Cleanup of imports and checking using pylint

gprMax/__init__.py

@@ -7,54 +7,32 @@ Electromagnetic wave propagation simulation software.
 
 """
 
-from ._version import __version__
-from .cmds_single_use import Discretisation
-from .cmds_single_use import Domain
-from .cmds_single_use import TimeWindow
-from .cmds_single_use import Title
-from .cmds_single_use import NumThreads
-from .cmds_single_use import TimeStepStabilityFactor
-from .cmds_single_use import PMLCells
-from .cmds_single_use import SrcSteps
-from .cmds_single_use import RxSteps
-from .cmds_single_use import ExcitationFile
-from .cmds_multiple import Waveform
-from .cmds_multiple import VoltageSource
-from .cmds_multiple import HertzianDipole
-from .cmds_multiple import MagneticDipole
-from .cmds_multiple import TransmissionLine
-from .cmds_multiple import Rx
-from .cmds_multiple import RxArray
-from .cmds_multiple import Snapshot
-from .cmds_multiple import Material
-from .cmds_multiple import AddDebyeDispersion
-from .cmds_multiple import AddLorentzDispersion
-from .cmds_multiple import AddDrudeDispersion
-from .cmds_multiple import SoilPeplinski
-from .cmds_multiple import GeometryView
-from .cmds_multiple import GeometryObjectsWrite
-from .cmds_multiple import PMLCFS
-from .subgrids.user_objects import SubGridHSG
-from .subgrids.user_objects import ReferenceRx
+import gprMax.config as config
 
-from .cmds_geometry.edge import Edge
-from .cmds_geometry.plate import Plate
-from .cmds_geometry.triangle import Triangle
+from ._version import __version__
+from .cmds_geometry.add_grass import AddGrass
+from .cmds_geometry.add_surface_roughness import AddSurfaceRoughness
+from .cmds_geometry.add_surface_water import AddSurfaceWater
 from .cmds_geometry.box import Box
 from .cmds_geometry.cylinder import Cylinder
 from .cmds_geometry.cylindrical_sector import CylindricalSector
-from .cmds_geometry.sphere import Sphere
+from .cmds_geometry.edge import Edge
 from .cmds_geometry.fractal_box import FractalBox
-from .cmds_geometry.add_surface_roughness import AddSurfaceRoughness
-from .cmds_geometry.add_surface_water import AddSurfaceWater
-from .cmds_geometry.add_grass import AddGrass
 from .cmds_geometry.geometry_objects_read import GeometryObjectsRead
-
-from .hash_cmds_file import user_libs_fn_to_scene_obj
-
-from .scene import Scene
+from .cmds_geometry.plate import Plate
+from .cmds_geometry.sphere import Sphere
+from .cmds_geometry.triangle import Triangle
+from .cmds_multiple import (PMLCFS, AddDebyeDispersion, AddDrudeDispersion,
+                            AddLorentzDispersion, GeometryObjectsWrite,
+                            GeometryView, HertzianDipole, MagneticDipole,
+                            Material, Rx, RxArray, Snapshot, SoilPeplinski,
+                            TransmissionLine, VoltageSource, Waveform)
+from .cmds_single_use import (Discretisation, Domain, ExcitationFile,
+                              NumThreads, PMLCells, RxSteps, SrcSteps,
+                              TimeStepStabilityFactor, TimeWindow, Title)
 from .gprMax import run as run
-
-import gprMax.config as config
+from .hash_cmds_file import user_libs_fn_to_scene_obj
+from .scene import Scene
+from .subgrids.user_objects import ReferenceRx, SubGridHSG
 
 __name__ = 'gprMax'

gprMax/cmds_geometry/add_grass.py

@@ -18,15 +18,14 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..exceptions import CmdInputError
-from ..fractals import FractalSurface
-from ..fractals import Grass
-from ..materials import Material
+from ..fractals import FractalSurface, Grass
+from ..materials import DispersiveMaterial
 from ..utilities import round_value
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 
@@ -175,15 +174,15 @@ class AddGrass(UserObjectGeometry):
 
         # Check to see if grass has been already defined as a material
         if not any(x.ID == 'grass' for x in grid.materials):
-            m = Material(len(grid.materials), 'grass')
+            m = DispersiveMaterial(len(grid.materials), 'grass')
             m.averagable = False
             m.type = 'builtin, debye'
-            m.er = Material.grasseri
-            m.deltaer.append(Material.grassdeltaer)
-            m.tau.append(Material.grasstau)
+            m.er = DispersiveMaterial.grasseri
+            m.deltaer.append(DispersiveMaterial.grassdeltaer)
+            m.tau.append(DispersiveMaterial.grasstau)
             grid.materials.append(m)
-            if Material.maxpoles == 0:
-                Material.maxpoles = 1
+            if config.get_model_config().materials['maxpoles'] == 0:
+                config.get_model_config().materials['maxpoles'] = 1
 
         # Check if time step for model is suitable for using grass
         grass = next((x for x in grid.materials if x.ID == 'grass'))

gprMax/cmds_geometry/add_surface_roughness.py

@@ -18,14 +18,13 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
-from ..cython.geometry_primitives import build_box
 from ..exceptions import CmdInputError
 from ..fractals import FractalSurface
 from ..utilities import round_value
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/add_surface_water.py

@@ -19,10 +19,11 @@
 import logging
 
 import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
+
 from ..exceptions import CmdInputError
-from ..materials import Material
+from ..materials import DispersiveMaterial
 from ..utilities import round_value
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 
@@ -126,15 +127,15 @@ class AddSurfaceWater(UserObjectGeometry):
 
         # Check to see if water has been already defined as a material
         if not any(x.ID == 'water' for x in grid.materials):
-            m = Material(len(grid.materials), 'water')
+            m = DispersiveMaterial(len(grid.materials), 'water')
             m.averagable = False
             m.type = 'builtin, debye'
-            m.er = Material.watereri
-            m.deltaer.append(Material.waterdeltaer)
-            m.tau.append(Material.watertau)
+            m.er = DispersiveMaterial.watereri
+            m.deltaer.append(DispersiveMaterial.waterdeltaer)
+            m.tau.append(DispersiveMaterial.watertau)
             grid.materials.append(m)
-            if Material.maxpoles == 0:
-                Material.maxpoles = 1
+            if config.get_model_config().materials['maxpoles'] == 0:
+                config.get_model_config().materials['maxpoles'] = 1
 
         # Check if time step for model is suitable for using water
         water = next((x for x in grid.materials if x.ID == 'water'))

gprMax/cmds_geometry/box.py

@@ -18,13 +18,13 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..cython.geometry_primitives import build_box
 from ..exceptions import CmdInputError
 from ..materials import Material
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/build_templates.py

@@ -16,9 +16,7 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from jinja2 import Environment
-from jinja2 import PackageLoader
-from jinja2 import select_autoescape
+from jinja2 import Environment, PackageLoader, select_autoescape
 
 env = Environment(
     loader=PackageLoader(__name__, 'templates'),

gprMax/cmds_geometry/cylinder.py

@@ -17,13 +17,14 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
-import numpy as np
 
 import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
+import numpy as np
+
 from ..cython.geometry_primitives import build_cylinder
 from ..exceptions import CmdInputError
 from ..materials import Material
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/cylindrical_sector.py

@@ -18,13 +18,13 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..cython.geometry_primitives import build_cylindrical_sector
 from ..exceptions import CmdInputError
 from ..materials import Material
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/edge.py

@@ -19,11 +19,11 @@
 import logging
 
 import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
-from ..cython.geometry_primitives import build_edge_x
-from ..cython.geometry_primitives import build_edge_y
-from ..cython.geometry_primitives import build_edge_z
+
+from ..cython.geometry_primitives import (build_edge_x, build_edge_y,
+                                          build_edge_z)
 from ..exceptions import CmdInputError
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/fractal_box.py

@@ -18,12 +18,12 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..exceptions import CmdInputError
 from ..fractals import FractalVolume
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/fractal_box_builder.py

@@ -16,13 +16,13 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
-from ..cython.geometry_primitives import build_voxels_from_array
-from ..cython.geometry_primitives import build_voxels_from_array_mask
+from ..cython.geometry_primitives import (build_voxels_from_array,
+                                          build_voxels_from_array_mask)
 from ..exceptions import CmdInputError
+from .cmds_geometry import UserObjectGeometry
 
 
 class FractalBoxBuilder(UserObjectGeometry):

gprMax/cmds_geometry/geometry_objects_read.py

@@ -19,14 +19,14 @@
 import logging
 from pathlib import Path
 
+import gprMax.config as config
 import h5py
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..cython.geometry_primitives import build_voxels_from_array
 from ..exceptions import CmdInputError
 from ..hash_cmds_file import get_user_objects
 from ..utilities import round_value
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/plate.py

@@ -19,11 +19,11 @@
 import logging
 
 import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
-from ..cython.geometry_primitives import build_face_yz
-from ..cython.geometry_primitives import build_face_xz
-from ..cython.geometry_primitives import build_face_xy
+
+from ..cython.geometry_primitives import (build_face_xy, build_face_xz,
+                                          build_face_yz)
 from ..exceptions import CmdInputError
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/sphere.py

