| Age | Commit message (Collapse) | Author | Files | Lines |
|---|
|
* Clean up examples folders
* Use `snake_case` names
* Rename `nci_corrector` as `nci_fdtd_stability`
|
|
* Start removing old BTD
* Remove GetCellCenteredData
* Remove do_backtransform_fields and do_backtransform_particles
* Remove more functions
* Remove more variables
* Update documentation
* Fix CI test `RigidInjection_BTD`
* Remove slicing from `BTD_ReducedSliceDiag`
* Rename `BTD_ReducedSliceDiag` as `LaserAcceleration_BTD`
* Query deprecated input and abort
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
|
|
plotfile/openPMD (#3424)
* print when writing openPMD, Ascent, Sensei
* remove unnecesssary variables, include min_digits
* print snapshot id when writing btd
* fix ascent print
* compile without warnings
* still working on Ascent
* still working Ascent
* Print when BTD buffer is flushed
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* print when writing openPMD, Ascent, Sensei
* remove unnecesssary variables, include min_digits
* print snapshot id when writing btd
* fix ascent print
* compile without warnings
* still working on Ascent
* still working Ascent
* Print when BTD buffer is flushed
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* add warning message if BTD not full
* adjust for CI, no in-situ vis BTD
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* revert to correct plotfile naming
* change warning topic to BTD
* nicer format for print statements
* extend examples to fill BTD
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Reset Checksums of BTD_ReducedSliceDiag
* Upgrade CI Test LaserAccelerationBoost
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* improve BTD warning notes
* edit final step notes
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix formatting
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
|
* BTD diagnostics specified by intervals
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* address CI errors
* refactor and test
* no duplicate or out-of-order snapshots
* update documentation and tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* clean for CI
* still fighting CI
* Update Source/Diagnostics/BTDiagnostics.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* refactor includes
* add an explicit constexpr
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* describe algorithm for BTD intervals list
* revert to old description of num_snapshots_lab
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* preserve behavior of num_snapshots_lab
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
|
|
* CI: Test New BTD in `BTD_ReducedSliceDiag`
* Compare Legacy BTD vs. New BTD
* Fix Bug in Loading of openPMD Array Data
* Fix CI Analysis
|
|
* fix BTD particle container BA, geom, and add assert for probhi == 0
* fix bug with mesh-refinement
* delete commented line
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* with offset added, we dont need the assert anymore
* similar to plotfile, openpmd also initializes tmp from pinned pc, and no need to reset BA
* commenting out the assert
* changes consistent with #3201
* unused var warning fix
* Compute snapshot box at init, expand and shrink buffer BA and particle BA before and after redistribute, close buffer when klab_current == k_lo for that buffer
* unused var
* turning off particle output in BTD CI tests for plotfiles
* reset particle BA only if species output is finite
* add particle output for plotfile format for BTD tests
* add openpmd diags back in 2d test case
* fix input to have the right format
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
|
|
* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
|
|
* move BTD call before Redistribute
* define particle buffer, BTD particle functor, particle filter
* select particles on the slice
* add particle functors
* add Lorentz Transform
* fix conflict
* add call to loretnz operator
* storing Particles in buffer
* This is WIP. Added particle buffers, filled them, sent them for flush with number already flushed. Does not work for multiple flushes. Crashes for OpenPMD.
* trailing endif after rebase
* adding print statements and not flushing particles in OPENPMD if numpart is 0
* last timestep flush is ensured at the end of evolve loop
* fix bug in declaring uy uy new and computing uzp
* set particle Geom, BA, and DMAP for particle flush with plotfile
* set Particle BA Geom DMAP for particle buffer and no BTD transform for force flush
* separate compute and pack from flush
* Fix Typo: resizeable -> resizable
Fixes HDF5 BTD particle output.
* new class for plotfile particles for BTD
* copy particle_H and DATA and Header. some WIP print statements
* Merge plotfile
* clean print statements
* fix warning message
* struct declaration in header, fix warning
* doxygen comments and copyright
* clean print statements
* fix eol and override function warning
* tile data
* fix output species array size bug
* fix access for particle buffer size
* clean and move time-update
* add cur_time update back
* remove cur time update which was called twice
* dont access particles flushed already for full diagnostics
* cur time must be updated for RigidInjection BTD CI test to pass
* temporarily move call to BTD
* updating time and calling BTD before movewindow
* cleanup
* reset benchmarks and analysis script
* clean and add comments
* fix particle box array, geom, dmap
* reset benchmarks for multi_J rz and ElectrostaticSphereEB_mixedBC
* wip commit
* wip commit
* add SI conversion
* abort for openpmd bp backend if species is selected. Also write particle output for BTD only if write_species is 1
* add documentation for aborting if adios is used with openpmd and add other BTD input parameters
* Apply suggestions from code review
commit Axel's suggestions from review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* use bool instead of int
* fix doxygen format
* using h5 as backend in example test to ensure consistency with abort for particle output.
