added example noh_3d

examples/noh_2d/check.py

@@ -50,7 +50,6 @@ while True:
         break
     
     """ get simulation data """
-    
     time = FloatType(data["Header"].attrs["Time"])
     ## simulation data
     Pos = np.array(data["PartType0"]["Coordinates"], dtype = FloatType)
@@ -74,7 +73,6 @@ while True:
     i_postshock, = np.where(Radius < r_shock)
     Density_ref[i_postshock] = 16.0    ## for 2d
     
-
     #### plot density profile
     if createFigures:
         fig, ax = plt.subplots(3, sharex=True, figsize=np.array([6.9,6.0]) )
@@ -109,7 +107,6 @@ while True:
         sys.exit(1)
     
     i_file += 1
-    
 
 ## if everything is ok
 sys.exit(0)

examples/noh_3d/Config.sh

+#!/bin/bash            # this line only there to enable syntax highlighting in this file
+
+## examples/noh_3d/Config.sh
+## config file for 3d Noh probelm
+
+#--------------------------------------- Basic operation mode of code
+REFLECTIVE_X=2                           # in-/outflow boundary conditions in x direction
+REFLECTIVE_Y=2                           # in-/outflow boundary conditions in y direction
+REFLECTIVE_Z=2                           # in-/outflow boundary conditions in z direction
+
+#--------------------------------------- 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/Input options
+HAVE_HDF5                                # needed when HDF5 I/O support is desired; should this be standard?
+
+#--------------------------------------- Testing and Debugging options
+DEBUG                                    # enables core-dumps, should this be standard?

examples/noh_3d/check.py

+""" @package ./examples/noh_3d/check.py
+Code that checks results of 3d Noh problem
+
+created by Rainer Weinberger, last modified 24.02.2019
+"""
+
+""" load libraries """
+import sys    ## load sys; needed for exit codes
+import numpy as np    ## load numpy
+import h5py    ## load h5py; needed to read snapshots
+import matplotlib.pyplot as plt    ## plot stuff
+
+createFigures = True
+
+simulation_directory = str(sys.argv[1])
+print("examples/noh_3d/check.py: checking simulation output in directory " + simulation_directory)
+
+FloatType = np.float64  # double precision: np.float64, for single use np.float32
+IntType = np.int32
+
+## 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 = IntType(data["Header"].attrs["NumPart_Total"][0]) 
+CellsPerDimension = NumberOfCells**(1./3.) ## 3d sim
+
+## parameters for initial state
+density_0 = 1.0
+velocity_radial_0 = -1.0    ## radial inflow velocity
+pressure_0 = 1.0e-4
+gamma = 5./3.  ## note: this has to be consistent with the parameter settings for Arepo!
+utherm_0 = pressure_0 / ( gamma - 1.0 ) / density_0
+
+## maximum L1 error after one propagation; empirically based
+DeltaMaxAllowed = 0.25
+
+""" 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 """
+    time = FloatType(data["Header"].attrs["Time"])
+    ## 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)
+    Uthermal = np.array(data["PartType0"]["InternalEnergy"], dtype = FloatType)
+    CellVolume = Mass / Density
+    
+    xPosFromCenter = (Pos[:,0] - 0.5 * Boxsize)
+    yPosFromCenter = (Pos[:,1] - 0.5 * Boxsize)
+    zPosFromCenter = (Pos[:,2] - 0.5 * Boxsize)
+    Radius = np.sqrt( xPosFromCenter**2 + yPosFromCenter**2 + zPosFromCenter**2 )
+    
+    vRad = Velocity[:,0] * xPosFromCenter / Radius \
+      + Velocity[:,1] * yPosFromCenter / Radius \
+      + Velocity[:,2] * zPosFromCenter / Radius
+    
+    r_shock = 1./3. * time
+    
+    ## exact solution, 2d
+    Radius[Radius == 0] = 1e-10
+    Density_ref = density_0 * (1.0 + time/Radius) * (1.0 + time/Radius) ## in 3d
+    i_postshock, = np.where(Radius < r_shock)
+    Density_ref[i_postshock] = 64.0    ## for 3d
+    
+    #### plot profiles
+    if createFigures:
+        fig, ax = plt.subplots(3, sharex=True, figsize=np.array([6.9,6.0]) )
+        fig.subplots_adjust(left = 0.13, bottom = 0.09,right = 0.98, top = 0.98)
+        
+        ax[0].scatter(Radius, Density, rasterized=True, s=0.2)
+        ax[1].scatter(Radius, vRad, rasterized=True, s=0.2)
+        ax[2].scatter(Radius, Uthermal, rasterized=True, s=0.2)
+        
+        i_sorted = np.argsort(Radius)
+        ax[0].plot(Radius[i_sorted], Density_ref[i_sorted], label="analytic solution")
+        ax[0].set_xlim(0,0.8)
+        ax[0].set_ylim(0,70)
+        ax[2].set_xlabel(r"radius")
+        ax[0].set_ylabel(r"density")
+        ax[1].set_ylabel(r"radial velocity")
+        ax[2].set_ylabel(r"spec. internal energy")
+        
+        fig.align_ylabels(ax[:])
+        fig.savefig(directory+"/figure_%03d.pdf"%i_file)
+
+    #### check against analytic solution
+    i_compare, = np.where(Radius < 0.8) ## only check inner region; boundary has spourious effects in this testcase
+    abs_delta_dens = np.abs(Density[i_compare] - Density_ref[i_compare]) / Density_ref[i_compare]
+    L1_dens = np.average(abs_delta_dens, weights=CellVolume[i_compare] )
+    
+    L1_max = DeltaMaxAllowed * time
+    print("examples/Noh_3d/check snapshot %d: L1_dens = %g, DeltaMaxAllowed = %g!" % (i_file, L1_dens, L1_max) )
+    
+    
+    if L1_dens > L1_max:
+        sys.exit(1)
+    
+    i_file += 1
+    
+## if everything is ok
+sys.exit(0)