@@ -18,13 +18,13 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..cython.geometry_primitives import build_sphere
 from ..exceptions import CmdInputError
 from ..materials import Material
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_geometry/triangle.py

@@ -18,13 +18,13 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .cmds_geometry import UserObjectGeometry
 from ..cython.geometry_primitives import build_triangle
 from ..exceptions import CmdInputError
 from ..materials import Material
+from .cmds_geometry import UserObjectGeometry
 
 logger = logging.getLogger(__name__)
 

gprMax/cmds_multiple.py

@@ -18,23 +18,22 @@
 
 import logging
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
 from .cmds_geometry.cmds_geometry import UserObjectGeometry
-from .exceptions import CmdInputError
+from .exceptions import CmdInputError, GeneralError
 from .geometry_outputs import GeometryObjects as GeometryObjectsUser
-from .materials import Material as MaterialUser
 from .materials import DispersiveMaterial as DispersiveMaterialUser
+from .materials import Material as MaterialUser
 from .materials import PeplinskiSoil as PeplinskiSoilUser
-from .pml import CFSParameter
-from .pml import CFS
+from .pml import CFS, CFSParameter
 from .receivers import Rx as RxUser
 from .snapshots import Snapshot as SnapshotUser
-from .sources import VoltageSource as VoltageSourceUser
 from .sources import HertzianDipole as HertzianDipoleUser
 from .sources import MagneticDipole as MagneticDipoleUser
 from .sources import TransmissionLine as TransmissionLineUser
+from .sources import VoltageSource as VoltageSourceUser
 from .subgrids.base import SubGridBase
 from .utilities import round_value
 from .waveforms import Waveform as WaveformUser
@@ -162,7 +161,7 @@ class VoltageSource(UserObjectMulti):
 
         # Check if there is a waveformID in the waveforms list
         if not any(x.ID == waveform_id for x in grid.waveforms):
-            raise CmdInputError(f"'{self.params_str()}' there is no waveform with the identifier {tmp[5]}")
+            raise CmdInputError(f"'{self.params_str()}' there is no waveform with the identifier {waveform_id}")
 
         v = VoltageSourceUser()
         v.polarisation = polarisation
@@ -594,7 +593,7 @@ class RxArray(UserObjectMulti):
                     r.zcoordorigin = z
                     r.ID = r.__class__.__name__ + '(' + str(x) + ',' + str(y) + ',' + str(z) + ')'
                     for key in RxUser.defaultoutputs:
-                        r.outputs[key] = np.zeros(grid.iterations, dtype=config.dtypes['float_or_double'])
+                        r.outputs[key] = np.zeros(grid.iterations, dtype=config.sim_config.dtypes['float_or_double'])
                     logger.info(f"  Receiver at {r.xcoord * grid.dx:g}m, {r.ycoord * grid.dy:g}m, {r.zcoord * grid.dz:g}m with output component(s) {', '.join(r.outputs)} created.")
                     grid.rxs.append(r)
 
@@ -1080,7 +1079,7 @@ class GeometryObjectsWrite(UserObjectMulti):
         try:
             p1 = self.kwargs['p1']
             p2 = self.kwargs['p2']
-            filename = self.kwargs['filename']
+            basefilename = self.kwargs['filename']
         except KeyError:
             raise CmdInputError(f"'{self.params_str()}' requires exactly seven parameters")
 
@@ -1088,9 +1087,9 @@ class GeometryObjectsWrite(UserObjectMulti):
         x0, y0, z0 = p1
         x1, y1, z1 = p2
 
-        g = GeometryObjectsUser(x0, y0, z0, x1, y1, z1, filename)
+        g = GeometryObjectsUser(x0, y0, z0, x1, y1, z1, basefilename)
 
-        logger.info(f'Geometry objects in the volume from {p1[0] * grid.dx:g}m, {p1[1] * grid.dy:g}m, {p1[2] * grid.dz:g}m, to {p2[0] * grid.dx:g}m, {p2[1] * grid.dy:g}m, {p2[2] * grid.dz:g}m, will be written to {g.filename}, with materials written to {g.materialsfilename}')
+        logger.info(f'Geometry objects in the volume from {p1[0] * grid.dx:g}m, {p1[1] * grid.dy:g}m, {p1[2] * grid.dz:g}m, to {p2[0] * grid.dx:g}m, {p2[1] * grid.dy:g}m, {p2[2] * grid.dz:g}m, will be written to {g.filename_hdf5}, with materials written to {g.filename_materials}')
 
         # Append the new GeometryView object to the geometry objects to write list
         grid.geometryobjectswrite.append(g)

gprMax/cmds_single_use.py

@@ -20,19 +20,16 @@ import inspect
 import logging
 from pathlib import Path
 
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
-import numpy as np
-from scipy.constants import c
-from scipy import interpolate
-
 import gprMax.config as config
+import numpy as np
+from colorama import Fore, Style, init
+init()
+from scipy import interpolate
+from scipy.constants import c
+
 from .exceptions import CmdInputError
+from .utilities import round_value, set_omp_threads
 from .waveforms import Waveform
-from .utilities import round_value
-from .utilities import set_omp_threads
 
 logger = logging.getLogger(__name__)
 
@@ -95,31 +92,31 @@ class Domain(UserObjectSingle):
         try:
             G.nx, G.ny, G.nz = uip.discretise_point(self.kwargs['p1'])
         except KeyError:
-            raise CmdInputError(f"'{self.params_str()}' please specify a point")
+            raise CmdInputError(self.__str__() + ' please specify a point')
 
         if G.nx == 0 or G.ny == 0 or G.nz == 0:
-            raise CmdInputError(f"'{self.params_str()}' requires at least one cell in every dimension")
+            raise CmdInputError(self.__str__() + ' requires at least one cell in every dimension')
 
         logger.info(f"Domain size: {self.kwargs['p1'][0]:g} x {self.kwargs['p1'][1]:g} x {self.kwargs['p1'][2]:g}m ({G.nx:d} x {G.ny:d} x {G.nz:d} = {(G.nx * G.ny * G.nz):g} cells)")
 
         # Calculate time step at CFL limit; switch off appropriate PMLs for 2D
         if G.nx == 1:
-            G.mode = '2D TMx'
+            config.get_model_config().mode = '2D TMx'
             G.pmlthickness['x0'] = 0
             G.pmlthickness['xmax'] = 0
         elif G.ny == 1:
-            G.mode = '2D TMy'
+            config.get_model_config().mode = '2D TMy'
             G.pmlthickness['y0'] = 0
             G.pmlthickness['ymax'] = 0
         elif G.nz == 1:
-            G.mode = '2D TMz'
+            config.get_model_config().mode = '2D TMz'
             G.pmlthickness['z0'] = 0
             G.pmlthickness['zmax'] = 0
         else:
-            G.mode = '3D'
+            config.get_model_config().mode = '3D'
         G.calculate_dt()
 
-        logger.info(f'Mode: {G.mode}')
+        logger.info(f'Mode: {config.get_model_config().mode}')
         logger.info(f'Time step (at CFL limit): {G.dt:g} secs')
 
 
@@ -140,14 +137,14 @@ class Discretisation(UserObjectSingle):
             G.dl = np.array(self.kwargs['p1'])
             G.dx, G.dy, G.dz = self.kwargs['p1']
         except KeyError:
-            raise CmdInputError(f"'{self.params_str()}' discretisation requires a point")
+            raise CmdInputError(self.__str__() + ' discretisation requires a point')
 
         if G.dl[0] <= 0:
-            raise CmdInputError(f"'{self.params_str()}' discretisation requires the x-direction spatial step to be greater than zero")
+            raise CmdInputError(self.__str__() + ' discretisation requires the x - direction spatial step to be greater than zero')
         if G.dl[1] <= 0:
-            raise CmdInputError(f"'{self.params_str()}' discretisation requires the y-direction spatial step to be greater than zero")
+            raise CmdInputError(self.__str__() + ' discretisation requires the y - direction spatial step to be greater than zero')
         if G.dl[2] <= 0:
-            raise CmdInputError(f"'{self.params_str()}' discretisation requires the z-direction spatial step to be greater than zero")
+            raise CmdInputError(self.__str__() + ' discretisation requires the z - direction spatial step to be greater than zero')
 
         logger.info(f'Spatial discretisation: {G.dl[0]:g} x {G.dl[1]:g} x {G.dl[2]:g}m')
 
@@ -182,12 +179,12 @@ class TimeWindow(UserObjectSingle):
                 G.timewindow = tmp
                 G.iterations = int(np.ceil(tmp / G.dt)) + 1
             else:
-                raise CmdInputError(f"'{self.params_str()}' must have a value greater than zero")
+                raise CmdInputError(self.__str__() + ' must have a value greater than zero')
         except KeyError:
             pass
 
         if not G.timewindow:
-            raise CmdInputError(f"'{self.params_str()}' specify a time or number of iterations")
+            raise CmdInputError(self.__str__() + ' specify a time or number of iterations')
 
         logger.info(f'Time window: {G.timewindow:g} secs ({G.iterations} iterations)')
 

gprMax/config.py

@@ -17,23 +17,19 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
-from pathlib import Path
 import sys
+from pathlib import Path
 
