added example gresho_2d

examples/gresho_2d/Config.sh

+#!/bin/bash            # this line only there to enable syntax highlighting in this file
+
+## examples/gresho_2d/Config.sh
+## config file for 2d Gresho vortex probelm
+
+
+#--------------------------------------- Basic operation mode of code
+TWODIMS                                  # 2d simulation
+
+#--------------------------------------- MPI/Threading Hybrid
+READ_MASS_AS_DENSITY_IN_INPUT            # Reads the mass field in the IC as density
+
+#--------------------------------------- Mesh motion and regularization
+REGULARIZE_MESH_CM_DRIFT                 # Mesh regularization; Move mesh generating point towards center of mass to make cells rounder.
+REGULARIZE_MESH_CM_DRIFT_USE_SOUNDSPEED  # Limit mesh regularization speed by local sound speed
+REGULARIZE_MESH_FACE_ANGLE               # Use maximum face angle as roundness criterion in mesh regularization
+
+#--------------------------------------- Time integration options
+TREE_BASED_TIMESTEPS                     # non-local timestep criterion (take 'signal speed' into account)
+
+#---------------------------------------- Single/Double Precision
+DOUBLEPRECISION=1                        # Mode of double precision: not defined: single; 1: full double precision 2: mixed, 3: mixed, fewer single precisions; unless short of memory, use 1.
+INPUT_IN_DOUBLEPRECISION                 # initial conditions are in double precision
+OUTPUT_IN_DOUBLEPRECISION                # snapshot files will be written in double precision
+
+#--------------------------------------- Output/Input options
+HAVE_HDF5                                # needed when HDF5 I/O support is desired (recommended)
+
+#--------------------------------------- Testing and Debugging options
+DEBUG                                    # enables core-dumps

