Merge pull request #115 from OpenSEMBA/dev

Updates dev with tagnumber changes in main

Author: Alberto-o

.devcontainer/Dockerfile

@@ -0,0 +1 @@
+FROM intel/oneapi-hpckit

.devcontainer/devcontainer.json

@@ -0,0 +1,46 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "OpenSEMBA dev. framework",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+	"features": {
+		"ghcr.io/msclock/features/vcpkg:2": {},
+		"ghcr.io/devcontainers/features/python:1": {}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postStartCommand": "git config --global --add safe.directory ${containerWorkspaceFolder}",
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"codespaces": {
+		  "repositories": {
+			"lmdiazangulo/json-fortran": { "permissions": "read-all" },
+			"opensemba/fhash": { "permissions": "read-all" },
+			"reference-lapack/lapack": { "permissions": "read-all" },
+			"opensemba/ngtest": {"permissions": "read-all" },
+			"google/googletest": { "permissions": "read-all" }
+		  }
+		},
+		"vscode": {
+			"extensions": [
+				"ms-toolsai.jupyter",
+				"fortran-lang.linter-gfortran",
+				"ms-vscode.cmake-tools",
+				"ms-python.autopep8",
+				"matepek.vscode-catch2-test-adapter"
+			]
+		}
+	  }
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.devcontainer/notes.md

@@ -0,0 +1,12 @@
+
+```
+git submodule init
+git submodule --recursive
+```
+
+Install python packages
+```
+python3 -m venv ~/py_envs
+source ~/py_envs/bin/activate
+python3 -m pip install -r requirements.txt
+```

.github/workflows/windows.yml

@@ -14,25 +14,20 @@ concurrency:
 jobs:
 
   builds-and-tests:
-    runs-on: windows-latest
+    
     strategy:
       matrix:
+        os: [windows-latest]
         compiler: [ {name: 'intel', version: '2024.0'} ]
         build-type: ["Debug", "Release"]
         mpi: ["No"]
         mtln: ["Yes"]
         hdf: ["Yes"]
 
-        include:
-          - compiler: {name: 'intel', version: '2024.0'}
-            build-type: "Release"
-            mpi: "No"
-            mtln: "No"
-            hdf: "Yes"
-
       fail-fast: false
+    runs-on: ${{matrix.os}}
 
-    name: ${{matrix.compiler.name}} / ${{matrix.build-type}}-mpi(${{matrix.mpi}})-mtln(${{matrix.mtln}})-hdf(${{matrix.hdf}})
+    name: ${{matrix.os}} / ${{matrix.compiler.name}} / ${{matrix.build-type}}-mpi(${{matrix.mpi}})-mtln(${{matrix.mtln}})-hdf(${{matrix.hdf}})
 
     steps:
 

.gitmodules

@@ -1,23 +1,23 @@
 [submodule "external/json-fortran"]
 	path = external/json-fortran
-	url = git@github.com:lmdiazangulo/json-fortran.git
+	url = https://github.com/lmdiazangulo/json-fortran.git
 	ignore = dirty
 
 [submodule "external/fhash"]
 	path = external/fhash
-	url = git@github.com:opensemba/fhash.git
+	url = https://github.com/OpenSEMBA/fhash.git
 	ignore = dirty
 
 [submodule "external/lapack"]
 	path = external/lapack
-	url = git@github.com:Reference-LAPACK/lapack.git
+	url = https://github.com/Reference-LAPACK/lapack.git
 	ignore = dirty
 
 [submodule "external/ngspice"]
 	path = external/ngspice
-	url = git@github.com:opensemba/ngspice
+	url = https://github.com/OpenSEMBA/ngspice.git
 	ignore = dirty
 
