Debugging movies

.github/workflows/automatic-release-ubuntu-gnu.yml

@@ -3,8 +3,7 @@ name: automatic-release-ubuntu-gnu
 on:
   push:
     branches:
-      - main
-
+      - main 
 
 jobs:
 

.github/workflows/windows-intelLLVM.yml → .github/workflows/windows.yml

@@ -1,4 +1,4 @@
-name: windows-intelLLVM
+name: windows
 
 on:
 
@@ -32,7 +32,7 @@ jobs:
 
       fail-fast: false
 
-    name: ${{matrix.build-type}}-mpi(${{matrix.mpi}})-mtln(${{matrix.mtln}})-hdf(${{matrix.hdf}})
+    name: ${{matrix.compiler.name}}-${{matrix.build-type}}-mpi(${{matrix.mpi}})-mtln(${{matrix.mtln}})-hdf(${{matrix.hdf}})
 
     steps:
 

.gitignore

@@ -61,3 +61,4 @@ src_pyWrapper/__pycache__/*
 tmp/
 tmp_cases/
 testData/outputs/paul/paul_8.6_square.txt
+testing_hdf5_writing_and_reading.h5

doc/development.md

@@ -29,9 +29,9 @@ You can compile HDF5 for your specific platform downloading the latest sources f
 Extract to a folder and build and install with the following commands
 
 ```shell
-  cmake -S . -B build-ifx --fresh -DHDF5_BUILD_FORTRAN=YES
-  cmake --build build-ifx -j 
-  cmake --install build-ifx --prefix ~/hdf5-installed 
+  cmake -S . -B build -DHDF5_BUILD_FORTRAN=YES -DHDF5_ENABLE_Z_LIB_SUPPORT=NO --fresh
+  cmake --build build -j 
+  cmake --install build --prefix ~/hdf5-installed 
 ```
 
 A specific HDF5 library can be set with the option `-DHDF5_ROOT=<path-to-library>`, e.g.
@@ -143,6 +143,7 @@ Once the environment is loaded, follow the steps in the next section.
 
 2. **Generate the Project with CMake GUI**:
    - In **CMake GUI**, select the option to create a project for **Visual Studio 2019** from the CMake files.
+   - Set `-T fortran=ifx` to use intelLLVM compiler.
    - Specify the output folder where the `.sln` file for the project will be generated.
 
 3. **Open the Project in Visual Studio**:

doc/smbjson.md

@@ -629,6 +629,7 @@ If not `magnitudeFile` is specified and only one `source` is defined, the `magni
 
 Probes of type `movie` record a vector field in a volume region indicated by `elementIds`. `[field]` can be `electric`, `magnetic`, or `currentDensity`; defaults to `electric`.
 `currentDensity` will store only the surface density currents on `pec` or lossy surfaces.
+For movies in time domain, the `initialTime`, `finalTime`, and `samplingPeriod` must be specified by the user; there is no default value.  
 The stored values can be selected using the `[component]` entry, which stores one of the following labels `x`, `y`, `z`, or `magnitude`; if no component is specified, defaults to `magnitude`.
 
 An example follows:

requirements.txt

@@ -2,4 +2,5 @@ pytest
 numpy
 matplotlib
 pandas
-pyvista
+pyvista
+h5py

set_precompiled_libraries.cmake

@@ -36,36 +36,6 @@ if (SEMBA_FDTD_ENABLE_MTLN)
 	MESSAGE(STATUS "Using lapack libraries at: " ${LAPACK_DIR})
 endif()
 
