Merge pull request #84 from OpenSEMBA/feature/smbjson

Adding dielectrics and thin gaps

.github/workflows/run_tests_windows.bat

@@ -19,5 +19,4 @@ IF "%VS_VER%"=="2017_build_tools" (
 for /f "tokens=* usebackq" %%f in (`dir /b "C:\Program Files (x86)\Intel\oneAPI\compiler\" ^| findstr /V latest ^| sort`) do @set "LATEST_VERSION=%%f"
 @call "C:\Program Files (x86)\Intel\oneAPI\compiler\%LATEST_VERSION%\env\vars.bat"
 
-build\bin\fdtd_tests.exe
 python -m pytest test

.github/workflows/windows-intelLLVM.yml

@@ -46,8 +46,13 @@ jobs:
       run: |
         python -m pip install -r requirements.txt
 
-    - name: Run all tests 
+    - name: Run unit tests 
       shell: bash
-      timeout-minutes: 120
+      timeout-minutes: 10
+      run: build/bin/fdtd_tests.exe
+
+    - name: Run system tests 
+      shell: bash
+      timeout-minutes: 30
       run: |
         .github/workflows/run_tests_windows.bat

doc/smbjson.md

@@ -51,7 +51,7 @@ The following entries are shared by several FDTD-JSON objects and have a common
 
 + `type` followed by a string, indicates the type of JSON object that. Some examples of types are `planewave` for `sources` objects, and `polyline` for `elements`.
 + `id` is a unique integer identifier for objects that belong to a list and which can be referenced by other objects. For instance, an element in the `elements` list must contain a `id` which can be referenced by a source in `sources` through its list of `elementIds`.
-+ `[name]` is an optional entry which is used to make the FDTD-JSON input human-readable, helping to identify inputs and outputs.
++ `[name]` is an optional entry which is used to make the FDTD-JSON input human-readable, helping to identify inputs and outputs. Leading and trailing blank spaces are removed. Blank spaces are substituted by underscroes. The following characters are reserved and can't be used in a `name`: `@`.
 
 ### `<general>`
 
@@ -85,12 +85,13 @@ These objects must contain a `<type>` label which can be:
 
 + `pec` for perfectly electric conducting termination.
 + `pmc` for perfectly magnetic conducting termination.
++ `periodic` for periodic boundary conditions. Must be paired with the opposite side. 
 + `mur` for Mur's first order absorbing boundary condition.
 + `pml` for perfectly matched layer termination. If this `type` is selected, it must also contain:
 
-  + `[layers]`: with an integer indicating the number of pml layers which will be used. TODO Change to an optional input which defaults to 10 layers
-  + `[order]`: TODO Change to an optional input which defaults to order 2.
-  + `[reflection]`: TODO Change to an optional input which defaults to 0.001 refl.
+  + `[layers]`: with an integer indicating the number of pml layers which will be used. Defaults to $10$ layers
+  + `[order]`: an integer indicating the order of the profile. defaults to order $2$.
+  + `[reflection]`: Computed reflection coefficient, defaults to $0.001$.
 
 **Example:**
 
@@ -253,9 +254,9 @@ These materials represent a perfectly electrically conducting (`pec`) and perfec
 "materials": [ {"id": 1, "type": "pec"} ]
 ```
 
-#### `simple`
+#### `isotropic`
 
-A `material` with `type` `simple` represents an isotropic material with constant (not frequency dependent) relative permittivity $\varepsilon_r$, relative permeability $\mu_r$, electric conductivity $\sigma$ and/or magnetic conductivity $\sigma_m$:
+A `material` with `type` `isotropic` represents an isotropic material with constant (not frequency dependent) relative permittivity $\varepsilon_r$, relative permeability $\mu_r$, electric conductivity $\sigma$ and/or magnetic conductivity $\sigma_m$:
 
 + `[relativePermittivity]` is a real which defaults to $1.0$. Must be greater than $1.0$.
 + `[relativePermeability]` is a real which defaults to $1.0$. Must be greater than $1.0$.
@@ -268,7 +269,7 @@ A `material` with `type` `simple` represents an isotropic material with constant
 {
     "name": "teflon"
     "id": 1, 
-    "type": "simple",
+    "type": "isotropic",
     "relativePermittivity": 2.5,
     "electricConducitivity": 1e-6
 } 
@@ -280,7 +281,7 @@ In surface materials, `elementIds` must reference `cell` elements. All `interval
 
 #### `multilayeredSurface`
 
-A `multilayeredSurface` must contain the entry `<layers>` which is an array indicating materials which are described in the same way as [simple materials](#simple) and a `<thickness>`.
+A `multilayeredSurface` must contain the entry `<layers>` which is an array indicating materials which are described in the same way as [isotropic materials](#isotropic) and a `<thickness>`.
 
 ```json
 {
@@ -289,22 +290,26 @@ A `multilayeredSurface` must contain the entry `<layers>` which is an array indi
     "id": 2,
     "layers": [
         {"thickness": 1e-3, "relativePermittivity": 1.3, "electricConductivity": 2e-4},
-        {"thickness": 5e-3, "relativePermittivity": 1.3}
+        {"thickness": 5e-3, "relativePermittivity": 1.3},
         {"thickness": 1e-3, "relativePermittivity": 1.3, "electricConductivity": 2e-4}
     ]
 }
 ```
 
-#### `frequencyDependentSurface`
+### Line materials
 
-The entry `<file>` is the path to a file containing the poles and residues which are used to model the surface impedance of the material.
+In line materials, `elementIds` must reference `cell` elements. All `intervals` modeling entities different to lines are ignored.
+
+#### `thinSlot`
+
+A `thinSlot` represents a gap between two conductive surfaces. Therefore it must be located at a surface and be defined using line cell elements only. Its `<width>` is a real number which defines the distance between the surfaces in meters.
 
