on neumann (Ice Front) -> none
 if (md.dim==2)
-        md.pressureload=zeros(0,4);
+        md.diagnostic.icefront=zeros(0,4);
 else
-        md.pressureload=zeros(0,6);
+        md.diagnostic.icefront=zeros(0,6);
 end
 

issm/trunk/src/m/utils/BC/SetIceShelfBC.m

@@ -28 +28 @@
 end
 pos=find(md.nodeonboundary & ~nodeonicefront);
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
-md.diagnostic_ref=NaN*ones(md.numberofnodes,6);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
+md.diagnostic.referential=NaN*ones(md.numberofnodes,6);
 
 %Dirichlet Values
 if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes)
         disp('      boundary conditions for diagnostic model: spc set as observed velocities');
-        md.spcvx(pos)=md.vx_obs(pos);
-        md.spcvy(pos)=md.vy_obs(pos);
+        md.diagnostic.spcvx(pos)=md.vx_obs(pos);
+        md.diagnostic.spcvy(pos)=md.vy_obs(pos);
 else
         disp('      boundary conditions for diagnostic model: spc set as zero');
@@ -62 +62 @@
 
 %plug onto model
-md.pressureload=pressureload;
+md.diagnostic.icefront=pressureload;
 
 %Create zeros basalforcings.melting_rate, surfaceforcings.ablation_rate, surfaceforcings.accumulation_rate

issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m

@@ -35 +35 @@
         warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually')
 end
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
-md.diagnostic_ref=NaN*ones(md.numberofnodes,6);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
+md.diagnostic.referential=NaN*ones(md.numberofnodes,6);
 
 %Dirichlet Values
 if (length(md.vx_obs)==md.numberofnodes & length(md.vy_obs)==md.numberofnodes)
         disp('      boundary conditions for diagnostic model: spc set as observed velocities');
-        md.spcvx(pos)=md.vx_obs(pos);
-        md.spcvy(pos)=md.vy_obs(pos);
+        md.diagnostic.spcvx(pos)=md.vx_obs(pos);
+        md.diagnostic.spcvy(pos)=md.vy_obs(pos);
 else
         disp('      boundary conditions for diagnostic model: spc set as zero');
@@ -72 +72 @@
 
 %plug onto model
-md.pressureload=pressureload;
+md.diagnostic.icefront=pressureload;
 
 

issm/trunk/template

@@ -61 +61 @@
         waterfraction
 }}}
-diagnostic{{{
-        spcvx
-        spcvy
-        spcvz
-        stokesreconditioning
-        shelf_dampening
-        viscosity_overshoot
-        pressureload -> rename icefront?
-        diagnostic_ref -> rename referential?
-        penalties -> rename vertex_pairing
-        penalty_offset -> rename penalty_factor and change to absolute value
-
-        eps_res -> rename following PETSc: restol
-        eps_rel -> rename following PETSc: reltol
-        eps_abs-> rename following PETSc:  abstol
-        max_nonlinear_iterations -> rename maxiter
-
-        penalty_lock -> rename rift_penalty_lock 
-        min_mechanical_constraints -> rename  rift_penalty_threshold
-        requested_outputs
-}}}
 inversion{{{ 
         private: 

issm/trunk/test/Miscellaneous/Bump/Bump.par

@@ -28 +28 @@
 %Deal with boundary conditions:
 md=SetIceSheetBC(md);
-md.spcvx=zeros(md.numberofnodes,1);
-md.spcvy=200*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=zeros(md.numberofnodes,1);
+md.diagnostic.spcvy=200*ones(md.numberofnodes,1);
 
 %Parallel options

issm/trunk/test/NightlyRun/test1101.m

@@ -21 +21 @@
 
         %Create dirichlet on the bed only
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
         pos=find(md.nodeonbed);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
 
         %Create MPCs to have periodic boundary conditions
@@ -36 +36 @@
         posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x));
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1102.m

@@ -29 +29 @@
         %Create dirichlet on the bed only
         pos=find(md.nodeonbed);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
-        md.spcvz(pos)=0;
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
+        md.diagnostic.spcvz(pos)=0;
 
