"Gradient descent" convergence to steady-state (#176)

* Added ArbitraryDistributionVolumeEmitter * Updated particle weight calculation * renamed thermionic_emission test directory to emission * arbitrary seed from uniform distribution * Bug fixes and changes to test * add test for arbitrary seeding * Changed position sampling, added test * Removed unused imports and code * revert traceback printout * Added comments for binning particle positions * increased rtol for test * Allow input of any 2d array, add interpolation of 2d array onto current simulation grid * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated changelog * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated changelog * update version * created steady_state_descent.py file * Added coarsening algorithm * Added ability to read numpy data and coarsen grid * Added regression function calculation * Solve system of equations rather than curve fit * Use skimage block_reduce * Hard coded inverse exponential solve * take mean if exponential equation can't be solved * Added special cases to use linear regression * Update docstring * Added command line arguments * Modified linear regression logic and added main function * Added entry point * Change output file name * Change output file name * Fixed interpolate grid * updated arbitrary distribution emitter test * Fix interpolation logic * Changed to take in exact prediction timestep rather than a multiple * Added ability to specify save directory * Updated docstrings, removed unneeded files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added gradient descent test, refactored code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Changed test parameters * Increase rtol of arbitrary seed test by 0.01 * Apply shift in BTD for zmax different than 0 (ECP-WarpX#3091) * Include shift in t_lab when `zmax` is different than 0 * Revert "Include shift in t_lab when `zmax` is different than 0" This reverts commit 5f786f2. * Apply shift in BTD for zmax > 0 * Update mewarpx/mewarpx/utils_store/plasma_density_oracle.py Co-authored-by: Roelof Groenewald <[email protected]> * Update changelog * AMReX: Weekly Update (ECP-WarpX#3095) * Update version * Add controller for plasma density oracle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix miscellaneous issues found with clang tidy (ECP-WarpX#3083) * fix miscellaneous issues found with clang tidy * fix miscellaneous issues found with clang tidy * moved default constructors and destructors to header * fix issue * Use default again * Add a python script to generate timestep duration plots (ECP-WarpX#3036) * add script to generate timestep duration plots * disable transparent background * fix bugs * fix bug in doc * Update plot_timestep_duration.rst * add permissions * using argparse * using if __name__ == __main__: * add page in workflows * Update Docs/source/usage/workflows.rst * added missing file * Formatting * Apply shift for zmax>0 in old BTD (ECP-WarpX#3094) * Apply shift for zmax>0 in old BTD * BTD: also shift t_slice_lab * Use uniform error message formatting for all the amrex::Abort() calls in WarpX.cpp (ECP-WarpX#2952) * use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp * fixed bug * fixed bug * Update Source/WarpX.cpp * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <[email protected]> * WIP oracle control * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use queryWithParser to Parse v_particle_pml (ECP-WarpX#3096) Use queryWithParser, instead of query, to parse v_particle_pml, in order to support functions like sin, cos, sqrt, etc. * Allow oracle control bins to be overridden * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Wrong Abort Message for PSATD w/ Time Averaging (ECP-WarpX#3098) * Doc: Improve Doxygen Links (ECP-WarpX#3099) * Doc: Improve Doxygen Links - download also openPMD-api tag files & link them - improve developer page: clearer links * Update: .gitignore * Added command line arguments * Fix Mirrors for RZ (NullifyMF) (ECP-WarpX#3101) * Fixed bugs, added info logging * added ability to modify run_script * removed unnecessary code * Cleaned up code * Fix Breaking Pip 22.1 Logic (ECP-WarpX#3106) * CI: Fix Windows Pip's `--no-build-isolation` says