Merge branch 'master' of https://github.com/gprMax/gprMax

default voxel and optional edge writing

gprMax/fields_update.pyx

@@ -19,6 +19,7 @@
 import numpy as np
 cimport numpy as np
 from cython.parallel import prange
+
 from gprMax.constants cimport floattype_t, complextype_t
 
 

gprMax/geometry_primitives.pyx

@@ -19,6 +19,7 @@
 import numpy as np
 cimport numpy as np
 np.seterr(divide='raise')
+
 from gprMax.utilities import round_value
 from gprMax.yee_cell_setget_rigid cimport set_rigid_Ex, set_rigid_Ey, set_rigid_Ez, set_rigid_Hx, set_rigid_Hy, set_rigid_Hz, set_rigid_E, unset_rigid_E, set_rigid_H, unset_rigid_H
 

gprMax/geometry_views.py

@@ -16,12 +16,14 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import os, sys
+import os
+import sys
+
 import numpy as np
 from struct import pack
-from gprMax.xdmf import write_output_file
 
 from gprMax.utilities import round_value
+from gprMax.xdmf import write_output_file
 
 
 class GeometryView(object):

gprMax/gprMax.py

@@ -67,7 +67,8 @@ def main():
 
 
 def api(inputfile, n=1, mpi=False, benchmark=False, geometry_only=False, geometry_fixed=False, write_processed=False, opt_taguchi=False):
-    """If you have installed gprMax as a module this is the entry point"""
+    """If installed as a module this is the entry point."""
+    
     class ImportArguments:
         pass
 
@@ -86,7 +87,12 @@ def api(inputfile, n=1, mpi=False, benchmark=False, geometry_only=False, geometr
 
 
 def run_main(args):
-
+    """Top-level function that controls what mode of simulation (standard/optimsation/benchmark etc...) is run.
+        
+    Args:
+        args (dict): Namespace with input arguments from command line or api.
+    """
+        
     numbermodelruns = args.n
     inputdirectory = os.path.dirname(os.path.abspath(args.inputfile))
     inputfile = os.path.abspath(os.path.join(inputdirectory, os.path.basename(args.inputfile)))
@@ -415,7 +421,7 @@ def run_model(args, modelrun, numbermodelruns, inputfile, usernamespace):
         tgeostart = perf_counter()
         for geometryview in G.geometryviews:
             geometryview.write_vtk(modelrun, numbermodelruns, G)
-            geometryview.write_xdmf(modelrun, numbermodelruns, G)
+        #geometryview.write_xdmf(modelrun, numbermodelruns, G)
         tgeoend = perf_counter()
         print('\nGeometry file(s) written in [HH:MM:SS]: {}'.format(datetime.timedelta(seconds=int(tgeoend - tgeostart))))
 

gprMax/grid.py

@@ -17,14 +17,14 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import matplotlib.pyplot as plt
 
 from gprMax.constants import c, floattype, complextype
 from gprMax.materials import Material
 
 
-class Grid():
-
+class Grid(object):
+    """Generic grid/mesh."""
+    
     def __init__(self, grid):
         self.nx = grid.shape[0]
         self.ny = grid.shape[1]

gprMax/input_cmds_file.py

@@ -16,7 +16,8 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import os, sys
+import os
+import sys
 
 from gprMax.exceptions import CmdInputError
 from gprMax.utilities import ListStream

gprMax/input_cmds_geometry.py

@@ -17,6 +17,7 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import os
+
 import h5py
 import numpy as np
 

gprMax/input_cmds_singleuse.py

@@ -16,8 +16,10 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import os, psutil
+import os
+import psutil
 import decimal as d
+
 import numpy as np
 
 from gprMax.constants import c, floattype

gprMax/optimisation_taguchi.py

@@ -16,7 +16,9 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import importlib, os, pickle
+import importlib
+import os
+import pickle
 from collections import OrderedDict
 
 import numpy as np

gprMax/pml_1order_update.pyx

@@ -19,6 +19,7 @@
 import numpy as np
 cimport numpy as np
 from cython.parallel import prange
+
 from gprMax.constants cimport floattype_t, complextype_t
 
 

gprMax/pml_2order_update.pyx

@@ -19,6 +19,7 @@
 import numpy as np
 cimport numpy as np
 from cython.parallel import prange
+
 from gprMax.constants cimport floattype_t, complextype_t
 
 

gprMax/snapshots.py

@@ -16,10 +16,12 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-import os, sys
-import numpy as np
+import os
+import sys
 from struct import pack
 
+import numpy as np
+
 from gprMax.constants import floattype
 from gprMax.grid import Ix, Iy, Iz
 from gprMax.utilities import round_value

gprMax/sources.py

@@ -17,6 +17,7 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 from copy import deepcopy
+
 import numpy as np
 
 from gprMax.constants import c, floattype

gprMax/utilities.py

@@ -18,6 +18,7 @@
 
 import sys
 import decimal as d
+
 from pyfiglet import Figlet
 
 

gprMax/writer_hdf5.py

@@ -18,7 +18,7 @@
 
 import h5py
 
-from ._version import __version__
+from gprMax._version import __version__
 from gprMax.constants import floattype
 from gprMax.grid import Ix, Iy, Iz
 

gprMax/xdmf.py

@@ -1,8 +1,11 @@
-import numpy as np
+import copy
+
 import h5py
 from lxml import etree
+import numpy as np
+
 from gprMax.grid import Grid
-import copy
+
 
 
 class Edges:

gprMax/yee_cell_build.pyx

@@ -18,6 +18,7 @@
 
 import numpy as np
 cimport numpy as np
+
 from gprMax.materials import Material
 from gprMax.yee_cell_setget_rigid cimport get_rigid_Ex, get_rigid_Ey, get_rigid_Ez, get_rigid_Hx, get_rigid_Hy, get_rigid_Hz