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* Added functionality to pass mpi comm from python script to amrex during initialization
* Fixed missing _ in MPI._sizeof()
* Added functions to get the current processor's rank and total number of processors
* Renamed MPI_Comm to _MPI_Comm_type and defined _MPI_Comm_type in except statement
* Updated comment to explain why mpi4py needs to be imported before loading libwarpx
* Removed ifdef flags that prevent amrex_init_with_inited_mpi from being declared when MPI is off
* Changed amrex_init_with_inited_mpi to be declared even when not using mpi, but will be defined to be functionally the same as amrex_init
* Defined MPI = None to signify whether MPI is used, to add another check when initializing amrex
* Changed ifdef blocks in WarpXWrappers.cpp/h to fix compile errors.
Added ifdef block to conditionally declare amrex_init_with_inited_mpi in WarpXWrappers.h to prevent compile error when not using MPI. Removed ifdef block to declare/define same function in WarpXWrappers.cpp since function needs to be declared even when MPI is not used, but will never be called in that case.
* Changed BL_USE_MPI to AMREX_USE_MPI and removed incorrect MPI=None statement
* Changed BL_USE_MPI to AMREX_USE_MPI
* Added test to verify correct passing of MPI communicator to amrex
* Added ability to pass mpi_comm to sim.step
* Change test to check for differeing outputs when passed different inputs
* Removed obsolete comments refactored program to use more shared code
* Refactored comments
* Updated description to match test
* Removed unecessary imports and updated comments
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* Add possibility to start and stop moving window
* Update Benchmark laserInjection_2d
* Update Source/Diagnostics/BTDiagnostics.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* modification of the MoveWindow function in the python interface
* False to True for move j in python function
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* initial tests with IWYU
* added a couple of forward declarations
* used iwyu on more files
* progress
* used iwyu on more files
* progress with iwyu
* progress with iwyu
* fixed bug
* progress with iwyu
* progress with IWYU
* progress with IWYU
* fixed bug
* fixed bug
* progress with IWYU
* progress with IWYU + use forward declarations in WarpX.H
* first try with .def files
* fix bugs
* progress with IWYU
* progress with IWYU
* progress with iwyu
* correct copyright
* fixed bug
* fixed bugs
* fix missing include
* fixed bug
* fix bug
* fix bug introduced during last bugfix
* use iwyu on newly added files
* add space
* fix bug
* fix missing include
* fix missing include
* fix missing include
* fixed bugs
* fixed bug
* attempt at fixing issue with math functions
* added missing include
* fixed missing include
* using _fwd.H
* fixed bug
* progress with iwyu
* update AMReX branch
* enforce alphabetic order
* progress with iwyu
* use right version of amrex
* use right version of amrex for tests
* fixed bug
* fix another bug
* fix missing include
* fix missing include
* fix missing include
* updated amrex
* initial work to document new include strategy
* updated documentation
* Fix rst & private includes
* Remove accidentially added files
* Fix rst code blocks
* one more rst block
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* added ReadBCParams() function call to python execution and added a test of the electrostatic solver executing from python
* added separate specification of particle boundary conditions in picmi setup and adjusted the inputs for existing tests to follow the new practice
* updated input for rz PICMI test and renamed the electrostatic test to follow standard practice
* added arguments for particle boundary conditions to Langmuir RZ test
* added dictionary to picmi.py to map from picmistandard field boundary condition specifications to that of WarpX
* fixes for failing unit tests; added key, pair 'none' to picmi dictionary of field BCs
* also using 'none' for upper boundary condition for RZ test Python_Langmuir_rz_multimode
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* Define: _OPENMP -> AMREX_USE_OMP
Replace the define check of `_OPENMP` with the explicit
backend control of `AMREX_USE_OMP` for parallel constructs.
Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency
pulls it in for linear algebra, I/O, etc. This can led to confusion if the
user explicitly requested a serial build. Also, we might want to use OpenMP
functionality here and there for auxiliary functions w/o having to use the
AMReX OpenMP backend, i.e. because we compile for GPUs.
* Add missing amrex::Gpu::notInLaunchRegion
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* Fixes to the Python interface for accessing field and particle data
* In Python wrapper, cleaned up how ngrow is handled
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* New reduced diag: number of macroparticles
* Add parentheses in header line
* Apply suggestions from code review
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Add some consts
* Fuse some lines with std::ofstream
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
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* Rename l_lower_order_in_v to galerkin_interpolation
* Changed galerkin_interpolation from int to bool
* ... and same for member versions.