examples/gresho_2d/check.py

+""" @package ./examples/gresho_2d/check.py
+Code that checks results of 2d Gresho vortex problem
+
+created by Rainer Weinberger, last modified 21.02.2019 -- comments welcome
+"""
+
+#### load libraries
+import sys    # system specific calls
+import numpy as np    ## load numpy
+import h5py    ## load h5py; needed to read snapshots
+
+simulation_directory = str(sys.argv[1])
+print("examples/gresho_2d/check.py: checking simulation output in directory " + simulation_directory)
+
+FloatType = np.float64  # double precision: np.float64, for single use np.float32
+
+## open initial conditiions to get parameters
+try:
+    data = h5py.File(simulation_directory + "/IC.hdf5", "r")
+except:
+    print("could not open initial  conditions!")
+    exit(-1)
+Boxsize = FloatType(data["Header"].attrs["BoxSize"])
+NumberOfCells = np.int32(data["Header"].attrs["NumPart_Total"][0]) 
+CellsPerDimension = np.sqrt(NumberOfCells)
+
+## parameters
+density_0 = 1.0
+velocity_0 = 3.0
+gamma = 5.0/3.0
+gamma_minus_one = gamma - 1.0
+
+## maximum L1 error after one propagation; empirically based
+DeltaMaxAllowed = 0.03 * (FloatType(CellsPerDimension) / 40.0)**-1.4
+
+""" loop over all output files """
+i_file = 0
+while True:
+    """ try to read in snapshot """
+    directory = simulation_directory+"/output/"
+    filename = "snap_%03d.hdf5" % (i_file)
+    try:
+        data = h5py.File(directory+filename, "r")
+    except:
+        break
+    
+    """ get simulation data """
+    ## simulation data
+    Pos = np.array(data["PartType0"]["Coordinates"], dtype = FloatType)
+    Density = np.array(data["PartType0"]["Density"], dtype = FloatType)
+    Mass = np.array(data["PartType0"]["Masses"], dtype = FloatType)
+    Velocity = np.array(data["PartType0"]["Velocities"], dtype = FloatType)
+    Velocity[:,0] -= velocity_0
+    Uthermal = np.array(data["PartType0"]["InternalEnergy"], dtype = FloatType)
+    Volume = Mass / Density
+    
+    xPosFromCenter = (Pos[:,0] - 0.5 * Boxsize)
+    yPosFromCenter = (Pos[:,1] - 0.5 * Boxsize)
+    Radius = np.sqrt( xPosFromCenter**2 + yPosFromCenter**2 )
+    i_select, = np.where(Radius != 0.0)
+    RotationVelocity = yPosFromCenter * Velocity[:,0] - xPosFromCenter * Velocity[:,1]
+    RotationVelocity[i_select] /= Radius[i_select]
+    RotationVelocity[Radius[:] == 0.0] = 0.0
+
+    """ calculate analytic solution """
+    ## density
+    Density_ref = np.full(Density.shape, density_0, dtype=FloatType)
+    
+    ## different zones
+    i1, = np.where( Radius < 0.2 )
+    i2, = np.where( (Radius >= 0.2) & (Radius < 0.4) )
+    i3, = np.where( Radius >= 0.4 )
+    
+    ## velocity
+    RotationVelocity_ref = np.zeros(Velocity.shape[0], dtype=FloatType)
+    RotationVelocity_ref[i1] = 5.0 * Radius[i1]
+    RotationVelocity_ref[i2] = 2.0 - 5.0 * Radius[i2]
+    RotationVelocity_ref[i3] = 0.0
+    Velocity_ref = np.zeros(Velocity.shape, dtype=FloatType )
+    i_select, = np.where(Radius != 0.0)
+    Velocity_ref[i_select,0] = RotationVelocity_ref[i_select] * (Pos[i_select,1] - 0.5 * Boxsize) / Radius[i_select]
+    Velocity_ref[i_select,1] = -RotationVelocity_ref[i_select] * (Pos[i_select,0] - 0.5 * Boxsize) / Radius[i_select]
+    
+    ## specific internal energy
+    Pressure_ref = np.zeros(Uthermal.shape, dtype=FloatType)
+    Pressure_ref[i1] = 5.0 + 12.5 * Radius[i1] * Radius[i1]
+    Pressure_ref[i2] = 9.0 + 12.5 * Radius[i2] * Radius[i2] - 20.0 * Radius[i2] + 4.0 * np.log(Radius[i2] / 0.2)
+    Pressure_ref[i3] = 3.0 + 4.0 * np.log(2.0)
+    Uthermal_ref = Pressure_ref / density_0 / gamma_minus_one
+    
+    """ compare data """
+    ## density
+    abs_delta_dens = np.abs(Density - Density_ref)
+    L1_dens = np.average(abs_delta_dens, weights = Volume)
+    
+    ## velocity
+    abs_delta_vel = np.abs(RotationVelocity - RotationVelocity_ref)
+    L1_vel = np.average(abs_delta_vel, weights = Volume)
+    
+    ## internal energy
+    abs_delta_utherm = np.abs(Uthermal - Uthermal_ref)
+    L1_utherm = np.average(abs_delta_utherm, weights = Volume)
+
+    """ printing results """
+    print("examples/Gresho_2d/check.py: L1 error of " + filename +":")
+    print("\t density: %g" % L1_dens)
+    print("\t velocity: %g" % L1_vel)
+    print("\t specific internal energy: %g" % L1_utherm)
+    print("\t tolerance: %g for %d cells per dimension" % (DeltaMaxAllowed, CellsPerDimension) )
+    
+    """ criteria for failing the test """
+    if L1_dens > DeltaMaxAllowed or L1_vel > DeltaMaxAllowed or L1_utherm > DeltaMaxAllowed:
+        sys.exit(-1)
+    i_file += 1
+    
+print("normal exit")
+""" normal exit """
+sys.exit(0)

