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John Wise committed 6cd4c87 Merge

Forgot to pull the latest changes. Merging again.

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run/Cosmology/Hydro/AMRCosmology/AMRCosmology.enzo

+#
+# AMR PROBLEM DEFINITION FILE: Cosmology Simulation (amr version)
+#
+#  define problem
+#
+ProblemType                = 30      // cosmology simulation
+TopGridRank                = 3
+TopGridDimensions          = 16 16 16
+SelfGravity                = 1       // gravity on
+TopGridGravityBoundary     = 0       // Periodic BC for gravity
+LeftFaceBoundaryCondition  = 3 3 3   // same for fluid
+RightFaceBoundaryCondition = 3 3 3
+#
+#  problem parameters
+#
+CosmologySimulationOmegaBaryonNow       = 0.04
+CosmologySimulationOmegaCDMNow          = 0.26
+CosmologySimulationDensityName          = GridDensity
+CosmologySimulationVelocity1Name        = GridVelocities
+CosmologySimulationVelocity2Name        = GridVelocities
+CosmologySimulationVelocity3Name        = GridVelocities
+CosmologySimulationParticlePositionName = ParticlePositions
+CosmologySimulationParticleVelocityName = ParticleVelocities
+#
+#  define cosmology parameters
+#
+ComovingCoordinates        = 1       // Expansion ON
+CosmologyOmegaMatterNow    = 0.3
+CosmologyOmegaLambdaNow    = 0.7
+CosmologyHubbleConstantNow = 0.5     // in 100 km/s/Mpc
+CosmologyComovingBoxSize   = 16.0    // in Mpc/h
+CosmologyMaxExpansionRate  = 0.015   // maximum allowed delta(a)/a
+CosmologyInitialRedshift   = 30      // 
+CosmologyFinalRedshift     = 0       //
+GravitationalConstant      = 1       // this must be true for cosmology
+#
+#  set I/O and stop/start parameters
+#
+StopCycle              = 1000          // stop after this many cycles
+dtDataDump             = 10.0         // dump at beginning and end
+#CycleSkipDataDump      = 20
+DataDumpName           = output_
+ParallelRootGridIO     = 1
+CosmologyOutputRedshift[0] = 10
+CosmologyOutputRedshift[1] = 8
+CosmologyOutputRedshift[2] = 6
+CosmologyOutputRedshift[3] = 4
+CosmologyOutputRedshift[4] = 3
+CosmologyOutputRedshift[5] = 2
+CosmologyOutputRedshift[6] = 1
+CosmologyOutputRedshift[7] = 0
+#
+#  set hydro parameters
+#
+Gamma                  = 1.6667
+PPMDiffusionParameter  = 0       // diffusion off
+DualEnergyFormalism    = 1       // use total & internal energy
+InterpolationMethod    = 1     // SecondOrderA
+CourantSafetyNumber    = 0.5
+ParticleCourantSafetyNumber = 0.8
+RadiativeCooling            = 0
+MultiSpecies                = 0
+#
+#  set grid refinement parameters
+#
+StaticHierarchy           = 0    // dynamic hierarchy
+MaximumRefinementLevel    = 2    // use up to 2 levels
+RefineBy                  = 2    // refinement factor
+CellFlaggingMethod        = 2 4    // use baryon mass for refinement 
+MinimumEfficiency         = 0.4  // fraction efficiency
+MinimumOverDensityForRefinement = 4.0 // times the initial density
+MinimumMassForRefinementLevelExponent = -0.3
+MinimumEnergyRatioForRefinement = 0.4 // min Egas/Etot for shock refinement
+#RefineRegionLeftEdge            = 0.15 0.20 0.41
+#RefineRegionRightEdge           = 0.35 0.45 0.79
+#
+#  set some global parameters
+#
+GreensFunctionMaxNumber   = 30   // # of greens function at any one time
+