* Add input parameter to control galerkin_interpolation
* Update documentation
* semicolon
* Update Docs/source/running_cpp/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/running_cpp/parameters.rst
Resolve ambiguity
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Fix doc
* Add references to documentation
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Forgot to also overwrite the initialization defines for Python
with my last PR.
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* Added CheckGriddingForRZSpectral
* Bug fix in check gridding for RZ Spectral, fixing handling of refinement ratio
* Change numprocs=2 for python reg tests and reset benchmarks (#1075)
* changing nprocs to 2 for Python_PlasmaAcceleration test
* Resetting benchmark for Python_PlasmaAcceleration test case due to change in nprocs=2 in reg test
* resetting benchmarks for Python test-cases except Python_Langmuir due to change in numprocs in WarpX-tests.ini
* changing numprocs=2 for Python tests
* resetting python reg test benchmarks after updating pywarpx
Co-authored-by: Revathi Jambunathan <revanathan@pop-os.localdomain>
Co-authored-by: Tools <warpx.lbl.gov>
Co-authored-by: Tools <warpx@lbl.gov>
* Updates to picmi, mostly related to fields, and add psatd (#1077)
* Fixed bad arguments in PICMI_inputs_laser_acceleration.py (#1074)
Note that polarization_angle was changed to 0 since that
was the value being used because the polarization_argument was bad.
* Fix typo for pml_ncell in parameters doc (#1071)
* remove #line wp_parser.l because it causes issues with AMReX make system (#1078)
* remove amrex namespace from diag functor cpp files and use amrex:: prefic (#1093)
* For RZ spectral, updated documentation regarding blocking factor and max grid size
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Revathi Jambunathan <revanathan@pop-os.localdomain>
Co-authored-by: Tools <warpx@lbl.gov>
Co-authored-by: NeilZaim <49716072+NeilZaim@users.noreply.github.com>
Co-authored-by: WeiqunZhang <WeiqunZhang@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* [skip travis] CMake: Add CMake Scripts
This add CMake scripts for the CMake build system generator.
* CUDA Support Achieved
Fastest compile via:
cmake .. -DENABLE_CUDA=ON -DCUDA_ARCH=6.0
* CMake: openPMD & QED
* CMake: Dimension Support
WarpX_DIMS=2,3,RZ
* CCache & Out-of-Source
Enable CCache when found and prevent in-root builds (in-source okay-ish).
* CMake: CUDA C++ Language Minimum
* Add new Files
* CI: Migrate macOS to CMake
* Fortran: Enable Because Transitive
... for now :)
* CI: Migrate Linux ICC to CMake
* CI: Verbose Make
* CMake: Add Missing PSATD Sources
* CMake: PSATD, Compute, Precision, Clean
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* Start removing nodal flags where possible
* Remove additional nodal flags
* Clean up getFieldNodalFlagData in Python wrappers
* Remove nodal flags from PML files
* Revert "Remove nodal flags from PML files"
This reverts commit 1d58519f9cee2e64df811f76f3d8a0aead1aa4ef.
