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2023-02-27Change plotfile RZ allowed diags to r,t from x,y (#3663)Gravatar Ryan Sandberg 1-1/+1
* change plotfile RZ allowed diag to r,t from x,y * Change labeling in checksums * add rz silver mueller analysis script * make analysis_silver_mueller_rz.py executable * change x,y fields to r,t in more tests * x->r in MR RZ checksums * correct analysis for plotfiles saved as 'boxlib' * add self to creator list * change rz diags in PICMI * correct PICMI changes * another y->t in an rz test * update picmi plotfile rz btd names * review suggestion to condense analysis * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-01-17Modify refined injection CI test for anisotropic ref ratio (#3605)Gravatar Prabhat Kumar 1-5/+6
* Modify refined ijection CI to account for anisotropic ref ratio * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * change n_move based on new dt * change variable name to be more specific * Update Regression/WarpX-tests.ini Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * reset benchmark for RefineInjection because now it uses anisotropic refinement ratio * add comment to show the formula for n_move * Reset benchmark of `RefinedInjection` * Remove wrong benchmark file Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-10-25Diagnostics: print when writing openPMD/Ascent/Sensei and BTD ↵Gravatar Ryan Sandberg 1-5/+8
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>
2022-10-12Correct particle positions outside refined injection (#3463)Gravatar Remi Lehe 1-2/+11
* Correct particle positions outside refined injection * Improve test * Update benchmark * Update Examples/Physics_applications/laser_acceleration/analysis_refined_injection.py
2022-09-23fix labels in inputfiles (#3422)Gravatar Luca Fedeli 3-3/+3
2022-08-22Remove outdated comments from example input files (#3332)Gravatar Luca Fedeli 4-4/+4
Update comments in example input files: moving window now available along x, y, z.
2022-08-17Allow filtering in z with RZ FDTD (#3281)Gravatar David Grote 1-1/+2
* Allow filtering in z with RZ FDTD * Update the error message about filtering in RZ * Turned z filtering on in laser_acceleration/inputs_rz * Update LaserAccelerationRZ benchmark, including z filtering
2022-08-04Species variables in diagnostics: deal with runtime components (#3218)Gravatar Neïl Zaim 1-1/+1
* Species variables in diagnostics: deal with runtime components * Remove ParticleStringNames namespace * Use const reference in iteration variable * Fix ion acc 2D test * Output extra (e.g. initialized later with python) comps by default * Always output theta in RZ * Fix QED tests * Fix Laser Acceleration RZ test
2022-04-04Moving Frame Field Probe Functionality (#2996)Gravatar Tiberius Rheaume 3-0/+42
* DRAFT for Moving Frame * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adds m_last_compute_step * Generalized SetParticlePosition, semicolons and formatting * Update Source/Diagnostics/ReducedDiags/FieldProbe.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Moved particle push before calculations. Condensed stuff. * Fixed Velocity, added start and stop time functionality * Documentation * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Empty-Commit * Fixed ParallelFor from review * FP moving window in laser_acceleration 1d, 2d, 3d test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Line detector instead of point 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>
2022-03-22openPMD RZ modes dumped in thetaMode (#2878)Gravatar Ryan Sandberg 1-1/+0
* [Draft] openPMD: RZ Modes * Change 'theta' to 't' and 'J' to 'j' * Docs: openPMD rz notes * editing docs openPMD RZ note * erase cartesian E,B,j from openPMD rz diags list * openpmd rz: theta->t, exclude xyz dumps * openpmd rz: axes r,z, save as comp[mode][r][z] * catch logic bugs tracking when in rz mode * change return type to c++17 tuple in helper fn * allow divB functor to store in theta mode * tuple bindings / account for theta mode variables * only r,t,z componets in RZ, separate rz field init * separate rz field init, arbitrary diags in RZ * docs: xyz comps in cartesian, rtz in rz geometry * docs : remove mention of dump_rz_modes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clarify documentation of InitializeFieldFunctorsRZ * n_rz_modes = 1 if not in RZ * style change for brackets * style, documentation, clarify magic constants * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add helper getVec * transpose RZ openPMD data for proper viewing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * safe for 2d and rz * fix transpose order of limits, add tinyProfiler * document transpose function, lack of optimization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix divB num components * keeping changes to openPMD+RZ, not general RZ * divB made more similar to divE * eliminate or document unused variables * fix openPMD+RZ documentation * change thetaMode parser to regex * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replace n_rz_azimuthal_modes with warpx variable ncomps * Ignore Unused Var in Cartesian * add rz openpmd analysis * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix warnings: unused vars * clarify documentation of dump_rz_modes * cleaning up before sending to PR * remove divB, divE, test in a different PR * Update Source/Diagnostics/WarpXOpenPMD.cpp fix Dxygen strings Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * clean up doxygen, note issue in divB * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixing rz_opmd test, still not passing * Fix: Unused <diag>.dump_rz_modes * updating openPMD+rz analysis * Regression Setup: set `outputFile` * Use HDF5 Backend This is most likely installed by all developers, so we use it for tests. * Code Style Updates * simplify test and reduce code redundancy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reduce redundancy 1 less line * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Keep HDF5 HDF5 is easier to install for developers and provided in CI. * Style fixes * Style fix 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>
2022-03-03Rename `serialize_ics` as `serialize_initial_conditions` (#2925)Gravatar Edoardo Zoni 7-7/+7
* Rename `serialize_ics` as `serialize_initial_conditions` * Add Backward Compatibility Check
2022-02-11User-defined integer and real particle attributes (#2735)Gravatar Revathi Jambunathan 3-0/+11
* define user attributes, parse them, initialize with respective parsers * fix warning by using static_cast for int attribute as parser returns real * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean-up from self-review * adding dimensionless velocity, gamma*v/c and time to parser argument * add documentation * typo in comment * unused var * device vector for kernels * particle attribute in developer doc * data ptr for device vector * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ignore_unused * Docs: Describe all particle attributes including pre-defined ones :) * Docs: Fix formatting (user params) * Add: 1D and RZ Support * Docs: Fix Typo in Function Declaration * Laser-Ion Example: User-Defined Attrib. Add two user-defined attributes to the laser-ion acceleration example. This is a 2D test. Documents the name in the table of commonly used, user-defined attribute names. The attribute added is the original position of particles, which I like to plot in "potential" plots that correlate original position in the target with final energy. * changing user-interface API with .attribute. and no need for separate 1D 2D 3D RZ code for parser. pos.x/y/z returns the right values * Adding 1D, 3D, and rz tests * attribute in inputs * at(i) * refinining names for inputs for laser ion and acceleration tests * typo in input * reset benchmarks for test-cases that included attributes Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-023D LWFA PICMI Test: Add Electron Beam (#2723)Gravatar Edoardo Zoni 1-0/+30
* LWFA PICMI Tests: Add Electron Beam * Remove Electron Beam from 1D Test
2022-01-25RZ FDTD: Filter Not Working (Abort) (#2775)Gravatar Edoardo Zoni 2-2/+2
* RZ FDTD: Filter Not Working (Abort) * Update CI Tests and Benchmarks
2022-01-12Make moving window dimensionality consistent in PICMI (#2721)Gravatar Prabhat Kumar 2-2/+2
* 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
2022-01-04Add PICMI Scripts for LWFA Tests (#2700)Gravatar Edoardo Zoni 9-160/+589
* Add PICMI Script for 2D Case * Add PICMI Script for 3D Case * Cleaning * Add PICMI Script for 1D Case * Add PICMI Script for RZ Case * Remove Old PICMI Script * Remove Old Test Python_LaserAccelerationMR * inputs_3d: Move Inputs From runtime_params * inputs_2d: Move Inputs From runtime_params * Update PICMI Script for 2D Case * Update PICMI Script for 3D Case * inputs_1d: Move Inputs From runtime_params * inputs_2d_rz: Move Inputs From runtime_params * Rename inputs_2d_rz as inputs_rz * Update PICMI Script for 1D Case * Update PICMI Script for RZ Case * inputs_rz: Fix Diagnostic Interval * Fix Diagnostic Interval For All Inputs * Add New Test For Each PICMI Script * Remove Old PICMI Script From Workflow yml Files * Dump RZ Modes for RZ Case * LWFA PICMI: Add Shellbang Add missing shellbang lines. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-21pre-commit: Python imports (#2686)Gravatar Axel Huebl 2-0/+4
* 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 5-5/+5
* 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>
2021-12-15Examples: Python ShellBang & Executable (#2673)Gravatar Axel Huebl 1-1/+1
* 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
2021-12-14Fix: `pre-commit run -a` (#2671)Gravatar Axel Huebl 1-1/+0
Prepare to enable autofix bot from https://pre-commit.ci
2021-12-091D tests for plasma acceleration (#2593)Gravatar Prabhat Kumar 2-1/+68
* 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>
2021-11-19add github ci compile check for ascent (#2483)Gravatar Cyrus Harrison 1-0/+76
* add github ci compile check for ascent * now with less whitespace * add ascent to insitu workflow * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * more style * try to run as existing user * new container * use env script * path fix * add ascent test * fix space * move test resources * get into style * style * Ascent CI: Cleanup (#1) - make sure inputs file stays up-to-date - locate alongside example * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * rename test file * fix for cp * improve color table for vol rendering * now with rotation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-08Install pre-commit (#2532)Gravatar Axel Huebl 3-3/+1