we have to have build-deps pre-installed. But Pip does offer no option to install those from `pyproject.toml`. * Pip 22.1: in-tree-build default And dropped the old option with a fatal error... classic. * Pip no-build isolation: pre-install build tools not installed in non-isolated builds - we want isolated builds, because they have a derministic path that we can cache with ccache * fix bug (ECP-WarpX#3110) * Fix Laser Injection in RZ (ECP-WarpX#3104) * Add STL files support in pywarpx (ECP-WarpX#3089) * Added STL files support in pywarpx * Add new EB bucket * Added name to file headers * Fixing year in file headers * Checking that stl file and imp function are not both specified * Renamed EB bucket to EB2 * Adding STL documentation * Implement suggestions from code review Co-authored-by: lgiacome <[email protected]> * Stricter Tolerance for 3D Langmuir Tests (ECP-WarpX#3097) * CI: HIP with https (ECP-WarpX#3111) Small update in HIP docs: now supports HTTPS: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu * Add Headers to Input File Written by PICMI (ECP-WarpX#3093) * Add Headers to Input File Written by PICMI * Commit Suggestion by @dpgrote * Add Comment * Add Empty Line * Slightly Better Readable with a newline * Refactored code to be clearer * AMReX/PICSAR: Weekly Update (ECP-WarpX#3112) * AMReX: Weekly Update * PICSAR: Weekly Update * [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#3113) updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.13 → v1.1.14](Lucas-C/pre-commit-hooks@v1.1.13...v1.1.14) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Use uniform error message formatting in more source files (ECP-WarpX#2964) * use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <[email protected]> * use more uniform text formatting * fixed bug * fixed bug * using Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed last merge conflict * fixed bug * fix indentation Co-authored-by: Axel Huebl <[email protected]> * Avoid resizing ParticleBoundaryBuffer allocation to total particle count (ECP-WarpX#3068) * Avoid resizing ParticleBoundaryBuffer allocation to total particle count * Switch atomic increments over to reductions * Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ (ECP-WarpX#3071) * Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ Document how to install ADIOS2 (for openPMD `.bp`) and BLAS++/LAPACK++ (for PSATD in RZ) on Lassen at LLNL. * Update: ADIOS2~SST, BLAS++/LAPACK++ w/ ESSL * Add workaround for Libfabric bug on Crusher to job script. (ECP-WarpX#3114) * Add workaround for Libfabric bug on Crusher to job script. * add known issues section for Crusher * Update docstrings * Added test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added documentation about oracle_control * Updated changelog * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed TOTAL_TIME calculation * ABLASTR: localIDtoGlobal (ECP-WarpX#3115) * ABLASTR: localIDtoGlobal Move the control of `localIDtoGlobal` to ABLASTR for particle IDs. * WarpX: Use ABLASTR now * update wheel in docker build * build image * change numpy to oldest-supported-numpy for docker * build image * Updated formatting and documentation Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <[email protected]> Co-authored-by: Roelof Groenewald <[email protected]> Co-authored-by: Axel Huebl <[email protected]> Co-authored-by: Luca Fedeli <[email protected]> Co-authored-by: amadou38 <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: David Grote <[email protected]> Co-authored-by: Lorenzo Giacomel <[email protected]> Co-authored-by: lgiacome <[email protected]> Co-authored-by: Phil Miller <[email protected]> Co-authored-by: Andrew Myers <[email protected]> Co-authored-by: roelof.groenewald <[email protected]>
ModernElectron · May 24, 2022 · e31338f · e31338f
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diff --git a/.github/workflows/cuda.yml b/.github/workflows/cuda.yml
@@ -106,7 +106,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd amrex && git checkout --detach 22.05 && cd -
+        cd amrex && git checkout --detach 843a7dff266273a0f5b7b9f6cc9233a278f41fe1 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_PSATD=TRUE USE_CCACHE=TRUE -j 2
 