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
 import cython
 import numpy as np
+from colorama import Fore, Style, init
+init()
 from scipy.constants import c
 from scipy.constants import epsilon_0 as e0
 from scipy.constants import mu_0 as m0
 
 from .exceptions import GeneralError
-from .utilities import detect_gpus
-from .utilities import get_host_info
-from .utilities import get_terminal_width
+from .utilities import detect_gpus, get_host_info, get_terminal_width
 
 logger = logging.getLogger(__name__)
 

gprMax/contexts.py

@@ -21,15 +21,12 @@ import logging
 import sys
 
 import gprMax.config as config
+
 from ._version import __version__, codename
 from .exceptions import GeneralError
 from .model_build_run import ModelBuildRun
-from .solvers import create_solver
-from .solvers import create_G
-from .utilities import get_terminal_width
-from .utilities import human_size
-from .utilities import logo
-from .utilities import timer
+from .solvers import create_G, create_solver
+from .utilities import get_terminal_width, human_size, logo, timer
 
 logger = logging.getLogger(__name__)
 

gprMax/cython/fields_updates_hsg.pyx

@@ -18,7 +18,6 @@
 
 import numpy as np
 cimport numpy as np
-
 from cython.parallel import prange
 
 

gprMax/exceptions.py

@@ -18,8 +18,7 @@
 
 import logging
 
-from colorama import init
-from colorama import Fore
+from colorama import Fore, init
 init()
 
 logger = logging.getLogger(__name__)

gprMax/fields_outputs.py

@@ -17,8 +17,8 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import logging
-from string import Template
 from pathlib import Path
+from string import Template
 
 import h5py
 

gprMax/fractals.py

@@ -16,12 +16,11 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
+import gprMax.config as config
 import numpy as np
 from scipy import fftpack
 
-import gprMax.config as config
-from .cython.fractals_generate import generate_fractal2D
-from .cython.fractals_generate import generate_fractal3D
+from .cython.fractals_generate import generate_fractal2D, generate_fractal3D
 from .utilities import round_value
 
 np.seterr(divide='raise')
@@ -220,7 +219,7 @@ class Grass:
 
         self.numblades = numblades
         self.geometryparams = np.zeros((self.numblades, 6),
-                                       dtype=config.dtypes['float_or_double'])
+                                       dtype=config.sim_config.dtypes['float_or_double'])
         self.seed = None
 
         # Randomly defined parameters that will be used to calculate geometry

gprMax/geometry_outputs.py

@@ -19,16 +19,15 @@
 import logging
 import os
 from pathlib import Path
-
-import h5py
-import numpy as np
 from struct import pack
 
 import gprMax.config as config
+import h5py
+import numpy as np
 
 from ._version import __version__
-from .cython.geometry_outputs import define_normal_geometry
-from .cython.geometry_outputs import define_fine_geometry
+from .cython.geometry_outputs import (define_fine_geometry,
+                                      define_normal_geometry)
 from .utilities import round_value
 
 logger = logging.getLogger(__name__)

gprMax/gprMax.py

@@ -20,8 +20,8 @@ import argparse
 import logging
 
 import gprMax.config as config
-from .contexts import Context
-from .contexts import MPIContext
+
+from .contexts import Context, MPIContext
 from .utilities import setup_logging
 
 logger = logging.getLogger(__name__)

gprMax/grid.py

@@ -16,22 +16,16 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from collections import OrderedDict
 import decimal as d
-
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
-import numpy as np
+from collections import OrderedDict
 
 import gprMax.config as config
+import numpy as np
+from colorama import Fore, Style, init
+init()
 from .exceptions import GeneralError
-from .pml import PML
-from .pml import CFS
-from .utilities import fft_power
-from .utilities import human_size
-from .utilities import round_value
+from .pml import CFS, PML
+from .utilities import fft_power, human_size, round_value
 
 np.seterr(invalid='raise')
 
@@ -274,13 +268,13 @@ class FDTDGrid:
 
     def calculate_dt(self):
         """Calculate time step at the CFL limit."""
-        if self.mode == '2D TMx':
+        if config.get_model_config().mode == '2D TMx':
             self.dt = 1 / (config.sim_config.em_consts['c'] *
                            np.sqrt((1 / self.dy**2) + (1 / self.dz**2)))
-        elif self.mode == '2D TMy':
+        elif config.get_model_config().mode == '2D TMy':
             self.dt = 1 / (config.sim_config.em_consts['c'] *
                            np.sqrt((1 / self.dx**2) + (1 / self.dz**2)))
-        elif self.mode == '2D TMz':
+        elif config.get_model_config().mode == '2D TMz':
             self.dt = 1 / (config.sim_config.em_consts['c'] *
                            np.sqrt((1 / self.dx**2) + (1 / self.dy**2)))
         else:
@@ -352,9 +346,12 @@ def dispersion_analysis(G):
         results (dict): Results from dispersion analysis
     """
 
-    # Physical phase velocity error (percentage); grid sampling density;
-    # material with maximum permittivity; maximum significant frequency; error message
-    results = {'deltavp': False, 'N': False, 'material': False, 'maxfreq': [], 'error': ''}
+    # deltavp: physical phase velocity error (percentage)
+    # N: grid sampling density
+    # material: material with maximum permittivity
+    # maxfreq: maximum significant frequency
+    # error: error message
+    results = {'deltavp': None, 'N': None, 'material': None, 'maxfreq': [], 'error': ''}
 
     # Find maximum significant frequency
     if G.waveforms:

gprMax/hash_cmds_file.py

@@ -16,13 +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/>.
 
-from io import StringIO
 import logging
 import os
-from pathlib import Path
 import sys
+from io import StringIO
+from pathlib import Path
 
 import gprMax.config as config
+
 from .exceptions import CmdInputError
 from .hash_cmds_geometry import process_geometrycmds
 from .hash_cmds_multiuse import process_multicmds

gprMax/hash_cmds_geometry.py

@@ -18,17 +18,18 @@
 
 import numpy as np
 
-from .cmds_geometry.edge import Edge
-from .cmds_geometry.plate import Plate
-from .cmds_geometry.triangle import Triangle
+from .cmds_geometry.add_grass import AddGrass
+from .cmds_geometry.add_surface_roughness import AddSurfaceRoughness
+from .cmds_geometry.add_surface_water import AddSurfaceWater
 from .cmds_geometry.box import Box
 from .cmds_geometry.cylinder import Cylinder
 from .cmds_geometry.cylindrical_sector import CylindricalSector
+from .cmds_geometry.edge import Edge
 from .cmds_geometry.fractal_box import FractalBox
+from .cmds_geometry.plate import Plate
 from .cmds_geometry.sphere import Sphere
-from .cmds_geometry.add_surface_roughness import AddSurfaceRoughness
-from .cmds_geometry.add_surface_water import AddSurfaceWater
-from .cmds_geometry.add_grass import AddGrass
+from .cmds_geometry.triangle import Triangle
+from .exceptions import CmdInputError
 from .utilities import round_value
 
 
@@ -181,15 +182,18 @@ def process_geometrycmds(geometry):
 
             # Isotropic case with no user specified averaging
             if len(tmp) == 10:
-                CylindricalSector(normal=normal, ctl1=ctl1, ctl2=ctl2, extent1=extent1, extent2=extent2, r=r, start=start, end=end, msterial_id=tmp[9])
+                cylindrical_sector = CylindricalSector(normal=normal, ctr1=ctr1, ctr2=ctr2, extent1=extent1,
+                                  extent2=extent2, r=r, start=start, end=end, msterial_id=tmp[9])
 
             # Isotropic case with user specified averaging
             elif len(tmp) == 11:
-                CylindricalSector(normal=normal, ctl1=ctl1, ctl2=ctl2, extent1=extent1, extent2=extent2, r=r, start=start, end=end, averaging=tmp[10], material_id=tmp[9])
+                cylindrical_sector = CylindricalSector(normal=normal, ctr1=ctr1, ctr2=ctr2, extent1=extent1, extent2=extent2,
+                                  r=r, start=start, end=end, averaging=tmp[10], material_id=tmp[9])
 
             # Uniaxial anisotropic case
             elif len(tmp) == 12:
-                CylindricalSector(normal=normal, ctl1=ctl1, ctl2=ctl2, extent1=extent1, extent2=extent2, r=r, start=start, end=end, material_ids=tmp[9:])
+                cylindrical_sector = CylindricalSector(normal=normal, ctr1=ctr1, ctr2=ctr2, extent1=extent1,
+                                  extent2=extent2, r=r, start=start, end=end, material_ids=tmp[9:])
 
             else:
                 raise CmdInputError("'" + ' '.join(tmp) + "'" + ' too many parameters have been given')

gprMax/hash_cmds_multiuse.py

@@ -16,21 +16,11 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from .cmds_multiple import Waveform
-from .cmds_multiple import VoltageSource
-from .cmds_multiple import HertzianDipole
-from .cmds_multiple import MagneticDipole
-from .cmds_multiple import TransmissionLine
-from .cmds_multiple import Material
-from .cmds_multiple import Snapshot
-from .cmds_multiple import AddDebyeDispersion
-from .cmds_multiple import AddLorentzDispersion
-from .cmds_multiple import AddDrudeDispersion
-from .cmds_multiple import SoilPeplinski
-from .cmds_multiple import GeometryView
-from .cmds_multiple import GeometryObjectsWrite
-from .cmds_multiple import PMLCFS
-from .cmds_multiple import Rx
+from .cmds_multiple import (PMLCFS, AddDebyeDispersion, AddDrudeDispersion,
+                            AddLorentzDispersion, GeometryObjectsWrite,
+                            GeometryView, HertzianDipole, MagneticDipole,
+                            Material, Rx, RxArray, Snapshot, SoilPeplinski,
+                            TransmissionLine, VoltageSource, Waveform)
 from .exceptions import CmdInputError
 
