Merge pull request #197 from OpenSEMBA/dev

Dev

Author: lmdiazangulo

.gitignore

@@ -65,3 +65,4 @@ tmp/
 tmp_cases/
 testData/outputs/paul/paul_8.6_square.txt
 testing_hdf5_writing_and_reading.h5
+build

CMakeLists.txt

@@ -56,7 +56,6 @@ if (CMAKE_SYSTEM_NAME MATCHES "Linux")
 	if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
 		message(STATUS "Using GNU flags")
 
-		add_definitions(-DCompileWithIncludeMpifh)
 		set(CMAKE_CXX_FLAGS "-fopenmp")
 		set(CMAKE_Fortran_FLAGS "-fopenmp -ffree-form -ffree-line-length-none -fdec -fallow-argument-mismatch")
 
@@ -173,6 +172,13 @@ add_library(semba-types
 	"src_wires_pub/wires_types.F90"
 	"src_main_pub/lumped_types.F90"
 )
+target_link_libraries(semba-types ${MPI_Fortran_LIBRARIES})
+
+add_library(semba-reports
+	"src_main_pub/errorreport.F90"
+	"src_main_pub/snapxdmf.F90"
+)
+target_link_libraries(semba-reports semba-types ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES})
 
 if(SEMBA_FDTD_ENABLE_SMBJSON)
 	add_subdirectory(src_json_parser)
@@ -200,7 +206,6 @@ endif()
 
 if(SEMBA_FDTD_COMPONENTS_LIB)
 	add_library(semba-components
-		"src_main_pub/errorreport.F90"
 		"src_main_pub/anisotropic.F90"
 		"src_main_pub/borderscpml.F90"
 		"src_main_pub/bordersmur.F90"
@@ -217,19 +222,21 @@ if(SEMBA_FDTD_COMPONENTS_LIB)
 		"src_wires_pub/wires.F90"
 		"src_wires_pub/wires_mtln.F90"
 	)
-	target_link_libraries(semba-components semba-types ${MTLN_LIBRARIES})
+	target_link_libraries(semba-components semba-types semba-reports ${MTLN_LIBRARIES})
 endif()
 
 if(SEMBA_FDTD_OUTPUTS_LIB)
 	add_library(semba-outputs
 		"src_main_pub/mpicomm.F90"
 		"src_main_pub/observation.F90"
 		"src_main_pub/vtk.F90"
-		"src_main_pub/snapxdmf.F90"
 		"src_main_pub/xdmf.F90"
 		"src_main_pub/xdmf_h5.F90"
 	)
-	target_link_libraries(semba-outputs semba-components ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES})
+	target_link_libraries(semba-outputs 
+		semba-components 
+		${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} 
+		${MPI_Fortran_LIBRARIES})
 endif()
 
 if(SEMBA_FDTD_MAIN_LIB)
@@ -247,14 +254,17 @@ if(SEMBA_FDTD_MAIN_LIB)
 		"src_main_pub/resuming.F90"	
 		"src_main_pub/timestepping.F90"
 	)
-	target_link_libraries(semba-main semba-outputs ${SMBJSON_LIBRARIES} ${MTLN_LIBRARIES})
+	target_link_libraries(semba-main
+		semba-outputs 
+		${SMBJSON_LIBRARIES} 
+		${MTLN_LIBRARIES})
 endif()
 
 if (SEMBA_FDTD_EXECUTABLE)
 	add_executable(semba-fdtd 
 		"src_main_pub/semba_fdtd.F90"
 	)
-	target_link_libraries(semba-fdtd semba-main)
+	target_link_libraries(semba-fdtd semba-main semba-reports)
 	target_link_libraries(semba-fdtd ${MPI_Fortran_LIBRARIES})
 endif()
 

README.md

@@ -39,6 +39,8 @@ In a nutshell, semba-fdtd capabilities are
 
 Compilation and debugging instructions can be found [here](doc/development.md).
 