run/Cosmology/Hydro/AMRCosmology/AMRCosmology.enzotest

+name = 'AMRCosmology'
+answer_testing_script = None
+nprocs = 1
+runtime = 'unknown'
+critical = True
+cadence = 'nightly'
+hydro = True
+gravity = True
+AMR = True
+cosmology = True
+dimensionality = 3

run/Cosmology/Hydro/AMRCosmologySimulation/AMRCosmologySimulation.enzo

-#
-# AMR PROBLEM DEFINITION FILE: Cosmology Simulation (amr version)
-#
-#  define problem
-#
-ProblemType                = 30      // cosmology simulation
-TopGridRank                = 3
-TopGridDimensions          = 16 16 16
-SelfGravity                = 1       // gravity on
-TopGridGravityBoundary     = 0       // Periodic BC for gravity
-LeftFaceBoundaryCondition  = 3 3 3   // same for fluid
-RightFaceBoundaryCondition = 3 3 3
-#
-#  problem parameters
-#
-CosmologySimulationOmegaBaryonNow       = 0.04
-CosmologySimulationOmegaCDMNow          = 0.26
-CosmologySimulationDensityName          = GridDensity
-CosmologySimulationVelocity1Name        = GridVelocities
-CosmologySimulationVelocity2Name        = GridVelocities
-CosmologySimulationVelocity3Name        = GridVelocities
-CosmologySimulationParticlePositionName = ParticlePositions
-CosmologySimulationParticleVelocityName = ParticleVelocities
-#
-#  define cosmology parameters
-#
-ComovingCoordinates        = 1       // Expansion ON
-CosmologyOmegaMatterNow    = 0.3
-CosmologyOmegaLambdaNow    = 0.7
-CosmologyHubbleConstantNow = 0.5     // in 100 km/s/Mpc
-CosmologyComovingBoxSize   = 16.0    // in Mpc/h
-CosmologyMaxExpansionRate  = 0.015   // maximum allowed delta(a)/a
-CosmologyInitialRedshift   = 30      // 
-CosmologyFinalRedshift     = 0       //
-GravitationalConstant      = 1       // this must be true for cosmology
-#
-#  set I/O and stop/start parameters
-#
-StopCycle              = 1000          // stop after this many cycles
-dtDataDump             = 10.0         // dump at beginning and end
-#CycleSkipDataDump      = 20
-DataDumpName           = output_
-ParallelRootGridIO     = 1
-CosmologyOutputRedshift[0] = 10
-CosmologyOutputRedshift[1] = 8
-CosmologyOutputRedshift[2] = 6
-CosmologyOutputRedshift[3] = 4
-CosmologyOutputRedshift[4] = 3
-CosmologyOutputRedshift[5] = 2
-CosmologyOutputRedshift[6] = 1
-CosmologyOutputRedshift[7] = 0
-#
-#  set hydro parameters
-#
-Gamma                  = 1.6667
-PPMDiffusionParameter  = 0       // diffusion off
-DualEnergyFormalism    = 1       // use total & internal energy
-InterpolationMethod    = 1     // SecondOrderA
-CourantSafetyNumber    = 0.5
-ParticleCourantSafetyNumber = 0.8
-RadiativeCooling            = 0
-MultiSpecies                = 0
-#
-#  set grid refinement parameters
-#
-StaticHierarchy           = 0    // dynamic hierarchy
-MaximumRefinementLevel    = 2    // use up to 2 levels
-RefineBy                  = 2    // refinement factor
-CellFlaggingMethod        = 2 4    // use baryon mass for refinement 
-MinimumEfficiency         = 0.4  // fraction efficiency
-MinimumOverDensityForRefinement = 4.0 // times the initial density
-MinimumMassForRefinementLevelExponent = -0.3
-MinimumEnergyRatioForRefinement = 0.4 // min Egas/Etot for shock refinement
-#RefineRegionLeftEdge            = 0.15 0.20 0.41
-#RefineRegionRightEdge           = 0.35 0.45 0.79
-#
-#  set some global parameters
-#
-GreensFunctionMaxNumber   = 30   // # of greens function at any one time
-