examples/gresho_2d/create.py

+""" @package ./examples/gresho_2d/create.py
+Code that creates 2d Gresho vortex initial conditions
+
+created by Rainer Weinberger, last modified 21.02.2019 -- comments welcome
+"""
+
+#### load libraries
+import sys    # system specific calls
+import numpy as np    ## load numpy
+import h5py    ## load h5py; needed to write initial conditions in hdf5 format
+
+simulation_directory = str(sys.argv[1])
+print("examples/gresho_2d/create.py: creating ICs in directory " + simulation_directory)
+
+""" initial condition parameters """
+FilePath = simulation_directory + '/IC.hdf5'
+
+FloatType = np.float64  # double precision: np.float64, for single use np.float32
+IntType = np.int32
+
+Boxsize = FloatType(1.0)
+CellsPerDimension = IntType(40)
+
+## parameters
+density_0 = 1.0
+velocity_0 = 3.0 ## bulk velocity
+gamma = 5.0/3.0
+gamma_minus_one = gamma - 1.0
+
+""" set up grid: equidistant polar 2d grid; similar to Pakmor et al (2016) """
+d_ring = Boxsize / CellsPerDimension
+## place central cell
+Radius = [0.0]
+xPosFromCenter = [0.0]
+yPosFromCenter = [0.0]
+
+i_ring = 0
+while d_ring * FloatType(i_ring) <= 0.71 * Boxsize:
+    i_ring += 1
+    ## place i_ring cells at this distance
+    phi = np.random.uniform(0,2.0*np.pi) ## random starting angle
+    #print "i_ring", i_ring
+    for i_cell in np.arange( IntType(2.0*np.pi*i_ring) ):
+        radius_this_cell = d_ring * FloatType(i_ring)
+        #print radius_this_cell
+        xcoord = radius_this_cell * np.sin(phi)
+        ycoord = radius_this_cell * np.cos(phi)
+        
+        ## only include the cell if coordinates are within the box
+        if xcoord >= -0.5*Boxsize and xcoord < 0.5*Boxsize and ycoord >= -0.5*Boxsize and ycoord < 0.5*Boxsize:
+            Radius.append( radius_this_cell )
+            xPosFromCenter.append( xcoord )
+            yPosFromCenter.append( ycoord )
+            
+        phi += (2.0*np.pi*i_ring) / IntType(2.0*np.pi*i_ring) / FloatType(i_ring)
+## convert to numpy arrays now that number of cells is known
+Radius = np.array(Radius, dtype=FloatType)
+xPosFromCenter = np.array(xPosFromCenter, dtype=FloatType)
+yPosFromCenter = np.array(yPosFromCenter, dtype=FloatType)
+NumberOfCells = Radius.shape[0]
+## set up structure for positions (in code coordinates, i.e. from 0 to Boxsize)
+Pos = np.zeros([NumberOfCells, 3])
+Pos[:,0] = xPosFromCenter + 0.5 * Boxsize
+Pos[:,1] = yPosFromCenter + 0.5 * Boxsize
+
+""" set up hydrodynamical quantitites """
+## mass insetad of density
+Density = np.full(NumberOfCells, density_0, dtype=FloatType) 
+## different zones
+i1, = np.where( Radius < 0.2 )
+i2, = np.where( (Radius >= 0.2) & (Radius < 0.4) )
+i3, = np.where( Radius >= 0.4 )
+
+## velocity
+RotationVelocity = np.zeros( NumberOfCells, dtype=FloatType )
+RotationVelocity[i1] = 5.0 * Radius[i1]
+RotationVelocity[i2] = 2.0 - 5.0 * Radius[i2]
+RotationVelocity[i3] = 0.0
+Vel = np.zeros([NumberOfCells, 3], dtype=FloatType )
+i_all_but_central = np.arange(1,NumberOfCells)
+Vel[i_all_but_central,0] = RotationVelocity[i_all_but_central] * yPosFromCenter[i_all_but_central] / Radius[i_all_but_central]
+Vel[i_all_but_central,1] = -RotationVelocity[i_all_but_central] * xPosFromCenter[i_all_but_central] / Radius[i_all_but_central]
+Vel[:,0] += velocity_0
+
+## specific internal energy
+Pressure = np.zeros( NumberOfCells, dtype=FloatType)
+Pressure[i1] = 5.0 + 12.5 * Radius[i1] * Radius[i1]
+Pressure[i2] = 9.0 + 12.5 * Radius[i2] * Radius[i2] - 20.0 * Radius[i2] + 4.0 * np.log(Radius[i2] / 0.2)
+Pressure[i3] = 3.0 + 4.0 * np.log(2.0)
+Uthermal = Pressure / density_0 / gamma_minus_one
+
+""" write *.hdf5 file; minimum number of fields required by Arepo """
+IC = h5py.File(simulation_directory+'/IC.hdf5', 'w')
+
+## create hdf5 groups
+header = IC.create_group("Header")
+part0 = IC.create_group("PartType0")
+
+## header entries
+NumPart = np.array([NumberOfCells, 0, 0, 0, 0, 0], dtype = IntType)
+header.attrs.create("NumPart_ThisFile", NumPart)
+header.attrs.create("NumPart_Total", NumPart)
+header.attrs.create("NumPart_Total_HighWord", np.zeros(6, dtype = IntType) )
+header.attrs.create("MassTable", np.zeros(6, dtype = IntType) )
+header.attrs.create("Time", 0.0)
+header.attrs.create("Redshift", 0.0)
+header.attrs.create("BoxSize", Boxsize)
+header.attrs.create("NumFilesPerSnapshot", 1)
+header.attrs.create("Omega0", 0.0)
+header.attrs.create("OmegaB", 0.0)
+header.attrs.create("OmegaLambda", 0.0)
+header.attrs.create("HubbleParam", 1.0)
+header.attrs.create("Flag_Sfr", 0)
+header.attrs.create("Flag_Cooling", 0)
+header.attrs.create("Flag_StellarAge", 0)
+header.attrs.create("Flag_Metals", 0)
+header.attrs.create("Flag_Feedback", 0)
+if Pos.dtype == np.float64:
+    header.attrs.create("Flag_DoublePrecision", 1)
+else:
+    header.attrs.create("Flag_DoublePrecision", 0)
+
+## copy datasets
+part0.create_dataset("ParticleIDs", data = np.arange(1, NumberOfCells+1) )
+part0.create_dataset("Coordinates", data = Pos)
+part0.create_dataset("Masses", data = Density)
+part0.create_dataset("Velocities", data = Vel)
+part0.create_dataset("InternalEnergy", data = Uthermal)
+
+## close file
+IC.close()
+sys.exit(0)