 
@@ -275,9 +265,9 @@ def process_multicmds(multicmds):
             if len(tmp) != 7:
                 raise CmdInputError("'" + cmdname + ': ' + ' '.join(tmp) + "'" + ' requires exactly seven parameters')
 
-                p1 = float(tmp[0]), float(tmp[1]), float(tmp[2])
-                p2 = float(tmp[3]), float(tmp[4]), float(tmp[5])
-                gow = GeometryObjectsWrite(p1=p1, p2=p2, filename=tmp[6])
-                scene_objects.append(gow)
+            p1 = float(tmp[0]), float(tmp[1]), float(tmp[2])
+            p2 = float(tmp[3]), float(tmp[4]), float(tmp[5])
+            gow = GeometryObjectsWrite(p1=p1, p2=p2, filename=tmp[6])
+            scene_objects.append(gow)
 
     return scene_objects

gprMax/hash_cmds_singleuse.py

@@ -16,17 +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/>.
 
-from .cmds_single_use import Title
-from .cmds_single_use import NumThreads
-from .cmds_single_use import Discretisation
-from .cmds_single_use import Domain
-from .cmds_single_use import TimeStepStabilityFactor
-from .cmds_single_use import TimeWindow
-from .cmds_single_use import PMLCells
-from .cmds_single_use import SrcSteps
-from .cmds_single_use import RxSteps
-from .cmds_single_use import ExcitationFile
-from .cmds_single_use import OutputDir
+from .cmds_single_use import (Discretisation, Domain, ExcitationFile,
+                              NumThreads, OutputDir, PMLCells, RxSteps,
+                              SrcSteps, TimeStepStabilityFactor, TimeWindow,
+                              Title)
 from .exceptions import CmdInputError
 
 

gprMax/model_build_run.py

@@ -19,37 +19,31 @@
 import datetime
 import itertools
 import logging
-from pathlib import Path
 import platform
-import psutil
 import sys
+from pathlib import Path
 
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
+import gprMax.config as config
 import numpy as np
+import psutil
+from colorama import Fore, Style, init
+init()
 from terminaltables import SingleTable
 from tqdm import tqdm
 
-import gprMax.config as config
-from .cython.yee_cell_build import build_electric_components
-from .cython.yee_cell_build import build_magnetic_components
+from .cython.yee_cell_build import (build_electric_components,
+                                    build_magnetic_components)
 from .exceptions import GeneralError
 from .fields_outputs import write_hdf5_outputfile
 from .grid import dispersion_analysis
 from .hash_cmds_file import parse_hash_commands
-from .materials import Material
-from .materials import process_materials
-from .pml import build_pml
-from .pml import print_pml_info
+from .materials import Material, process_materials
+from .pml import build_pml, print_pml_info
 from .scene import Scene
 from .snapshots import Snapshot
 from .solvers import create_solver
-from .utilities import get_terminal_width
-from .utilities import human_size
-from .utilities import mem_check_all
-from .utilities import set_omp_threads
+from .utilities import (get_terminal_width, human_size, mem_check_all,
+                        set_omp_threads)
 
 logger = logging.getLogger(__name__)
 

gprMax/mpi.py

@@ -16,9 +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/>.
 
-from enum import IntEnum
 import logging
 import time
+from enum import IntEnum
 
 from mpi4py import MPI
 

gprMax/pml.py

@@ -18,9 +18,8 @@
 
 from importlib import import_module
 
-import numpy as np
-
 import gprMax.config as config
+import numpy as np
 
 
 class CFSParameter:

gprMax/receivers.py

@@ -16,9 +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 numpy as np
-
 import gprMax.config as config
+import numpy as np
 
 
 class Rx:

gprMax/scene.py

@@ -21,11 +21,9 @@ import logging
 from .cmds_geometry.cmds_geometry import UserObjectGeometry
 from .cmds_geometry.fractal_box_builder import FractalBoxBuilder
 from .cmds_multiple import UserObjectMulti
-from .cmds_single_use import UserObjectSingle
-from .cmds_single_use import Domain
-from .cmds_single_use import Discretisation
-from .cmds_single_use import TimeWindow
-from .exceptions import CmdInputError
+from .cmds_single_use import (Discretisation, Domain, TimeWindow,
+                              UserObjectSingle)
+from .exceptions import CmdInputError, GeneralError
 from .materials import create_built_in_materials
 from .subgrids.user_objects import SubGridBase as SubGridUserBase
 from .user_inputs import create_user_input_points

gprMax/snapshots.py

@@ -16,12 +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/>.
 
-from struct import pack
 import sys
-
-import numpy as np
+from struct import pack
 
 import gprMax.config as config
+import numpy as np
+
 from .cython.snapshots import calculate_snapshot_fields
 from .utilities import round_value
 

gprMax/solvers.py

@@ -17,11 +17,10 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import gprMax.config as config
-from .grid import FDTDGrid
-from .grid import CUDAGrid
+
+from .grid import CUDAGrid, FDTDGrid
 from .subgrids.updates import create_updates as create_subgrid_updates
-from .updates import CPUUpdates
-from .updates import CUDAUpdates
+from .updates import CPUUpdates, CUDAUpdates
 
 
 def create_G():

gprMax/sources.py

@@ -18,12 +18,10 @@
 
 from copy import deepcopy
 
+import gprMax.config as config
 import numpy as np
 
-import gprMax.config as config
-from .grid import Ix
-from .grid import Iy
-from .grid import Iz
+from .grid import Ix, Iy, Iz
 from .utilities import round_value
 
 

gprMax/subgrids/subgrid_hsg.py

@@ -16,16 +16,16 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from colorama import init
-from colorama import Fore
-from colorama import Style
+import gprMax.config as config
+from colorama import Fore, Style, init
+
+from ..cython.fields_updates_hsg import (cython_update_electric_os,
+                                         cython_update_is,
+                                         cython_update_magnetic_os)
+from .base import SubGridBase
+
 init()
 
-import gprMax.config as config
-from .base import SubGridBase
-from ..cython.fields_updates_hsg import cython_update_is
-from ..cython.fields_updates_hsg import cython_update_magnetic_os
-from ..cython.fields_updates_hsg import cython_update_electric_os
 
 
 class SubGridHSG(SubGridBase):

gprMax/subgrids/updates.py

@@ -19,10 +19,9 @@
 import logging
 
 from ..exceptions import GeneralError
-from .precursor_nodes import PrecursorNodes
-from .precursor_nodes import PrecursorNodesFiltered
-from .subgrid_hsg import SubGridHSG
 from ..updates import CPUUpdates
+from .precursor_nodes import PrecursorNodes, PrecursorNodesFiltered
+from .subgrid_hsg import SubGridHSG
 
 log = logging.getLogger(__name__)
 

gprMax/subgrids/user_objects.py

@@ -19,11 +19,10 @@
 from copy import copy
 
 import numpy as np
-
 from gprMax import config
+
 from ..cmds_geometry.cmds_geometry import UserObjectGeometry
-from ..cmds_multiple import UserObjectMulti
-from ..cmds_multiple import Rx
+from ..cmds_multiple import Rx, UserObjectMulti
 from ..exceptions import CmdInputError
 from .multi import ReferenceRx as ReferenceRxUser
 from .subgrid_hsg import SubGridHSG as SubGridHSGUser

gprMax/updates.py

@@ -16,27 +16,26 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from importlib import import_module
 import logging
-
-import numpy as np
+from importlib import import_module
 
 import gprMax.config as config
+import numpy as np
+
 from .cuda.fields_updates import kernel_template_fields
 from .cuda.snapshots import kernel_template_store_snapshot
 from .cuda.source_updates import kernel_template_sources
-from .cython.fields_updates_normal import update_electric as update_electric_cpu
-from .cython.fields_updates_normal import update_magnetic as update_magnetic_cpu
-from .fields_outputs import store_outputs as store_outputs_cpu
+from .cython.fields_updates_normal import \
+    update_electric as update_electric_cpu
+from .cython.fields_updates_normal import \
+    update_magnetic as update_magnetic_cpu
+from .exceptions import GeneralError
 from .fields_outputs import kernel_template_store_outputs
-from .receivers import htod_rx_arrays
-from .receivers import dtoh_rx_array
-from .snapshots import Snapshot
-from .snapshots import htod_snapshot_array
-from .snapshots import dtoh_snapshot_array
+from .fields_outputs import store_outputs as store_outputs_cpu
+from .receivers import dtoh_rx_array, htod_rx_arrays
+from .snapshots import Snapshot, dtoh_snapshot_array, htod_snapshot_array
 from .sources import htod_src_arrays
-from .utilities import round32
-from .utilities import timer
+from .utilities import human_size, round32, timer
 
 
 class CPUUpdates:
@@ -692,7 +691,7 @@ class CUDAUpdates:
         # Copy data from any snapshots back to correct snapshot objects
         if self.grid.snapshots and not config.get_model_config().cuda['snapsgpu2cpu']:
             for i, snap in enumerate(self.grid.snapshots):
-                dtoh_snapshot_arra(self.snapEx_gpu.get(),
+                dtoh_snapshot_array(self.snapEx_gpu.get(),
                                    self.snapEy_gpu.get(),
                                    self.snapEz_gpu.get(),
                                    self.snapHx_gpu.get(),

gprMax/user_inputs.py

@@ -18,19 +18,17 @@
 
 import logging
 
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
-import numpy as np
-
 import gprMax.config as config
+import numpy as np
+from colorama import Fore, Style, init
+init()
 from .exceptions import CmdInputError
 from .subgrids.base import SubGridBase
 from .utilities import round_value
 
 logger = logging.getLogger(__name__)
 