   build_nvhpc21-11-nvcc:

diff --git a/.github/workflows/dependencies/hip.sh b/.github/workflows/dependencies/hip.sh
@@ -8,13 +8,14 @@
 set -eu -o pipefail
 
 # Ref.: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
-wget -q -O - http://repo.radeon.com/rocm/rocm.gpg.key \
+wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key \
   | sudo apt-key add -
-echo 'deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
+echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
   | sudo tee /etc/apt/sources.list.d/rocm.list
 
 echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
   | sudo tee -a /etc/profile.d/rocm.sh
+
 # we should not need to export HIP_PATH=/opt/rocm/hip with those installs
 
 sudo apt-get update

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -37,6 +37,7 @@ jobs:
         cmake --build build --config Debug --parallel 2
 
         python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade cmake
         $env:PYWARPX_LIB_DIR="$(Get-Location | Foreach-Object { $_.Path })\build\lib\Debug\"
         python3 -m pip install . -vv --no-build-isolation
 
@@ -81,6 +82,7 @@ jobs:
         cmake --build build --config Release --parallel 2
 
         python3 -m pip install --upgrade pip setuptools wheel
+        python3 -m pip install --upgrade cmake
         set "PYWARPX_LIB_DIR=%cd%\build\lib\"
         python3 -m pip install . -vv --no-build-isolation
 

diff --git a/.gitignore b/.gitignore
@@ -35,6 +35,7 @@ pywarpx.egg-info/
 ##########
 Docs/amrex-doxygen-web.tag.xml
 Docs/warpx-doxygen-web.tag.xml
+Docs/openpmd-api-doxygen-web.tag.xml
 Docs/doxyhtml/
 Docs/doxyxml/
 Docs/source/_static/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -48,7 +48,7 @@ repos:
 
 # Changes tabs to spaces
 - repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.1.13
+  rev: v1.1.14
   hooks:
   - id: remove-tabs
     exclude: 'Make.WarpX|Make.package|Makefile|GNUmake'

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -423,7 +423,7 @@ if(WarpX_LIB)
         ${CMAKE_COMMAND} -E rm -f ${WarpX_BINARY_DIR}/pywarpx*whl
         COMMAND
             ${CMAKE_COMMAND} -E env PYWARPX_LIB_DIR=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-                python3 -m pip wheel -v --no-build-isolation --use-feature=in-tree-build ${WarpX_SOURCE_DIR}
+                python3 -m pip wheel -v --no-build-isolation ${WarpX_SOURCE_DIR}
         WORKING_DIRECTORY
             ${WarpX_BINARY_DIR}
         DEPENDS

diff --git a/Docs/Doxyfile b/Docs/Doxyfile
@@ -2104,7 +2104,8 @@ SKIP_FUNCTION_MACROS   = YES
 # the path). If a tag file is not located in the directory in which doxygen is
 # run, you must also specify the path to the tagfile here.
 
-TAGFILES               = amrex-doxygen-web.tag.xml=https://amrex-codes.github.io/amrex/doxygen/
+TAGFILES               = amrex-doxygen-web.tag.xml=https://amrex-codes.github.io/amrex/doxygen/  \
+                         openpmd-api-doxygen-web.tag.xml=https://openpmd-api.readthedocs.io/en/latest/_static/doxyhtml/
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create a
 # tag file that is based on the input files it reads. See section "Linking to

diff --git a/Docs/source/conf.py b/Docs/source/conf.py
@@ -188,10 +188,12 @@
 # Tell sphinx what the pygments highlight language should be.
 highlight_language = 'cpp'
 
-# Download AMReX Doxygen Tagfile to interlink Doxygen docs
+# Download AMReX & openPMD-api Doxygen Tagfile to interlink Doxygen docs
 url = 'https://amrex-codes.github.io/amrex/docs_xml/doxygen/amrex-doxygen-web.tag.xml'
 urllib.request.urlretrieve(url, '../amrex-doxygen-web.tag.xml')
 
+url = 'https://openpmd-api.readthedocs.io/en/latest/_static/doxyhtml/openpmd-api-doxygen-web.tag.xml'
+urllib.request.urlretrieve(url, '../openpmd-api-doxygen-web.tag.xml')
 
 # Build Doxygen
 subprocess.call('cd ../; doxygen;'

diff --git a/Docs/source/developers/doxygen.rst b/Docs/source/developers/doxygen.rst
@@ -5,4 +5,10 @@ C++ Objects & Functions
 
 We generate the documentation of C++ objects and functions *from our C++ source code* by adding :ref:`Doxygen strings <developers-docs>`.
 
