updated 2d examples

examples/current_sheet_2d/Config.sh

@@ -33,4 +33,4 @@ HAVE_HDF5                                # needed when HDF5 I/O support is desir
 DEBUG                                    # enables core-dumps, should this be standard?
 
 #--------------------------------------- Output options
-OUTPUT_BFIELD_GRADIENT                   # gradient estimates of B-field
+OUTPUT_BFIELD_GRADIENT                   # gradient estimates of B-field
\ No newline at end of file

examples/current_sheet_2d/check.py

@@ -8,12 +8,19 @@ created by Rainer Weinberger, last modified 13.03.2019
 import sys    ## system calls
 import numpy as np    ## load numpy
 import h5py    ## load h5py; needed to read snapshots
-import matplotlib.pyplot as plt
+import os      # file specific calls
+import matplotlib.pyplot as plt    # needs to be active for plotting!
+plt.rcParams['text.usetex'] = True
 
-createFigures = True
+makeplots = True
+if len(sys.argv) > 2:
+  if sys.argv[2] == "True":
+    makeplots = True
+  else:
+    makeplots = False
 
 simulation_directory = str(sys.argv[1])
-print("examples/current_sheet_2d/check.py: checking simulation output in directory " + simulation_directory) 
+print("current_sheet_2d: checking simulation output in directory " + simulation_directory) 
 
 FloatType = np.float64  # double precision: np.float64, for single use np.float32
 
@@ -68,10 +75,44 @@ while True:
 Time = np.array(Time)
 MagneticEnergy = np.array(MagneticEnergy)
 
-if createFigures:
+if makeplots:
+    if not os.path.exists( simulation_directory+"/plots" ):
+        os.mkdir( simulation_directory+"/plots" )
+  
     fig, ax = plt.subplots(1)
     ax.plot(Time, MagneticEnergy/MagneticEnergy[0])
-    fig.savefig(simulation_directory+'/MagneticEnergy.pdf')
+    fig.savefig(simulation_directory+'/plots/MagneticEnergy.pdf')
+    
+    for i_file in [0,2,4,8]:
+        filename = "snap_%03d.hdf5" % (i_file)
+        try:
+            data = h5py.File(directory+filename, "r")
+        except:
+            break
+    
+        VoronoiPos    = np.array(data["PartType0"]["Coordinates"], dtype = np.float64)
+        MagneticField = np.array(data["PartType0"]["MagneticField"], dtype = np.float64)
+        Time          = data["Header"].attrs["Time"]
+        Boxsize       = data["Header"].attrs["BoxSize"]
+        NumberOfCells = np.int32(data["Header"].attrs["NumPart_Total"][0])
+    
+        Nplot = 256
+        from scipy import spatial # needed for KDTree that we use for nearest neighbour search
+        Edges1d = np.linspace(0., Boxsize, Nplot+1, endpoint=True, dtype=np.float64)
+        Grid1d = 0.5 * (Edges1d[1:] + Edges1d[:-1])
+        xx, yy = np.meshgrid(Grid1d, Grid1d)
+        Grid2D = np.array( [xx.reshape(Nplot**2), yy.reshape(Nplot**2)] ).T
+        dist, cells = spatial.KDTree( VoronoiPos[:,:2] ).query( Grid2D, k=1 )
+  
+        fig = plt.figure( figsize=(3.5,3.5), dpi=300 )
+        ax = plt.axes( [0,0,1,1] )
+        ax.streamplot( Grid1d, Grid1d, MagneticField[cells,0].reshape((Nplot,Nplot)), MagneticField[cells,1].reshape((Nplot,Nplot)), density=2., linewidth=0.5, arrowsize=1e-6, integration_direction='both', minlength=0.3 )
+        ax.set_xlim( 0, Boxsize )
+        ax.set_ylim( 0, Boxsize )
+        plt.text( 0.02, 0.95, "$N=%d^2,\ t=%3.1f$" % (np.int32(np.sqrt(NumberOfCells)), Time), color='k', transform=fig.transFigure, bbox={'boxstyle':'round', 'facecolor':'w'} )
+    
+        fig.savefig( simulation_directory+"plots/streamlines_%03d.pdf" % (i_file), dpi=300 )
+        plt.close(fig)
 
 ## if everything is ok
 if np.min(MagneticEnergy/MagneticEnergy[0]) > 0.92:

examples/current_sheet_2d/param.txt

 %% examples/current_sheet_2d.txt
 % parameter file for 2d current sheet problem
 
-InitCondFile                          IC
+InitCondFile                          ./IC
 ICFormat                              3
 