+
 """Module contains classes to handle points supplied by a user. The
     classes implement a common interface such that geometry building objects
     such as box or triangle do not need to have any knowledge which grid to

gprMax/utilities.py

@@ -16,34 +16,30 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from contextlib import contextmanager
 import codecs
 import decimal as d
 import logging
 import os
 import platform
-import psutil
 import re
 import subprocess
-from shutil import get_terminal_size
 import sys
 import textwrap
+from contextlib import contextmanager
+from shutil import get_terminal_size
+
+import gprMax.config as config
+import numpy as np
+import psutil
+from colorama import Fore, Style, init
+init()
+from .exceptions import GeneralError
 
 try:
     from time import thread_time as timer_fn
 except ImportError:
     from time import perf_counter as timer_fn
 
-
-from colorama import init
-from colorama import Fore
-from colorama import Style
-init()
-import numpy as np
-
-import gprMax.config as config
-from .exceptions import GeneralError
-
 logger = logging.getLogger(__name__)
 
 
@@ -525,7 +521,7 @@ def detect_gpus():
     else:
         deviceIDsavail = range(drv.Device.count())
 
-    # Gather information about selected/detected GPUs
+    # Gather information about detected GPUs
     gpus = []
     for ID in deviceIDsavail:
         gpu = GPU(deviceID=ID)
@@ -535,24 +531,24 @@ def detect_gpus():
     return gpus
 
 
-def check_gpus(gpus):
-    """Check if requested Nvidia GPU(s) deviceID(s) exist.
+# def check_gpus(gpus):
+#     """Check if requested Nvidia GPU(s) deviceID(s) exist.
 
-    Args:
-        gpus (list): List of GPU object(s).
-    """
+#     Args:
+#         gpus (list): List of GPU object(s).
+#     """
 
-    # Check if requested device ID(s) exist
-    for ID in deviceIDs:
-        if ID not in deviceIDsavail:
-            raise GeneralError(f'GPU with device ID {ID} does not exist')
+#     # Check if requested device ID(s) exist
+#     for ID in deviceIDs:
+#         if ID not in deviceIDsavail:
+#             raise GeneralError(f'GPU with device ID {ID} does not exist')
 
-    # Gather information about selected/detected GPUs
-    gpus = []
-    for ID in deviceIDsavail:
-        gpu = GPU(deviceID=ID)
-        gpu.get_gpu_info(drv)
-        gpus.append(gpu)
+#     # Gather information about selected/detected GPUs
+#     gpus = []
+#     for ID in deviceIDsavail:
+#         gpu = GPU(deviceID=ID)
+#         gpu.get_gpu_info(drv)
+#         gpus.append(gpu)
 
 
 def timer():

gprMax/waveforms.py

@@ -16,8 +16,11 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
+import logging
 import numpy as np
 
+logger = logging.getLogger(__name__)
+
 
 class Waveform:
     """Definitions of waveform shapes that can be used with sources."""
@@ -129,5 +132,5 @@ class Waveform:
         return ampvalue
 
     def __str__(self):
-        log.debug('Do we need this?')
+        logger.debug('Do we need this?')
         return f'Waveform: ID={self.ID}, type={self.type}, amp{self.amp}, freq={self.freq}'

tests/analytical_solutions.py

@@ -1,7 +1,6 @@
 import numpy as np
 
-from gprMax.config import c
-from gprMax.config import e0
+import gprMax.config as config
 from gprMax.waveforms import Waveform
 
 
@@ -52,52 +51,41 @@ def hertzian_dipole_fs(iterations, dt, dxdydz, rx):
     x = rx[0]
     y = rx[1]
     z = rx[2]
-    if z == 0:
-        sign_z = 1
-    else:
-        sign_z = np.sign(z)
 
     # Coordinates of Rx for Ex FDTD component
     Ex_x = x + 0.5 * dx
     Ex_y = y
     Ex_z = z - 0.5 * dz
     Er_x = np.sqrt((Ex_x**2 + Ex_y**2 + Ex_z**2))
-    tau_Ex = Er_x / c
+    tau_Ex = Er_x / config.sim_config.em_consts['c']
 
     # Coordinates of Rx for Ey FDTD component
     Ey_x = x
     Ey_y = y + 0.5 * dy
     Ey_z = z - 0.5 * dz
     Er_y = np.sqrt((Ey_x**2 + Ey_y**2 + Ey_z**2))
-    tau_Ey = Er_y / c
+    tau_Ey = Er_y / config.sim_config.em_consts['c']
 
     # Coordinates of Rx for Ez FDTD component
     Ez_x = x
     Ez_y = y
     Ez_z = z
     Er_z = np.sqrt((Ez_x**2 + Ez_y**2 + Ez_z**2))
-    tau_Ez = Er_z / c
+    tau_Ez = Er_z / config.sim_config.em_consts['c']
 
     # Coordinates of Rx for Hx FDTD component
     Hx_x = x
     Hx_y = y + 0.5 * dy
     Hx_z = z
     Hr_x = np.sqrt((Hx_x**2 + Hx_y**2 + Hx_z**2))
-    tau_Hx = Hr_x / c
+    tau_Hx = Hr_x / config.sim_config.em_consts['c']
 
     # Coordinates of Rx for Hy FDTD component
     Hy_x = x + 0.5 * dx
     Hy_y = y
     Hy_z = z
     Hr_y = np.sqrt((Hy_x**2 + Hy_y**2 + Hy_z**2))
-    tau_Hy = Hr_y / c
-
-    # Coordinates of Rx for Hz FDTD component
-    Hz_x = x + 0.5 * dx
-    Hz_y = y + 0.5 * dy
-    Hz_z = z - 0.5 * dz
-    Hr_z = np.sqrt((Hz_x**2 + Hz_y**2 + Hz_z**2))
-    tau_Hz = Hr_z / c
+    tau_Hy = Hr_y / config.sim_config.em_consts['c']
 
     # Initialise fields
     fields = np.zeros((iterations, 6))
@@ -118,30 +106,24 @@ def hertzian_dipole_fs(iterations, dt, dxdydz, rx):
         f_Ez = w.calculate_value((timestep * dt) - tau_Ez, dt) * dl
         fdot_Ez = wdot.calculate_value((timestep * dt) - tau_Ez, dt) * dl
 
-        fint_Hx = wint.calculate_value((timestep * dt) - tau_Hx, dt) * dl
         f_Hx = w.calculate_value((timestep * dt) - tau_Hx, dt) * dl
         fdot_Hx = wdot.calculate_value((timestep * dt) - tau_Hx, dt) * dl
 
-        fint_Hy = wint.calculate_value((timestep * dt) - tau_Hy, dt) * dl
         f_Hy = w.calculate_value((timestep * dt) - tau_Hy, dt) * dl
         fdot_Hy = wdot.calculate_value((timestep * dt) - tau_Hy, dt) * dl
 
-        fint_Hz = wint.calculate_value((timestep * dt) - tau_Hz, dt) * dl
-        f_Hz = w.calculate_value((timestep * dt) - tau_Hz, dt) * dl
-        fdot_Hz = wdot.calculate_value((timestep * dt) - tau_Hz, dt) * dl
-
         # Ex
-        fields[timestep, 0] = ((Ex_x * Ex_z) / (4 * np.pi * e0 * Er_x**5)) * (3 * (fint_Ex + (tau_Ex * f_Ex)) + (tau_Ex**2 * fdot_Ex))
+        fields[timestep, 0] = ((Ex_x * Ex_z) / (4 * np.pi * config.sim_config.em_consts['e0'] * Er_x**5)) * (3 * (fint_Ex + (tau_Ex * f_Ex)) + (tau_Ex**2 * fdot_Ex))
 
         # Ey
         try:
             tmp = Ey_y / Ey_x
         except ZeroDivisionError:
             tmp = 0
-        fields[timestep, 1] = tmp * ((Ey_x * Ey_z) / (4 * np.pi * e0 * Er_y**5)) * (3 * (fint_Ey + (tau_Ey * f_Ey)) + (tau_Ey**2 * fdot_Ey))
+        fields[timestep, 1] = tmp * ((Ey_x * Ey_z) / (4 * np.pi * config.sim_config.em_consts['e0'] * Er_y**5)) * (3 * (fint_Ey + (tau_Ey * f_Ey)) + (tau_Ey**2 * fdot_Ey))
 