-# if (SEMBA_FDTD_ENABLE_MTLN)
-# 	if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
-# 		if (${CMAKE_Fortran_COMPILER_ID} STREQUAL "GNU")
-# 			set(NGSPICE_DIR "${PRECOMPILED_DIR}/linux-gcc/ngspice/")
-# 			set(NGSPICE_LIB ${NGSPICE_DIR}libngspice.a)
-# 		elseif (${CMAKE_Fortran_COMPILER_ID} STREQUAL "NVHPC")
-# 			set(NGSPICE_DIR "${PRECOMPILED_DIR}/linux-gcc/ngspice/")
-# 			set(NGSPICE_LIB ${NGSPICE_DIR}libngspice.a)
-# 		elseif (${CMAKE_Fortran_COMPILER_ID} STREQUAL "Intel")
-# 			set(NGSPICE_DIR "${PRECOMPILED_DIR}/linux-intel/ngspice/")
-# 			set(NGSPICE_LIB ${NGSPICE_DIR}libngspice.a)
-# 		elseif (${CMAKE_Fortran_COMPILER_ID} STREQUAL "IntelLLVM")
-# 			set(NGSPICE_DIR "${PRECOMPILED_DIR}/linux-intelLLVM/ngspice/")
-# 			set(NGSPICE_LIB ${NGSPICE_DIR}libngspice.a)
-# 		endif()
-# 	elseif(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-# 		set(NGSPICE_DIR "${PRECOMPILED_DIR}/windows-intel/ngspice/")
-# 		set(NGSPICE_LIB ${NGSPICE_DIR}ngspice.lib)
-# 		add_library(ngspice SHARED IMPORTED)
-# 		set_target_properties(ngspice PROPERTIES 
-# 			IMPORTED_LOCATION "${NGSPICE_DIR}ngspice.dll"
-# 			IMPORTED_IMPLIB "${NGSPICE_DIR}ngspice.lib"
-# 		)
-# 	endif()
-# 	if (NOT NGSPICE_DIR)
-# 		message(FATAL_ERROR "ngspice libraries for this platform and/or compiler have not been found.")
-# 	endif()
-# 	MESSAGE(STATUS "Using ngspice libraries at: " ${NGSPICE_DIR})
-# endif()
-
 if (SEMBA_FDTD_ENABLE_HDF AND NOT HDF5_FOUND)
 	if (NOT HDF5_ROOT)
 		if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")

src_json_parser/smbjson.F90

@@ -58,7 +58,6 @@ module smbjson
       procedure, private :: readThinSlots
       !
       !
-      !
       procedure, private :: getLogicalAt
       procedure, private :: getIntAt
       procedure, private :: getIntsAt

test/CMakeLists.txt

@@ -25,5 +25,6 @@ target_link_libraries(fdtd_tests
     ${MTLN_TESTS_LIBRARY}
     ${SMBJSON_TESTS_LIBRARY}
     ${SYSTEM_TESTS_LIBRARY}
+    ${HDF_TESTS_LIBRARY}
     GTest::gtest_main
 )

test/pyWrapper/test_full_system.py

@@ -129,7 +129,24 @@ def test_sphere(tmp_path):
     assert len(electric_field_movie_files) == 3
     p = Probe(electric_field_movie_files[0])
     assert p.type == 'movie'
+
+@no_hdf_skip
+@pytest.mark.hdf 
+def test_movie_in_planewave_in_box(tmp_path):    
+    fn = CASE_FOLDER + 'planewave/pw-in-box-with-movie.fdtd.json'
+    solver = FDTD(fn, path_to_exe=SEMBA_EXE, run_in_folder=tmp_path)
+    solver.run()
+    assert solver.hasFinishedSuccessfully()
 
+    h5file = solver.getSolvedProbeFilenames("electric_field_movie")[2]
+    with h5py.File(h5file, "r") as f:
+        time_key = list(f.keys())[0]
+        field_key = list(f.keys())[1]
+        time_ds = f[time_key][()] 
+        field_ds = f[field_key][()]
+
+    assert np.isclose(np.max(field_ds), 1.0, rtol=1e-2)
+    assert np.min(field_ds) == 0.0
 
 def test_planewave_in_box(tmp_path):    
     fn = CASE_FOLDER + 'planewave/pw-in-box.fdtd.json'

test/pyWrapper/utils.py

@@ -5,6 +5,7 @@
 import matplotlib.pyplot as plt
 import pyvista as pv
 import pytest
+import h5py
 from os import environ as env
 from sys import platform
 

test/smbjson/smbjson_tests.h

@@ -18,12 +18,13 @@ extern "C" int test_read_dielectricslab();
 extern "C" int test_read_thinslot();
 extern "C" int test_read_holland1981();
 extern "C" int test_read_towelhanger();
-extern "C" int test_read_connectedwires();
 extern "C" int test_read_currentinjection();
-extern "C" int test_read_shieldedpair();
-extern "C" int test_read_mtln();
 extern "C" int test_read_sphere();
 extern "C" int test_read_airplane();
+extern "C" int test_read_mtln();
+extern "C" int test_read_holland1981();
+extern "C" int test_read_connectedwires();
+extern "C" int test_read_shieldedpair();
 extern "C" int test_read_large_airplane_mtln();
 