-OutputDir                             output
+OutputDir                             ./output/
 SnapshotFileBase                      snap
 SnapFormat                            3
 NumFilesPerSnapshot                   1

examples/gresho_2d/Config.sh

 #!/bin/bash            # this line only there to enable syntax highlighting in this file
 
-## examples/gresho_2d/Config.sh
+## 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
@@ -22,6 +20,7 @@ TREE_BASED_TIMESTEPS                     # non-local timestep criterion (take 's
 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_CENTER_OF_MASS                    # output centers of cells
 
 #--------------------------------------- Output/Input options
 HAVE_HDF5                                # needed when HDF5 I/O support is desired (recommended)

examples/gresho_2d/check.py

-""" @package ./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
@@ -8,9 +8,19 @@ created by Rainer Weinberger, last modified 21.02.2019 -- comments welcome
 import sys    # system specific calls
 import numpy as np    ## load numpy
 import h5py    ## load h5py; needed to read snapshots
+import os      # file specific calls
+import matplotlib.pyplot as plt    ## needs to be active for plotting!
+plt.rcParams['text.usetex'] = True
+
+makeplots = True
+if len(sys.argv) > 2:
+  if sys.argv[2] == "True":
+    makeplots = True
+  else:
+    makeplots = False
 
 simulation_directory = str(sys.argv[1])
-print("examples/gresho_2d/check.py: checking simulation output in directory " + simulation_directory)
+print("Gresho_2d: checking simulation output in directory " + simulation_directory) 
 
 FloatType = np.float64  # double precision: np.float64, for single use np.float32
 
@@ -46,7 +56,9 @@ while True:
     
     """ get simulation data """
     ## simulation data
-    Pos = np.array(data["PartType0"]["Coordinates"], dtype = FloatType)
+    Time = FloatType(data["Header"].attrs["Time"])
+    Pos = np.array(data["PartType0"]["CenterOfMass"], dtype = FloatType)
+    VoronoiPos = 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)
@@ -102,12 +114,67 @@ while True:
     L1_utherm = np.average(abs_delta_utherm, weights = Volume)
 
     """ printing results """
-    print("examples/Gresho_2d/check.py: L1 error of " + filename +":")
+    print("Gresho_2d: 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) )
     
+    if makeplots:
+      ## plot:
+      fig = plt.figure( figsize=np.array([7.0,3.5]), dpi=300 )
+      
+      Nplot = 256
+      from scipy import spatial # needed for KDTree that we use for nearest neighbour search
+      Edges1d = np.linspace(0., Boxsize, Nplot+1, endpoint=True, dtype=FloatType)
+      Grid1d = 0.5 * (Edges1d[1:] + Edges1d[:-1])
+      xx, yy = np.meshgrid(Grid1d, Grid1d)
+      Grid2D = np.array( [xx.reshape(Nplot**2), yy.reshape(Nplot**2)] ).T
+      
+      vor = spatial.Voronoi( VoronoiPos[:,:2] )
+      dist, cells = spatial.KDTree( VoronoiPos[:,:2] ).query( Grid2D, k=1 )
+      
+      ax  = plt.axes( [0.05,0.15,0.35,0.7] )
+      pc  = ax.pcolormesh( Edges1d, Edges1d, RotationVelocity[cells].reshape((Nplot,Nplot)), rasterized=True )
+      cax = plt.axes( [0.42,0.15,0.01,0.7] )
+      plt.colorbar( pc, cax=cax )
+      ax.set_title( 'Rotation velocity' )
+      spatial.voronoi_plot_2d( vor, ax=ax, line_colors='w', show_points=False, show_vertices=False, line_width=0.5 )
+      ax.set_xlim( 0, Boxsize )
+      ax.set_ylim( 0, Boxsize )
+      
+      error = RotationVelocity[cells]-RotationVelocity_ref[cells]
+      ax  = plt.axes( [0.53,0.15,0.35,0.7] )
+      pc  = ax.pcolormesh( Edges1d, Edges1d, error.reshape((Nplot,Nplot)), rasterized=True )
+      cax = plt.axes( [0.90,0.15,0.01,0.7] )
+      plt.colorbar( pc, cax=cax )
+      ax.set_title( 'Rotation velocity error' )
+      spatial.voronoi_plot_2d( vor, ax=ax, line_colors='w', show_points=False, show_vertices=False, line_width=0.5 )
+      ax.set_xlim( 0, Boxsize )
+      ax.set_ylim( 0, Boxsize )
+      
+      plt.text( 0.5, 0.92, "$t=%4.1f,\ L_1=%5.1e$" % (Time,L1_dens), ha='center', size=12, transform=fig.transFigure )
+
+      if not os.path.exists( simulation_directory+"/plots" ):
+        os.mkdir( simulation_directory+"/plots" )
+
+      print(simulation_directory+"/plots/figure_%03d.pdf" % (i_file) )
+      fig.savefig(simulation_directory+"/plots/figure_%03d.pdf" % (i_file), dpi=300)
+      plt.close(fig)
+      
+      fig = plt.figure( figsize=np.array([3.5,3.5]), dpi=300 )
+      ax = plt.axes( [0.19, 0.12, 0.75, 0.75] )
+      ax.plot( [0.,0.2,0.4], [0.,1.,0.], 'k--', label='Analytic solution' )
+      ax.plot( Radius, RotationVelocity, 'o', label='Arepo cells', mec='b', mfc="None", mew=0.3 )
+      ax.set_ylabel( "$v_\phi$" )
+      ax.set_xlabel( "$r$" )
+      ax.set_ylim( 0, 1 )
+      ax.legend( loc='upper right', frameon=False, fontsize=8 )
+      ax.set_title( "$\mathrm{Gresho\_2d:}\ \mathrm{N}=%d^2,\ \mathrm{L1}=%4.1e$" % (np.int32(CellsPerDimension),L1_vel), loc='right', size=8 )
+      plt.ticklabel_format( axis='y', style='sci', scilimits=(0,0) )
+      fig.savefig( simulation_directory+"plots/velocity_%03d.pdf" % (i_file) )
+      plt.close(fig)
+    
     """ criteria for failing the test """
     if L1_dens > DeltaMaxAllowed or L1_vel > DeltaMaxAllowed or L1_utherm > DeltaMaxAllowed:
         sys.exit(-1)