run/Cosmology/Hydro/AMRCosmologySimulation/AMRCosmologySimulation.enzotest

-name = 'AMRCosmologySimulation'
-answer_testing_script = None
-nprocs = 1
-runtime = 'unknown'
-critical = True
-cadence = 'nightly'
-hydro = True
-gravity = True
-AMR = True
-cosmology = True
-dimensionality = 3

run/Cosmology/Hydro/AMRNestedCosmology/AMRNestedCosmology.enzo

+#
+# nested cosmology simulation
+#
+ProblemType                    = 30
+TopGridRank                    = 3
+SelfGravity                    = 1
+TopGridGravityBoundary         = 0
+LeftFaceBoundaryCondition      = 3 3 3
+RightFaceBoundaryCondition     = 3 3 3
+BaryonSelfGravityApproximation = 1
+TopGridDimensions              = 32 32 32
+
+#
+#  problem parameters
+#
+CosmologySimulationOmegaBaryonNow       = 0.04
+CosmologySimulationOmegaCDMNow          = 0.26
+CosmologySimulationInitialTemperature   = 140.0  // DEBATABLE
+CosmologySimulationDensityName          = GridDensity
+CosmologySimulationVelocity1Name        = GridVelocities
+CosmologySimulationVelocity2Name        = GridVelocities
+CosmologySimulationVelocity3Name        = GridVelocities
+CosmologySimulationParticlePositionName = ParticlePositions
+CosmologySimulationParticleVelocityName = ParticleVelocities
+CosmologySimulationNumberOfInitialGrids = 3
+CosmologySimulationGridDimension[1]     = 32 32 32
+CosmologySimulationGridLeftEdge[1]      = 0.25 0.25 0.25
+CosmologySimulationGridRightEdge[1]     = 0.75 0.75 0.75
+CosmologySimulationGridLevel[1]         = 1
+CosmologySimulationGridDimension[2]     = 32 32 32
+CosmologySimulationGridLeftEdge[2]      = 0.375 0.375 0.375 
+CosmologySimulationGridRightEdge[2]     = 0.625 0.625 0.625
+CosmologySimulationGridLevel[2]         = 2
+
+#
+#  define cosmology parameters
+#
+ComovingCoordinates        = 1
+CosmologyOmegaMatterNow    = 0.3
+CosmologyOmegaLambdaNow    = 0.7
+CosmologyHubbleConstantNow = 0.70
+CosmologyComovingBoxSize   = 0.3
+CosmologyMaxExpansionRate  = 0.02
+CosmologyInitialRedshift   = 99
+CosmologyFinalRedshift     = 15
+GravitationalConstant      = 1
+
+#
+#  set I/O and stop/start parameters
+#
+
+dtDataDump                = 1.0
+RedshiftDumpName          = RD
+RedshiftDumpDir           = RD
+DataDumpName              = DD
+DataDumpDir               = DD
+
+CosmologyOutputRedshift[0] = 99
+CosmologyOutputRedshift[1] = 40
+CosmologyOutputRedshift[2] = 35
+CosmologyOutputRedshift[3] = 30
+CosmologyOutputRedshift[4] = 25
+CosmologyOutputRedshift[5] = 24
+CosmologyOutputRedshift[6] = 23
+CosmologyOutputRedshift[7] = 22
+CosmologyOutputRedshift[8] = 21
+CosmologyOutputRedshift[9] = 20
+CosmologyOutputRedshift[10] = 19
+CosmologyOutputRedshift[11] = 18
+CosmologyOutputRedshift[12] = 17
+CosmologyOutputRedshift[13] = 16
+CosmologyOutputRedshift[14] = 15
+
+#
+#  set hydro parameters
+#
+Gamma                        = 1.6667
+PPMDiffusionParameter        = 0
+DualEnergyFormalism          = 1
+HydroMethod                  = 0
+InterpolationMethod          = 1 
+CourantSafetyNumber          = 0.4
+ParticleCourantSafetyNumber  = 0.6
+UseMinimumPressureSupport    = 0
+MultiSpecies                 = 2
+RadiativeCooling             = 1    
+RadiationFieldType           = 0
+FluxCorrection               = 1
+ConservativeInterpolation    = 0
+
+#
+#  set grid refinement parameters
+#
+StaticHierarchy                 = 0
+MaximumRefinementLevel          = 6
+MaximumGravityRefinementLevel   = 6
+OutputFirstTimeAtLevel          = 6
+RefineBy                        = 2
+CellFlaggingMethod              = 2 4 
+MinimumEfficiency               = 0.35
+MinimumOverDensityForRefinement = 0.125 0.125
+RefineRegionLeftEdge            = 0.375 0.375 0.375
+RefineRegionRightEdge           = 0.625 0.625 0.625
+MinimumMassForRefinementLevelExponent = -0.3
+MinimumEnergyRatioForRefinement = 0.4 
+
+#
+#  set some global parameters
+#
+GreensFunctionMaxNumber   = 40
+ParallelRootGridIO        = 1
+ParallelParticleIO        = 1

