| Age | Commit message (Collapse) | Author | Files | Lines |
|---|
|
particle creation in AddNParticles() (#2115)
* exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index
* added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation
* added function to get index of a particle component given the PID name
* changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id
* changed warpx_addRealComp to accept a species name as input and only add the new component for that species
* added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime
* changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index
* updated test according to PR #2119 changes
* removed unneeded BL_ASSERT(nattr == 1) statement
* fixed bug in add_particles to correctly determine the number of extra attributes
* fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species
* use isinstance(attr, ndarray) rather than type(attr) is np.ndarray
* generalize_runtime_comps_io
* fix OpenPMD
* fix OpenPMD
* fix plot flags in WritePlotFile
* fix offset and comment
* changed extra pid test to not use an underscore in the pid name
* switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays
* License update in test file
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* fix typo
* added a test with unique_particles=False
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* updated docstring and comments
Co-authored-by: atmyers <atmyers2@gmail.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
|
* Added ParticleBoundaries and reflecting boundary conditions
* Added ParticleBoundaries::AllNone
* Allowed different particle boundary conditions on each side of the domain
* Updated the documentation for particle boundaries
* Fix end of line space in Docs/source/running_cpp/parameters.rst
* Updated the reflecting BC to use boundary input group
* Fixes to reflective boundary conditions
* Bug fix in AsStored
* Added particle boundaries regression test particle_boundaries_3d
* Fixed particle_boundaries_3d.json
* Minor updates
* Added algo.particle_shape to test case
* Remove do_pml from test case
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
* Need to explicitly turn off pml in CI test
* Re-add include
* Fixed includes
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
|
(#2046)
|
|
* Introduce new option skip_deposition
* Properly implement the option to skip deposition
* Skip deposition for electrostatic solver
* Correct typo
* Add Index Enumerator and Equations for F/G Without Averaging
* Define new functions for current deposition and charge deposition
* Disable interpolation between levels
* Correct compilation error in RZ mode
* Add argument for relative time
* Add Index Enumerator and Equations for F/G With Averaging
* [skip ci] Add new OneStep function
* Fix compilation errors
* Correct more compilation errors
* [skip ci] Fix compilation
* Split the PSATD push into separate functions
* Add guards for rho field
* [skip ci] Use new functions in OneStep
* [skip ci] Separate the inverse transform of E_avg, B_avg
* Add deposition of rho
* [skip ci] Prevent deposition of rho if unallocated
* Fix error in deposition function
* Add subcycling of current deposition
* [skip ci] Add inverse transform of averaged fields
* [skip ci] Move component of rho
* Add function to copy J
* Temporarily deactivate contribution from F
* [skip ci] Implement call to linear in J
* Add psatd time averaging for multiJ
* [skip ci] Fix implementation of averaging
* [skip ci] Implement divE cleaning
* Fix Bug for RZ Builds
* Fix Bug for RZ Builds
* Fix Bug in Init of PML Spectral Solvers
* Cleaning
* Cleaning
* Add div(B) Cleaning (G Equation)
* Multi-J Not Implemented with Galilean PSATD or PMLs
* Add 2D CI Test Using Multi-J Scheme
* Add More Inline Comments
* Add More Inline Comments & Doxygen
