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2022-12-02Clean up examples folders (#3545)Gravatar Edoardo Zoni 4-314/+0
* Clean up examples folders * Use `snake_case` names * Rename `nci_corrector` as `nci_fdtd_stability`
2022-11-09BTD: remove old/legacy back-transformed diagnostics (#3485)Gravatar Remi Lehe 2-30/+9
* 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>
2022-10-25Diagnostics: print when writing openPMD/Ascent/Sensei and BTD ↵Gravatar Ryan Sandberg 1-1/+1
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>
2022-09-24BTD diagnostics specified by intervals (#3367)Gravatar Ryan Sandberg 1-1/+1
* 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>
2022-09-07CI: Test New v. Legacy BTD in `RigidInjection_BTD` (#3327)Gravatar Edoardo Zoni 2-38/+85
* Improve Testing of New v. Legacy BTD * openPMD: Flush Series before Accessing Arrays Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> * Add Checksums for RigidInjection_BTD (BTD data) * Compare Also Particle Momenta (BTD data) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-08-10Initialize particle runtime attributes inside AddNParticles (#3272)Gravatar Neïl Zaim 2-0/+19
* Initialize particle runtime attributes before calling AddNParticles * Avoid Multiplication result converted to larger type warning * Directly initialize runtime attributes inside AddNParticles * Update doxygen comment
2022-07-24Bug fix for BTD - particle BA, and geom, same as field buffer (#3056)Gravatar Revathi Jambunathan 1-1/+2
* 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>
2022-03-03Rename `serialize_ics` as `serialize_initial_conditions` (#2925)Gravatar Edoardo Zoni 2-2/+2
* Rename `serialize_ics` as `serialize_initial_conditions` * Add Backward Compatibility Check
2022-01-19RigidInjection_BTD: Specify H5 Backend (#2761)Gravatar Axel Huebl 1-1/+2
We default to `.bp` files when available. This results for this test in: ``` amrex::Abort::0:: Currently BackTransformed diagnostics type does not support species output for ADIOS backend. Please select h5 as openpmd backend !!! ```
2021-12-21pre-commit: Python imports (#2686)Gravatar Axel Huebl 2-3/+6
* 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>
2021-12-21Inputs: `geometry.dims` option (#2685)Gravatar Axel Huebl 2-2/+2
* 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>
2021-12-16Generalize Analysis Scripts: Number of Digits (plt) (#2683)Gravatar Axel Huebl 1-1/+2
* Update Scripts to Handle New File Names * Use glob in Analysis of Collision Tests * Use rstrip in Analysis of Collision Tests * Regex: Match ends-in-digits Thanks Phil! :) Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
2021-12-15Examples: Python ShellBang & Executable (#2673)Gravatar Axel Huebl 2-2/+2
* 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
2021-09-30Rigid injected species: Remove unused function and variables (#2350)Gravatar Remi Lehe 2-4/+0
* Remove unused function * Remove `focused` and `projected` for rigid particles
2021-07-21Use new boundary input (#2110)Gravatar Revathi Jambunathan 2-4/+10
* 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
2021-07-01Filter Always ON by Default (#2031)Gravatar Edoardo Zoni 1-0/+1
* 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
2021-05-20CI: Add BTD Tests (#1973)Gravatar Axel Huebl 1-4/+22
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
2021-05-11New Input Parameter for Order of Shape Factors (#1934)Gravatar Edoardo Zoni 2-0/+8
* 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
2021-01-14Unify intervals notation (#1485)Gravatar NeilZaim 2-2/+2
* 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
2020-07-27Input: Remove n<something> options (#1217)Gravatar Axel Huebl 2-2/+0
* 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>
2020-06-03Add checksum regression tests (#1065)Gravatar MaxThevenet 1-0/+5
* 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>
2020-05-01Delete old diagnostics (#933)Gravatar MaxThevenet 2-2/+10
* 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>
2020-05-01Most fun PR ever: print error and tolerance before ASSERT in CI (#967)Gravatar MaxThevenet 2-6/+15
* always print error and tolerance before ASSERT in CI tests * eol * fix typos * more typo * typo
2020-01-27Automatically add copyright header with update_copyright.shGravatar Tools 2-0/+15
2020-01-14Merge pull request #605 from EZoni/cleanup_examples_input_filesGravatar MaxThevenet 2-0/+0
Clean up input files in Examples/
2020-01-13fix lgtm warningsGravatar Luca Fedeli 2-3/+1
2020-01-09Clean up input files in Examples/:Gravatar Edoardo Zoni 2-0/+0
- 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)
2020-01-08Clean up input files in /Examples/Modules/:Gravatar Edoardo Zoni 2-0/+0
- 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
2019-10-25replace 'boosted frame diags' with 'back-transformed diags'Gravatar MaxThevenet 1-1/+1
2019-10-07move test to boosted_diags and use relative error for assertGravatar MaxThevenet 2-156/+0
2019-10-07Removing commented out line in inputs.BoostedFrame_testSliceGravatar RevathiJambunathan 1-1/+1
2019-10-07Merge branch 'ChangeOutputDirectoryForLabFrameSnapshotData' of ↵Gravatar RevathiJambunathan 1-2/+2
https://github.com/RevathiJambunathan/WarpX into SliceInLabFrameForBoostedSim
2019-10-01fixing EOL spaceGravatar RevathiJambunathan 2-4/+4
2019-10-01Adding files to automatically test the reduced back-transformed diagnostics ↵Gravatar RevathiJambunathan 2-0/+156
and fixing EOL space
2019-09-23use read_raw_data functions in tests instead of redefiningGravatar MaxThevenet 1-14/+2
2019-09-20Changing the output directory for the boosted frame diag tests from ↵Gravatar RevathiJambunathan 1-2/+2
lab_frame_diag/ to lab_frame_diag/snapshots/
2019-09-11Source & Tools: No EOL WhitespacesGravatar Tools 1-2/+2
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 ```
2019-08-15re-define assert since fix to rigid injection has been mergedGravatar MaxThevenet 2-4/+2
2019-08-15relax assertion until rigid injection is fixed in other PRGravatar MaxThevenet 2-2/+4
2019-08-15add comments in analysis scriptsGravatar MaxThevenet 2-0/+29
2019-08-15some renamingGravatar MaxThevenet 4-0/+0
2019-08-15RigidInjection test in boosted frame using back-transformed diagsGravatar MaxThevenet 2-0/+88
2019-08-15update read_raw_data to avoid warning for deprecated Python syntaxGravatar MaxThevenet 1-0/+0
2019-08-14add inputs and analysis for rigid injection test in LAB FRAMEGravatar MaxThevenet 2-84/+92
2019-05-29Use new algorithm string in examplesGravatar Remi Lehe 1-4/+0
2019-05-07updated Examples and picmiGravatar MaxThevenet 1-5/+0
2018-09-28Created subdirectories in Examples and move examples in these subdirectories.Gravatar Jean-Luc Vay 1-0/+97
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