* Fix issue when removing nodal flags from PML files
* Remove nodal flags from (OLD) slice diagnostics
* Nodal flags are now local variables in WarpX::AllocLevelMFs
* Trigger Travis CI build after AMReX bug fix
* Void commit: trigger Travis CI build
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* Create subsection for diags documentation in input parameters list
* Replace old diags with new ones IN DOC ONLY
* eol whitespace
* Check first CI test with new diags, before changing all of them
* use diags in all CI
* oops, had forgotten all examples except Tests/
* Updated picmi interface to use the new diagnostics
* fix bug in how field functors are initialized for diags
* fix bug: should always dump output at the end of simulation
* eol
* update test parameters in ini file
* Further fixes to picmi for new diagnostics
* Updates PICMI input files to use the new diagnostics
* avoid dumping final plotfile twoce
* update test to run with new diags
* fix typo introduced when fixing merge conflicts
* had accidentally removed the max_step here, so the run never ended on TravisCI
* Add Diagnostics.py for picmi with new diagnostics
* Adding m_ for member variables in new diags (#934)
* fixing bug to initialize CellCenterFunctor for Bx
* diag_name renamed to m_diag_name
* some more diag members made m_
* renaming member variable mf_avg to m_mf_output
* fixing m_mf_output to mf_dst in comments
* Python documentation updates (#936)
* Update Python documentation
* Added numpy as a requirement for the Python installation
* Cleaned EOL white space in Python documentation
* Add periodictable to the Python packages required
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Added periodictable to required packages for pure Python version
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add hostname to LoadBalanceCosts reduced diagnostic (#902)
* Add hostname to reduced diags
EOL
Fix rd loadbalancecosts test
AMREX_USE_MPI
EOL
move macro to source file
Review changes
eol
add GPU ID if running on GPU
eol
Typo in comment
use vectors to get rid of C-style memory management
Fix for test
eol
* Compute number of unique box data fields in analysis script
* analysis script
* Use amrex Tokenize to split string
* Update WarpXUtil.cpp
* Update WarpXUtil.H
* [mini] Add contact us section to documentation (#941)
* add contact us section to doc
* Update Docs/source/contact_us.rst
Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov>
* Update Docs/source/contact_us.rst
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
* stop calling the old WritePlotFile functions
* fix new diags, problem with rho and PSATD and particle output variables
* remove more deprecated code for old diags
* Move checkpoint capability to new diagnostics
* error if user asks custom output for checkpoint
* eol
* some more old diags code deleted
* further cleaning
* eol
* further cleaning, make sure that WarpX compiles with USE_OPENPMD
* remove old diags parameters
* use new option to change the plotfile name
* typo
* do not need checkpoint files
* adapt to new option for checkpoint
* removed unread options as they make tests crash
* remove warpx_checkInt from the Python layer
* remove some more python wrappers
* add checkpoint capability with 2 diags in new output
* fix bug in MultiDiagnostics, and (should) fix checkpoint-restart test
* fix restart CI test
* avoid issue when writing the last plotfile twice
* dpgrote's fix for the Python tests
* update doc for diagnostics
* stop requesting ndiags, this is read from the list of diags
* awk to remove ndiags from all example input files
* Removed diagnostics.ndiags from picmi interface
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
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* Includes: Only From `Source/`
Avoid adding all directories to include paths:
- automatically structure includes more clearly, e.g. a util include
with a short name is clearly seen as such
- should have some small positive impact on compile time, since the
compiler has to search less directories for an include file
* Includes: Fix Non-Local Paths
Add missing prefix relative to `Source/` for WarpX-local includes.
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Remove the listing of all header-files from the Make-buildsystem.
Listing public header files here tells the AMReX Makefile build
system to install those in an install step after build. WarpX is
currently not building a public library which can be consumed by
users for their projects and only an executable.
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* Added nodal and cell size data to the Python interface and updates the Python_Langmuir_rz_multimode regression test
* Cleanup of PICMI_inputs_langmuir_rz_multimode_analyze.py
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- Use `""` for WarpX-local includes
- Order: WarpX `""`, AMReX `<>`, other third party includes `<>`
- Add dir prefixes for WarpX
Add order to includes by including from `Source/` onward and keeping
directory prefixes of non-local includes for clarity.
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Add Copyright header in all source files
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Remove the `dump_plotfile` switch and only control via
interval value in `plot_int` for plotfiles.
Remove the `dump_openpmd` switch and only control via
interval value in `plot_openpmd` for openPMD data dumps.
openPMD: pick first available backend if unspecified.
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Adds Python wrapper of PML fields
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Manually fix tabs to four spaces and alignments for consistent
prepresentation of source code over all machines.
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End-of-line (EOL) whitespaces are verbose and increase diffs and
merge conflicts over time.
Cleaned them up for the `Source/`, `Examples/` and `Tools/` directory
with the following bash one-liner:
```bash
find . -type f -not -path './.git*' \
-exec sed -i 's/[[:blank:]]*$//' {} \;
```
Committed as generic user so git does not credit the many lines
to me:
```bash
GIT_AUTHOR_NAME="Tools" GIT_AUTHOR_EMAIL="warpx@lbl.gov" \
git commit
```
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files
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KZhu-ME
thomas clark
Luca Fedeli
roelof-groenewald
Axel Huebl
David Grote
Weiqun Zhang
NeilZaim
danielbelkin
Edoardo Zoni
MaxThevenet
Remi Lehe
Tools