 [submodule "external/googletest"]
 	path = external/googletest
-	url = git@github.com:google/googletest.git
+	url = https://github.com/google/googletest.git

src_main_pub/observation.F90

@@ -1746,7 +1746,7 @@ subroutine launch_simulation(sgg,sggMtag,tag_numbers, sggMiNo,sggMiEx,sggMiEy,sg
          !Update observation matrices !MUST GO AFTER THE MPI EXCHANGING INFO, SINCE Bloque CURRENTS NEED UPDATED INFO
          IF (Thereare%Observation) then
             !se le pasan los incrementos autenticos (bug que podia aparecer en NF2FF y Bloque currents 17/10/12)
-            call UpdateObservation(sgg,sggMiEx,sggMiEy,sggMiEz,sggMiHx,sggMiHy,sggMiHz,sggMtag, n,ini_save, Ex, Ey, Ez, Hx, Hy, Hz, dxe, dye, dze, dxh, dyh, dzh,wiresflavor,SINPML_FULLSIZE,wirecrank, &
+            call UpdateObservation(sgg,sggMiEx,sggMiEy,sggMiEz,sggMiHx,sggMiHy,sggMiHz,sggMtag,tag_numbers, n,ini_save, Ex, Ey, Ez, Hx, Hy, Hz, dxe, dye, dze, dxh, dyh, dzh,wiresflavor,SINPML_FULLSIZE,wirecrank, &
                                    Exvac, Eyvac, Ezvac, Hxvac, Hyvac, Hzvac,Excor, Eycor, Ezcor, Hxcor, Hycor, Hzcor,planewavecorr,noconformalmapvtk,b)
 
             if (n>=ini_save+BuffObse)  then

src_main_pub/timestepping.F90

@@ -38,34 +38,34 @@ def __init__(self, probe_filename):
 
         tag = self._getTagFromFilename(self.filename)
         if tag not in Probe.MOVIE_TAGS:
-            self.df = pd.read_csv(self.filename, sep='\\s+')
+            self.data = pd.read_csv(self.filename, sep='\\s+')
 
         position_str = self._getPositionStrFromFilename(self.filename)
         if tag in Probe.CURRENT_PROBE_TAGS:
             self.type = 'wire'
             self.cell = self._positionStrToCell(position_str)
             self.segment = int(position_str.split('_s')[1])
             if self.domainType == 'time':
-                self.df = self.df.rename(columns={
+                self.data = self.data.rename(columns={
                     't': 'time',
-                    self.df.columns[1]: 'current'
+                    self.data.columns[1]: 'current'
                 })
             elif self.domainType == 'frequency':
-                self.df = self.df.rename(columns={
-                    self.df.columns[0]: 'frequency',
-                    self.df.columns[1]: 'magnitude',
-                    self.df.columns[2]: 'phase'
+                self.data = self.data.rename(columns={
+                    self.data.columns[0]: 'frequency',
+                    self.data.columns[1]: 'magnitude',
+                    self.data.columns[2]: 'phase'
                 })
         elif tag in Probe.POINT_PROBE_TAGS:
             self.type = 'point'
             self.cell = self._positionStrToCell(position_str)
             self.field = tag[1]
             self.direction = tag[2]
             if self.domainType == 'time':
-                self.df = self.df.rename(columns={
+                self.data = self.data.rename(columns={
                     't': 'time',
-                    self.df.columns[1]: 'field',
-                    self.df.columns[2]: 'incident'
+                    self.data.columns[1]: 'field',
+                    self.data.columns[2]: 'incident'
                 })
         elif tag in Probe.FAR_FIELD_TAG:
             self.type = 'farField'
@@ -81,11 +81,10 @@ def __init__(self, probe_filename):
             self.type = 'mtln'
             self.cell = self._positionStrToCell(position_str)
         else:
-            raise ValueError(
-                "Unable to determine probe name or type for a probe with name:" + basename)
+            raise ValueError("Unable to determine probe type")
 
     def __getitem__(self, key):
-        return self.df[key]
+        return self.data[key]
 
     @staticmethod
     def _getCaseNameFromFilename(fn):
@@ -224,7 +223,9 @@ def run(self):
         case_name = self.getCaseName() + ".json"
         self.output = subprocess.run(
             [self.path_to_exe, "-i", case_name]+self.flags)
+        
         self._hasRun = True
+        assert self.hasFinishedSuccessfully()
 
     def hasFinishedSuccessfully(self):
         if self._hasRun and (self.output.returncode == 0):

src_pyWrapper/pyWrapper.py

@@ -11,7 +11,6 @@ def test_shieldedPair(tmp_path):
                   flags=['-mtlnwires'],
                   run_in_folder=tmp_path)
     solver.run()
-    assert solver.hasFinishedSuccessfully() == True
 
     probe_files = ['shieldedPair.fdtd_wire_start_bundle_line_0_V_75_74_74.dat',
                    'shieldedPair.fdtd_wire_start_bundle_line_0_I_75_74_74.dat',
@@ -26,11 +25,11 @@ def test_shieldedPair(tmp_path):
 
