Output issue heterogeneous soil model

[LeWerner42]

First of all thanks for actively maintaining and developing this tool. It is a pleasure to use.
When running the heterogeneous soil example with V4.0.0, one of the preprocessing steps takes really long (2 min) and all output data fields in the resulting .h5 file are plain zero. No data is contained in any field. If I run the same input file with V3.1.6 I get the expected result.
When using the new python api to run the same simulation, it does not proceed to the solving step at all.
I am using the -gpu option for all tests.

I am using following input:

#title: Heterogeneous soil using a stochastic distribution of dielectric properties given by a mixing model from Peplinski
#domain: 0.15 0.15 0.1
#dx_dy_dz: 0.001 0.001 0.001
#time_window: 6e-9

#waveform: ricker 1 1.5e9 my_ricker
#hertzian_dipole: y 0.045 0.075 0.085 my_ricker
#rx: 0.105 0.075 0.085

#soil_peplinski: 0.5 0.5 2.0 2.66 0.001 0.25 my_soil
#fractal_box: 0 0 0 0.15 0.15 0.070 1.5 1 1 1 50 my_soil my_soil_box
#add_surface_roughness: 0 0 0.070 0.15 0.15 0.070 1.5 1 1 0.065 0.080 my_soil_box

#geometry_view: 0 0 0 0.15 0.15 0.1 0.001 0.001 0.001 heterogeneous_soil n

From the python api, I get stuck with the following output:

=== Electromagnetic modelling software based on the Finite-Difference Time-Domain (FDTD) method 

    www.gprmax.com   __  __
     __ _ _ __  _ __|  \/  | __ ___  __
    / _` | '_ \| '__| |\/| |/ _` \ \/ /
   | (_| | |_) | |  | |  | | (_| |>  <
    \__, | .__/|_|  |_|  |_|\__,_/_/\_\
    |___/|_|
                     v4.0.0b0 (Càrn Mòr)

 Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley

 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 www.gnu.org/licenses.

Rechenschieber | Gigabyte Technology Co., Ltd. Z790 GAMING X AX | 1 x 13th Gen Intel(R) Core(TM) i9-13900K (24 cores) | 62.6 GiB | Linux-5.15.0-84-generic-x86_64-with-glibc2.31
|--->OpenMP: 24 threads
|--->CUDA:
     |--->Device 0: NVIDIA TITAN X (Pascal) | 11.9 GiB

--- Model 1/1, input file: simulationData/B-ScanTest --------------------------

Model title: 0.1
Spatial discretisation: 0.002 x 0.002 x 0.002m
Domain size: 1 x 0.4 x 0.4m (500 x 200 x 200 = 2e+07 cells)
Mode: 3D
Time step (at CFL limit): 3.85167e-12 secs
Time window: 9e-09 secs (2338 iterations)
Waveform mypulse of type ricker with maximum amplitude scaling 1, frequency 1e+09Hz created.
Hertzian dipole with polarity y at 0.1m, 0.18m, 0.35m, using waveform mypulse created.
Receiver at 0.1m, 0.22m, 0.35m with output component(s) Ex, Ey, Ez, Hx, Hy, Hz created.
Mixing model (Peplinski) used to create my_soil with sand fraction 0.8, clay fraction 0.2, bulk density 2g/cm3, sand particle density 2.66g/cm3, and water volumetric fraction 0.05 to 0.25 created.
#fractal_box: 0 0 0 1 0.4 0.3 2.5 1 1 1 50 my_soil fractalBox n no value for seed detected. This means you will get a different fractal distribution every time the model runs.
Fractal box fractalBox from 0m, 0m, 0m, to 1m, 0.4m, 0.3m with my_soil, fractal dimension 2.5, fractal weightings 1, 1, 1, fractal seeding None, with 50 material(s) created, dielectric smoothing is on.
Cylinder with face centres 0.5m, 0m, 0.07m and 0.5m, 0.002m, 0.07m, with radius 0.05m, of material(s) pec created, dielectric smoothing is off.

Memory required (estimated): ~1.7 GB [main_grid] + ~65.0 MB overhead = 1.7 GB

PML boundaries [main_grid]: {formulation: HORIPML, order: 1, thickness (cells): 10}
Building PML boundaries [main_grid]: 100%|█████| 6/6 [00:00<00:00, 2219.99it/s]

Building Yee cells [main_grid]:   0%|                    | 0/2 [00:00<?, ?it/s]

Cheers

[craig-warren]

@LeWerner42 can you try this again. I've made some updates to the CUDA solver in the v4 to fix an issue with dispersive materials.