examples/gresho_2d/param.txt

+%% ./examples/gresho_2d/param.txt
+% parameter file for 2d Gresho vortex problem
+
+InitCondFile                          ./run/examples/gresho_2d/IC
+ICFormat                              3
+
+OutputDir                             ./run/examples/gresho_2d/output/
+SnapshotFileBase                      snap
+SnapFormat                            3
+NumFilesPerSnapshot                   1
+NumFilesWrittenInParallel             1
+
+ResubmitOn                            0
+ResubmitCommand                       my-scriptfile
+OutputListFilename                    ol
+OutputListOn                          0
+
+CoolingOn                             0
+StarformationOn                       0
+
+Omega0                                0.0
+OmegaBaryon                           0.0
+OmegaLambda                           0.0
+HubbleParam                           1.0
+
+BoxSize                               1.0
+PeriodicBoundariesOn                  1
+ComovingIntegrationOn                 0
+
+MaxMemSize                            2500
+TimeOfFirstSnapshot                   0.0
+CpuTimeBetRestartFile                 9000
+TimeLimitCPU                          90000
+
+TimeBetStatistics                     0.5
+TimeBegin                             0.0
+TimeMax                               3.0
+TimeBetSnapshot                       3.0
+
+UnitVelocity_in_cm_per_s              1.0
+UnitLength_in_cm                      1.0
+UnitMass_in_g                         1.0
+GravityConstantInternal               0.0
+
+ErrTolIntAccuracy                     0.1
+ErrTolTheta                           0.1
+ErrTolForceAcc                        0.1
+
+MaxSizeTimestep                       1.0
+MinSizeTimestep                       1e-5
+CourantFac                            0.3
+
+LimitUBelowThisDensity                0.0
+LimitUBelowCertainDensityToThisValue  0.0
+DesNumNgb                             64
+MaxNumNgbDeviation                    2
+
+MultipleDomains                       2
+TopNodeFactor                         4
+ActivePartFracForNewDomainDecomp      0.5
+
+TypeOfTimestepCriterion               0
+TypeOfOpeningCriterion                1
+GasSoftFactor                         0.01
+
+SofteningComovingType0                0.1
+SofteningComovingType1                0.1
+SofteningComovingType2                0.1
+SofteningComovingType3                0.1
+SofteningComovingType4                0.1
+SofteningComovingType5                0.1
+
+SofteningMaxPhysType0                 0.1
+SofteningMaxPhysType1                 0.1
+SofteningMaxPhysType2                 0.1
+SofteningMaxPhysType3                 0.1
+SofteningMaxPhysType4                 0.1
+SofteningMaxPhysType5                 0.1
+
+SofteningTypeOfPartType0              0
+SofteningTypeOfPartType1              0
+SofteningTypeOfPartType2              0
+SofteningTypeOfPartType3              0
+SofteningTypeOfPartType4              0
+SofteningTypeOfPartType5              0
+
+InitGasTemp                           0.0
+MinGasTemp                            0.0
+MinEgySpec                            0.0
+MinimumDensityOnStartUp               0.0
+
+CellShapingSpeed                      0.5
+CellMaxAngleFactor                    2.25 

examples/yee_2d/param.txt

@@ -28,7 +28,6 @@ PeriodicBoundariesOn         1
 ComovingIntegrationOn                 0
 
 MaxMemSize                            2500
-
 TimeOfFirstSnapshot                   0.0
 CpuTimeBetRestartFile                 9000
 TimeLimitCPU                          90000

test.sh

@@ -17,6 +17,7 @@ TESTS+="wave_1d "
 TESTS+="shocktube_1d "
 
 ## available 2d examples
+TESTS+="gresho_2d "
 TESTS+="yee_2d "
 
 ## loop over all tests