examples/noh_3d/create.py

+""" @package ./examples/noh_3d/create.py
+Code that creates 3d Noh test problem initial conditions
+
+created by Rainer Weinberger, last modified 24.02.2019
+"""
+
+""" load libraries """
+import sys    # system specific calls
+import numpy as np    # scientific computing package
+import h5py    # hdf5 format
+
+simulation_directory = str(sys.argv[1])
+print("examples/noh_3d/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(6.0)
+CellsPerDimension = IntType(30)
+NumberOfCells = CellsPerDimension * CellsPerDimension * CellsPerDimension
+
+## initial state
+density_0 = 1.0
+velocity_radial_0 = -1.0    ## radial inflow velocity
+pressure_0 = 1.0e-4
+gamma = 5./3.  ## note: this has to be consistent with the parameter settings for Arepo!
+utherm_0 = pressure_0 / ( gamma - 1.0 ) / density_0
+
+""" set up grid: cartesian 3d grid """
+## spacing
+dx = Boxsize / FloatType(CellsPerDimension)
+## position of first and last cell
+pos_first, pos_last = 0.5 * dx, Boxsize - 0.5 * dx
+
+## set up grid
+Grid1d = np.linspace(pos_first, pos_last, CellsPerDimension, dtype=FloatType)
+xx, yy, zz = np.meshgrid(Grid1d, Grid1d, Grid1d)
+Pos = np.zeros([NumberOfCells, 3], dtype=FloatType)
+Pos[:,0] = xx.reshape(NumberOfCells)
+Pos[:,1] = yy.reshape(NumberOfCells)
+Pos[:,2] = zz.reshape(NumberOfCells)
+## calculate distance from center
+xPosFromCenter = (Pos[:,0] - 0.5 * Boxsize)
+yPosFromCenter = (Pos[:,1] - 0.5 * Boxsize)
+zPosFromCenter = (Pos[:,2] - 0.5 * Boxsize)
+Radius = np.sqrt( xPosFromCenter**2 + yPosFromCenter**2 + zPosFromCenter**2 )
+
+""" set up hydrodynamical quantitites """
+## mass insetad of density
+Mass = np.full(NumberOfCells, density_0*dx*dx*dx, dtype=FloatType)
+## velocity
+Velocity = np.zeros([NumberOfCells,3], dtype=FloatType)
+Velocity[:,0] = velocity_radial_0 * xPosFromCenter / Radius
+Velocity[:,1] = velocity_radial_0 * yPosFromCenter / Radius
+Velocity[:,2] = velocity_radial_0 * zPosFromCenter / Radius
+## specific internal energy
+Uthermal = np.full(NumberOfCells, utherm_0, dtype=FloatType)
+
+""" 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=Mass)
+part0.create_dataset("Velocities", data=Velocity)
+part0.create_dataset("InternalEnergy", data=Uthermal)
+
+## close file
+IC.close()

examples/noh_3d/param.txt

+%% examples/noh_3d/param.txt
+% parameter file for 3d Noh problem
+
+InitCondFile                          ./run/examples/noh_3d/IC
+ICFormat                              3
+
+OutputDir                             ./run/examples/noh_3d/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                               6.0
+PeriodicBoundariesOn                  1
+ComovingIntegrationOn                 0
+
+MaxMemSize                            2500
+
+TimeOfFirstSnapshot                   0.0
+CpuTimeBetRestartFile                 9000
+TimeLimitCPU                          90000
+
+TimeBetStatistics                     0.005
+TimeBegin                             0.0
+TimeMax                               2.0
+TimeBetSnapshot                       0.5
+
+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                       0.5
+MinSizeTimestep                       1e-5
+CourantFac                            0.3
+
+LimitUBelowThisDensity                0.0
+LimitUBelowCertainDensityToThisValue  0.0
+DesNumNgb                             64
+MaxNumNgbDeviation                    2
+
+MultipleDomains                       2
+TopNodeFactor                         4
+ActivePartFracForNewDomainDecomp      0.1
+
+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              1
+SofteningTypeOfPartType2              1
+SofteningTypeOfPartType3              1
+SofteningTypeOfPartType4              1
+SofteningTypeOfPartType5              1
+
+InitGasTemp                           0.0
+MinGasTemp                            0.0
+MinEgySpec                            0.0
+MinimumDensityOnStartUp               0.0
+
+CellShapingSpeed                      0.5
+CellMaxAngleFactor                    2.25 
+

test.sh

@@ -21,6 +21,9 @@ TESTS+="gresho_2d "
 TESTS+="noh_2d "
 TESTS+="yee_2d "
 
+## available 3d examples
+TESTS+="noh_3d "
+
 ## loop over all tests
 for TEST in $TESTS
 do