run/Cosmology/Hydro/AMRNestedCosmology/AMRNestedCosmology.enzotest

+name = 'AMRNestedCosmology'
+answer_testing_script = None
+nprocs = 1
+runtime = 'unknown'
+critical = True
+cadence = 'nightly'
+hydro = True
+gravity = True
+AMR = True
+cosmology = True
+dimensionality = 3

run/Cosmology/Inits/AMRCosmology/AMRCosmology.inits

+#  Generates initial grid and particle fields for a single-grid
+#    CDM simulation
+#
+#  Cosmology Parameters
+#
+
+# PREVIOUS (1998)
+
+# CosmologyOmegaMatterNow      = 1
+# CosmologyOmegaLambdaNow      = 0
+# CosmologyOmegaBaryonNow      = 0.06
+
+# CURRENT (WMAP)
+
+CosmologyOmegaMatterNow      = 0.3
+CosmologyOmegaLambdaNow      = 0.7
+CosmologyOmegaBaryonNow      = 0.04
+
+CosmologyComovingBoxSize     = 16       // in Mpc/h
+CosmologyHubbleConstantNow   = 0.5      // in units of 100 km/s/Mpc
+CosmologyInitialRedshift     = 30
+#
+#  Power spectrum Parameters
+#
+PowerSpectrumType            = 1             // BBKS
+PowerSpectrumSigma8          = 0.7
+PowerSpectrumPrimordialIndex = 1.0
+PowerSpectrumRandomSeed      = -123456789
+#
+#  Grid info
+#
+Rank                = 3
+GridDims            = 16 16 16
+InitializeGrids     = 1
+GridRefinement      = 1
+#
+#  Particle info
+#
+ParticleDims        = 16 16 16
+InitializeParticles = 1
+ParticleRefinement  = 1
+#
+#  Overall field parameters
+#
+MaxDims             = 16 16 16
+#NewCenter           = 0.5 0.5 0.5
+#StartIndex          = 0 0 0
+#
+#  Names
+#
+ParticlePositionName = ParticlePositions
+ParticleVelocityName = ParticleVelocities
+GridDensityName      = GridDensity
+GridVelocityName     = GridVelocities

