example wave_1d

examples/wave_1d/Config.sh

+#!/bin/bash            # this line only there to enable syntax highlighting in this file
+
+## ./examples/wave_1d/Config.sh
+## config file for 1d wave propagation probelm
+
+#--------------------------------------- Basic operation mode of code
+ONEDIMS                                  # 1d simulation
+
+#--------------------------------------- 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
+FORCE_EQUAL_TIMESTEPS                    # variable but global timestep
+
+#---------------------------------------- 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/wave_1d/check.py

+""" @package ./examples/wave_1d/check.py
+Code that checks results of 1d wave propagation problem
+
+created by Rainer Weinberger, last modified 19.2.2019 -- comments welcome
+"""
+
+""" 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/wave_1d/check.py: checking simulation output in directory " + simulation_directory) 
+
+FloatType = np.float64  # double precision: np.float64, for single use np.float32
+IntType = np.int32 # integer type
+
+""" 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])
+
+""" maximum L1 error after one propagation; empirically motivated """
+DeltaMaxAllowed = 5e-5 * FloatType(NumberOfCells)**-2
+
+""" initial state -- copied from create.py """
+density_0 = FloatType(1.0)
+velocity_0 = FloatType(0.0)
+pressure_0 = FloatType(3.0) / FloatType(5.0)
+gamma = FloatType(5.0) / FloatType(3.0)
+gamma_minus_one = gamma - FloatType(1.0)
+delta = FloatType(1e-6)    # relative density perturbation
+uthermal_0 = pressure_0 / density_0 / gamma_minus_one
+
+""" 
+    loop over all output files; need to be at times when analytic
+    solution equals the initial conditions
+"""
+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)
+    Velocity = np.array(data["PartType0"]["Velocities"], dtype = FloatType)
+    Uthermal = np.array(data["PartType0"]["InternalEnergy"], dtype = FloatType)
+
+    """ calculate analytic solution at new cell positions """
+    Density_ref = np.full(Pos.shape[0], density_0, dtype=FloatType)
+    Velocity_ref = np.zeros(Pos.shape, dtype=FloatType)
+    Uthermal_ref = np.full(Pos.shape[0], uthermal_0, dtype=FloatType)
+    ## perturbations
+    Density_ref *=  FloatType(1.0) + delta * np.sin( FloatType(2.0) * FloatType(np.pi) * Pos[:,0] / Boxsize )
+    Velocity_ref[:,0] = velocity_0
+    Uthermal_ref *= (Density / density_0)**gamma_minus_one
+
+    """ compare data """
+    ## density
+    abs_delta_dens = np.abs(Density - Density_ref) / Density_ref
+    L1_dens = np.average(abs_delta_dens)
+    
+    ## velocity, here, use absolute error (velocity should be zero!)
+    abs_delta_vel = np.abs(Velocity - Velocity_ref)
+    L1_vel = np.average(abs_delta_vel)
+    
+    ## internal energy
+    abs_delta_utherm = np.abs(Uthermal - Uthermal_ref) / Uthermal_ref
+    L1_utherm = np.average(abs_delta_utherm)
+
+    """ printing results """
+    print("examples/wave_1d/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" % (DeltaMaxAllowed, NumberOfCells) )
+    
+    """ criteria for failing the test """
+    if L1_dens > DeltaMaxAllowed or L1_vel > DeltaMaxAllowed or L1_utherm > DeltaMaxAllowed:
+        sys.exit(1)
+    i_file += 1
+
+""" normal exit """
+sys.exit(0) 

examples/wave_1d/create.py

+""" @package examples/wave_1d/create.py
+Code that creates 1d wave test problem;
+supposed to be as siple as possible and self-contained
+
+created by Rainer Weinberger, last modified 19.2.2019 -- comments welcome
+"""
+
+""" 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/wave_1d/create.py: creating ICs in directory " + simulation_directory)
+
+""" initial condition parameters """
+FilePath = simulation_directory + '/IC.hdf5'
+
+## ensure calculations happen with predefined precision
+FloatType = np.float64  # double precision: np.float64, for single use np.float32
+IntType = np.int32 # integer type
+
+## computational domain
+Boxsize = FloatType(1.0)
+NumberOfCells = IntType(32)
+
+## initial state
+density_0 = FloatType(1.0)
+velocity_0 = FloatType(0.0)
+pressure_0 = FloatType(3.0) / FloatType(5.0)
+gamma = FloatType(5.0) / FloatType(3.0)
+gamma_minus_one = gamma - FloatType(1.0)
+delta = FloatType(1e-6)    # relative density perturbation
+uthermal_0 = pressure_0 / density_0 / gamma_minus_one
+
+""" set up grid: uniform 1d grid """
+## spacing
+dx = Boxsize / FloatType(NumberOfCells)
+
+## position of first and last cell
+pos_first, pos_last = FloatType(0.5) * dx, Boxsize - FloatType(0.5) * dx
+
+## set up grid
+Pos = np.zeros([NumberOfCells, 3], dtype=FloatType)
+Pos[:,0] = np.linspace(pos_first, pos_last, NumberOfCells, dtype=FloatType)
+Volume = np.full(NumberOfCells, dx, dtype=FloatType)
+
+""" set up hydrodynamical quantitites """
+## set up unperturbed system; density, velocity and specific internal energy
+Density = np.full(Pos.shape[0], density_0, dtype=FloatType)
+Velocity = np.zeros(Pos.shape, dtype=FloatType)
+Uthermal = np.full(Pos.shape[0], uthermal_0, dtype=FloatType)
+
+## perturbations
+Density *=  FloatType(1.0) + delta * np.sin( FloatType(2.0) * FloatType(np.pi) * Pos[:,0] / Boxsize )
+Velocity[:,0] = velocity_0
+Uthermal *= (Density / density_0)**gamma_minus_one
+
+## mass instead of density needed for input
+Mass = Density * Volume
+
+""" write *.hdf5 file; minimum number of fields required by Arepo """
+IC = h5py.File(FilePath, 'w')    # open/create file
+
+## create hdf5 groups
+header = IC.create_group("Header")    # create header group
+part0 = IC.create_group("PartType0")    # create particle group for gas cells
+
+## write 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)
+
+## write cell data
+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()
+
+""" normal exit """
+sys.exit(0)

