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2022-08-15Move handling of do_not_deposit to physics callers (#3225)Gravatar Phil Miller 1-0/+1
* Rearrange in preparation for lifting do_not_deposit higher in the call stack * Make do_not_deposit public, so callers can test on it * Make all DepositCharge call sites respect WarpXParticleContainer::do_not_deposit * Drop check for do_not_deposit in DepositCharge * Fix comment to accurately describe np_to_depose * Fix logic to account for other logic in AddSpaceChargeField * Match zero charge density array to filled array in RZ PSATD case * Structure control flow per @dpgrote's preference * Reword comment for clarity
2022-08-10Initialize particle runtime attributes inside AddNParticles (#3272)Gravatar Neïl Zaim 1-3/+5
* Initialize particle runtime attributes before calling AddNParticles * Avoid Multiplication result converted to larger type warning * Directly initialize runtime attributes inside AddNParticles * Update doxygen comment
2022-08-02`SyncCurrent`: Pass References To Current MultiFabs (#3277)Gravatar Edoardo Zoni 1-2/+4
* `SyncCurrent`: Pass References To Current MultiFabs * Add Doxygen for `SyncCurrent`
2022-06-02Move warning logger in ablastr (#3154)Gravatar Luca Fedeli 1-2/+5
* initial work to move the Warning Logger into ablastr * progress with warn manager class * moved Warning Logger in ablastr * fixed bugs * Fix: `SpectralFieldDataRZ.cpp` Missing include for `WarpX::getCosts(lev);` Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-06-01Clean-up in python wrappers to access particle data (#2531)Gravatar Roelof Groenewald 1-30/+15
* use numLocalTilesAtLevel instead of an empty particle iterator loop to determine the number of non-empty tiles * explicitly zero out the `*particles_per_tile` array
2022-02-24Remove (almost) all residual "dangerous" c-style casts in WarpX (#2889)Gravatar Luca Fedeli 1-15/+15
* remove almost all c-style casts in WarpX * add comment * Fix `getMultiFabPointers`: `const` cast Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-11Rename ngE as ngEB (used for E,B) (#2841)Gravatar Edoardo Zoni 1-2/+2
2022-02-04added `local` flag to `warpx_getNumParticles` (#2828)Gravatar Roelof Groenewald 1-2/+3
2022-01-26style fixes in WarpXWrappers.cpp (#2792)Gravatar Roelof Groenewald 1-17/+17
2022-01-26expose WarpXParticleContainer::sumParticleCharge to Python (#2790)Gravatar Roelof Groenewald 1-0/+8
2022-01-25Add SyncRho call to warpx_depositChargeDensity (#2777)Gravatar Roelof Groenewald 1-3/+4
* add SyncRho call to warpx_depositChargeDensity * expose SyncRho to Python; add warpx_clearChargeDensity to reset rho_fp before deposition * remove unneeded warpx_clearChargeDensity function * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add (default) option to depositChargeDensity to call SyncRho after deposition * added option to depositChargeDensity to zero out rho_fp before deposition * code cleanup * import fields from inside depositChargeDensity Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-21Access species specific charge density from python (#2710)Gravatar Roelof Groenewald 1-0/+31
* added python wrapper function to deposit a specific species density in rho_fp * added 1D ES input file with MCC that uses the charge deposition functionality * reset rho_fp[lev] before depositing * updated documentation * switch to using simulation.extension in Poisson solver * Apply suggestion from code review Co-authored-by: Phil Miller <phil.miller@intensecomputing.com> * suggested changes from code review * add comment explaining why a direct Poisson solver is used * removed direct solver in 1D example since it is actually slower than the MLMG solver * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * added docstring for warpx_depositChargeDensity * fixed order of imports in new PICMI input file Co-authored-by: Phil Miller <phil.miller@intensecomputing.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-19Refactor python callback handling (#2703)Gravatar Roelof Groenewald 1-56/+10
* added support to uninstall an external Poisson solver and return to using the default MLMG solver; also updated some callbacks.py calls to Python3 * refactor callback handling - use a map to handle all the different callbacks * warpx_callback_py_map does not need to link to C * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * further suggested changes from code review * added function ExecutePythonCallback to reduce code duplication * moved ExecutePythonCallback to WarpX_py * added function IsPythonCallbackInstalled Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-21Inputs: `geometry.dims` option (#2685)Gravatar Axel Huebl 1-1/+1
