| Age | Commit message (Collapse) | Author | Files | Lines |
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* 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>
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* Make moving window dimensionality consistent in PICMI
* update PICMI_inputs_plasma_acceleration_1d.py
* two elements for moving window velocity in RZ
* update RZ laser_acceration test
* update PICMI version
* update PICMI Langmuir RZ test
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* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
`.editorconfig`: isort options
https://github.com/PyCQA/isort/wiki/isort-Settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleaning: double np and lib
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* 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>
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* 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
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Hard coded, undocumented convention: turns out this must be the name
of the test that we define in the ini file. Logical, isn't it. Not.
Follow-up to #2593
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* modify requirements.txt and add input file for 1D Python pwfa
* add 1D Python plasma acceleration test to CI
* picmi version
* USE_PSATD=OFF for 1D
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Regression/WarpX-tests.ini
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Cartesian1D class in pywarpx/picmi.py
* requirements.txt: update picmistandard
* update picmi version
* requirements.txt: revert unintended changes
* 1D Laser Acceleration Test
* Update Examples/Physics_applications/laser_acceleration/inputs_1d
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add data_list to PICMI laser_acceleration test
* increase max steps and fix bug in pywarpx/picmi.py 1DCartesian moving window direction
* add data_lust to Python laser acceleration test
* picmistandard update
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Add pre-commit
Add basis for automated pre-commit checks.
Install locally via:
```bash
python3 -m pip install -U pre-commit
pre-commit install
```
See: https://pre-commit.com
* Cleanup: Whitespaces
* Cleanup: requirements.txt order
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* 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>
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* Remove unused function
* Remove `focused` and `projected` for rigid particles
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* do_pml not parsed. remove code that was added to support both types of boundary interface
* add paranthesis
* fix eol and move to BackwardCompatibility
* missing semicolon
* Update Source/WarpX.cpp
* clean input files in examples
* delete do_pml in performance test input
* fixing an example input file in docs
* Update Source/WarpX.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* cleaning up docs
* Update Docs/source/usage/parameters.rst
* fix eol
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* 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
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* Filter Always ON by Default
* Fix CI Tests
* Update Docs
* Fix CI Test dirichletbc
* Default WarpX::use_filter = 0 with RZ FDTD, Add Warnings
* Set WarpX::use_kspace_filter = true by Default, too
* RZ: Fix Bug with PSATD Binary and FDTD Runtime Solver
* Default use_kspace_filter = true, Fix Runtime Issue with Rho Functor
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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 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
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* Read boundary and set periodicity, enumerate BC types, added support for periodic
* separate particle and field boudnary structs
* Update comment for particle struct
* default pml is 0, and reset lo, hi, and do_pml to 1
* turn on pml for MR
* eol
* remove duplication
* resolving commit conflict
* explicitly setting pml_HI_MR
* default pml lo and hi to 0, and set MR pml lo and hi to the domain values if fine patch coincides with domain boundary
* set lo and hi flag for pml when do pml = 1 and domain is non-periodic
* remove commented line
* add doc
* Update Source/Utils/WarpXUtil.cpp
remove empty line
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/usage/parameters.rst
lower case for input
* add do_pml flags for IonAcc2d and PlasmaMirror
* add pml = true in PICMI for gaussian beam and plasma acceleration
* pml is the default field BC
* adding temporary defaults for field and particle BC using periodicity
* fix temp initialization
* set default to pec if input sets pml to 0
* fix typo
* logic for both old and new pml interface
* fix eol
* change examples to original pml input with default values
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* fix comments
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Docs: fix .rst list
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* 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
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* picmi - convert True/False to 1/0
* picmi - update picmi input files to use True/False for booleans
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* 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>
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* 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>
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* 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>
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* add a checksum module for regtests
* All capabilities to checksum tests
* update tests to generate a clean benchmark
* call checksum tests from analysis scripts
* Add checksum json benchmarks
* add missing script, better printing and increase tol
* eol
* fix permission, and bump tolerance
* chmod +x checksumAPI.py
* update benchmarks, probably old ones were wrong due to parallelization
* remove unused variable, thanks lgtm
* special handling when the benchmark is 0
* non-zero but very small CFL for 1 step for init tests
* reset erroneous Python benchmarks
* slightly bump tolerance for initial distribution test
* too small dr results in nans
* improve prints, tolerance handling, and fix tests
* typo
* enable tolerance and fields/particles optional comparison to fix tests
* more minor cleaning in space charge initialization tests
* update Python benchmarks for serial runs
* Run Python tests with 1 rank instead of 2
* fields that are zero should not be in reg tests
* Add developer documentation on checksum regression tests
Co-authored-by: Tools <warpx@lbl.gov>
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* Implemented new particle diagnostics in picmi
* Cleaned up picmi adding new particle diagnostics
* In PICMI examples, use name option for diagnostics
* For travis, update ubuntu version to bionic
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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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(#893)
Co-authored-by: David Grote <dpgrote@lbl.gov>
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* first implementation, doesnt link
* fix species type and use it in some examples
* eol
* typo in input file
* Apply suggestions from code review
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-Authored-By: Yinjian Zhao <yinjianzhao@lbl.gov>
* changes suggested by review
* put species functions into a namespace
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-authored-by: Yinjian Zhao <yinjianzhao@lbl.gov>
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* avoid duplicate tests and plot less often
* fix tests I broke when trying to save plotfiles
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Clean up input files in Examples/
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- 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)
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- 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
- change wrong permissions from executable to read/write
- update entries in /Regression/WarpX-tests.ini for Travis CI
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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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driverback doesn't need the rigid injection stuff
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Luca Fedeli
Remi Lehe
Prabhat Kumar
Axel Huebl
Neïl Zaim
Revathi Jambunathan
Edoardo Zoni
roelof-groenewald
David Grote
Andrew Myers
MaxThevenet
Edoardo Zoni
Tools
Andrew Myers
Weiqun Zhang