examples/wave_1d/param.txt

+%% ./examples/wave_1d/param.txt
+% parameter file for 1d wave propagation problem
+
+InitCondFile                          ./run/examples/wave_1d/IC
+ICFormat                              3
+
+OutputDir                             ./run/examples/wave_1d/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                     1.0
+TimeBegin                             0.0
+TimeMax                               1.0
+TimeBetSnapshot                       1.0
+
+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                       0.5
+MinSizeTimestep                       1e-5
+CourantFac                            0.3
+
+CellShapingSpeed                      0.5
+CellMaxAngleFactor                    2.25
+
+LimitUBelowThisDensity                0.0
+LimitUBelowCertainDensityToThisValue  0.0
+
+DesNumNgb                             64
+
+MultipleDomains                       2
+TopNodeFactor                         4
+
+ActivePartFracForNewDomainDecomp      0.01
+
+MaxNumNgbDeviation                    2
+
+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

test.sh

+#!/bin/bash            # this line only there to enable syntax highlighting in this file
+## shell script for code testing
+
+#################################
+## perform predefined examples ##
+#################################
+
+## Number of cores to compile and run the problem on
+## use NUMBER_OF_TASKS=1 for 1d test problems!
+NUMBER_OF_TASKS=1
+
+## choose your tests
+TESTS=""
+## available 1d test cases
+TESTS+="wave_1d "
+
+## loop over all tests
+for TEST in $TESTS
+do
+  DIR="./examples/"${TEST}"/"
+  RUNDIR="./run/examples/"${TEST}"/"
+  
+  ## clean up 
+  rm -rf ./run
+
+  ## create run directory
+  mkdir ./run
+  mkdir ./run/examples
+  mkdir ${RUNDIR}
+  
+  ## create ICs in run directory
+  echo ${DIR}
+  python ${DIR}/create.py ${RUNDIR}
+  ((return_value=$?))    ## get return value
+  if [ $return_value != 0 ]    ## check return value
+  then echo "ERROR: test.sh:\t" $DIR "\t python create.py failed!"
+  exit $return_value
+  fi
+  
+  ## copy Config and parameter file to run directory
+  cp ${DIR}/Config.sh ${RUNDIR}
+  cp ${DIR}/param.txt ${RUNDIR}
+
+  ## compile Arepo
+  make -j ${NUMBER_OF_TASKS} CONFIG=${RUNDIR}/Config.sh BUILD_DIR=${RUNDIR}/build EXEC=${RUNDIR}/Arepo
+  ((return_value=$?))    ## get return value
+  if [ $return_value != 0 ]    ## check return value
+  then echo "ERROR: test.sh:\t" $DIR "\t make failed!"
+  exit $return_value
+  fi
+  
+  ## execute test simulation
+  mpiexec -np ${NUMBER_OF_TASKS} ${RUNDIR}/Arepo ${RUNDIR}/param.txt
+  ((return_value=$?))    ## get return value
+  if [ $return_value != 0 ]    ## check return value
+  then echo "ERROR: test.sh:\t" $DIR "\t execution failed!"
+  exit $return_value
+  fi
+  
+  ## check result in example directory, this also creates some check plots
+  python ${DIR}/check.py ${RUNDIR}
+  ((return_value=$?))    ## get return value
+  if [ $return_value != 0 ]    ## check return value
+  then echo "ERROR: test.sh: test failed!"
+  exit $return_value
+  else echo "test.sh:\t" $DIR "\t test passed!"
+  echo "cleaning up..."
+  fi
+  
+  ## clean up
+  rm -rf ./run
+done
+
+echo "tests"
+echo ${TESTS}
+echo "passed!"
+
+exit ${return_value}