         %Create MPCs to have periodic boundary conditions
@@ -42 +42 @@
         %posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x) & ~md.nodeonbed);
 
-        %md.penalties=[posx,posx2;posy,posy2];
+        %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic
         md.eps_abs=NaN;
-        md.eps_rel=NaN;
-        md.eps_res=1;
+        md.diagnostic.reltol=NaN;
+        md.diagnostic.restol=1;
         md.cluster=generic('name',oshostname(),'np',8);
         md=solve(md,DiagnosticSolutionEnum);

issm/trunk/test/NightlyRun/test1103.m

@@ -19 +19 @@
 
         %Create dirichlet on the bed only
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
         pos=find(md.nodeonbed);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
 
         %Create MPCs to have periodic boundary conditions
@@ -33 +33 @@
         posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x));
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1104.m

@@ -18 +18 @@
 
         %Create dirichlet on the bed only
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
         pos=find(md.nodeonbed);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
 
         %Create MPCs to have periodic boundary conditions
@@ -33 +33 @@
         posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x));
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1105.m

@@ -21 +21 @@
 
         %Create MPCs to have periodic boundary conditions
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
         posx=find(md.x==0 & md.y~=0 & md.y~=L);
@@ -31 +31 @@
         posy2=find(md.y==L & md.x~=0 & md.x~=L);
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Add spc on the corners
         pos=find((md.x==0 | md.x==L) & (md.y==0 | md.y==L) & md.nodeonbed);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
         if(L==5000),
-                md.spcvx(pos)=15.66;
-                md.spcvy(pos)=-0.1967;
+                md.diagnostic.spcvx(pos)=15.66;
+                md.diagnostic.spcvy(pos)=-0.1967;
         elseif(L==10000),
-                md.spcvx(pos)=16.04;
-                md.spcvy(pos)=-0.1977;
+                md.diagnostic.spcvx(pos)=16.04;
+                md.diagnostic.spcvy(pos)=-0.1977;
         elseif(L==20000),
-                md.spcvx(pos)=16.53;
-                md.spcvy(pos)=-1.27;
+                md.diagnostic.spcvx(pos)=16.53;
+                md.diagnostic.spcvy(pos)=-1.27;
         elseif(L==40000),
-                md.spcvx(pos)=17.23;
-                md.spcvy(pos)=-3.17;
+                md.diagnostic.spcvx(pos)=17.23;
+                md.diagnostic.spcvy(pos)=-3.17;
         elseif(L==80000),
-                md.spcvx(pos)=16.68;
-                md.spcvy(pos)=-2.69;
+                md.diagnostic.spcvx(pos)=16.68;
+                md.diagnostic.spcvy(pos)=-2.69;
         elseif(L==160000),
-                md.spcvx(pos)=16.03;
-                md.spcvy(pos)=-1.27;
+                md.diagnostic.spcvx(pos)=16.03;
+                md.diagnostic.spcvy(pos)=-1.27;
         end
         
         %Spc the bed at zero for vz
         pos=find(md.nodeonbed);
-        md.spcvz(pos)=0;
+        md.diagnostic.spcvz(pos)=0;
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1106.m

@@ -25 +25 @@
         %posy2=find(md.y==L & md.x~=0 & md.x~=L);
 
-        %md.penalties=[posx,posx2;posy,posy2];
+        %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1107.m

@@ -21 +21 @@
 
         %We need one grd on dirichlet: the 4 corners are set to zero
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
         %Create MPCs to have periodic boundary conditions
@@ -32 +32 @@
         posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x));
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Add spc on the corners
         pos=find((md.x==0 | md.x==L) & (md.y==0 | md.y==L) & md.nodeonbed);
-        md.spcvy(:)=0;
-        md.spcvx(pos)=0;
+        md.diagnostic.spcvy(:)=0;
+        md.diagnostic.spcvx(pos)=0;
         if(L==5000),
-                md.spcvx(pos)=16.0912;
+                md.diagnostic.spcvx(pos)=16.0912;
         elseif(L==10000),
-                md.spcvx(pos)=16.52;
+                md.diagnostic.spcvx(pos)=16.52;
         elseif(L==20000),
-                md.spcvx(pos)=17.77;
+                md.diagnostic.spcvx(pos)=17.77;
         elseif(L==40000),
-                md.spcvx(pos)=19.88;
+                md.diagnostic.spcvx(pos)=19.88;
         elseif(L==80000),
-                md.spcvx(pos)=18.65;
+                md.diagnostic.spcvx(pos)=18.65;
         elseif(L==160000),
-                md.spcvx(pos)=16.91;
+                md.diagnostic.spcvx(pos)=16.91;
         end
         