-Our Doxygen C++ API documentation in classic formatting `is located here <../_static/doxyhtml/index.html>`_.
+* **WarpX and ABLASTR**: `C++ Doxygen <../_static/doxyhtml/index.html>`__
+
+This documentation dynamically links to objects described in dependencies:
+
+* **AMReX**: `C++ Doxygen <https://amrex-codes.github.io/amrex/doxygen>`__ and `Manual <https://amrex-codes.github.io/amrex/docs_html/>`__
+* **openPMD-api**: `C++ Doxygen <https://openpmd-api.readthedocs.io/en/latest/_static/doxyhtml/index.html>`__ and `Manual <https://openpmd-api.readthedocs.io>`__
+* **PICSAR-QED**: C++ Doxygen is *TODO*
diff --git a/Docs/source/install/cmake.rst b/Docs/source/install/cmake.rst
@@ -199,6 +199,7 @@ PICMI Python Bindings
    .. code-block:: bash
 
       python3 -m pip install -U pip setuptools wheel
+      python3 -m pip install -U cmake
 
 For PICMI Python bindings, configure WarpX to produce a library and call our ``pip_install`` *CMake target*:
 

diff --git a/Docs/source/install/hpc/crusher.rst b/Docs/source/install/hpc/crusher.rst
@@ -86,3 +86,19 @@ Post-Processing
 For post-processing, most users use Python via OLCFs's `Jupyter service <https://jupyter.olcf.ornl.gov>`__ (`Docs <https://docs.olcf.ornl.gov/services_and_applications/jupyter/index.html>`__).
 
 Please follow the same guidance as for :ref:`OLCF Summit post-processing <post-processing-summit>`.
+
+.. _known-crusher-issues:
+
+Known System Issues
+-------------------
+
+.. warning::
+
+   May 16th, 2022 (OLCFHELP-6888):
+   There is a caching bug in Libfrabric that causes WarpX simulations to occasionally hang on Crusher on more than 1 node.
+
+   As a work-around, please export the following environment variable in your job scripts unti the issue is fixed:
+
+   .. code-block:: bash
+
+      export FI_MR_CACHE_MAX_COUNT=0  # libfabric disable caching
diff --git a/Docs/source/install/hpc/lassen.rst b/Docs/source/install/hpc/lassen.rst
@@ -37,6 +37,34 @@ We recommend to store the above lines in a file, such as ``$HOME/lassen_warpx.pr
 
    source $HOME/lassen_warpx.profile
 
+And since Lassen does not yet provide a module for them, install ADIOS2, BLAS++ and LAPACK++:
+
+.. code-block:: bash
+
+   # c-blosc (I/O compression)
+   git clone -b v1.21.1 https://github.com/Blosc/c-blosc.git src/c-blosc
+   rm -rf src/c-blosc-lassen-build
+   cmake -S src/c-blosc -B src/c-blosc-lassen-build -DBUILD_TESTS=OFF -DBUILD_BENCHMARKS=OFF -DDEACTIVATE_AVX2=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/lassen/c-blosc-1.21.1
+   cmake --build src/c-blosc-lassen-build --target install --parallel 16
+
+   # ADIOS2
+   git clone -b v2.7.1 https://github.com/ornladios/ADIOS2.git src/adios2
+   rm -rf src/adios2-lassen-build
+   cmake -S src/adios2 -B src/adios2-lassen-build -DADIOS2_USE_Blosc=ON -DADIOS2_USE_Fortran=OFF -DADIOS2_USE_Python=OFF -DADIOS2_USE_SST=OFF -DADIOS2_USE_ZeroMQ=OFF -DCMAKE_INSTALL_PREFIX=$HOME/sw/lassen/adios2-2.7.1
+   cmake --build src/adios2-lassen-build --target install -j 16
+
+   # BLAS++ (for PSATD+RZ)
+   git clone https://bitbucket.org/icl/blaspp.git src/blaspp
+   rm -rf src/blaspp-lassen-build
+   cmake -S src/blaspp -B src/blaspp-lassen-build -Duse_openmp=ON -Dgpu_backend=CUDA -Duse_cmake_find_blas=ON -DBLA_VENDOR=IBMESSL -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=$HOME/sw/lassen/blaspp-master
+   cmake --build src/blaspp-lassen-build --target install --parallel 16
+
+   # LAPACK++ (for PSATD+RZ)
+   git clone https://bitbucket.org/icl/lapackpp.git src/lapackpp
+   rm -rf src/lapackpp-lassen-build
+   CXXFLAGS="-DLAPACK_FORTRAN_ADD_" cmake -S src/lapackpp -B src/lapackpp-lassen-build -Duse_cmake_find_lapack=ON -DBLA_VENDOR=IBMESSL -DCMAKE_CXX_STANDARD=17 -Dbuild_tests=OFF -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON -DCMAKE_INSTALL_PREFIX=$HOME/sw/lassen/lapackpp-master -DLAPACK_LIBRARIES=/usr/lib64/liblapack.so
+   cmake --build src/lapackpp-lassen-build --target install --parallel 16
+
 Then, ``cd`` into the directory ``$HOME/src/warpx`` and use the following commands to compile:
 