 TEST(smbjson, idchildtable_fhash)     {EXPECT_EQ(0, test_idchildtable_fhash()); }

test/smbjson/test_read_holland1981.F90

@@ -123,8 +123,7 @@ function expectedProblemDescription() result (expected)
 
       expected%tWires%n_tw = 1
       expected%tWires%n_tw_max = 1
-
-      ! expected mtln bundles
+
       expected%mtln%time_step = 30e-12
       expected%mtln%number_of_steps = 1000
 

testData/cases/.gitignore

@@ -3,4 +3,7 @@
 *.txt
 *.vtk
 *.bin
-*.log
+*.log
+*.h5
+*.xdmf
+*.bin

testData/cases/planewave/pw-in-box-with-movie.fdtd.json

@@ -0,0 +1,56 @@
+{
+    "format": "FDTD Input file",
+    "__comments": "Planewave passing through an empty box.",
+
+    "general": {
+        "timeStep": 0.05e-9,
+        "numberOfSteps": 400
+    },
+
+    "boundary": {
+        "all": {"type": "mur"}
+    },
+
+    "mesh": {
+        "grid": {
+            "numberOfCells": [6, 6, 6],
+            "steps": { "x": [0.01], "y": [0.01], "z": [0.01] }
+        },
+        "elements": [
+            {"id": 1, "type": "cell", "name": "pw-box", "intervals": [ [ [2, 2, 2], [4, 4, 4] ] ]},
+            {"id": 2, "type": "cell", "name": "movie-box", "intervals": [ [ [0, 0, 0], [6, 6, 6] ] ]}
+        ]
+    },
+
+    "sources": [
+        {
+            "type": "planewave",
+            "magnitudeFile": "gauss_1GHz.exc",
+            "elementIds": [1],
+            "direction": {
+                "theta": 0.0,
+                "phi": 0.0
+            },
+            "polarization": {
+                "theta": 1.5708,
+                "phi": 0.0
+            }
+        }
+    ],
+
+    "probes": [
+        {
+            "name": "electric_field_movie",
+            "type": "movie",
+            "field": "electric",
+            "component": "magnitude",
+            "elementIds": [2],
+            "domain": {
+                "type": "time",
+                "initialTime": 0.0,
+                "finalTime": 5e-9,
+                "samplingPeriod": 1.5e-12
+            }
+        }
+    ]
+}

testData/cases/planewave/pw_prepost.py

@@ -12,11 +12,8 @@
 
 
 # %% Prepare solver
-# solver = FDTD(input_filename = 'pw-in-box.fdtd.json', path_to_exe=SEMBA_EXE)
-solver = FDTD(input_filename = 'pw-with-periodic.fdtd.json', path_to_exe=SEMBA_EXE)
+solver = FDTD(input_filename = 'pw-in-box.fdtd.json', path_to_exe=SEMBA_EXE)
 solver.cleanUp()
-
-# %% Run solver
 solver.run()
 assert solver.hasFinishedSuccessfully()
 
@@ -33,4 +30,20 @@
 plt.xlim(0,4e-9)
 
 
+
+# %%
+# %% Prepare solver
+solver = FDTD(input_filename = 'pw-in-box-with-movie.fdtd.json', path_to_exe=SEMBA_EXE)
+solver.cleanUp()
+solver.run()
+assert solver.hasFinishedSuccessfully()
+
+# %% Postprocess
+import h5py
+fn = solver.getSolvedProbeFilenames("electric_field_movie")[2]
+with h5py.File(fn, "r") as f:
+    time_key = list(f.keys())[0]
+    field_key = list(f.keys())[1]
+    time_ds = f[time_key][()] 
+    field_ds = f[field_key][()]
 # %%