 ```json
 {
-    "name": "carbon_fiber_model",
-    "type": "frequencyDependentSurface",
-    "id": 3,
-    "file": "cfc.dat"
+    "name": "3mm-gap",
+    "type": "thinSlot",
+    "id": 2,
+    "width": 3e-3
 }
 ```
 
@@ -469,7 +474,7 @@ This entry stores associations between `materials` and `elements` using their re
 
 ### `bulk`
 
-Bulk materials such as `pec`, `pmc` or `simple` can be assigned to one or many elements of type `cell`. If the `cell` contains `intervals` representing points, these will be ignored.
+Bulk materials such as `pec`, `pmc` or `isotropic` can be assigned to one or many elements of type `cell`. If the `cell` contains `intervals` representing points, these will be ignored.
 
 ```json
 "materialAssociations": [
@@ -488,6 +493,16 @@ Surface materials can only be assigned to elements of type `cell`. If the `cell`
 ]
 ```
 
+### `line`
+
+Line materials can only be assigned to elements of type `cell`. If the `cell` contains `intervals` representing entities different to segments these will be ignored.
+
+```json
+"materialAssociations": [
+    {"type": "line", "materialId": 2, "elementIds": [4]}
+]
+```
+
 ### `cable`
 
 This object establishes the relationship between the physical models described in a `material` and parts of the geometry. Besides a `type`, `materialId` and `elementIds`; a `cable` can contain the following inputs:
@@ -579,8 +594,6 @@ Performs a loop integral along on the contour of the surface reference in the `e
 
 Due to Ampere's law, the loop integral of the magnetic field is equal to the total electric current passing through the surfaces. `[field]`, can be `electric` or `magnetic`. Defaults to `electric`, which gives the total current passing through the surface.
 
-TODO REVIEW DO BULK CURRENTS DO AVERAGES OF MAGNETIC FIELDS IN CELLS NEXT TO THE SELECTED?
-
 In the following example `elementId` points an element describing a single oriented surface, therefore `direction` does not need to be stated explicitly.
 
 ```json
@@ -602,8 +615,6 @@ In this example `elementId` points to a volume element, therefore `direction` mu
 }
 ```
 
-TODO EXAMPLE IMAGE
-
 #### `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). 
@@ -649,7 +660,7 @@ An example follows:
 
 ### `[domain]`
 
-If `domain` is not specified, it defaults to record from the beginning to the end of the simulation.
+If `domain` is not specified, it defaults to a time domain recording from the beginning to the end of the simulation.
 The domain must specify a `<type>` from the following ones:
 
 + `time`, means recording only in time domain. A probe with a `domain` of this `type` can contain the following entries:

src_json_parser/idchildtable.F90

@@ -11,7 +11,8 @@ module idchildtable_mod
       type(fhash_tbl_t) :: idToChilds
    contains
       procedure :: getId 
-      procedure :: count
+      procedure :: totalSize
+      procedure :: checkId
    end type
 
    interface IdChildTable_t
@@ -42,9 +43,17 @@ function ctor(core, root, path) result(res)
       end do
    end function
 
-   integer function count(this)
+   function totalSize(this) result(res)
       class(IdChildTable_t) :: this
-      call this%idToChilds%stats(num_items=count)
+      integer :: res
+      call this%idToChilds%stats(num_items=res)
+   end function
+
+   function checkId(this, id) result(stat)
+      class(IdChildTable_t) :: this
+      integer, intent(in) :: id
+      integer :: stat
+      call this%idToChilds%check_key(key(id), stat)
    end function
 
    function getId(this, id) result(res)
@@ -66,5 +75,6 @@ function getId(this, id) result(res)
          res = d
       end select
    end function
+
 #endif
 end module

src_json_parser/mesh.F90

@@ -37,7 +37,8 @@ module mesh_mod
    contains
       procedure :: addCoordinate => mesh_addCoordinate
       procedure :: getCoordinate => mesh_getCoordinate
-      procedure :: checkId => mesh_checkId
+      procedure :: checkCoordinateId => mesh_checkCoordinateId
+      procedure :: checkElementId => mesh_checkElementId
 
       procedure :: addElement => mesh_addElement
       procedure :: addCellRegion  => mesh_addCellRegion
@@ -86,12 +87,20 @@ subroutine mesh_printCoordHashInfo(this)
 
    end subroutine
 
-   subroutine mesh_checkId(this, id, stat)
+   function mesh_checkCoordinateId(this, id) result(stat)
       class(mesh_t) :: this
       integer, intent(in) :: id
-      integer, intent(inout) :: stat
+      integer :: stat
       call this%coordinates%check_key(key(id), stat)
-   end subroutine
+   end function
+
+
+   function mesh_checkElementId(this, id) result(stat)
+      class(mesh_t) :: this
+      integer, intent(in) :: id
+      integer :: stat
+      call this%elements%check_key(key(id), stat)
+   end function
 
    subroutine mesh_addCoordinate(this, id, coordinate)
       class(mesh_t) :: this