Merge branch 'devel-reframe' into mpi

2025-08-07 15:10:13 +08:00 · 2025-03-18 13:31:49 +00:00
--- a/testing/analytical_solutions.py
+++ b/testing/analytical_solutions.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -164,7 +164,9 @@ def hertzian_dipole_fs(iterations, dt, dxdydz, rx):
            tmp = Hy_x / Hy_y
        except ZeroDivisionError:
            tmp = 0
-        fields[timestep, 4] = -tmp * (-(Hy_y / (4 * np.pi * Hr_y**3)) * (f_Hy + (tau_Hy * fdot_Hy)))
+        fields[timestep, 4] = -tmp * (
+            -(Hy_y / (4 * np.pi * Hr_y**3)) * (f_Hy + (tau_Hy * fdot_Hy))
+        )

        # Hz
        fields[timestep, 5] = 0
--- a/testing/benchmarking/bench_simple.py
+++ b/testing/benchmarking/bench_simple.py
@@ -1,9 +1,8 @@
 """A series of models with different domain sizes used for benchmarking.
-    The domain is free space with a simple source (Hertzian Dipole) and
-    receiver at the centre.
+The domain is free space with a simple source (Hertzian Dipole) and
+receiver at the centre.
 """

-
 import itertools
 from pathlib import Path

--- a/testing/diff_output_files.py
+++ b/testing/diff_output_files.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -82,7 +82,10 @@ def diff_output_files(filename1, filename2):
    for i in range(len(outputs2)):
        maxi = np.amax(np.abs(data1[:, i]))
        datadiffs[:, i] = np.divide(
-            np.abs(data2[:, i] - data1[:, i]), maxi, out=np.zeros_like(data1[:, i]), where=maxi != 0
+            np.abs(data2[:, i] - data1[:, i]),
+            maxi,
+            out=np.zeros_like(data1[:, i]),
+            where=maxi != 0,
        )  # Replace any division by zero with zero

        # Calculate power (ignore warning from taking a log of any zero values)
--- a/testing/models_pmls/pml_3D_pec_plate/plot_pml_comparison.py
+++ b/testing/models_pmls/pml_3D_pec_plate/plot_pml_comparison.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -46,12 +46,16 @@ maxerrors = []
 testmodels = [basename + "_" + s for s in PMLIDs]

 fig, ax = plt.subplots(
-    subplot_kw=dict(xlabel="Iterations", ylabel="Error [dB]"), figsize=(20, 10), facecolor="w", edgecolor="w"
+    subplot_kw=dict(xlabel="Iterations", ylabel="Error [dB]"),
+    figsize=(20, 10),
+    facecolor="w",
+    edgecolor="w",
 )

 for x, model in enumerate(testmodels):
    time, datadiffs = diff_output_files(
-        fn.parent.joinpath(basename + "_ref.h5"), fn.parent.joinpath(basename + str(x + 1) + ".h5")
+        fn.parent.joinpath(basename + "_ref.h5"),
+        fn.parent.joinpath(basename + str(x + 1) + ".h5"),
    )

    # Print maximum error value
@@ -60,7 +64,14 @@ for x, model in enumerate(testmodels):
    logger.info(f"{model}: Max. error {maxerrors[x]}")

    # Plot diffs (select column to choose field component, 0-Ex, 1-Ey etc..)
-    ax.plot(time[start::], datadiffs[start::, 1], color=next(colors), lw=2, ls=next(lines), label=model)
+    ax.plot(
+        time[start::],
+        datadiffs[start::, 1],
+        color=next(colors),
+        lw=2,
+        ls=next(lines),
+        label=model,
+    )
    ax.set_xticks(np.arange(0, 2200, step=100))
    ax.set_xlim([0, 2100])
    ax.set_yticks(np.arange(-160, 0, step=20))
--- a/testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate.py
+++ b/testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate.py
@@ -22,7 +22,9 @@ time_window = gprMax.TimeWindow(iterations=2100)
 tssf = gprMax.TimeStepStabilityFactor(f=0.99)

 waveform = gprMax.Waveform(wave_type="gaussiandotnorm", amp=1, freq=9.42e9, id="mypulse")
-hertzian_dipole = gprMax.HertzianDipole(polarisation="z", p1=(0.013, 0.013, 0.014), waveform_id="mypulse")
+hertzian_dipole = gprMax.HertzianDipole(
+    polarisation="z", p1=(0.013, 0.013, 0.014), waveform_id="mypulse"
+)
 rx = gprMax.Rx(p1=(0.038, 0.114, 0.013))

 plate = gprMax.Plate(p1=(0.013, 0.013, 0.013), p2=(0.038, 0.113, 0.013), material_id="pec")
--- a/testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate_ref.py
+++ b/testing/models_pmls/pml_3D_pec_plate/pml_3D_pec_plate_ref.py
@@ -22,7 +22,9 @@ time_window = gprMax.TimeWindow(iterations=2100)
 tssf = gprMax.TimeStepStabilityFactor(f=0.99)

 waveform = gprMax.Waveform(wave_type="gaussiandotnorm", amp=1, freq=9.42e9, id="mypulse")
-hertzian_dipole = gprMax.HertzianDipole(polarisation="z", p1=(0.088, 0.088, 0.089), waveform_id="mypulse")
+hertzian_dipole = gprMax.HertzianDipole(
+    polarisation="z", p1=(0.088, 0.088, 0.089), waveform_id="mypulse"
+)
 rx = gprMax.Rx(p1=(0.113, 0.189, 0.088))

 plate = gprMax.Plate(p1=(0.088, 0.088, 0.088), p2=(0.113, 0.188, 0.088), material_id="pec")
--- a/testing/models_pmls/pml_basic/plot_pml_comparison.py
+++ b/testing/models_pmls/pml_basic/plot_pml_comparison.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -74,7 +74,13 @@ for x, PMLID in enumerate(PMLIDs):
        ax.set_ylabel(f"{output} error [dB]")