* Add Doxygen for Constructor of SpectralSolver
* More Doxygen in Class SpectralSolver
* Add Doxygen for New Functions in WarpXPushFieldsEM.cpp
* Add Doxygen for New Functions in WarpX/MultiParticleContainer
* do_dive/b_cleaning Must Be True With linear_in_J Option
* Cast multij_n_depose to Real in Divisions
* New Input Syntax
* Add const where Possible, Fix Warnings
* Docs for New Input Syntax, Fix Abort Messages
* Consistent Use of Idx, IdxAvg, IdxLin
* Improve Documentation of psatd.J_linear_in_time
* Use const Type Qualifier whenever Possible
* Simplify Initialization of Pointer ion_lev
* Improve Doxygen
* Update documentation
* Add Note on NCI to Docs
* Make warpx.do_multi_J_n_depositions Not Optional
* Simplify Logic in getRequiredNumberOfFields
* Use More const Type Qualifiers
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
|
|
* 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>
|
|
|
|
* Introduce relative_time for deposition
* Deposit current at arbitrary time
* Update documentation
* Combine parameters in DepositCurrent
* Explicitly show the time at which the current is deposited
|
|
|
|
|
|
* merge
* wip
* namespace
* eol
* cost
* eol
* fix
* eol
|
|
* Use IntVect for ng_J and ng_rho
* Compute guard cells for J and rho based on dt
* Reset some CI benchmarks
* Fix rebase commit
* Add back +1 cell for rho: fix remaining out-of-bound accesses
* Simplify ASSERTS using new interface of amrex::numParticlesOutOfRange
|
|
* 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
|
|
* Avoid stringent assert statement on GPU
* Fix Pointer Member Access
* fix nGrow with Vector
* Update Source/Particles/WarpXParticleContainer.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
|
|
|
|
* Docs: PSATD Runtime Option
* Tests: PSATD Runtime Option
Add new runtime option to PSATD regression test matrix.
* PICMI: PSATD runtime option
* Source: PSATD Runtime Option
|
|
* CI: Windows
Add an MSVC build to CI.
* Windows: _USE_MATH_DEFINES
Fix:
```
error C2065: 'M_PI': undeclared identifier
```
* Windows: no unistd.h
fix:
```
fatal error C1083: Cannot open include file: 'unistd.h':
No such file or directory
```
* Injector: Trivially Copyable only GPU
Only strictly required when we memcopy to accelerator devices.
* Flex: never-interactive
We don't use the interactive mode, so we can save some performance
and address:
```
Parser\wp_parser.lex.cpp(1503,40): error C3861: 'isatty': identifier not found
```
Alternatively, we can include `<io.h>` on Windows.
* MSVC: Vector<Long> != Vector<long>
Fix return and assignment issues with `amrex::Long` != `long`
in `amrex::Vector`.
```
Particles\MultiParticleContainer.cpp(438,13): error C2440: 'return': cannot convert from 'const amrex::Vector<amrex::Long,std::allocator<__int64>>' to 'amrex::Vector<long,std::allocator<long>>'
Particles\MultiParticleContainer.cpp(452,94): error C2440: 'initializing': cannot convert from 'amrex::Vector<amrex::Long,std::allocator<__int64>>' to 'amrex::Vector<long,std::allocator<long>>'
Particles\MultiParticleContainer.cpp(459,60): error C2665: 'amrex::ParallelDescriptor::ReduceLongSum': none of the 6 overloads could convert all the argument types
Particles\WarpXParticleContainer.cpp(782,51): error C2665: 'amrex::ParallelDescriptor::ReduceLongSum': none of the 6 overloads could convert all the argument types
```
* Windows CI: Parallel Build
|
|
|
|
* replace wherever possible .reset(new with = make_unique
* fixed bug
* fixed bug
* revert WarpXOpenPMD.cpp to the original version
* removed another .reset(new
|
|
* Fix warnings for 2D/3D PSATD builds
* Fix warnings for RZ PSATD builds
* Update FIXME comment: no known bug
* Fix remaining warning for RZ PSATD builds
|
|
* Use fewer guard cells for deposition
* Update some CI benchmarks
* Revert "Update some CI benchmarks"
This reverts commit 2f40062557d75e3f6b2d3ba284332b8a92a0d404.