+A short tutorial on usage can be found [here](doc/tutorials/veritasium/veritasium.md).
+
 The main binary is `semba-fdtd` which uses [the SMBJSON format](doc/smbjson.md) as input files.
 It can be run with
 
@@ -48,6 +50,7 @@ It can be run with
 
 Tests must be run from the root folder. `python` wrapper test assumes that `semba-fdtd` has been compiled successfully and is located in folder `build/bin/`. For intel compilation it also assumes that the intel runtime libraries are accessible.
 
+
 # License
 
 This code is licensed under the terms of the [MIT License](LICENSE). All rights reserved by the University of Granada (Spain)

doc/smbjson.md

@@ -453,7 +453,17 @@ Each entry in `terminations` is specified by a `type`
 
 + `short` if the wire is short-circuited with another wire or with any surface which might be present.
 + `open` if the wire does not end in an ohmic contact with any other structure.
-+ Different configurations of passive circuit elements R, L, and C can be defined with `series` (for RLC series circuits), `LCpRs` (LC parallel in series with a resistance) and `RLsCp` (for series RL in parallel with C). The are defined as follows:
++ Different configurations of passive circuit elements R, L, and C can be defined:
+  + `series` (for RLC series circuits), 
+  + `parallel` (for RLC parallel circuits), 
+  + `RsLCp` (LC parallel in series with R), 
+  + `RLsCp` (RL series in parallel with C), 
+  + `LsRCp` (RC parallel in series with L), 
+  + `CsLRp` (LR parallel in parallel with C),
+  + `RCsLp` (RC series in parallel with L), and 
+  + `LCsRp` (LC series in parallel with R). 
+
+The values are defined defined as follows:
   + `[resistance]` which defaults to `0.0`,
   + `[inductance]` which defaults to `0.0`,
   + `[capacitance]` which defaults to `1e22`.
@@ -597,7 +607,9 @@ Records a vector field a single position referenced by `elementIds` which must c
 
 Records a scalar field at a single position referenced by `elementIds`. `elementIds` must contain a single `id` referencing an element of type `node`. Additionally, this `node` must point to a `coordinateId` belonging to at least one `polyline`. 
 If the node's `coordinateId` is shared by more than one `polyline` a probe will be defined for each one of them
-The `[field]` can be `voltage` or `current`. Defaults to `current`. When `current` is selected, the orientation of the `polyline` on which the probe is located indicates the direction of the current. Voltages are well defined at polyline points. However, currents are defined over segments so:
+The `[field]` can be `voltage`, `current` or `charge`  (defaults to `current`). Voltage probes are properly defined only when used placed on `shieldedMultiwires`. The voltage on a conductor will be referred to the shield surrounding that conductor. In an unshielded wire, there is not a well defined reference, and thus the probe is not reliable. Charge probes are implemented only for wires not treated with the MTL module.
+
+When `current` is selected, the orientation of the `polyline` on which the probe is located indicates the direction of the current. Voltages are well defined at polyline points. However, currents are defined over segments so:
 
 - If the point is in the interior of the wire, the output will be an average on the currents of the segments which are contiguous to it.
 - If the point is at one wire end, the current will be the output of the last segment.
@@ -657,6 +669,19 @@ On the other hand, the coordinate **parallel** to the current also experiences a
 
 Again, with the current flowing in the direction of the red line, the blue line represents a cross-sectional view of the plane where the `bulkCurrent` is defined, while the green line shows the actual location used for current evaluation by the method.
 
+#### `line`
+
+A `line` probe computes the electric field line integral along a given `polyline`. At low frequencies, this quantity can be equivalent to a DC voltage difference between the extremes of the line. At higher frequencies, "voltage" is no longer a proper name. The integral is performed along a geometric line, hence the `polyline` does not have to be associated with any material. `[field]` defaults to `electric`, the only field supported at this point. The probe is only valid in the time domain.
+
+```json
+    {
+        "name" : "vprobe",
+        "type" : "line",
+        "elementIds" : [4],
+        "field" : "electric"
+    }
+```
+
 #### `farField`
 