 .. code-block:: bash

diff --git a/Docs/source/install/hpc/lxplus.rst b/Docs/source/install/hpc/lxplus.rst
@@ -137,6 +137,7 @@ Now, ensure Python tooling is up-to-date:
 .. code-block:: bash
 
    python3 -m pip install -U pip setuptools wheel
+   python3 -m pip install -U cmake
 
 Then we compile WarpX as in the previous section (with or without CUDA) adding ``-DWarpX_LIB=ON`` and then we install it into our Python:
 

diff --git a/Docs/source/usage/parameters.rst b/Docs/source/usage/parameters.rst
@@ -345,6 +345,9 @@ Additional PML parameters
     Whether to damp current in PML. Can only be used if particles are propagated in PML,
     i.e. if `warpx.pml_has_particles = 1`.
 
+* ``warpx.v_particle_pml`` (`float`; default: 1)
+    When ``warpx.do_pml_j_damping = 1``, the assumed velocity of the particles to be absorbed in the PML, in units of the speed of light `c`.
+
 * ``warpx.do_pml_dive_cleaning`` (`bool`; default: 1)
     Whether to use divergence cleaning for E in the PML region.
     The value must match ``warpx.do_pml_divb_cleaning`` (either both false or both true).

diff --git a/Docs/source/usage/workflows.rst b/Docs/source/usage/workflows.rst
@@ -11,6 +11,7 @@ This section collects typical user workflows and best practices for WarpX.
    workflows/parallelization
    workflows/debugging
    workflows/libensemble
+   workflows/plot_timestep_duration
    workflows/plot_distribution_mapping
    workflows/psatd_stencil
    workflows/archiving
diff --git a/Docs/source/usage/workflows/plot_timestep_duration.rst b/Docs/source/usage/workflows/plot_timestep_duration.rst
@@ -0,0 +1,18 @@
+.. _plot-timestep-duration:
+
+Plot timestep duration
+======================
+We provide a simple python script to generate plots of the timestep duration
+from the stdandard output of WarpX (provided that ``warpx.verbose`` is set to 1):
+`plot_timestep_duration.py <../../../../Tools/PostProcessing/plot_timestep_duration.py>`__ .
+
+If the standard output of a simulation has been redirected to a file named ``log_file``,
+the script can be used as follows:
+
+::
+
+    python plot_timestep_duration.py log_file
+
+The script generates two pictures: ``log_file_ts_duration.png``, which shows the duration
+of each timestep in seconds as a function of the timestep number, and ``log_file_ts_cumulative_duration.png``,
+which shows the total duration of the simulation as a function of the timestep number.
diff --git a/Examples/Tests/Langmuir/analysis_langmuir_multi.py b/Examples/Tests/Langmuir/analysis_langmuir_multi.py
@@ -142,7 +142,7 @@ def get_theoretical_field( field, t ):
 fig.tight_layout()
 fig.savefig('Langmuir_multi_analysis.png', dpi = 200)
 