* Check if shapes and guard cells are compatible only for rho
* Do not allocate one extra guard cell for J
* Add more relaxed check on shapes and guard cells for J
|
|
* option to have absorbing BC for particles, regarless of field BC
* document input parameter particles.absorbing_bc
* minor, just add a small comment
* clarify doc and use better input parameter
* clarify documentation
|
|
* fix << declaration of galilean_shift shadows a member of WarpX >>
* fix << unused mu_stag >>
* fix << unused uxp, uyp, uzp >>
* renamed galilean_shift (member variable of WarpX class) into m_galilean_shift
* renamed v_galilean to m_v_galilean when appropriate
* fixed bug introduced in latest commit
* fix <<comparison of integer expressions of different signedness>>
* Update Source/FieldSolver/FiniteDifferenceSolver/MacroscopicEvolveE.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
|
|
|
Resolves #1279.
|
|
(DIM=2, openMP+MPI, double precision, no advanced solvers, no QED, native output) (#1264)
Depends on #1263
|
|
openMP+MPI, double precision, no advanced solvers, no QED, native output) (#1263)
This PR should fix almost all the compilation warnings in the default configuration (DIM=3, openMP+MPI, double precision, no advanced solvers, no QED, native output...). Or at least it does that on my system (my compiler is `g++ (Ubuntu 9.3.0-10ubuntu2) 9.3.0` ).
I have just two residual warnings:
### 1
```
[ 89%] Building CXX object CMakeFiles/WarpX.dir/Source/Parser/wp_parser.lex.cpp.o
wp_parser.lex.c:1356:17: warning: ‘void yyunput(int, char*)’ defined but not used [-Wunused-function]
```
I don't know if `yyunput(int, char*)` is there for a reason, even if it is not used. So I didn't do anything.
### 2
```
[ 96%] Building CXX object CMakeFiles/WarpX.dir/Source/Utils/CoarsenIO.cpp.o
/home/luca/Projects/warpx_dir/WarpX/Source/Particles/WarpXParticleContainer.cpp: In member function ‘void WarpXParticleContainer::AddNParticles(int, int, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, const ParticleReal*, int, const ParticleReal*, int, int)’:
/home/luca/Projects/warpx_dir/WarpX/Source/Particles/WarpXParticleContainer.cpp:102:44: warning: unused parameter ‘nattr’ [-Wunused-parameter]
102 | int nattr, const ParticleReal* attr, int uniqueparticles, int id)
```
The first line of `AddNParticles` is `BL_ASSERT(nattr == 1); //! @fixme nattr is unused below: false sense of safety` . So I thought that there might be something to fix here and I didn't do anything.
|
|
(#1276)
|
|
|
|
getter / setter methods. These members are implemented using an anonymous struct that will be going away soon in amrex, so this type of access is deprecated. (#1208)
|
|
* Added stub for current correction in RZ spectral solver
* Start implementation of Vay deposition
* Continue implementation of Vay deposition
* Correct deposition of D
* Add phase shift for staggered currents
* Small clean-up
* Fix units in deposition of D
* Implement average of cumulative sum (needs bug fix)
* Start fixing bug in average of cumulative sum
* Still debugging
* Cumulative sums should be correct now
* Subtract averages of cumulative sums:
- current implementation: cumulative sums, inverse Fourier transform, subtraction of averages
- needs to be tested (including units of D after Vay deposition)
- needs to be shortened (too many loops over boxes and ParallelFors)
* [skip CI] Clean up and fix units
* Still fixing units
* [skip CI] Remove temporarily averages of cumulative sums
* [skip CI] Remove distinction between staggered and nodal
* Vay and Esirkepov similar results on periodic single box:
TODO:
- debug (charge not conserved);
- try using compute_shifted_shape_factor as in Esirkepov deposition;
- clean up;
- try on multiple boxes and with correction of mode at 0 frequency.