     for i in [2, 3]:
         p_solved = Probe(probe_files[i])
-        assert np.allclose(p_expected[i].df.to_numpy()[:, 0:3], p_solved.df.to_numpy()[
+        assert np.allclose(p_expected[i].data.to_numpy()[:, 0:3], p_solved.data.to_numpy()[
                            :, 0:3], rtol=5e-2, atol=0.2)
     for i in [0, 1, 4, 5]:
         p_solved = Probe(probe_files[i])
-        assert np.allclose(p_expected[i].df.to_numpy()[:, 0:4], p_solved.df.to_numpy()[
+        assert np.allclose(p_expected[i].data.to_numpy()[:, 0:4], p_solved.data.to_numpy()[
                            :, 0:4], rtol=5e-2, atol=0.2)
 
 
@@ -45,7 +44,6 @@ def test_coated_antenna(tmp_path):
         flags=['-mtlnwires'],
         run_in_folder=tmp_path)
     solver.run()
-    assert solver.hasFinishedSuccessfully() == True
 
     probe_current = solver.getSolvedProbeFilenames("mid_point_Wz")[0]
     probe_files = [probe_current]
@@ -55,16 +53,16 @@ def test_coated_antenna(tmp_path):
 
     p_solved = Probe(probe_files[0])
     assert np.allclose(
-        p_expected.df.to_numpy()[:, 0],
-        p_solved.df.to_numpy()[:, 0],
+        p_expected.data.to_numpy()[:, 0],
+        p_solved.data.to_numpy()[:, 0],
         rtol=0.0, atol=10e-8)
     assert np.allclose(
-        p_expected.df.to_numpy()[:, 1],
-        p_solved.df.to_numpy()[:, 1],
+        p_expected.data.to_numpy()[:, 1],
+        p_solved.data.to_numpy()[:, 1],
         rtol=0.0, atol=10e-8)
     assert np.allclose(
-        p_expected.df.to_numpy()[:, 2],
-        p_solved.df.to_numpy()[:, 2],
+        p_expected.data.to_numpy()[:, 2],
+        p_solved.data.to_numpy()[:, 2],
         rtol=0.0, atol=10e-6)
 
 
@@ -75,7 +73,6 @@ def test_holland(tmp_path):
                   run_in_folder=tmp_path)
 
     solver.run()
-    assert solver.hasFinishedSuccessfully() == True
 
     probe_current = solver.getSolvedProbeFilenames("mid_point_Wz")[0]
     probe_files = [probe_current]
@@ -85,8 +82,8 @@ def test_holland(tmp_path):
 
     p_solved = Probe(probe_files[0])
     assert np.allclose(
-        p_expected.df.to_numpy()[:, 0:3], 
-        p_solved.df.to_numpy()[:, 0:3], 
+        p_expected.data.to_numpy()[:, 0:3], 
+        p_solved.data.to_numpy()[:, 0:3], 
         rtol=1e-5, atol=1e-6)
 
 
@@ -98,7 +95,6 @@ def test_holland_mtln(tmp_path):
                   flags=['-mtlnwires'], run_in_folder=tmp_path)
 
     solver.run()
-    assert solver.hasFinishedSuccessfully() == True
 
     probe_current = solver.getSolvedProbeFilenames("mid_point_Wz")[0]
     probe_files = [probe_current]
@@ -108,8 +104,8 @@ def test_holland_mtln(tmp_path):
 
     p_solved = Probe(probe_files[0])
     assert np.allclose(
-        p_expected.df.to_numpy()[:, 0:3], 
-        p_solved.df.to_numpy()[:, 0:3], 
+        p_expected.data.to_numpy()[:, 0:3], 
+        p_solved.data.to_numpy()[:, 0:3], 
         rtol=1e-5, atol=1e-6)
 