         # Ez
-        fields[timestep, 2] = (1 / (4 * np.pi * e0 * Er_z**5)) * ((2 * Ez_z**2 - (Ez_x**2 + Ez_y**2)) * (fint_Ez + (tau_Ez * f_Ez)) - (Ez_x**2 + Ez_y**2) * tau_Ez**2 * fdot_Ez)
+        fields[timestep, 2] = (1 / (4 * np.pi * config.sim_config.em_consts['e0'] * Er_z**5)) * ((2 * Ez_z**2 - (Ez_x**2 + Ez_y**2)) * (fint_Ez + (tau_Ez * f_Ez)) - (Ez_x**2 + Ez_y**2) * tau_Ez**2 * fdot_Ez)
 
         # Hx
         fields[timestep, 3] = - (Hx_y / (4 * np.pi * Hr_x**3)) * (f_Hx + (tau_Hx * fdot_Hx))

tests/test_experimental.py

@@ -17,13 +17,12 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import argparse
-from pathlib import Path
 import sys
+from pathlib import Path
 
 import h5py
-import numpy as np
 import matplotlib.pyplot as plt
-
+import numpy as np
 from gprMax.exceptions import CmdInputError
 
 """Plots a comparison of fields between given simulation output and experimental data files."""

tests/test_models.py

@@ -16,21 +16,21 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from pathlib import Path
 import sys
+from pathlib import Path
 
-from colorama import init, Fore, Style
-init()
+import gprMax
 import h5py
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+from colorama import Fore, Style, init
+init()
+from gprMax.exceptions import GeneralError
+from tests.analytical_solutions import hertzian_dipole_fs
 
 if sys.platform == 'linux':
     plt.switch_backend('agg')
 
-import gprMax
-from gprMax.exceptions import GeneralError
-from tests.analytical_solutions import hertzian_dipole_fs
 
 """Compare field outputs
 

tools/HPC_scripts/gprmax_omp_mpi.sh

@@ -16,7 +16,7 @@
 #$ -pe mpi 176
 
 ### Job script name:
-#$ -N gprmax_omp_mpi.sh
+#$ -N gprmax_omp_mpi_no_spawn.sh
 #####################################################################################
 
 ### Initialise environment module
@@ -34,4 +34,4 @@ export OMP_NUM_THREADS=16
 
 ### Run gprMax with input file
 cd $HOME/gprMax
-python -m gprMax mymodel.in -n 10 -mpi 11
+mpirun -n 11 python -m gprMax mymodel.in -n 10 -mpi

tools/HPC_scripts/gprmax_omp_mpi_no_spawn.sh

@@ -1,37 +0,0 @@
-#!/bin/sh
-#####################################################################################
-### Change to current working directory:
-#$ -cwd
-
-### Specify runtime (hh:mm:ss):
-#$ -l h_rt=01:00:00
-
-### Email options:
-#$ -m ea -M joe.bloggs@email.com
-
-### Resource reservation:
-#$ -R y
-
-### Parallel environment ($NSLOTS):
-#$ -pe mpi 176
-
-### Job script name:
-#$ -N gprmax_omp_mpi_no_spawn.sh
-#####################################################################################
-
-### Initialise environment module
-. /etc/profile.d/modules.sh
-
-### Load and activate Anaconda environment for gprMax, i.e. Python 3 and required packages
-module load anaconda
-source activate gprMax
-
-### Load OpenMPI
-module load openmpi
-
-### Set number of OpenMP threads per MPI task (each gprMax model)
-export OMP_NUM_THREADS=16
-
-### Run gprMax with input file
-cd $HOME/gprMax
-mpirun -n 11 python -m gprMax mymodel.in -n 10 --mpi-no-spawn

tools/inputfile_old2new.py

@@ -223,7 +223,7 @@ while(lindex < len(inputlines)):
             lindex += 1
 
         elif cmdname == '#bowtie':
-            print("Command '{}', is no longer supported. You can create the bowtie shape using two triangle commands.".format(inputlines[lindex], replacement))
+            print("Command '{}', is no longer supported. You can create the bowtie shape using two triangle commands.".format(inputlines[lindex]))
             inputlines.pop(lindex)
 
         elif cmdname == '#cylinder':

tools/outputfiles_merge.py

@@ -23,8 +23,8 @@ from pathlib import Path
 
 import h5py
 import numpy as np
-
 from gprMax._version import __version__
+from gprMax.exceptions import CmdInputError
 
 
 def get_output_data(filename, rxnumber, rxcomponent):

tools/plot_Ascan.py

@@ -20,10 +20,9 @@ import argparse
 from pathlib import Path
 
 import h5py
-import numpy as np
-import matplotlib.pyplot as plt
 import matplotlib.gridspec as gridspec
-
+import matplotlib.pyplot as plt
+import numpy as np
 from gprMax.exceptions import CmdInputError
 from gprMax.receivers import Rx
 from gprMax.utilities import fft_power

tools/plot_Bscan.py

@@ -20,10 +20,10 @@ import argparse
 from pathlib import Path
 
 import h5py
-import numpy as np
 import matplotlib.pyplot as plt
-
+import numpy as np
 from gprMax.exceptions import CmdInputError
+
 from .outputfiles_merge import get_output_data
 
 

tools/plot_antenna_params.py

@@ -20,10 +20,9 @@ import argparse
 from pathlib import Path
 
 import h5py
-import numpy as np
-import matplotlib.pyplot as plt
 import matplotlib.gridspec as gridspec
-
+import matplotlib.pyplot as plt
+import numpy as np
 from gprMax.exceptions import CmdInputError
 
 
@@ -412,10 +411,10 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
     # ax.grid(which='both', axis='both', linestyle='-.')
 
     # Save a PDF/PNG of the figure
-    savename1 = file.stem + '_tl_params'
-    savename1 = file.parent / savename1
-    savename2 = file.stem + '_ant_params'
-    savename2 = file.parent / savename2
+    savename1 = filename.stem + '_tl_params'
+    savename1 = filename.parent / savename1
+    savename2 = filename.stem + '_ant_params'
+    savename2 = filename.parent / savename2
     # fig1.savefig(savename1.with_suffix('.png'), dpi=150, format='png',
     #              bbox_inches='tight', pad_inches=0.1)
     # fig2.savefig(savename2.with_suffix('.png'), dpi=150, format='png',