         %Spc the bed at zero for vz
         pos=find(md.nodeonbed);
-        md.spcvz(pos)=0;
+        md.diagnostic.spcvz(pos)=0;
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1108.m

@@ -18 +18 @@
 
         %We need one grd on dirichlet: the 4 corners are set to zero
-        %md.spcvx=NaN*ones(md.numberofnodes,1);
-        %md.spcvy=NaN*ones(md.numberofnodes,1);
-        %md.spcvz=NaN*ones(md.numberofnodes,1);
+        %md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        %md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        %md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
         
         %pos=find((md.x==0 | md.x==max(md.x)) & (md.y==0 | md.y==max(md.y)));
-        %md.spcvx(pos)=0;
-        %md.spcvy(pos)=0;
-        %md.spcvz(pos)=0;
+        %md.diagnostic.spcvx(pos)=0;
+        %md.diagnostic.spcvy(pos)=0;
+        %md.diagnostic.spcvz(pos)=0;
 
         %%Create MPCs to have periodic boundary conditions
@@ -34 +34 @@
         %posy2=find(md.y==max(md.y) & md.x~=0 & md.x~=max(md.x));
 
-        %md.penalties=[posx,posx2;posy,posy2];
+        %md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1109.m

@@ -28 +28 @@
         posx=find(md.x==0);
         posx2=find(md.x==max(md.x));
-        md.penalties=[posx,posx2];
+        md.diagnostic.vertex_pairing=[posx,posx2];
 
         %Create spcs on the bed 
         pos=find(md.nodeonbed);
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
-        md.spcvx(pos)=0;
-        md.spcvy(pos)=0;
-        md.spcvz(pos)=0;
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx(pos)=0;
+        md.diagnostic.spcvy(pos)=0;
+        md.diagnostic.spcvz(pos)=0;
 
         %Remove the spc where there is some sliding (case 3 and 4):
         if i==3 | i==4,
                 pos=find(md.y/max(md.y)>=0.44 & md.y/max(md.y)<=0.5);
-                md.spcvx(pos)=NaN;
-                md.spcvy(pos)=NaN;
-                md.spcvz(pos)=NaN;
+                md.diagnostic.spcvx(pos)=NaN;
+                md.diagnostic.spcvy(pos)=NaN;
+                md.diagnostic.spcvz(pos)=NaN;
         end
 

issm/trunk/test/NightlyRun/test1110.m

@@ -20 +20 @@
         end
 
-        md.spcvx=NaN*ones(md.numberofnodes,1);
-        md.spcvy=NaN*ones(md.numberofnodes,1);
-        md.spcvz=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+        md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
         if (i==1 | i==3),
                 %Create dirichlet on the bed if no slip
                 pos=find(md.nodeonbed);
-                md.spcvx(pos)=0;
-                md.spcvy(pos)=0;
-                md.spcvz(pos)=0;
+                md.diagnostic.spcvx(pos)=0;
+                md.diagnostic.spcvy(pos)=0;
+                md.diagnostic.spcvz(pos)=0;
         else
                 pos=find(md.nodeonbed & (md.x==0 | md.x==max(md.x)) & (md.y==0 | md.y==max(md.y)));
-                md.spcvx(pos)=100; %because we need a dirichlet somewhere
-                md.spcvy(pos)=0;
-                md.spcvz(pos)=0;
+                md.diagnostic.spcvx(pos)=100; %because we need a dirichlet somewhere
+                md.diagnostic.spcvy(pos)=0;
+                md.diagnostic.spcvz(pos)=0;
         end
         pos=find(~md.nodeonbed);
@@ -45 +45 @@
         posy2=find(md.y==max(md.y));
 