 
@@ -118,7 +114,6 @@ def test_towelHanger(tmp_path):
     solver = FDTD(input_filename=fn, path_to_exe=SEMBA_EXE,
                   run_in_folder=tmp_path)
     solver.run()
-    assert solver.hasFinishedSuccessfully() == True
 
     probe_files = [solver.getSolvedProbeFilenames("wire_start")[0],
                    solver.getSolvedProbeFilenames("wire_mid")[0],
@@ -131,7 +126,7 @@ def test_towelHanger(tmp_path):
 
     for i in range(3):
         p_solved = Probe(probe_files[i])
-        assert np.allclose(p_expected[i].df.to_numpy()[:, 0:3], p_solved.df.to_numpy()[
+        assert np.allclose(p_expected[i].data.to_numpy()[:, 0:3], p_solved.data.to_numpy()[
                            :, 0:3], rtol=5e-2, atol=5e-2)
 
 
@@ -146,18 +141,15 @@ def test_sphere(tmp_path):
     solver['probes'][0]['domain']['finalFrequency'] = 1e9
 
     solver.run()
-    assert solver.hasFinishedSuccessfully()
 
     # semba-fdtd seems to always use the name Far for "far field" probes.
     far_field_probe_files = solver.getSolvedProbeFilenames("Far")
-    assert solver.hasFinishedSuccessfully() == True
     assert len(far_field_probe_files) == 1
     p = Probe(far_field_probe_files[0])
     assert p.type == 'farField'
 
     electric_field_movie_files = solver.getSolvedProbeFilenames(
         "electric_field_movie")
-    assert solver.hasFinishedSuccessfully() == True
     assert len(electric_field_movie_files) == 3
     p = Probe(electric_field_movie_files[0])
     assert p.type == 'movie'
@@ -169,7 +161,6 @@ def test_movie_in_planewave_in_box(tmp_path):
     fn = CASES_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:
@@ -187,50 +178,47 @@ def test_planewave_in_box(tmp_path):
     solver = FDTD(fn, path_to_exe=SEMBA_EXE, run_in_folder=tmp_path)
 
     solver.run()
-    assert solver.hasFinishedSuccessfully()
 
     before = Probe(solver.getSolvedProbeFilenames("before")[0])
     inbox = Probe(solver.getSolvedProbeFilenames("inbox")[0])
     after = Probe(solver.getSolvedProbeFilenames("after")[0])
 
-    np.allclose(inbox.df['field'], inbox.df['incident'])
-    zeros = np.zeros_like(before.df['field'])
-    np.allclose(before.df['field'], zeros)
-    np.allclose(after.df['field'], zeros)
+    np.allclose(inbox.data['field'], inbox.data['incident'])
+    zeros = np.zeros_like(before.data['field'])
+    np.allclose(before.data['field'], zeros)
+    np.allclose(after.data['field'], zeros)
 
 
 def test_planewave_with_periodic_boundaries(tmp_path):
     fn = CASES_FOLDER + 'planewave/pw-with-periodic.fdtd.json'
     solver = FDTD(fn, path_to_exe=SEMBA_EXE, run_in_folder=tmp_path)
 
     solver.run()
-    assert solver.hasFinishedSuccessfully()
-
+    
     before = Probe(solver.getSolvedProbeFilenames("before")[0])
     inbox = Probe(solver.getSolvedProbeFilenames("inbox")[0])
     after = Probe(solver.getSolvedProbeFilenames("after")[0])
 
-    np.allclose(inbox.df['field'], inbox.df['incident'])
-    zeros = np.zeros_like(before.df['field'])
-    np.allclose(before.df['field'], zeros)
-    np.allclose(after.df['field'], zeros)
+    np.allclose(inbox.data['field'], inbox.data['incident'])
+    zeros = np.zeros_like(before.data['field'])
+    np.allclose(before.data['field'], zeros)
+    np.allclose(after.data['field'], zeros)
 
 
 def test_sgbc_shielding_effectiveness(tmp_path):
     fn = CASES_FOLDER + 'sgbcShieldingEffectiveness/shieldingEffectiveness.fdtd.json'
     solver = FDTD(fn, path_to_exe=SEMBA_EXE, run_in_folder=tmp_path)
 
     solver.run()
-    assert solver.hasFinishedSuccessfully()
 
     # FDTD results
     back = Probe(solver.getSolvedProbeFilenames("back")[0])
 
-    t = back.df['time']
+    t = back.data['time']
     dt = t[1] - t[0]
     fq = fftfreq(len(t))/dt
-    INC = fft(back.df['incident'])
-    BACK = fft(back.df['field'])
+    INC = fft(back.data['incident'])
+    BACK = fft(back.data['field'])
     S21 = BACK/INC
 
     fmin = 8e6