examples/gresho_2d/create.py

-""" @package ./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
@@ -10,7 +10,7 @@ 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)
+print("examples/Gresho_2d/create.py: creating ICs in directory " + simulation_directory)
 
 """ initial condition parameters """
 FilePath = simulation_directory + '/IC.hdf5'

examples/gresho_2d/param.txt

-%% ./examples/gresho_2d/param.txt
+%% ./examples/Gresho_2d/param.txt
 % parameter file for 2d Gresho vortex problem
 
-InitCondFile                          IC
+InitCondFile                          ./IC
 ICFormat                              3
 
-OutputDir                             output
+OutputDir                             ./output/
 SnapshotFileBase                      snap
 SnapFormat                            3
 NumFilesPerSnapshot                   1

examples/noh_2d/Config.sh

 #!/bin/bash            # this line only there to enable syntax highlighting in this file
 
-## examples/noh_2d/Config.sh
+## examples/Noh_2d/Config.sh
 ## config file for 2d Noh probelm
 
 #--------------------------------------- Basic operation mode of code
@@ -19,6 +19,7 @@ TREE_BASED_TIMESTEPS                     # non-local timestep criterion (take 's
 #---------------------------------------- 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_CENTER_OF_MASS                    # output centers of cells
 
 #--------------------------------------- Output/Input options
 HAVE_HDF5                                # needed when HDF5 I/O support is desired (recommended)

examples/noh_2d/check.py

-""" @package ./examples/noh_2d/check.py
+""" @package ./examples/Noh_2d/check.py
 Code that checks results of 2d Noh problem
 
 created by Rainer Weinberger, last modified 23.02.2019
@@ -8,12 +8,19 @@ created by Rainer Weinberger, last modified 23.02.2019
 import sys    # system specific calls
 import numpy as np    ## load numpy
 import h5py    ## load h5py; needed to read snapshots
-import matplotlib.pyplot as plt    ## plot stuff
+import os      # file specific calls
+import matplotlib.pyplot as plt    # needs to be active for plotting!
+plt.rcParams['text.usetex'] = True
 
-createFigures = False
+makeplots = True
+if len(sys.argv) > 2:
+  if sys.argv[2] == "True":
+    makeplots = True
+  else:
+    makeplots = False
 
 simulation_directory = str(sys.argv[1])
-print("examples/noh_2d/check.py: checking simulation output in directory " + simulation_directory) 
+print("Noh_2d: checking simulation output in directory " + simulation_directory) 
 