 Probes of type `farField` perform a near to far field transformation of the electric and magnetic vector fields and are typically located in the scattered field region which is defined by a total/scatterd field excitation, e.g. [a planewave](#planewave). 
@@ -771,8 +796,7 @@ This object represents a time-varying vector field applied along an oriented lin
     "type": "nodalSource", 
     "magnitudeFile": "gauss.exc", 
     "elementIds": [1],
-    "hardness": "soft",
-    "field": "electric"
+    "hardness": "soft"
 }
 ```
 

doc/tutorials/veritasium/circuit_layout.png

@@ -0,0 +1,104 @@
+import json
+import numpy as np
+import matplotlib.pyplot as plt
+from pathlib import Path
+
+def validate_json_structure(json_data):
+    """Validate the basic structure of the FDTD JSON file"""
+    required_sections = ['format', 'general', 'boundary', 'materials', 
+                        'mesh', 'probes', 'sources', 'materialAssociations']
+    
+    for section in required_sections:
+        if section not in json_data:
+            print(f"Error: Missing required section '{section}'")
+            return False
+    return True
+
+def validate_parameters(json_data):
+    """Validate specific parameters in the simulation"""
+    # Check time step and number of steps
+    time_step = json_data['general']['timeStep']
+    num_steps = json_data['general']['numberOfSteps']
+    total_time = time_step * num_steps
+    
+    # Calculate expected propagation delay
+    wire_length = 30  # meters (from mesh configuration)
+    speed_of_light = 3e8  # m/s
+    expected_delay = wire_length / speed_of_light
+    
+    print(f"\nSimulation Parameters:")
+    print(f"Time step: {time_step:.2e} s")
+    print(f"Number of steps: {num_steps}")
+    print(f"Total simulation time: {total_time:.2e} s")
+    print(f"Expected propagation delay: {expected_delay:.2e} s")
+    
+    if total_time < expected_delay:
+        print(f"Warning: Total simulation time ({total_time:.2e} s) is less than expected propagation delay ({expected_delay:.2e} s)")
+        return False
+    return True
+
+def visualize_circuit(json_data):
+    """Create a simple visualization of the circuit layout"""
+    # Extract coordinates
+    coords = json_data['mesh']['coordinates']
+    elements = json_data['mesh']['elements']
+    
+    # Create figure
+    plt.figure(figsize=(12, 4))
+    
+    # Plot wires
+    for element in elements:
+        if element['type'] == 'polyline':
+            coord_ids = element['coordinateIds']
+            x = [coords[coord_ids[0]-1]['relativePosition'][0], 
+                 coords[coord_ids[1]-1]['relativePosition'][0]]
+            z = [coords[coord_ids[0]-1]['relativePosition'][2], 
+                 coords[coord_ids[1]-1]['relativePosition'][2]]
+            plt.plot(z, x, 'b-', linewidth=2)
+    
+    # Plot nodes
+    for element in elements:
+        if element['type'] == 'node':
+            coord_id = element['coordinateIds'][0]
+            pos = coords[coord_id-1]['relativePosition']
+            plt.plot(pos[2], pos[0], 'ro', markersize=10)
+    
+    plt.title('Circuit Layout')
+    plt.xlabel('Z position (cells)')
+    plt.ylabel('X position (cells)')
+    plt.grid(True)
+    plt.savefig('circuit_layout.png')
+    plt.close()
+
+def main():
+    # Load JSON file
+    json_path = Path(__file__).parent / 'closedCircuit.fdtd.json'
+    try:
+        with open(json_path, 'r') as f:
+            json_data = json.load(f)
+    except Exception as e:
+        print(f"Error loading JSON file: {e}")
+        return
+    
+    print("Validating FDTD simulation file...")
+    
+    # Validate structure
+    if not validate_json_structure(json_data):
+        print("JSON structure validation failed!")
+        return
+    
+    # Validate parameters
+    if not validate_parameters(json_data):
+        print("Parameter validation failed!")
+        return
+    
+    # Create visualization
+    print("\nCreating circuit visualization...")
+    visualize_circuit(json_data)