-        md.penalties=[posx,posx2;posy,posy2];
+        md.diagnostic.vertex_pairing=[posx,posx2;posy,posy2];
         md.prognostic.vertex_pairing=[posx,posx2;posy,posy2];
 
@@ -52 +52 @@
         md.output_frequency=50;
         md.prognostic.stabilization=1;
-        md.max_nonlinear_iterations=1;
+        md.diagnostic.maxiter=1;
 
         %Compute the diagnostic

issm/trunk/test/NightlyRun/test1203.m

@@ -11 +11 @@
 %Impose a non zero velocity on the upper boundary condition (y=max(y))
 pos=find(md.y==max(md.y));
-md.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2);
+md.diagnostic.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2);
 
 %Compute solution for MacAyeal's model 

issm/trunk/test/NightlyRun/test1204.m

@@ -11 +11 @@
 %Impose a non zero velocity on the upper boundary condition (y=max(y))
 pos=find(md.y==max(md.y));
-md.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2);
+md.diagnostic.spcvy(pos)=400*(((md.x(pos)-100000)/25000).^2-ones(size(pos,1),1)).*heaviside((1+eps)*ones(size(pos,1),1)-((md.x(pos)-100000)/25000).^2);
 
 %Compute solution for MacAyeal's model 

issm/trunk/test/NightlyRun/test1205.m

@@ -23 +23 @@
 %Spc the nodes on the bed
 pos=find(md.nodeonbed);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
 
 %Now we can solve the problem 

issm/trunk/test/NightlyRun/test1206.m

@@ -23 +23 @@
 %Spc the nodes on the bed
 pos=find(md.nodeonbed);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
 
 %Now we can solve the problem 

issm/trunk/test/NightlyRun/test1207.m

@@ -23 +23 @@
 %Spc the nodes on the bed
 pos=find(md.nodeonbed);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
 
 %Now we can solve the problem 

issm/trunk/test/NightlyRun/test1208.m

@@ -14 +14 @@
 %Spc the nodes on the bed
 pos=find(md.nodeonbed);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
 
 %Adapt the time steps to the resolution

issm/trunk/test/NightlyRun/test221.m

@@ -4 +4 @@
 md=extrude(md,3,1);
 md=setflowequation(md,'stokes','all');
-md.eps_rel=NaN;
+md.diagnostic.reltol=NaN;
 md.cluster=none;
 md=solve(md,TransientSolutionEnum);

issm/trunk/test/NightlyRun/test222.m

@@ -4 +4 @@
 md=extrude(md,3,1);
 md=setflowequation(md,'stokes','all');
-md.eps_rel=NaN;
+md.diagnostic.reltol=NaN;
 md.cluster=generic('name',oshostname(),'np',3);
 md=solve(md,TransientSolutionEnum);

issm/trunk/test/NightlyRun/test232.m

@@ -9 +9 @@
 md.rifts.riftstruct.fill=MelangeEnum();
 md.rifts.riftstruct.fraction=0;
-md.penalty_lock=2;
-md.min_mechanical_constraints=0;
+md.rift_penalty_lock=2;
+md.rift_penalty_threshold=0;
 md.rifts.riftstruct.fractionincrement=.1;
 md=solve(md,DiagnosticSolutionEnum);

issm/trunk/test/NightlyRun/test233.m

@@ -10 +10 @@
 
 %tighten
-md.eps_res=10^-4;
+md.diagnostic.restol=10^-4;
 
 %needed later
@@ -37 +37 @@
 
 %Boundary conditions:
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
 %constrain flanks to 0 normal velocity
 pos=find(md.x==xmin | md.x==xmax);
-md.spcvx(pos)=0;
-md.spcvz(pos)=NaN;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvz(pos)=NaN;
 
 %constrain grounding line to 0 velocity
 pos=find(md.y==ymin);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
 
 %icefront
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); pressureload=md.segments(pos,:);
-pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))];
-md.pressureload=pressureload;
+pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
+md.diagnostic.icefront=diagnostic.icefront;
 
 md=solve(md,DiagnosticSolutionEnum);

issm/trunk/test/NightlyRun/test234.m

@@ -10 +10 @@
 
 %tighten
-md.eps_res=10^-4;
+md.diagnostic.restol=10^-4;
 