* [skip CI] Clean up
* Fix bug in 3D deposition
* [skip CI] Clean up
* Fix 2D and 3D implementation:
- simulation results agree between direct and Vay deposition in both 2D and 3D
- Travis CI tests should pass except for check of charge conservation (debug)
* Small clean-up
* Fix bug when compiling in RZ geometry
* Add benchmark json files (will be reset later)
* Do not set zero current at zero frequency
* [skip CI] Revert last commit and clean up
* Fix small bug after reverting commit
* Set nodal test first on Travis
* Fix benchmark for nodal test in 3D
* Fix particle output for nodal test in 3D
* Fix bugs due to staggering
* Rename current nodal Travis tests
* Add Travis tests staggered in 2D and 3D
* Further clean-up after bug fix
* Abort when using Vay deposition with domain decomposition
* Add optional argument of index type to forward FFT
* Fourier shifts can be private members as before
* Small clean-up
* Clean up and improve Doxygen documentation
* Fix small bug in analysis script for 2D tests
* Fix tests (remove E and B fields from particle diags)
* Add option to fill guard cells and docs
* Fix value of last guard cell by enforcing periodicity
* Revert changes merged from #1121
* Clean up style
* Improve docs
* Fix forgotten alignment
* Improve docs
* Make base class functions VayDeposition pure
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
|
|
|
|
* add functor for doing the tmp particles copy for the back-transformed diagnosti
* merge the particle push options into one kernel
* EOL
* fix assertion
* add a FieldGatherandPushPX method to PhysicalParticleContainer
* handle offset in copyAttribs
* allow this functor to be constructed even it we aren't doing the back transformed diagnostics
* EOL
* update the overloads of PushPX for the Photon and RigidInjected ParticleContainers
* function for dispatching the right field gather
* init this val to 0.0
* fix some typos
* handle scaling the fields for rigid injection
* EOL
* don't need to get pointers to E and B arrays in PushPX any more.
* actually I can't remove these yet
* EOL
* variable order bug
* move the QED stuff to the proper place
* EOL
* make sure we don't build these functors unless the runtime options are toggled
* EOL
* perform the field gather prior to the photon particle push
* remove E and B components and FieldGather methods. Reimplement PushP for rigid injected and physical particles
* update ionization to do field gather inline
* remove E and B from the particle diagnostics
* don't write E or B in these tests for particles
* add missing files
* remove EB from the Regtest ini file too
* no need to do this twice
* important typo
* also do the gather inline for the QED processes that need to
* move these sources inside ifdef for QED
* fix bug in RZ
* remove some fields from the Python tests.
* remove all particle E and B comps from json benchmarks
* don't assert that Ey is the langmuir output
* remove uy from this output
* update test
* restore the mesh fields I turned off by mistake
* turn off field IO for a few python tests I missed
* fix typo
* reset Langmuir_multi benchmark
* update Langmuir_multi_nodal benchmark
* update single precision langmuir bench
* update psatd single precision languir one too
* also do ionization_lab
* finally, ionizaiton_boost
* update benchmarks_json/Langmuir_multi_psatd.json
* update benchmarks_json/Langmuir_multi_psatd_current_correction.json
* update benchmarks_json/Langmuir_multi_psatd_momentum_conserving.json
* update benchmarks_json/Langmuir_multi_psatd_nodal.json
* remove the particle E and B from the choices in the docs
* fix offset bug
* also add the Gather subdirectory
* Update Source/WarpX.H
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* add docstring for LowerCornerWithGalilean
* add new source files to CMakeLists.txt
* also need to update the GPU regression tests
* update the name of the output file for this python test
* remove field gather call from FieldDiagnostics
* fix typo in docstring
* init fields to 0
* add docstring to the CopyParticleAttribs constructor
* some explicit amrex::namepace
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
|
|
* Move interpolation functions for MR to new folder
* Preparatory clean-up of old namespace Average for future MR functions
* Add interpolation for MR in new namespace Coarsen
* Change file names Average.H/.cpp to Coarsen.H/.cpp
* Remove Source/Parallelization/WarpXComm.H (not necessary anymore)