+    print("Circuit layout saved as 'circuit_layout.png'")
+    
+    print("\nValidation complete! The simulation file appears to be correctly configured.")
+    print("You can now run the FDTD simulation.")
+
+if __name__ == "__main__":
+    main() 

doc/tutorials/veritasium/circuit_layout_test.py

@@ -0,0 +1,123 @@
+{
+    "format": "FDTD Input file",
+    "__comments": "Veritasium's circuit demonstration - The Big Misconception About Electricity",
+    
+    "general": {
+        "timeStep": 2.0e-9,
+        "numberOfSteps": 100
+    },
+      
+    "boundary": {
+        "all": {
+            "type": "pml",
+            "layers": 10,
+            "order": 2.0,
+            "reflection": 0.001
+        }
+    },
+
+    "mesh": {
+        "grid": {
+            "numberOfCells": [210, 300, 200],
+            "steps": {"x": [0.1], "y": [0.1], "z": [0.1]}
+        },
+
+        "coordinates": [
+            {"id": 1, "relativePosition": [100, 149, 100]},
+            {"id": 2, "relativePosition": [100, 100, 100]},
+            {"id": 3, "relativePosition": [110, 100, 100]},
+            {"id": 4, "relativePosition": [110, 150, 100]},
+            {"id": 5, "relativePosition": [110, 200, 100]},
+            {"id": 6, "relativePosition": [100, 200, 100]},
+            {"id": 7, "relativePosition": [100, 151, 100]}
+        ],
+        
+        "elements": [
+            {"id": 1, "type": "polyline", "coordinateIds": [1, 2, 3, 4, 5, 6, 7]},
+            {"id": 2, "type": "node", "coordinateIds": [4]},
+            {"id": 3, "type": "cell", "name": "cube", "intervals": [ [ [99, 149, 99], [101, 151, 101] ] ]},
+            {"id": 4, "type": "cell", "name": "wire-plane", "intervals": [ [ [105, 99, 99], [105, 101, 101] ] ]},
+            {"id": 5, "type": "cell", "name": "source-plane", "intervals": [ [ [109, 150, 99], [111, 150, 101] ] ]},
+            {"id": 6, "type": "cell", "name": "cube-plane", "intervals": [ [ [98, 150, 98], [102, 150, 102] ] ]},
+            {"id": 7, "type": "cell", "name": "movie-domain", "intervals": [ [ [80, 80, 80], [130, 220, 120] ] ]}
+        ]
+    },
+
+    "materials": [
+        {
+            "id": 1,
+            "name": "wire_material",
+            "type": "wire",
+            "radius": 0.0001,
+            "resistancePerMeter": 22.9e-3
+        },
+        {
+            "id": 2,
+            "name": "resistance_material",
+            "type": "terminal",
+            "terminations": [
+                {"type": "series", "resistance": 50.0}
+            ]
+        },
+        {
+            "id": 3,
+            "name": "cube_material",
+            "type": "pec"
+        }
+    ],
+
+    "materialAssociations": [
+        {
+            "name": "wire_association",
+            "elementIds": [1],
+            "materialId": 1,
+            "initialTerminalId": 2,
+            "endTerminalId": 2
+        },
+        {
+            "name": "cube_association",
+            "elementIds": [3],
+            "materialId": 3
+        }
+    ],
+
+    "sources": [
+        {
+            "name": "source_generator",
+            "type": "generator",
+            "magnitudeFile": "step.exc",
+            "elementIds": [2],
+            "field": "voltage"
+        }
+    ],
+
+    "probes": [
+        {
+            "name": "wire_current",
+            "type": "bulkCurrent",
+            "elementIds": [4]
+        },
+        {
+            "name": "source_current",
+            "type": "bulkCurrent",
+            "elementIds": [5]
+        },
+        {
+            "name": "cube_current",
+            "type": "bulkCurrent",
+            "elementIds": [6]
+        },
+        {
+            "name": "movie_electric",
+            "type": "movie",
+            "field": "electric",
+            "component": "magnitude",
+            "elementIds": [7],
+            "domain": {
+                "initialTime": 0.0, 
+                "finalTime": 2e-7, 
+                "samplingPeriod": 1.5e-10
+            }
+        }
+    ]
+}