 %needed later
@@ -37 +37 @@
 
 %Boundary conditions:
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
 %constrain flanks to 0 normal velocity
 pos=find(md.x==xmin | md.x==xmax);
-md.spcvx(pos)=0;
-md.spcvz(pos)=NaN;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvz(pos)=NaN;
 
 %constrain grounding line to 0 velocity
 pos=find(md.y==ymin);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
 
 %icefront
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); pressureload=md.segments(pos,:);
-pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))];
-md.pressureload=pressureload;
+pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
+md.diagnostic.icefront=diagnostic.icefront;
 
 md=solve(md,DiagnosticSolutionEnum);

issm/trunk/test/NightlyRun/test235.m

@@ -34 +34 @@
 
 %Boundary conditions:
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
 %constrain flanks to 0 normal velocity
 pos=find(md.x==xmin | md.x==xmax);
-md.spcvx(pos)=0;
-md.spcvz(pos)=NaN;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvz(pos)=NaN;
 
 %constrain grounding line to 0 velocity
 pos=find(md.y==ymin);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
 
 %icefront
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); pressureload=md.segments(pos,:);
-pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))];
-md.pressureload=pressureload;
+pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
+md.diagnostic.icefront=diagnostic.icefront;
 
 %partitioning
@@ -77 +77 @@
 
 %imperative! 
-md.eps_rel=10^-10; %tighten for qmu analysese
+md.diagnostic.reltol=10^-10; %tighten for qmu analysese
 md.qmu.isdakota=1;
 

issm/trunk/test/NightlyRun/test236.m

@@ -34 +34 @@
 
 %Boundary conditions:
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
 %constrain flanks to 0 normal velocity
 pos=find(md.x==xmin | md.x==xmax);
-md.spcvx(pos)=0;
-md.spcvz(pos)=NaN;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvz(pos)=NaN;
 
 %constrain grounding line to 0 velocity
 pos=find(md.y==ymin);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
 
 %icefront
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); pressureload=md.segments(pos,:);
-pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))];
-md.pressureload=pressureload;
+pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
+md.diagnostic.icefront=diagnostic.icefront;
 
 %partitioning
@@ -77 +77 @@
 
 %imperative! 
-md.eps_rel=10^-10; %tighten for qmu analysese
+md.diagnostic.reltol=10^-10; %tighten for qmu analysese
 md.qmu.isdakota=1;
 

issm/trunk/test/NightlyRun/test423.m

@@ -31 +31 @@
 
 %imperative! 
-md.eps_rel=10^-5; %tighten for qmu analysese
+md.diagnostic.reltol=10^-5; %tighten for qmu analysese
 
 %solve

issm/trunk/test/NightlyRun/test424.m

@@ -30 +30 @@
 
 %imperative! 
-md.eps_rel=10^-5; %tighten for qmu analysese
+md.diagnostic.reltol=10^-5; %tighten for qmu analysese
 
 %solve

issm/trunk/test/NightlyRun/test425.m

@@ -30 +30 @@
 
 %imperative!
-md.eps_rel=10^-5; %tighten for qmu analyses
+md.diagnostic.reltol=10^-5; %tighten for qmu analyses
 md.qmu.isdakota=1;
 

issm/trunk/test/NightlyRun/test426.m

@@ -30 +30 @@
 
 %imperative!
-md.eps_rel=10^-5; %tighten for qmu analyses
+md.diagnostic.reltol=10^-5; %tighten for qmu analyses
 md.qmu.isdakota=1;
 

issm/trunk/test/NightlyRun/test427.m

@@ -8 +8 @@
 
 %constrain all velocities to 1 m/yr, in the y-direction
-md.spcvx(:)=0;
-md.spcvy(:)=1;
-md.spcvz(:)=0;
+md.diagnostic.spcvx(:)=0;
+md.diagnostic.spcvy(:)=1;
+md.diagnostic.spcvz(:)=0;
 
 %Dakota options
@@ -44 +44 @@
 md.qmu.params.interval_type='forward';
 md.qmu.isdakota=1;
-md.eps_rel=10^-5; %tighten for qmu analyses
+md.diagnostic.reltol=10^-5; %tighten for qmu analyses
 