    # Save a PDF/PNG of the figure
-    fig.savefig(basename + "_diffs_" + PMLID + ".pdf", dpi=None, format="pdf", bbox_inches="tight", pad_inches=0.1)
+    fig.savefig(
+        basename + "_diffs_" + PMLID + ".pdf",
+        dpi=None,
+        format="pdf",
+        bbox_inches="tight",
+        pad_inches=0.1,
+    )
    # fig.savefig(basename + "_diffs_" + PMLID + ".png", dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

 plt.show()
--- a/testing/models_pmls/pml_basic/pml_basic.py
+++ b/testing/models_pmls/pml_basic/pml_basic.py
@@ -18,7 +18,9 @@ dxdydz = gprMax.Discretisation(p1=(dl, dl, dl))
 time_window = gprMax.TimeWindow(time=3e-9)

 waveform = gprMax.Waveform(wave_type="gaussian", amp=1, freq=1e9, id="mypulse")
-hertzian_dipole = gprMax.HertzianDipole(polarisation="z", p1=(0.050, 0.050, 0.050), waveform_id="mypulse")
+hertzian_dipole = gprMax.HertzianDipole(
+    polarisation="z", p1=(0.050, 0.050, 0.050), waveform_id="mypulse"
+)
 rx = gprMax.Rx(p1=(0.070, 0.070, 0.070))

 # PML cases
--- a/testing/other_codes/vs_MoM_MATLAB/antenna_bowtie_fs/antenna_bowtie_fs.py
+++ b/testing/other_codes/vs_MoM_MATLAB/antenna_bowtie_fs/antenna_bowtie_fs.py
@@ -31,7 +31,10 @@ tx_pos = (x / 2, y / 2, z / 2)
 # Source excitation and type
 wave = gprMax.Waveform(wave_type="gaussian", amp=1, freq=1.5e9, id="mypulse")
 tl = gprMax.TransmissionLine(
-    p1=(tx_pos[0], tx_pos[1], tx_pos[2]), polarisation="x", resistance=50, waveform_id="mypulse"
+    p1=(tx_pos[0], tx_pos[1], tx_pos[2]),
+    polarisation="x",
+    resistance=50,
+    waveform_id="mypulse",
 )
 scene.add(wave)
 scene.add(tl)
@@ -59,8 +62,16 @@ scene.add(t2)

 # Detailed geometry view around bowtie and feed position
 gv1 = gprMax.GeometryView(
-    p1=(tx_pos[0] - bowtie_dims[0] - 2 * dl, tx_pos[1] - bowtie_dims[1] / 2 - 2 * dl, tx_pos[2] - 2 * dl),
-    p2=(tx_pos[0] + bowtie_dims[0] + 2 * dl, tx_pos[1] + bowtie_dims[1] / 2 + 2 * dl, tx_pos[2] + 2 * dl),
+    p1=(
+        tx_pos[0] - bowtie_dims[0] - 2 * dl,
+        tx_pos[1] - bowtie_dims[1] / 2 - 2 * dl,
+        tx_pos[2] - 2 * dl,
+    ),
+    p2=(
+        tx_pos[0] + bowtie_dims[0] + 2 * dl,
+        tx_pos[1] + bowtie_dims[1] / 2 + 2 * dl,
+        tx_pos[2] + 2 * dl,
+    ),
    dl=(dl, dl, dl),
    filename="antenna_bowtie_fs_pcb",
    output_type="f",
--- a/testing/test_experimental.py
+++ b/testing/test_experimental.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -32,7 +32,8 @@ logger = logging.getLogger(__name__)

 # Parse command line arguments
 parser = argparse.ArgumentParser(
-    description="Plots a comparison of fields between " + "given simulation output and experimental data files.",
+    description="Plots a comparison of fields between "
+    + "given simulation output and experimental data files.",
    usage="cd gprMax; python -m testing.test_experimental modelfile realfile output",
 )
 parser.add_argument("modelfile", help="name of model output file including path")
--- a/testing/test_models.py
+++ b/testing/test_models.py
@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2024: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2025: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
@@ -113,7 +113,11 @@ for i, model in enumerate(testmodels):
        # Tx/Rx position to feed to analytical solution
        rxpos = filetest[path].attrs["Position"]
        txpos = filetest["/srcs/src1/"].attrs["Position"]
-        rxposrelative = ((rxpos[0] - txpos[0]), (rxpos[1] - txpos[1]), (rxpos[2] - txpos[2]))
+        rxposrelative = (
+            (rxpos[0] - txpos[0]),
+            (rxpos[1] - txpos[1]),
+            (rxpos[2] - txpos[2]),
+        )

        # Analytical solution of a dipole in free space
        dataref = hertzian_dipole_fs(