* 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
2021-10-23Add automated test of refined injection feature. (#2473)Gravatar Andrew Myers 1-0/+51
* Add automated test of refined injection feature. * revert accidental changes * missing import * fix typo in analysis script * add checksum stuff to analysis script * add benchmark file
2021-10-19Simplify momentum initialization in example input files (#2309)Gravatar Neïl Zaim 4-5/+5
* 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>
2021-09-30Rigid injected species: Remove unused function and variables (#2350)Gravatar Remi Lehe 1-2/+0
* Remove unused function * Remove `focused` and `projected` for rigid particles
2021-09-02Bug fix in call to RhoFunctor for RZ modes (#2271)Gravatar David Grote 1-0/+1
2021-07-21Use new boundary input (#2110)Gravatar Revathi Jambunathan 4-8/+21
* 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 1-1/+2
* 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
2021-06-07Call function ReadBCParams() during python execution (#1972)Gravatar roelof-groenewald 1-0/+2
* 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
2021-05-11New Input Parameter for Order of Shape Factors (#1934)Gravatar Edoardo Zoni 4-12/+12
* 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
2021-02-10new setup.py: PYWARPX_LIB_DIR support (#1698)Gravatar Axel Huebl 1-0/+2
* new setup.py: PYWARPX_LIB_DIR support Add support to build in a quick and modular way against pre-built C++ WarpX libraries through a `PYWARPX_LIB_DIR` hint to the root `setup.py`. * new setup.py: add WarpX_PRECISION * CI: PYWARPX_LIB_DIR in new setup.py
2021-01-14Unify intervals notation (#1485)Gravatar NeilZaim 4-4/+4
* 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
2020-10-22Docs: Ascent Replay Workflow (#1331)Gravatar lge0303 1-0/+93
* Document for ascent replay * ascent replated repository * Apply suggestions from code review * Review of replay - rendering plot without run simulation * modify Review of replay - accept Axel suggestion * modify replay - remove png file * Remove PNG Too large for git * Replay: Restructure Workflow * Remove duplicated files Well documented in the LWFA example and text now. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-07-27Input: Remove n<something> options (#1217)Gravatar Axel Huebl 4-8/+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>
2020-07-27Rename Input to `algo.maxwell_solver` (#1188)Gravatar Axel Huebl 1-1/+1
* 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>
2020-07-17LWFA: Diag add Charge Density (#1048)Gravatar Axel Huebl 4-1/+6
* LWFA: Diag add Charge Density Dump the charge density in the LWFA example by default. This is a common quantity to visualize when getting started, so we adjust this to be generated by default. * reset benchmark: LaserAcceleration (add rho) Co-authored-by: Tools <warpx@lbl.gov>
2020-07-09Fix bug and test with LaserAccelerationRZ (#1150)Gravatar Edoardo Zoni 1-0/+1
2020-06-05Fixed bad arguments in PICMI_inputs_laser_acceleration.py (#1074)Gravatar David Grote 1-3/+2
Note that polarization_angle was changed to 0 since that was the value being used because the polarization_argument was bad.
2020-06-03Add checksum regression tests (#1065)Gravatar MaxThevenet 1-1/+3
* 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>
2020-05-14Implemented new particle diagnostics in picmi (#984)Gravatar David Grote 1-2/+4
* 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
2020-05-01Delete old diagnostics (#933)Gravatar MaxThevenet 5-17/+21
* 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>
2020-03-13Add limit to #parts in theta in RZ (#765)Gravatar L. Diana Amorim 1-1/+1
* Added abort error for insufficient #cells in phi * Fixed language in error message * Added #parts per theta limit in docs * Fixed initialization of n_rz_azimuthal_modes * Fixed abort message cpp errors * Fix n_rz_azimuthal_modes read from WarpX class * Fix wrong index in num_particles_per_cell_each_dim * Fix PR# and abort message without additional variable * Fixed LWFA RZ example * Changed Abort to AssertWithMessage * Corrected inequality to include case of x2 * RZ #modes=1 by default. Fix #parts in theta =2 * Fix to LWFA RZ #modes=2 #parts in theta=4 * Added limitation in #parts in theta for NRandomPerCell style
2020-03-02Option to specify the type of physical species (#746)Gravatar MaxThevenet 1-4/+2
* 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>
2020-02-19avoid duplicate tests and plot less often (#726)Gravatar MaxThevenet 1-1/+1
* avoid duplicate tests and plot less often * fix tests I broke when trying to save plotfiles
2020-01-23OCD fix: Laser sectionGravatar L. Diana Amorim 1-1/+1
2020-01-09Clean up input files in Examples/:Gravatar Edoardo Zoni 4-0/+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/Physics_applications/:Gravatar Edoardo Zoni 4-0/+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 - change wrong permissions from executable to read/write - update entries in /Regression/WarpX-tests.ini for Travis CI
2020-01-03Fix diagnostic period in PICMI_inputs_laser_acceleration.pyGravatar Dave Grote 1-2/+2
2019-12-10Changed several Python tests to run simulationGravatar Dave Grote 1-2/+2
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