-tolerance_rel = 0.15
+tolerance_rel = 5e-2
 
 print("error_rel    : " + str(error_rel))
 print("tolerance_rel: " + str(tolerance_rel))

diff --git a/Python/pywarpx/EB2.py b/Python/pywarpx/EB2.py
@@ -0,0 +1,9 @@
+# Copyright 2022 Lorenzo Giacomel
+#
+# This file is part of WarpX.
+#
+# License: BSD-3-Clause-LBNL
+
+from .Bucket import Bucket
+
+eb2 = Bucket('eb2')
diff --git a/Python/pywarpx/WarpX.py b/Python/pywarpx/WarpX.py
@@ -1,10 +1,12 @@
-# Copyright 2016-2020 Andrew Myers, David Grote, Maxence Thevenet
-# Remi Lehe
+# Copyright 2016-2022 Andrew Myers, David Grote, Maxence Thevenet
+# Remi Lehe, Lorenzo Giacomel
 #
 # This file is part of WarpX.
 #
 # License: BSD-3-Clause-LBNL
 
+import re
+
 from . import Particles
 from .Algo import algo
 from .Amr import amr
@@ -13,6 +15,7 @@
 from .Collisions import collisions, collisions_list
 from .Constants import my_constants
 from .Diagnostics import diagnostics
+from .EB2 import eb2
 from .Geometry import geometry
 from .Interpolation import interpolation
 from .Langmuirwave import langmuirwave
@@ -38,6 +41,7 @@ def create_argv_list(self):
         argv += langmuirwave.attrlist()
         argv += interpolation.attrlist()
         argv += psatd.attrlist()
+        argv += eb2.attrlist()
 
         # --- Search through species_names and add any predefined particle objects in the list.
         particles_list_names = [p.instancename for p in particles_list]
@@ -101,7 +105,17 @@ def write_inputs(self, filename='inputs', **kw):
 
         with open(filename, 'w') as ff:
 
+            prefix_old = ''
             for arg in argv:
+                # This prints the name of the input group (prefix) as a header
+                # before each group to make the input file more human readable
+                prefix_new = re.split(' |\.', arg)[0]
+                if prefix_new != prefix_old:
+                    if prefix_old != '':
+                        ff.write('\n')
+                    ff.write(f'# {prefix_new}\n')
+                    prefix_old = prefix_new
+
                 ff.write(f'{arg}\n')
 
 warpx = WarpX('warpx')
diff --git a/Python/pywarpx/__init__.py b/Python/pywarpx/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2016-2019 Andrew Myers, David Grote
+# Copyright 2016-2022 Andrew Myers, David Grote, Lorenzo Giacomel
 #
 # This file is part of WarpX.
 #
@@ -10,6 +10,7 @@
 from .Collisions import collisions
 from .Constants import my_constants
 from .Diagnostics import diagnostics
+from .EB2 import eb2
 from .Geometry import geometry
 from .Interpolation import interpolation
 from .Langmuirwave import langmuirwave