tools/plot_antenna_params_UtEl.py

@@ -0,0 +1,429 @@
+# Copyright (C) 2015-2020: The University of Edinburgh
+#                 Authors: Craig Warren and Antonis Giannopoulos
+#
+# This file is part of gprMax.
+#
+# gprMax is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# gprMax is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
+
+import argparse
+from pathlib import Path
+
+import h5py
+import matplotlib.gridspec as gridspec
+import matplotlib.pyplot as plt
+import numpy as np
+from gprMax.exceptions import CmdInputError
+from scipy.io import loadmat
+
+
+def calculate_antenna_params(filename, tltxnumber=1, tlrxnumber=None, rxnumber=None, rxcomponent=None):
+    """Calculates antenna parameters - incident, reflected and total volatges and currents; s11, (s21) and input impedance.
+
+    Args:
+        filename (string): Filename (including path) of output file.
+        tltxnumber (int): Transmitter antenna - transmission line number
+        tlrxnumber (int): Receiver antenna - transmission line number
+        rxnumber (int): Receiver antenna - output number
+        rxcomponent (str): Receiver antenna - output electric field component
+
+    Returns:
+        antennaparams (dict): Antenna parameters.
+    """
+
+    # Open output file and read some attributes
+    file = Path(filename)
+    f = h5py.File(file, 'r')
+    dxdydz = f.attrs['dx_dy_dz']
+    dt = f.attrs['dt']
+    iterations = f.attrs['Iterations']
+
+    # Calculate time array and frequency bin spacing
+    time = np.linspace(0, (iterations - 1) * dt, num=iterations)
+    df = 1 / np.amax(time)
+
+    print(f'Time window: {np.amax(time):g} s ({iterations} iterations)')
+    print(f'Time step: {dt:g} s')
+    print(f'Frequency bin spacing: {df:g} Hz')
+
+    # Read/calculate voltages and currents from transmitter antenna
+    tltxpath = '/tls/tl' + str(tltxnumber) + '/'
+
+    # Incident voltages/currents
+    Vinc = f[tltxpath + 'Vinc'][:]
+    Iinc = f[tltxpath + 'Iinc'][:]
+
+    # Total (incident + reflected) voltages/currents
+    Vtotal = f[tltxpath + 'Vtotal'][:]
+    Itotal = f[tltxpath + 'Itotal'][:]
+
+    # Reflected voltages/currents
+    Vref = Vtotal - Vinc
+    Iref = Itotal - Iinc
+
+    # If a receiver antenna is used (with a transmission line or receiver), get received voltage for s21
+    if tlrxnumber:
+        tlrxpath = '/tls/tl' + str(tlrxnumber) + '/'
+        Vrec = f[tlrxpath + 'Vtotal'][:]
+
+    elif rxnumber:
+        rxpath = '/rxs/rx' + str(rxnumber) + '/'
+        availableoutputs = list(f[rxpath].keys())
+
+        if rxcomponent not in availableoutputs:
+            raise CmdInputError(f"{rxcomponent} output requested, but the available output for receiver {rxnumber} is {', '.join(availableoutputs)}")
+
+        rxpath += rxcomponent
+
+        # Received voltage
+        if rxcomponent == 'Ex':
+            Vrec = f[rxpath][:] * -1 * dxdydz[0]
+        elif rxcomponent == 'Ey':
+            Vrec = f[rxpath][:] * -1 * dxdydz[1]
+        elif rxcomponent == 'Ez':
+            Vrec = f[rxpath][:] * -1 * dxdydz[2]
+    f.close()
+
+    # Frequency bins
+    freqs = np.fft.fftfreq(Vinc.size, d=dt)
+
+    # Delay correction - current lags voltage, so delay voltage to match current timestep
+    delaycorrection = np.exp(1j * 2 * np.pi * freqs * (dt / 2))
+
+    # Calculate s11 and (optionally) s21
+    s11 = np.abs(np.fft.fft(Vref) / np.fft.fft(Vinc))
+    if tlrxnumber or rxnumber:
+        s21 = np.abs(np.fft.fft(Vrec) / np.fft.fft(Vinc))
+
+    # Calculate input impedance
+    zin = (np.fft.fft(Vtotal) * delaycorrection) / np.fft.fft(Itotal)
+
+    # Calculate input admittance
+    yin = np.fft.fft(Itotal) / (np.fft.fft(Vtotal) * delaycorrection)
+
+    # Convert to decibels (ignore warning from taking a log of any zero values)
+    with np.errstate(divide='ignore'):
+        Vincp = 20 * np.log10(np.abs((np.fft.fft(Vinc) * delaycorrection)))
+        Iincp = 20 * np.log10(np.abs(np.fft.fft(Iinc)))
+        Vrefp = 20 * np.log10(np.abs((np.fft.fft(Vref) * delaycorrection)))
+        Irefp = 20 * np.log10(np.abs(np.fft.fft(Iref)))
+        Vtotalp = 20 * np.log10(np.abs((np.fft.fft(Vtotal) * delaycorrection)))
+        Itotalp = 20 * np.log10(np.abs(np.fft.fft(Itotal)))
+        s11 = 20 * np.log10(s11)
+
+    # Replace any NaNs or Infs from zero division
+    Vincp[np.invert(np.isfinite(Vincp))] = 0
+    Iincp[np.invert(np.isfinite(Iincp))] = 0
+    Vrefp[np.invert(np.isfinite(Vrefp))] = 0
+    Irefp[np.invert(np.isfinite(Irefp))] = 0
+    Vtotalp[np.invert(np.isfinite(Vtotalp))] = 0
+    Itotalp[np.invert(np.isfinite(Itotalp))] = 0
+    s11[np.invert(np.isfinite(s11))] = 0
+
+    # Create dictionary of antenna parameters
+    antennaparams = {'time': time, 'freqs': freqs, 'Vinc': Vinc, 'Vincp': Vincp, 'Iinc': Iinc, 'Iincp': Iincp,
+                     'Vref': Vref, 'Vrefp': Vrefp, 'Iref': Iref, 'Irefp': Irefp,
+                     'Vtotal': Vtotal, 'Vtotalp': Vtotalp, 'Itotal': Itotal, 'Itotalp': Itotalp,
+                     's11': s11, 'zin': zin, 'yin': yin}
+    if tlrxnumber or rxnumber:
+        with np.errstate(divide='ignore'): # Ignore warning from taking a log of any zero values
+            s21 = 20 * np.log10(s21)
+        s21[np.invert(np.isfinite(s21))] = 0
+        antennaparams['s21'] = s21
+
+    return antennaparams
+
+
+def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref, Irefp, Vtotal, Vtotalp, Itotal, Itotalp, s11, zin, yin, s21=None):
+    """Plots antenna parameters - incident, reflected and total volatges and currents; s11, (s21) and input impedance.
+
+    Args:
+        filename (string): Filename (including path) of output file.
+        time (array): Simulation time.
+        freq (array): Frequencies for FFTs.
+        Vinc, Vincp, Iinc, Iincp (array): Time and frequency domain representations of incident voltage and current.
+        Vref, Vrefp, Iref, Irefp (array): Time and frequency domain representations of reflected voltage and current.
+        Vtotal, Vtotalp, Itotal, Itotalp (array): Time and frequency domain representations of total voltage and current.
+        s11, s21 (array): s11 and, optionally, s21 parameters.
+        zin, yin (array): Input impedance and input admittance parameters.
+
+    Returns:
+        plt (object): matplotlib plot object.
+    """
+
+    # Set plotting range
+    pltrangemin = 1
+    # To a certain drop from maximum power
+    pltrangemax = np.where((np.amax(Vincp[1::]) - Vincp[1::]) > 60)[0][0] + 1
+    # To a maximum frequency
+    pltrangemax = np.where(freqs > 3e9)[0][0]
+    pltrange = np.s_[pltrangemin:pltrangemax]
+
+    # Print some useful values from s11, and input impedance
+    s11minfreq = np.where(s11[pltrange] == np.amin(s11[pltrange]))[0][0]
+    print(f's11 minimum: {np.amin(s11[pltrange]):g} dB at {freqs[s11minfreq + pltrangemin]:g} Hz')
+    print(f'At {freqs[s11minfreq + pltrangemin]:g} Hz...')
+    print(f'Input impedance: {np.abs(zin[s11minfreq + pltrangemin]):.1f}{zin[s11minfreq + pltrangemin].imag:+.1f}j Ohms')
+    # print(f'Input admittance (mag): {np.abs(yin[s11minfreq + pltrangemin]):g} S')
+    # print(f'Input admittance (phase): {np.angle(yin[s11minfreq + pltrangemin], deg=True):.1f} deg')
+
+    # Figure 1
+    # Plot incident voltage
+    # fig1, ax = plt.subplots(num='Transmitter transmission line parameters', figsize=(20, 12), facecolor='w', edgecolor='w')
+    # gs1 = gridspec.GridSpec(4, 2, hspace=0.7)
+    # ax = plt.subplot(gs1[0, 0])
+    # ax.plot(time, Vinc, 'r', lw=2, label='Vinc')
+    # ax.set_title('Incident voltage')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Voltage [V]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot frequency spectra of incident voltage
+    # ax = plt.subplot(gs1[0, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Vincp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'r')
+    # plt.setp(markerline, 'markerfacecolor', 'r', 'markeredgecolor', 'r')
+    # ax.plot(freqs[pltrange], Vincp[pltrange], 'r', lw=2)
+    # ax.set_title('Incident voltage')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot incident current
+    # ax = plt.subplot(gs1[1, 0])
+    # ax.plot(time, Iinc, 'b', lw=2, label='Vinc')
+    # ax.set_title('Incident current')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Current [A]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot frequency spectra of incident current
+    # ax = plt.subplot(gs1[1, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Iincp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'b')
+    # plt.setp(markerline, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
+    # ax.plot(freqs[pltrange], Iincp[pltrange], 'b', lw=2)
+    # ax.set_title('Incident current')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot total voltage
+    # ax = plt.subplot(gs1[2, 0])
+    # ax.plot(time, Vtotal, 'r', lw=2, label='Vinc')
+    # ax.set_title('Total (incident + reflected) voltage')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Voltage [V]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot frequency spectra of total voltage
+    # ax = plt.subplot(gs1[2, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Vtotalp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'r')
+    # plt.setp(markerline, 'markerfacecolor', 'r', 'markeredgecolor', 'r')
+    # ax.plot(freqs[pltrange], Vtotalp[pltrange], 'r', lw=2)
+    # ax.set_title('Total (incident + reflected) voltage')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot total current
+    # ax = plt.subplot(gs1[3, 0])
+    # ax.plot(time, Itotal, 'b', lw=2, label='Vinc')
+    # ax.set_title('Total (incident + reflected) current')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Current [A]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot frequency spectra of total current
+    # ax = plt.subplot(gs1[3, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Itotalp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'b')
+    # plt.setp(markerline, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
+    # ax.plot(freqs[pltrange], Itotalp[pltrange], 'b', lw=2)
+    # ax.set_title('Total (incident + reflected) current')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot reflected (reflected) voltage
+    # ax = plt.subplot(gs1[4, 0])
+    # ax.plot(time, Vref, 'r', lw=2, label='Vref')
+    # ax.set_title('Reflected voltage')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Voltage [V]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot frequency spectra of reflected voltage
+    # ax = plt.subplot(gs1[4, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Vrefp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'r')
+    # plt.setp(markerline, 'markerfacecolor', 'r', 'markeredgecolor', 'r')
+    # ax.plot(freqs[pltrange], Vrefp[pltrange], 'r', lw=2)
+    # ax.set_title('Reflected voltage')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot reflected (reflected) current
+    # ax = plt.subplot(gs1[5, 0])
+    # ax.plot(time, Iref, 'b', lw=2, label='Iref')
+    # ax.set_title('Reflected current')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Current [A]')
+    # ax.set_xlim([0, np.amax(time)])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot frequency spectra of reflected current
+    # ax = plt.subplot(gs1[5, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Irefp[pltrange], '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'b')
+    # plt.setp(markerline, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
+    # ax.plot(freqs[pltrange], Irefp[pltrange], 'b', lw=2)
+    # ax.set_title('Reflected current')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Figure 2
+    # Load measured s11
+    s11_meas = loadmat('/Volumes/Users/cwarren/Dropbox (Northumbria University)/Research/GPR-antennas/Utsi Electronics/500MHz_Vivaldi_antenna/measured/s11_measured.mat')
+
+    # Plot frequency spectra of s11
+    fig2, ax = plt.subplots(num='Antenna parameters', figsize=(20, 12), facecolor='w', edgecolor='w')
+    gs2 = gridspec.GridSpec(1, 1, hspace=0.3)
+    ax = plt.subplot(gs2[0, 0])
+    markerline, stemlines, baseline = ax.stem(freqs[pltrange], s11[pltrange], '-.', use_line_collection=True)
+    markerline2, stemlines2, baseline2 = ax.stem(s11_meas['f'], s11_meas['s11_t'], '-.', use_line_collection=True)
+    plt.setp(baseline, 'linewidth', 0)
+    plt.setp(stemlines, 'color', 'w')
+    plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    plt.setp(baseline2, 'linewidth', 0)
+    plt.setp(stemlines2, 'color', 'w')
+    plt.setp(markerline2, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
+    ax.plot(freqs[pltrange], s11[pltrange], 'g', lw=2, label='Simulation (Debye, 50$\Omega$)')
+    ax.plot(s11_meas['f'], s11_meas['s11_t'], 'b', lw=2, label='Measured')
+    ax.set_title('s11')
+    ax.set_xlabel('Frequency [Hz]')
+    ax.set_ylabel('Power [dB]')
+    ax.set_xlim([0, 3e9])
+    ax.set_ylim([-40, 0])
+    ax.grid(which='both', axis='both', linestyle='-.')
+    ax.legend(fontsize=12, frameon=False)
+
+    # Plot frequency spectra of s21
+    if s21 is not None:
+        ax = plt.subplot(gs2[0, 1])
+        markerline, stemlines, baseline = ax.stem(freqs[pltrange], s21[pltrange], '-.', use_line_collection=True)
+        plt.setp(baseline, 'linewidth', 0)
+        plt.setp(stemlines, 'color', 'g')
+        plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+        ax.plot(freqs[pltrange], s21[pltrange], 'g', lw=2)
+        ax.set_title('s21')
+        ax.set_xlabel('Frequency [Hz]')
+        ax.set_ylabel('Power [dB]')
+        # ax.set_xlim([0.88e9, 1.02e9])
+        # ax.set_ylim([-25, 50])
+        ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot input resistance (real part of impedance)
+    # ax = plt.subplot(gs2[1, 0])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], zin[pltrange].real, '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], zin[pltrange].real, 'g', lw=2)
+    # ax.set_title('Input impedance (resistive)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Resistance [Ohms]')
+    # # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim(bottom=0)
+    # # ax.set_ylim([0, 300])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+    #
+    # # Plot input reactance (imaginery part of impedance)
+    # ax = plt.subplot(gs2[1, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], zin[pltrange].imag, '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], zin[pltrange].imag, 'g', lw=2)
+    # ax.set_title('Input impedance (reactive)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Reactance [Ohms]')
+    # # ax.set_xlim([0.88e9, 1.02e9])
+    # # ax.set_ylim([-300, 300])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot input admittance (magnitude)
+    # ax = plt.subplot(gs2[2, 0])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.abs(yin[pltrange]), '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], np.abs(yin[pltrange]), 'g', lw=2)
+    # ax.set_title('Input admittance (magnitude)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Admittance [Siemens]')
+    # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim([0, 0.035])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Plot input admittance (phase)
+    # ax = plt.subplot(gs2[2, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.angle(yin[pltrange], deg=True), '-.', use_line_collection=True)
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], np.angle(yin[pltrange], deg=True), 'g', lw=2)
+    # ax.set_title('Input admittance (phase)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Phase [degrees]')
+    # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim([-40, 100])
+    # ax.grid(which='both', axis='both', linestyle='-.')
+
+    # Save a PDF/PNG of the figure
+    # fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig2.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_ant_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    fig2.savefig(filename.with_suffix('.pdf'), dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+
+    return plt
+
+
+if __name__ == "__main__":
+
+    # Parse command line arguments
+    parser = argparse.ArgumentParser(description='Plots antenna parameters (s11, s21 parameters and input impedance) from an output file containing a transmission line source.', usage='cd gprMax; python -m tools.plot_antenna_params outputfile')
+    parser.add_argument('outputfile', help='name of output file including path')
+    parser.add_argument('--tltx-num', default=1, type=int, help='transmitter antenna - transmission line number')
+    parser.add_argument('--tlrx-num', type=int, help='receiver antenna - transmission line number')
+    parser.add_argument('--rx-num', type=int, help='receiver antenna - output number')
+    parser.add_argument('--rx-component', type=str, help='receiver antenna - output electric field component', choices=['Ex', 'Ey', 'Ez'])
+    args = parser.parse_args()
+
+    antennaparams = calculate_antenna_params(args.outputfile, args.tltx_num, args.tlrx_num, args.rx_num, args.rx_component)
+    plthandle = mpl_plot(args.outputfile, **antennaparams)
+    plthandle.show()