 FloatType = np.float64  # double precision: np.float64, for single use np.float32
 IntType = np.int32
@@ -50,9 +57,11 @@ while True:
         break
     
     """ get simulation data """
+    
     time = FloatType(data["Header"].attrs["Time"])
     ## simulation data
-    Pos = np.array(data["PartType0"]["Coordinates"], dtype = FloatType)
+    Pos = np.array(data["PartType0"]["CenterOfMass"], dtype = FloatType)
+    VoronoiPos = 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)
@@ -74,25 +83,65 @@ while True:
     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]) )
-        fig.subplots_adjust(left = 0.13, bottom = 0.09,right = 0.98, top = 0.98)
+    if makeplots:
+        fig = plt.figure( figsize=np.array([7.5,6.0]), dpi=300 )
+        i_sorted = np.argsort(Radius)
         
-        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)
+        if r_shock == 0:
+          r_shock = 0.1 * Boxsize
         
-        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(0,22)
-        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")
+        Nplot = 512
+        from scipy import spatial # needed for KDTree that we use for nearest neighbour search and Voronoi mesh
+        Edges1d = np.linspace(0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.4*r_shock, Nplot+1, endpoint=True, dtype=FloatType)
+        Grid1d = 0.5 * (Edges1d[1:] + Edges1d[:-1])
+        xx, yy = np.meshgrid(Grid1d, Grid1d)
+        Grid2D = np.array( [xx.reshape(Nplot**2), yy.reshape(Nplot**2)] ).T      
+        dist, cells = spatial.KDTree( VoronoiPos[:,:2] ).query( Grid2D, k=1 )
+        
+        ax = plt.axes( [0.08,0.70,0.52,0.25] )
+        ax.plot(Radius[i_sorted], Density_ref[i_sorted], 'k', label="Analytic solution")
+        ax.plot(Radius, Density, 'b.', rasterized=True, ms=0.2)
+        ax.set_ylabel(r"Density")
+        ax.set_ylim( 0, 20 )
+      
+        ax  = plt.axes( [0.65,0.70,0.20,0.25] )
+        pc  = ax.pcolormesh( Edges1d, Edges1d, Density[cells].reshape((Nplot,Nplot)), rasterized=True, cmap=plt.get_cmap('viridis'), vmin=0, vmax=20. )
+        cax = plt.axes( [0.88,0.70,0.02,0.25] )
+        plt.colorbar( pc, cax=cax )
+        ax.set_xlim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
+        ax.set_ylim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
+       
+        ax = plt.axes( [0.08,0.38,0.52,0.25] )
+        ax.plot(Radius, vRad, 'b.', rasterized=True, ms=0.2)
+        ax.set_ylabel(r"Radial velocity")
+        ax.set_ylim( -1.1, 1.1 )
+        
+        ax  = plt.axes( [0.65,0.38,0.20,0.25] )
+        pc  = ax.pcolormesh( Edges1d, Edges1d, vRad[cells].reshape((Nplot,Nplot)), rasterized=True, cmap=plt.get_cmap('plasma'), vmin=-1.1, vmax=1.1 )
+        cax = plt.axes( [0.88,0.38,0.02,0.25] )
+        plt.colorbar( pc, cax=cax )
+        ax.set_xlim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
+        ax.set_ylim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
         
-        fig.align_ylabels(ax[:])
-        fig.savefig(directory+"/figure_%03d.pdf"%i_file)
+        ax = plt.axes( [0.08,0.07,0.52,0.25] )
+        ax.plot(Radius, Uthermal, 'b.', rasterized=True, ms=0.2)
+        ax.set_xlabel(r"Radius")
+        ax.set_ylabel(r"Spec. internal energy")
+        ax.set_ylim( -0.05, 0.8 )
+        
+        ax  = plt.axes( [0.65,0.07,0.20,0.25] )
+        pc  = ax.pcolormesh( Edges1d, Edges1d, Uthermal[cells].reshape((Nplot,Nplot)), rasterized=True, cmap=plt.get_cmap('magma'), vmin=-0.05, vmax=0.8 )
+        cax = plt.axes( [0.88,0.07,0.02,0.25] )
+        plt.colorbar( pc, cax=cax )
+        ax.set_xlim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
+        ax.set_ylim( 0.5*Boxsize-1.3*r_shock, 0.5*Boxsize+1.3*r_shock )
+        
+        if not os.path.exists( simulation_directory+"/plots" ):
+          os.mkdir( simulation_directory+"/plots" )
+
+        print(simulation_directory+"/plots/figure_%03d.pdf" % (i_file) )
+        fig.savefig(simulation_directory+"/plots/figure_%03d.pdf" % (i_file), dpi=300)
+        plt.close(fig)
 