run/Cosmology/Inits/AMRCosmologySimulation.inits

-#  Generates initial grid and particle fields for a single-grid
-#    CDM simulation
-#
-#  Cosmology Parameters
-#
-
-# PREVIOUS (1998)
-
-# CosmologyOmegaMatterNow      = 1
-# CosmologyOmegaLambdaNow      = 0
-# CosmologyOmegaBaryonNow      = 0.06
-
-# CURRENT (WMAP)
-
-CosmologyOmegaMatterNow      = 0.3
-CosmologyOmegaLambdaNow      = 0.7
-CosmologyOmegaBaryonNow      = 0.04
-
-CosmologyComovingBoxSize     = 16       // in Mpc/h
-CosmologyHubbleConstantNow   = 0.5      // in units of 100 km/s/Mpc
-CosmologyInitialRedshift     = 30
-#
-#  Power spectrum Parameters
-#
-PowerSpectrumType            = 1             // BBKS
-PowerSpectrumSigma8          = 0.7
-PowerSpectrumPrimordialIndex = 1.0
-PowerSpectrumRandomSeed      = -123456789
-#
-#  Grid info
-#
-Rank                = 3
-GridDims            = 16 16 16
-InitializeGrids     = 1
-GridRefinement      = 1
-#
-#  Particle info
-#
-ParticleDims        = 16 16 16
-InitializeParticles = 1
-ParticleRefinement  = 1
-#
-#  Overall field parameters
-#
-MaxDims             = 16 16 16
-#NewCenter           = 0.5 0.5 0.5
-#StartIndex          = 0 0 0
-#
-#  Names
-#
-ParticlePositionName = ParticlePositions
-ParticleVelocityName = ParticleVelocities
-GridDensityName      = GridDensity
-GridVelocityName     = GridVelocities

run/Cosmology/Inits/AMRNestedCosmology/AMRNestedCosmology_SubGrid.inits

+#
+#  Cosmology Parameters
+#
+CosmologyOmegaMatterNow      = 0.3
+CosmologyOmegaLambdaNow      = 0.7
+CosmologyOmegaBaryonNow      = 0.04
+CosmologyComovingBoxSize     = 0.3       // in Mpc/h
+CosmologyHubbleConstantNow   = 0.70      // in units of 100 km/s/Mpc
+CosmologyInitialRedshift     = 99
+#
+#  Power spectrum Parameters
+#
+PowerSpectrumType            = 11             // Eisenstein & Hu
+PowerSpectrumSigma8          = 0.9
+PowerSpectrumPrimordialIndex = 1.0
+PowerSpectrumRandomSeed      = -267478895
+#
+#  Grid info
+#
+Rank                = 3
+InitializeGrids     = 1
+GridRefinement      = 2
+GridDims = 32 32 32
+#
+#  Particle info
+#
+InitializeParticles = 1
+ParticleRefinement  = 2
+ParticleDims = 32 32 32
+
+#
+#  Overall field parameters
+#
+MaxDims = 128 128 128
+NewCenterFloat = 0.480763 0.674363 0.285945
+StartIndexInNewCenterTopGridSystem = 8 8 8
+EndIndexInNewCenterTopGridSystem   = 23 23 23
+RootGridDims = 32 32 32
+#
+#  Names
+#
+ParticlePositionName = ParticlePositions.1
+ParticleVelocityName = ParticleVelocities.1
+GridDensityName      = GridDensity.1
+GridVelocityName     = GridVelocities.1

run/Cosmology/Inits/AMRNestedCosmology/AMRNestedCosmology_SubSubGrid.inits

+#
+#  Cosmology Parameters
+#
+CosmologyOmegaMatterNow      = 0.3
+CosmologyOmegaLambdaNow      = 0.7
+CosmologyOmegaBaryonNow      = 0.04
+CosmologyComovingBoxSize     = 0.3       // in Mpc/h
+CosmologyHubbleConstantNow   = 0.70      // in units of 100 km/s/Mpc
+CosmologyInitialRedshift     = 99
+#
+#  Power spectrum Parameters
+#
+PowerSpectrumType            = 11             // Eisenstein & Hu
+PowerSpectrumSigma8          = 0.9
+PowerSpectrumPrimordialIndex = 1.0
+PowerSpectrumRandomSeed      = -267478895
+#
+#  Grid info
+#
+Rank                = 3
+InitializeGrids     = 1
+GridRefinement      = 1
+GridDims = 32 32 32
+#
+#  Particle info
+#
+InitializeParticles = 1
+ParticleRefinement  = 1
+ParticleDims = 32 32 32
+
+#
+#  Overall field parameters
+#
+MaxDims = 128 128 128
+NewCenterFloat = 0.480763 0.674363 0.285945
+StartIndexInNewCenterTopGridSystem = 12 12 12
+EndIndexInNewCenterTopGridSystem   = 19 19 19
+RootGridDims = 32 32 32
+#
+#  Names
+#
+ParticlePositionName = ParticlePositions.2
+ParticleVelocityName = ParticleVelocities.2
+GridDensityName      = GridDensity.2
+GridVelocityName     = GridVelocities.2