diff --git a/Python/pywarpx/picmi.py b/Python/pywarpx/picmi.py
@@ -1,5 +1,5 @@
-# Copyright 2018-2020 Andrew Myers, David Grote, Ligia Diana Amorim
-# Maxence Thevenet, Remi Lehe, Revathi Jambunathan
+# Copyright 2018-2022 Andrew Myers, David Grote, Ligia Diana Amorim
+# Maxence Thevenet, Remi Lehe, Revathi Jambunathan, Lorenzo Giacomel
 #
 #
 # This file is part of WarpX.
@@ -917,21 +917,43 @@ class EmbeddedBoundary(picmistandard.base._ClassWithInit):
     """
     Custom class to handle set up of embedded boundaries specific to WarpX.
     If embedded boundary initialization is added to picmistandard this can be
-    changed to inherit that functionality.
+    changed to inherit that functionality. The geometry can be specified either as
+    an implicit function or as an STL file (ASCII or binary). In the latter case the
+    geometry specified in the STL file can be scaled, translated and inverted.
     - implicit_function: Analytic expression describing the embedded boundary
+    - stl_file: STL file path (string), file contains the embedded boundary geometry
+    - stl_scale: factor by which the STL geometry is scaled (pure number)
+    - stl_center: vector by which the STL geometry is translated (in meters)
+    - stl_reverse_normal: if True inverts the orientation of the STL geometry
     - potential: Analytic expression defining the potential. Can only be specified
                  when the solver is electrostatic. Optional, defaults to 0.
      Parameters used in the expressions should be given as additional keyword arguments.
     """
-    def __init__(self, implicit_function, potential=None, **kw):
+    def __init__(self, implicit_function=None, stl_file=None, stl_scale=None, stl_center=None, stl_reverse_normal=False,
+                 potential=None, **kw):
+
+        assert stl_file is None or implicit_function is None, Exception('Only one between implicit_function and '
+                                                                            'stl_file can be specified')
+
         self.implicit_function = implicit_function
+        self.stl_file = stl_file
+
+        if stl_file is None:
+            assert stl_scale is None, Exception('EB can only be scaled only when using an stl file')
+            assert stl_center is None, Exception('EB can only be translated only when using an stl file')
+            assert stl_reverse_normal is False, Exception('EB can only be reversed only when using an stl file')
+
+        self.stl_scale = stl_scale
+        self.stl_center = stl_center
+        self.stl_reverse_normal = stl_reverse_normal
+
         self.potential = potential
 
         # Handle keyword arguments used in expressions
         self.user_defined_kw = {}
         for k in list(kw.keys()):
-            if (re.search(r'\b%s\b'%k, implicit_function) or
-                (potential is not None and re.search(r'\b%s\b'%k, potential))):
+            if (implicit_function is not None and re.search(r'\b%s\b'%k, implicit_function) or
+               (potential is not None and re.search(r'\b%s\b'%k, potential))):
                 self.user_defined_kw[k] = kw[k]
                 del kw[k]
 
@@ -944,8 +966,16 @@ def initialize_inputs(self, solver):
         # defined in my_constants with the same name but different value.
         self.mangle_dict = pywarpx.my_constants.add_keywords(self.user_defined_kw)
 
-        expression = pywarpx.my_constants.mangle_expression(self.implicit_function, self.mangle_dict)
-        pywarpx.warpx.eb_implicit_function = expression
+        if self.implicit_function is not None:
+            expression = pywarpx.my_constants.mangle_expression(self.implicit_function, self.mangle_dict)
+            pywarpx.warpx.eb_implicit_function = expression
+
+        if self.stl_file is not None:
+            pywarpx.eb2.geom_type = "stl"
+            pywarpx.eb2.stl_file = self.stl_file
+            pywarpx.eb2.stl_scale = self.stl_scale
+            pywarpx.eb2.stl_center = self.stl_center
+            pywarpx.eb2.stl_reverse_normal = self.stl_reverse_normal
 
         if self.potential is not None:
             assert isinstance(solver, ElectrostaticSolver), Exception('The potential is only supported with the ElectrostaticSolver')

diff --git a/Regression/WarpX-GPU-tests.ini b/Regression/WarpX-GPU-tests.ini
@@ -60,7 +60,7 @@ emailBody = Check https://ccse.lbl.gov/pub/GpuRegressionTesting/WarpX/ for more
 
 [AMReX]
 dir = /home/regtester/git/amrex/
-branch = 22.05
+branch = 843a7dff266273a0f5b7b9f6cc9233a278f41fe1
 
 [source]
 dir = /home/regtester/git/WarpX

diff --git a/Regression/WarpX-tests.ini b/Regression/WarpX-tests.ini
@@ -59,7 +59,7 @@ emailBody = Check https://ccse.lbl.gov/pub/RegressionTesting/WarpX/ for more det
 
 [AMReX]
 dir = /home/regtester/AMReX_RegTesting/amrex/
-branch = 22.05
+branch = 843a7dff266273a0f5b7b9f6cc9233a278f41fe1
 
 [source]
 dir = /home/regtester/AMReX_RegTesting/warpx