* Coarsening for IO and MR in separate files
* Clean up IO and MR Coarsen namespaces
* Remove old interpolation functions (charge and current)
* Void commit: trigger Travis CI build
* Fix GPU build
* Void commit: trigger Travis CI build
* Add Python script to test interpolation points/weights in 1D
* Move using-directives inside namespaces
* Add Doxygen documentation and comments
* Minor style changes
* Improve new Python script
|
|
Cleanup
Cleanup
|
|
* 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
|
|
|
|
|
|
* port rigid injection to the gpu
* eol
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* define csqi
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
|
|
* Fix compiler warnings with DIM=2
* Fix compiler warnings with USE_RZ=TRUE
* Fix compiler warnings with USE_PSATD=TRUE and DIM=2
* Fix compiler warnings with USE_PSATD=TRUE and DIM=3
* Fix bug: discard only return value when calling DefineAndReturnParticleTile
* Remove unused variables not triggering warnings
|
|
* [WIP] costs mf --> costs vector
* [WIP] costs vector
* [WIP] vector costs
* formatting
* makefile
* [WIP] costs vector
* [WIP] *= costs
* wts do not need to divide by num cells
* Tiling safety on CPU
* Add tests
* EOL
* Remove unneeded input
* Update Source/WarpX.H costs documentation
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update timers with times only if user Timers update
* warpx.-->WarpX::
* warpx.-->WarpX::
* warpx.-->WarpX::
* warpx.-->WarpX::
* warpx.-->WarpX::
* add dev synch
* Update Regression/WarpX-tests.ini
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Delete inputs_loadbalance_costs_heuristic
* Update and rename inputs_loadbalancecosts_timers to inputs_loadbalancecosts
* Update WarpX-tests.ini
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
|
|
|
|
* Allowed for more general centering of charge density
* Used rho_nodal_flag in ApplyInverseVolumeScalingToChargeDensity
* Simplify declaration of rho_nodal_flag
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Fix documentation for doChargeDepositionShapeN
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
|
|
Use the `clang-tidy` pass `misc-unused-parameters` to remove unused
parameter warnings.
https://clang.llvm.org/extra/clang-tidy/checks/misc-unused-parameters.html)
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
```
|
|
- 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.
|
|
* add warpx profiler wrapper
* call WX profiler wrapper instead of BL
* EOL and cleaning
* add doc on profile syncs
* do not use PROFILE macros in .H files
* replace WX_PROFILE with WARPX_PROFILE and use bool instead of int
* typo
* this file shouldn't be there
|
|
* Read Galilean velocity
* Prepare structures for Galilean solver
* Started implementing Galilean equations
* Analytical limits for X1, X2, X3, X4 coefficients added
* Slight changes added
* Added Galilean position pusher
* Scale galilean velocity
* Remove unneeded Abort
* Fix Galilean pusher
* Allocate Theta2 array
* Fix definition of coefficients
* Increase guard cells for Galilean
* Add guard cell in particle exchange
* Type corrected
* v_gal added to warpx_current_deposition
* v_gal added to WarpXParticleContainer.H
* Bug fixed - update particle x-position over one time step
* Fix issues with merge from dev
* Preparation for merging dev into galilean.
* Adding galilean shift
* Implemented galilean shift
* Changed method's name from GalileanShift to ShiftGalileanBoundary
* Added doxygen string for ShiftGalileanBoundary
* Removed never used method LowerCornerWithCentering
* Removed temporary comments
* Removed dt as a variable from DepositCharge method and its dependencies
* Converted tab to spaces
* Removed EOL white space
* Add documentation and automated tests
* Fix compilation error
* Add automated test
* Update automated test
* Removed temporary used galilean shift
* Removed temporary used particle's push for Galilean PSATD
* Removed unused statement
* Remove EOL white space.
* Added zero shift for LowerCorner in RZ geometry
* Minor changes to Galilean implementation
* Modifications for GPU
* Fix typo
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
|
|
Fortran to C++: build buffer masks
|
|
|
|
|
|
|
Roelof Groenewald
David Grote
Remi Lehe
Luca Fedeli
Axel Huebl
Edoardo Zoni
Michael E Rowan
Andrew Myers
Weiqun Zhang
MaxThevenet
MaxThevenet
Olga Shapoval
Edoardo Zoni
Andrew Myers
