Merge branch 'development' into add_external_particle_fields_ohms_law…

…_hybrid

.readthedocs.yml

@@ -9,14 +9,17 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "mambaforge-latest"
+    # python: "3.11"
 
 sphinx:
-   configuration: Docs/source/conf.py
+  configuration: Docs/source/conf.py
 
-python:
-   install:
-   - requirements: Docs/requirements.txt
+conda:
+  environment: Docs/conda.yml
+# python:
+#   install:
+#   - requirements: Docs/requirements.txt
 
 formats:
   - htmlzip

Docs/Doxyfile

@@ -2245,15 +2245,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -2305,14 +2305,16 @@ PREDEFINED             = AMREX_Linux=1 \
                          WARPX_QED=1 \
                          WARPX_QED_TABLE_GEN=1
 
+PREDEFINED           += "AMREX_ENUM(CLASS,...)=\"enum class CLASS : int { __VA_ARGS__ };\""
+
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The
 # macro definition that is found in the sources will be used. Use the PREDEFINED
 # tag if you want to use a different macro definition that overrules the
 # definition found in the source code.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_AS_DEFINED      =
+EXPAND_AS_DEFINED      = AMREX_ENUM
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
 # remove all references to function-like macros that are alone on a line, have

Docs/README.md

@@ -9,12 +9,13 @@ More information can be found in Docs/source/developers/documentation.rst.
 
 Install the Python requirements for compiling the documentation:
 ```
-python3 -m pip install -r Docs/requirements.txt
+cd Docs/
+python3 -m pip install -r requirements.txt
 ```
 
 ### Compiling the documentation
 
-`cd` into the `Docs/` directory and type
+Still in the `Docs/` directory, type
 ```
 make html
 ```

Docs/conda.yml

@@ -0,0 +1,12 @@
+name: readthedocs
+
+channels:
+  - conda-forge
+  - nodefaults
+
+dependencies:
+  - python
+  - doxygen
+  - pip
+  - pip:
+    - -r requirements.txt

Docs/requirements.txt

@@ -5,7 +5,7 @@
 # License: BSD-3-Clause-LBNL
 
 # WarpX PICMI bindings w/o C++ component (used for autoclass docs)
--e Python
+-e ../Python
 breathe
 docutils>=0.17.1
 

Docs/source/developers/documentation.rst

@@ -56,16 +56,15 @@ First, make sure you are in the root directory of WarpX's source and install the
 
 .. code-block:: sh
 
-    python3 -m pip install -r Docs/requirements.txt
+    cd Docs/
+    python3 -m pip install -r requirements.txt
 
 You will also need Doxygen (macOS: ``brew install doxygen``; Ubuntu: ``sudo apt install doxygen``).
 
-Then, to compile the documentation, use
+Still in the ``Docs/`` directory, compile the documentation via
 
 .. code-block:: sh
 
-    cd Docs/
-
     make html
     # This will first compile the Doxygen documentation (execute doxygen)
     # and then build html pages from rst files using sphinx and breathe.

Docs/source/developers/fields.rst

@@ -37,6 +37,13 @@ The ``MultiFab`` constructor (for, e.g., ``Ex`` on level ``lev``) is called in `
 
 By default, the ``MultiFab`` are set to ``0`` at initialization. They can be assigned a different value in ``WarpX::InitLevelData``.
 
+Field Names
+-----------
+
+The commonly used WarpX field names are defined in:
+
+.. doxygenenum:: warpx::fields::FieldType
+
 Field solver
 ------------
 

Docs/source/usage/workflows/python_extend.rst

@@ -134,9 +134,12 @@ This example accesses the :math:`E_x(x,y,z)` field at level 0 after every time s
        warpx = sim.extension.warpx
 
        # data access
-       E_x_mf = warpx.multifab(f"Efield_fp[x][level=0]")
+       #   vector field E, component x, on the fine patch of MR level 0
+       E_x_mf = warpx.multifab("Efield_fp", dir=0, level=0)
+       #   scalar field rho, on the fine patch of MR level 0
+       rho_mf = warpx.multifab("rho_fp", level=0)
 
-       # compute
+       # compute on E_x_mf
        # iterate over mesh-refinement levels
        for lev in range(warpx.finest_level + 1):
            # grow (aka guard/ghost/halo) regions