tools/plot_source_wave.py

@@ -19,12 +19,10 @@
 import argparse
 from pathlib import Path
 
-import numpy as np
 import matplotlib.pyplot as plt
-
+import numpy as np
 from gprMax.exceptions import CmdInputError
-from gprMax.utilities import fft_power
-from gprMax.utilities import round_value
+from gprMax.utilities import fft_power, round_value
 from gprMax.waveforms import Waveform
 
 

user_libs/antenna_patterns/initial_save.py

@@ -9,13 +9,10 @@ import argparse
 import os
 import sys
 
+import gprMax.config as config
 import h5py
-import numpy as np
 import matplotlib.pyplot as plt
-
-from gprMax.config import c
-from gprMax.config import z0
-
+import numpy as np
 
 # Parse command line arguments
 parser = argparse.ArgumentParser(description='Calculate and store (in a Numpy file) field patterns from a simulation with receivers positioned in circles around an antenna.', usage='cd gprMax; python -m user_libs.antenna_patterns.initial_save outputfile')
@@ -55,9 +52,9 @@ traceno = np.s_[:]  # All traces
 # Critical angle and velocity
 if epsr:
     mr = 1
-    z1 = np.sqrt(mr / epsr) * z0
-    v1 = c / np.sqrt(epsr)
-    thetac = np.round(np.arcsin(v1 / c) * (180 / np.pi))
+    z1 = np.sqrt(mr / epsr) * config.sim_config.em_consts['z0']
+    v1 = config.sim_config.em_consts['c'] / np.sqrt(epsr)
+    thetac = np.round(np.arcsin(v1 / config.sim_config.em_consts['c']) * (180 / np.pi))
     wavelength = v1 / f
 
 # Print some useful information
@@ -164,8 +161,8 @@ for radius in range(0, len(radii)):
             Ethetasum[index] = np.sum(Etheta[:, index]**2) / z1
             Hthetasum[index] = np.sum(Htheta[:, index]**2) / z1
         else:
-            Ethetasum[index] = np.sum(Etheta[:, index]**2) / z0
-            Hthetasum[index] = np.sum(Htheta[:, index]**2) / z0
+            Ethetasum[index] = np.sum(Etheta[:, index]**2) / config.sim_config.em_consts['z0']
+            Hthetasum[index] = np.sum(Htheta[:, index]**2) / config.sim_config.em_consts['z0']
 
         index += 1
 

user_libs/antenna_patterns/plot_fields.py

@@ -9,12 +9,9 @@ import argparse
 import os
 import sys
 
-import numpy as np
+import gprMax.config as config
 import matplotlib.pyplot as plt
-
-from gprMax.config import c
-from gprMax.config import z0
-
+import numpy as np
 
 # Parse command line arguments
 parser = argparse.ArgumentParser(description='Plot field patterns from a simulation with receivers positioned in circles around an antenna. This module should be used after the field pattern data has been processed and stored using the initial_save.py module.', usage='cd gprMax; python -m user_libs.antenna_patterns.plot_fields numpyfile')
@@ -52,9 +49,9 @@ step = 12
 # Critical angle and velocity
 if epsr:
     mr = 1
-    z1 = np.sqrt(mr / epsr) * z0
-    v1 = c / np.sqrt(epsr)
-    thetac = np.round(np.rad2deg(np.arcsin(v1 / c)))
+    z1 = np.sqrt(mr / epsr) * config.sim_config.em_consts['z0']
+    v1 = config.sim_config.em_consts['c'] / np.sqrt(epsr)
+    thetac = np.round(np.rad2deg(np.arcsin(v1 / config.sim_config.em_consts['c'])))
     wavelength = v1 / f
 
 # Print some useful information