* fix doxygen comment
* reset benchmark again for comoving_2d_psatd galilean_2d_psatd multi_J_rz_psatd
* reset benchmark for background_mcc
* self-review suggestions
* reset benchmarks. Update with last snapshot full info
* Axel's PR suggestions
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's doxygen fix
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add comments
* fix eol
* improved exception handling for stringsteam
* PR suggestions
* Axels' suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's suggestions :)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* simplify logic
* suggestions from review (Axel/Reva)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* variable name change for clarity
* if num particles in tmp array is 0, return
* Use new BTD inputs to set up BTD for particles in the corresponding particle container
* unused var
* fix logic error
* speciesID undefined
* separate particle and field buffer calls and initialization for BTD. Data common to both are initialized separately
* rename variable so it does not ghost existing varname
* add more comments
* Assert that fields are on
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* redundant function definition
* unused variable
* unused variable zp
* 1D 2D 3D definition
* fix else
* Apply suggestions from code review
Add Prabhat's suggestion
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
* missing semicolon and ignore xp yp for 1D
* resetting benchmarks for boosted sims and mcc sim
* temporarily changing tolerance since the relative difference for momentum_z is 3.68e-3 and the current tolerance is 2.5e-3
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
|
|
* Docs: `geometry.dims` option
Add a new, required option to specify the geometry of an
inputs file at runtime.
* Check & Report Runtime Dims Mismatch
* Examples: add `geometry.dims`
* Deprecation Warning: `geometry.coord_sys`
* PICMI: `geometry.dims`
* Improve error message
sounds a bit better
* Improve Doc Description
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
|
|
* Examples: Python ShellBang & Executable
Make sure that all PICMI scripts and all analysis Python scripts
in `Examples/` are:
- executable (`chmod a+x`)
- start with a shell-bang to `python3`
Now, all scripts can be run directly without a `python3 ...` prefix
and also default to the only right executable of Python on older
systems. (New systems always have a `python3` alias, too.)
* Revert a moved numpy
|
|
* Simplify momentum initialization in example input files
* Update benchmarks
* Trigger Build
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Add more amrex prefix
* Remove using namespace amrex in PlasmaInjector.cpp
* Fix compilation with OpenPMD
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
|
|
By accident, the 2nd test did not use plotfile output.
|
|
* support only new boundary interface. set pml flags to 0 as default
* use new boundary interface in Examples/Modules/
* use new boundary interface in the input for tests in Examples/Physical_applications
* use new boundary interface in the input for tests in Examples/Tests
* use new bc
* fix typo
* fix typo
* Update Examples/Tests/SingleParticle/inputs_2d
* fix bc in input
* specific bc for electrostatic inputs
* resetting benchmark for PEC particle CI test after fixing the default pml flags from 1 to 0
* Update Examples/Physics_applications/laser_acceleration/inputs_2d_rz
* remove documentation on previous boundary input
* Comment to clarify where in the code is_periodic is appended and how it is defined
* add default parameters for BC in doc
|
|
Add tests for the new BTD diagnostics, so that parallely working
developers can easier test this.
Currently covered features:
- field BTD (particles are still WIP)
- openPMD & plotfiles
|
|
* Implemented query and getArrWithParser
* Updated parameters.rst regarding expressions for multiple floats
|
|
* Define New Input Parameter interpolation.shape_factors_order
* Use New Input Parameter, Remove Obsolete Ones
* Add New Input Parameter to PICMI Interface
* Update Docs, Use New Input Parameter in Remaining Input Files
* Cleaning
* New Name: algo.particle_shape
|
|
* Unify intervals notation
* Fix diagnostic intervals with PICMI
* Use new syntax in updated Larmor test
* Update PICMI to comply with the standard
* Update new hybrid test
* Update particles_in_PML test input files
|
|
* Input: Remove n<something> options
The information in
- lasers.nlasers
- particles.nspecies
- collisions.ncollisions
is redundant with their `<...>.names` counter-part and requires users
to change info at two locations. We just remove this now since we can
query the size of names automatically in the parser.
* Examples: remove n<something>
Removes:
- lasers.nlasers
- particles.nspecies
- collisions.ncollisions
from examples.
* QED: Update nspecies
* Removed nspecies and nlasers from the Python interface
Co-authored-by: Dave Grote <grote1@llnl.gov>
|
|
* Rename Input to `algo.maxwell_solver`
Rename the input option `algo.maxwell_fdtd_solver` to
`algo.maxwell_solver` and throw a useful error message for users
using the old option.
This is in preparation to unify FDTD and PSATD input control to
reduce mutually exclusive binary variants of WarpX.
* MW Solver Name: Update Examples
Update all example to use the new algo.maxwell_solver option.
* Fix typo in comutation of dt
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
|
|
* 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>
|
|
* always print error and tolerance before ASSERT in CI tests
* eol
* fix typos
* more typo
* typo
|
|
|
|
|
|
- remove wrong extension '.rt' from previous commits ('rt' string
denotes regression tests and does not represent a file extension)
- put back string 'rt' in input file names wherever needed
- update entries in Regression/WarpX-tests.ini for Travis CI
- add entries in Regression/WarpX-tests.ini corresponding to input files
previously not tested: now testing only run (no analysis)
|
|
- add strings '2d' or '3d' for dimensionality of test case
- use '.' only to separate file names from file extensions
- use uniform file extension '.rt' in all input files
- match few input file names with corresponding Python scripts names
- update entries in /Regression/WarpX-tests.ini for Travis CI
|
|
back-transformed
|
|
|
|
|
|
|
|
CopyParticlesInZBoostSliceUsingGPU
|
|
option.
|
|
|
|
|
|
input for the automated test.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Edoardo Zoni
Remi Lehe
Ryan Sandberg
Revathi Jambunathan
Axel Huebl
Neïl Zaim
David Grote
MaxThevenet
LDAmorim
Tools
Edoardo Zoni
RevathiJambunathan
Weiqun Zhang
Revathi Jambunathan
Jean-Luc Vay