     #### check against analytic solution
     i_compare, = np.where(Radius < 0.8) ## only check inner region; boundary has spourious effects in this testcase
@@ -100,13 +149,14 @@ while True:
     L1_dens = np.average(abs_delta_dens, weights=CellVolume[i_compare] )
     
     L1_max = DeltaMaxAllowed * time
-    print("examples/Noh_2d/check snapshot %d:  L1_dens = %g, DeltaMaxAllowed = %g!" % (i_file, L1_dens, L1_max) )
+    print("Noh_2d: snapshot %d: DEBUG: L1_dens = %g, DeltaMaxAllowed = %g!" % (i_file, L1_dens, L1_max) )
     
-    if L1_dens > L1_max:
-        print("examples/Noh_2d/check: ERROR: snaphshot %d: L1_dens = %g, DeltaMaxAllowed = %g!" % (i_file, L1_dens, L1_max) )
+    if L1_dens > L1_max and time > 0.:
+        print("Noh_2d: ERROR: snaphshot %d: L1_dens = %g, DeltaMaxAllowed = %g!" % (i_file, L1_dens, L1_max) )
         sys.exit(1)
     
     i_file += 1
+    
 
 ## if everything is ok
 sys.exit(0)

examples/noh_2d/create.py

-""" @package ./examples/noh_2d/create.py
+""" @package ./examples/Noh_2d/create.py
 Code that creates 2d Noh test problem initial conditions
 
 created by Rainer Weinberger, last modified 24.02.2019
@@ -10,7 +10,7 @@ import numpy as np    # scientific computing package
 import h5py    # hdf5 format
 
 simulation_directory = str(sys.argv[1])
-print("examples/noh_2d/create.py: creating ICs in directory " + simulation_directory)
+print("examples/Noh_2d/create.py: creating ICs in directory " + simulation_directory)
 
 """ initial condition parameters """
 FilePath = simulation_directory + '/IC.hdf5'
@@ -95,4 +95,4 @@ part0.create_dataset("Velocities", data = Velocity)
 part0.create_dataset("InternalEnergy", data = Uthermal)
 
 ## close file
-IC.close()
+IC.close()
\ No newline at end of file

examples/noh_2d/param.txt

-%% examples/noh_2d/param.txt
+%% examples/Noh_2d/param.txt
 % parameter file for 2d Noh problem
 
-InitCondFile                          IC
+InitCondFile                          ./IC
 ICFormat                              3
 
-OutputDir                             output
+OutputDir                             ./output/
 SnapshotFileBase                      snap
 SnapFormat                            3
 NumFilesPerSnapshot                   1

examples/yee_2d/Config.sh

 #!/bin/bash            # this line only there to enable syntax highlighting in this file
 
-## examples/yee_2d/Config.sh
+## examples/Yee_2d/Config.sh
 ## config file for 2d Yee vortex probelm
 
 
@@ -21,6 +21,7 @@ TREE_BASED_TIMESTEPS                     # non-local timestep criterion (take 's
 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_CENTER_OF_MASS                    # output centers of cells
 
 #--------------------------------------- Output/Input options
 HAVE_HDF5                                # needed when HDF5 I/O support is desired (recommended)

examples/yee_2d/check.py

-""" @package ./examples/yee_2d/check.py
+""" @package ./examples/Yee_2d/check.py
 Code that checks results of 2d Yee vortex problem
 
-created by Rainer Weinberger, last modified 21.02.2019 -- comments welcome
+created by Rainer Weinberger, last modified 07.01.2018 -- comments welcome
 """
 
 #### 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 os      # file specific calls
+import matplotlib.pyplot as plt    ## needs to be active for plotting!
+plt.rcParams['text.usetex'] = True
+
+makeplots = True
+if len(sys.argv) > 2:
+  if sys.argv[2] == "True":
+    makeplots = True
+  else:
+    makeplots = False
 
 simulation_directory = str(sys.argv[1])
-print("examples/yee_2d/check.py: checking simulation output in directory " + simulation_directory)
+print("Yee_2d: 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
@@ -45,7 +55,9 @@ while True:
     
     """ get simulation data """