 %solve

issm/trunk/test/NightlyRun/test428.m

@@ -8 +8 @@
 
 %constrain all velocities to 1 m/yr, in the y-direction
-md.spcvx=zeros(md.numberofnodes,1);
-md.spcvy=ones(md.numberofnodes,1);
-md.spcvz=zeros(md.numberofnodes,1);
+md.diagnostic.spcvx=zeros(md.numberofnodes,1);
+md.diagnostic.spcvy=ones(md.numberofnodes,1);
+md.diagnostic.spcvz=zeros(md.numberofnodes,1);
 
 %Dakota options
@@ -44 +44 @@
 md.qmu.params.interval_type='forward';
 md.qmu.isdakota=1;
-md.eps_rel=10^-5; %tighten for qmu analyses
+md.diagnostic.reltol=10^-5; %tighten for qmu analyses
 
 %solve

issm/trunk/test/NightlyRun/test434.m

@@ -8 +8 @@
 
 %constrain all velocities to 1 m/yr, in the y-direction
-md.spcvx(:)=0;
-md.spcvy(:)=1;
-md.spcvz(:)=0;
+md.diagnostic.spcvx(:)=0;
+md.diagnostic.spcvy(:)=1;
+md.diagnostic.spcvz(:)=0;
 
 %Dakota options
@@ -47 +47 @@
 md.qmu.isdakota=1;
 
-md.eps_rel=10^-5; %tighten for qmu analyses
+md.diagnostic.reltol=10^-5; %tighten for qmu analyses
 
 md=solve(md,DiagnosticSolutionEnum,'overwrite','y');

issm/trunk/test/NightlyRun/test439.m

@@ -29 +29 @@
 
 %imperative! 
-md.eps_rel=10^-5; %tighten for qmu analysese
+md.diagnostic.reltol=10^-5; %tighten for qmu analysese
 
 %solve

issm/trunk/test/NightlyRun/test440.m

@@ -29 +29 @@
 
 %imperative! 
-md.eps_rel=10^-5; %tighten for qmu analysese
+md.diagnostic.reltol=10^-5; %tighten for qmu analysese
 
 %solve

issm/trunk/test/NightlyRun/test443.m

@@ -5 +5 @@
 md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','tiling');
 md.cluster=none;
-md.eps_rel=0.4;
+md.diagnostic.reltol=0.4;
 md=solve(md,DiagnosticSolutionEnum);
 

issm/trunk/test/NightlyRun/test444.m

@@ -5 +5 @@
 md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','macayeal');
 md.cluster=generic('name',oshostname(),'np',3);
-md.eps_rel=0.4;
+md.diagnostic.reltol=0.4;
 md=solve(md,DiagnosticSolutionEnum);
 

issm/trunk/test/Par/79North.par

@@ -30 +30 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.3;
+md.diagnostic.viscosity_overshoot=0.3;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
@@ -37 +37 @@
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;
-md.eps_res=0.05;
-md.eps_rel=0.005;
+md.diagnostic.restol=0.05;
+md.diagnostic.reltol=0.005;
 md.steadystate.reltol=0.005;
-md.eps_abs=NaN;
+md.diagnostic.abstol=NaN;
 
 %Boundary conditions:

issm/trunk/test/Par/ISMIPF.par

@@ -21 +21 @@
 %Create node on boundary fist (because we cannot use mesh)
 md=SetIceSheetBC(md);
-md.spcvx=100*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=100*ones(md.numberofnodes,1);
 md.vx=zeros(md.numberofnodes,1);
 md.vy=zeros(md.numberofnodes,1);

issm/trunk/test/Par/Pig.par

@@ -28 +28 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.3;
+md.diagnostic.viscosity_overshoot=0.3;
 md.prognostic.stabilization=1;
 md.verbose=verbose(0);
@@ -34 +34 @@
 md.timestepping.time_step=1;
 md.timestepping.final_time=2;
-md.eps_res=0.05;
-md.eps_rel=1;
+md.diagnostic.restol=0.05;
+md.diagnostic.reltol=1;
 md.steadystate.reltol=1;
-md.eps_abs=NaN;
+md.diagnostic.abstol=NaN;
 