run/Cosmology/Inits/AMRNestedCosmology/AMRNestedCosmology_TopGrid.inits

+#
+#  Cosmology Parameters
+#
+CosmologyOmegaMatterNow      = 0.3
+CosmologyOmegaLambdaNow      = 0.7
+CosmologyOmegaBaryonNow      = 0.04
+CosmologyComovingBoxSize     = 0.3       // in Mpc/h
+CosmologyHubbleConstantNow   = 0.70      // in units of 100 km/s/Mpc
+CosmologyInitialRedshift     = 99
+
+#
+#  Power spectrum Parameters
+#
+PowerSpectrumType            = 11             // Eisenstein & Hu
+PowerSpectrumSigma8          = 0.9
+PowerSpectrumPrimordialIndex = 1.0
+PowerSpectrumRandomSeed      = -267478895
+
+#
+#  Grid info
+#
+Rank                = 3
+GridDims = 32 32 32 
+GridRefinement      = 4
+InitializeGrids     = 1
+
+#
+#  Particle info
+#
+InitializeParticles = 1
+ParticleRefinement  = 4
+ParticleDims = 32 32 32 
+
+#
+#  Overall field parameters
+#
+MaxDims = 128 128 128
+NewCenterFloat =  0.480763 0.674363 0.285945
+StartIndex = 0 0 0
+RootGridDims = 32 32 32
+
+#
+#  Names
+#
+ParticlePositionName = ParticlePositions.0
+ParticleVelocityName = ParticleVelocities.0
+GridDensityName      = GridDensity.0
+GridVelocityName     = GridVelocities.0

src/enzo/Grid_CopyParentToGravitatingFieldBoundary.C

      the region dim (in parent units). */
  
   for (dim = 0; dim < GridRank; dim++) {
-    // SubGridExtra[dim] = nint((GridLeftEdge[dim] -
-    // 			      GravitatingMassFieldLeftEdge[dim])
-    // 			     /GravitatingMassFieldCellSize);
-       SubGridExtra[dim] = nint((CellLeftEdge[dim][0] -
-    			      GravitatingMassFieldLeftEdge[dim])
+    SubGridExtra[dim] = nint((GridLeftEdge[dim] -
+			      GravitatingMassFieldLeftEdge[dim])
     			     /GravitatingMassFieldCellSize);
+    // SubGridExtra[dim] = nint((CellLeftEdge[dim][0] -
+    //  			      GravitatingMassFieldLeftEdge[dim])
+    //  			     /GravitatingMassFieldCellSize);
     ParentOffset[dim] = nint((GravitatingMassFieldLeftEdge[dim] -
 		  ParentGrid->GravitatingMassFieldLeftEdge[dim])/
 			     GravitatingMassFieldCellSize);

src/enzo/ReadParameterFile.C

     if (strstr(line, "ConductionBubble")) ret++;
     if (strstr(line, "ConductionCloud")) ret++;
     if (strstr(line, "CoolingTest")) ret++;
+    if (strstr(line, "OneZoneFreefall")) ret++;
     if (strstr(line, "ShearingBox")) ret++;
     if (strstr(line, "PoissonSolverTest")) ret++;
     /* 7.22.10 - CBH: Added 5 following lines to avoid runtime warnings from