Examples/Physics_applications/spacecraft_charging/inputs_test_rz_spacecraft_charging_picmi.py

@@ -121,13 +121,13 @@ def compute_virtual_charge_on_spacecraft():
     # Compute integral of rho over volume of the domain
     # (i.e. total charge of the plasma particles)
     rho_integral = (
-        (rho[1 : nr - 1, 1 : nz - 1] * r[1 : nr - 1, np.newaxis]).sum() * dr * dz
+        (rho[1 : nr - 1, 1 : nz - 1] * r[1 : nr - 1, np.newaxis]).sum()
+        * 2
+        * np.pi
+        * dr
+        * dz
     )
 
-    # Due to an oddity in WarpX (which will probably be solved later)
-    # we need to multiply `rho` by `-epsilon_0` to get the correct charge
-    rho_integral *= 2 * np.pi * -scc.epsilon_0  # does this oddity still exist?
-
     # Compute charge of the spacecraft, based on Gauss theorem
     q_spacecraft = -rho_integral - scc.epsilon_0 * grad_phi_integral
     print("Virtual charge on the spacecraft: %e" % q_spacecraft)

Source/BoundaryConditions/PML.cpp

@@ -1234,7 +1234,7 @@ PML::CheckPoint (
 {
     using ablastr::fields::Direction;
 
-    if (fields.has(FieldType::pml_E_fp, Direction{0}, 0))
+    if (fields.has_vector(FieldType::pml_E_fp, 0))
     {
         ablastr::fields::VectorField pml_E_fp = fields.get_alldirs(FieldType::pml_E_fp, 0);
         ablastr::fields::VectorField pml_B_fp = fields.get_alldirs(FieldType::pml_B_fp, 0);
@@ -1246,7 +1246,7 @@ PML::CheckPoint (
         VisMF::AsyncWrite(*pml_B_fp[2], dir+"_Bz_fp");
     }
 
-    if (fields.has(FieldType::pml_E_cp, Direction{0}, 0))
+    if (fields.has_vector(FieldType::pml_E_cp, 0))
     {
         ablastr::fields::VectorField pml_E_cp = fields.get_alldirs(FieldType::pml_E_cp, 0);
         ablastr::fields::VectorField pml_B_cp = fields.get_alldirs(FieldType::pml_B_cp, 0);
@@ -1267,7 +1267,7 @@ PML::Restart (
 {
     using ablastr::fields::Direction;
 
-    if (fields.has(FieldType::pml_E_fp, Direction{0}, 0))
+    if (fields.has_vector(FieldType::pml_E_fp, 0))
     {
         ablastr::fields::VectorField pml_E_fp = fields.get_alldirs(FieldType::pml_E_fp, 0);
         ablastr::fields::VectorField pml_B_fp = fields.get_alldirs(FieldType::pml_B_fp, 0);
@@ -1279,7 +1279,7 @@ PML::Restart (
         VisMF::Read(*pml_B_fp[2], dir+"_Bz_fp");
     }
 
-    if (fields.has(FieldType::pml_E_cp, Direction{0}, 0))
+    if (fields.has_vector(FieldType::pml_E_cp, 0))
     {
         ablastr::fields::VectorField pml_E_cp = fields.get_alldirs(FieldType::pml_E_cp, 0);
         ablastr::fields::VectorField pml_B_cp = fields.get_alldirs(FieldType::pml_B_cp, 0);

Source/Diagnostics/BTDiagnostics.H

@@ -241,7 +241,7 @@ private:
      *  will be used by all snapshots to obtain lab-frame data at the respective
      *  z slice location.
      */
-    amrex::Vector<std::unique_ptr<amrex::MultiFab> > m_cell_centered_data;
+    std::string const m_cell_centered_data_name;
     /** Vector of pointers to compute cell-centered data, per level, per component
      *  using the coarsening-ratio provided by the user.
      */
@@ -346,7 +346,7 @@ private:
      *  \param[in] i_buffer snapshot index
      */
     void SetSnapshotFullStatus (int i_buffer);
-    /** Vector of field-data stored in the cell-centered multifab, m_cell_centered_data.
+    /** Vector of field-data stored in the cell-centered MultiFab.
      *  All the fields are stored regardless of the specific fields to plot selected
      *  by the user.
      */