 %Boundary conditions:

issm/trunk/test/Par/RoundSheetEISMINT.par

@@ -45 +45 @@
 md.x(pos)=0; md.y(pos)=0; %the closest node to the center is changed to be exactly at the center
 
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;
 
 %parallel options

issm/trunk/test/Par/RoundSheetShelf.par

@@ -57 +57 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.0;
+md.diagnostic.viscosity_overshoot=0.0;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
 md.waitonlock=30;
-md.eps_res=0.05;
-md.eps_rel=0.05;
+md.diagnostic.restol=0.05;
+md.diagnostic.reltol=0.05;
 md.steadystate.reltol=0.05;
-md.eps_abs=NaN;
+md.diagnostic.abstol=NaN;
 md.timestepping.time_step=.1;
 md.timestepping.final_time=5;
@@ -75 +75 @@
 
 %Deal with boundary conditions:
-md.spcvx=NaN*ones(md.numberofnodes,1);
-md.spcvy=NaN*ones(md.numberofnodes,1);
-md.spcvz=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
+md.diagnostic.spcvz=NaN*ones(md.numberofnodes,1);
 
 pos=find(md.x==0 & md.y==0);
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
 
 pressureload=md.segments;
 pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end)) + 0*md.mask.elementongroundedice(pressureload(:,end))];
-md.pressureload=pressureload;
+md.diagnostic.icefront=pressureload;
 md.balancethickness.spcthickness=NaN*ones(md.numberofnodes,1);
 md.prognostic.spcthickness=NaN*ones(md.numberofnodes,1);

issm/trunk/test/Par/RoundSheetStaticEISMINT.par

@@ -50 +50 @@
 md.x(pos)=0; md.y(pos)=0; %the closest node to the center is changed to be exactly at the center
 
-md.spcvx(pos)=0;
-md.spcvy(pos)=0;
-md.spcvz(pos)=0;
+md.diagnostic.spcvx(pos)=0;
+md.diagnostic.spcvy(pos)=0;
+md.diagnostic.spcvz(pos)=0;

issm/trunk/test/Par/SquareSheetConstrained.par

@@ -31 +31 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.0;
+md.diagnostic.viscosity_overshoot=0.0;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
 md.waitonlock=30;
-md.eps_res=0.05;
+md.diagnostic.restol=0.05;
 md.steadystate.reltol=0.05;
-md.eps_rel=0.05;
-md.eps_abs=NaN;
+md.diagnostic.reltol=0.05;
+md.diagnostic.abstol=NaN;
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;

issm/trunk/test/Par/SquareSheetShelf.par

@@ -38 +38 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.0;
+md.diagnostic.viscosity_overshoot=0.0;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
 md.waitonlock=30;
-md.eps_res=0.05;
+md.diagnostic.restol=0.05;
 md.steadystate.reltol=0.05;
-md.eps_rel=0.05;
-md.eps_abs=NaN;
+md.diagnostic.reltol=0.05;
+md.diagnostic.abstol=NaN;
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;

issm/trunk/test/Par/SquareShelf.par

@@ -31 +31 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.3;
+md.diagnostic.viscosity_overshoot=0.3;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
 md.waitonlock=30;
 md.verbose=verbose(0);
-md.eps_res=0.10;
+md.diagnostic.restol=0.10;
 md.steadystate.reltol=0.02;
-md.eps_rel=0.02;
-md.eps_abs=NaN;
+md.diagnostic.reltol=0.02;
+md.diagnostic.abstol=NaN;
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;

issm/trunk/test/Par/SquareShelfConstrained.par

@@ -35 +35 @@
 
 %Numerical parameters
-md.viscosity_overshoot=0.0;
+md.diagnostic.viscosity_overshoot=0.0;
 md.prognostic.stabilization=1;
 md.thermal.stabilization=1;
 md.verbose=verbose(0);
 md.waitonlock=30;
-md.eps_res=0.05;
-md.eps_rel=0.05;
+md.diagnostic.restol=0.05;
+md.diagnostic.reltol=0.05;
 md.steadystate.reltol=0.05;
-md.eps_abs=NaN;
+md.diagnostic.abstol=NaN;
 md.timestepping.time_step=1;
 md.timestepping.final_time=3;