* 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>
2021-12-13Adding EB multifabs to the Python interface (#2647)Gravatar Lorenzo Giacomel 1-0/+12
* Adding edge_lengths and face_areas to the Python interface * Added wrappers for the two new arrays of data * Adding a CI test * Fixed test name * Added customRunCmd * Added mpi in test
2021-12-03extern 'C': Only in Headers (#2624)Gravatar Axel Huebl 1-7/+2
* extern 'C': Only in Headers This does not belong in source files. Seen as missing symbols on CI for macOS and Intel, both clang compiles. ``` File "/usr/local/lib/python3.9/site-packages/pywarpx/_libwarpx.py", line 94, in <module> from ._libwarpx import * File "/usr/local/lib/python3.9/site-packages/pywarpx/_libwarpx.py", line 94, in <module> libwarpx.warpx_Real_size.restype = ctypes.c_int File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py", line 387, in __getattr__ libwarpx.warpx_Real_size.restype = ctypes.c_int File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py", line 387, in __getattr__ func = self.__getitem__(name) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x7f89a3edb820, warpx_Real_size): symbol not found func = self.__getitem__(name) File "/usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py", line 392, in __getitem__ func = self._FuncPtr((name_or_ordinal, self)) AttributeError: dlsym(0x7fe5d36c5190, warpx_Real_size): symbol not found AttributeError: /home/runner/.local/lib/python3.8/site-packages/pywarpx/libwarpx.3d.so: undefined symbol: warpx_Real_size ``` Refs.: - https://stackoverflow.com/questions/2168241/is-it-required-to-add-extern-c-in-source-file-also - https://isocpp.org/wiki/faq/mixing-c-and-cpp#call-cpp * Fix: Declare amrex_init_with_inited_mpi AMReX mocks out MPI anyway in serial builds. * Wrapper: Add Missing Declarations - fields - PML fields * Wrapper: More Missing Declarations - `warpx_getCellSize`
2021-11-18Add WARPX_PROFILE calls to each python callback. (#2573)Gravatar Peter Scherpelz 1-2/+9
When python callbacks take some time, this is useful as otherwise many callbacks are lumped together in WarpX::Evolve::step.
2021-11-05added wrappers to get particle structs for the particles in the boundary ↵Gravatar Roelof Groenewald 1-0/+24
buffers (#2498)
2021-11-05Add Python Wrappers for F,G in PML (#2481)Gravatar Edoardo Zoni 1-0/+44
* Add Python Wrappers for F,G in PML * Add Getters for F,G Nodal Flags * Fix Bug in <F,G>FPPMLWrapper (Default Level) * Fix Bug in F,G Nodal Flags * Use GetPML Method for F,G Nodal Flags
2021-10-25Raise an exception if an MultiFab was not intialized (#2476)Gravatar David Grote 1-75/+88
2021-10-21Add Python Wrappers for F,G (#2460)Gravatar Edoardo Zoni 1-0/+12
2021-09-22External Poisson solver: wrappers to copy the full domain rho and phi ↵Gravatar Roelof Groenewald 1-0/+5
between C++ and Python (#2285) * added missing parts to allow an external Poisson solver to be used instead of the MLMG solver * added rho and phi wrappers to fields.py * added an example of using an external Poisson solver * need to run PICMI test on 2 processors same as non-PICMI version in order to compare plotfiles * changes requested during PR review * pass dictionary to eval statement when calculating boundary potential
2021-09-20Rename WarpXWrappers.(h->H) (#2261)Gravatar Axel Huebl 1-1/+1
* Rename WarpXWrappers.(h->H) All our other header files use `.H`, so renaming this one for consistency. * Remove unused includes of WarpXWrappers.H
2021-08-30Make buffer of scraped particles available to Python code (#2164)Gravatar Phil Miller 1-0/+67
* Added wrapper to get number of particle species tracked by the scraper Not sure if this is going to be useful, but it demonstrates a method to get information from the ParticleBoundaryBuffer into Python. * Stubbed out the main wrapper functions * Added parameters to wrapper * Added wrapper for getting the number of particles scraped of a species on a boundary * added picmi arguments to scrape particles at the domain boundary * Added wrapper to get the full particle buffer into python * rearanged the getBuffer properties code a little * Added docstrings +other suggested changes * Added num_particles_impacted_boundary docstring * fixed mistake in docstring * Changed boundary parameter to be a string for clarity * Fixed issue with the boundary parameter for scraping * Fixed issue with the boundary input for scraping stats wrapper * Added demonstration of particle scraping wrapper * Added analysis.py file * Fix typo in one of the dimension maps Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Added before esolve to warpx evolve * added test for the scraped particle buffer wrappers * Moved python PICMI particle boundary scrape test * Renamed test file to the correct name * Removed old test * added special functionality to get the timestep at which particles were scraped * removed debug print * added python wrapper for the clearParticles() function of the scraper buffer * added special wrapper function to get the timesteps at which the particles in the boundary buffer were scraped * updated test to match the non-PICMI test for the particle scraper buffer * Fix uncaught rebase mistake * re-activated picmi test of accessing the scraped particle buffers via python * added documentation for the new parameters involved in the scraped particle buffer and fixed remaining issue with picmi test * changes requested during code review Co-authored-by: mkieburtz <michaelkieburtz@gmail.com> Co-authored-by: Roelof <roelof.groenewald@modernelectron.com> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
2021-08-26Improvement in electrostic field solve when using EB & a small refactoring ↵Gravatar Roelof Groenewald 1-0/+4
of the Electrostatic solver (#2143) * refactored parts of the electrostatic solver to allow an outside Poisson solver to be installed * added callback to install a Poisson solver that can be used instead of the MLMG solver * added call to the poissonsolver callback if one is installed and updated ElectrostaticSolver.cpp to calculate the electric field directly in amrex if EBs are used * fixed issue causing ElectrostaticSphereEB test to crash * fixed the logic for when to call computeE * added function to allow charge density to be deposited in rho_fp from outside WarpX * fixed inconsistency between labframe and relativistic electrostatic simulation setup * fixed typo * fixed issue that caused ElectrostaticSphere test to fail and removed unnecessary call to multiply E_y by -1 when doing a 2d simulation * revert edit to error handling string * changes requested during PR review * additional change requested during PR review * fixed typo * revert unnecessary changes
2021-08-02Allow extra particle attributes (besides ux, uy, uz and w) to be set at ↵Gravatar Roelof Groenewald 1-0/+8
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>
2021-07-21Use only species name in libwarpx (#2119)Gravatar Roelof Groenewald 1-30/+18
* 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 * removed unneeded function declaration
2021-07-20Python - add new particle attributes at runtime (#2112)Gravatar Roelof Groenewald 1-0/+50
* 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 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
2021-07-13Interface silver mueller (#2051)Gravatar Revathi Jambunathan 1-2/+2
* interface silvermueller with refactored boundary interface * add interface in silver mueller input files * define first and second half for EvolveB * add do_pml parse snce RZ needs do_pml to be st to false * Silver-Mueller boundary condition in docs * add firsthalf in ApplyBfieldBoundary within PushPSATD as only first first half is used to apply silvermueller * CallSilverMueller once for all boundaries * remove unused do silvermueller flag * fix typo in input file * Apply suggestions from code review Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * abort message if silver-mueller is not selected on all valid boundaries * fix typo * fix eol * remove ifdef from inside the Assert message * check silver-mueller selection after reading all boundaries Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-07-09Feature pass MPI comm from Python script to AMReX during initialization (#2034)Gravatar KZhu-ME 1-2/+8
* Added functionality to pass mpi comm from python script to amrex during initialization * Fixed missing _ in MPI._sizeof() * Added functions to get the current processor's rank and total number of processors * Renamed MPI_Comm to _MPI_Comm_type and defined _MPI_Comm_type in except statement * Updated comment to explain why mpi4py needs to be imported before loading libwarpx * Removed ifdef flags that prevent amrex_init_with_inited_mpi from being declared when MPI is off * Changed amrex_init_with_inited_mpi to be declared even when not using mpi, but will be defined to be functionally the same as amrex_init * Defined MPI = None to signify whether MPI is used, to add another check when initializing amrex * Changed ifdef blocks in WarpXWrappers.cpp/h to fix compile errors. Added ifdef block to conditionally declare amrex_init_with_inited_mpi in WarpXWrappers.h to prevent compile error when not using MPI. Removed ifdef block to declare/define same function in WarpXWrappers.cpp since function needs to be declared even when MPI is not used, but will never be called in that case. * Changed BL_USE_MPI to AMREX_USE_MPI and removed incorrect MPI=None statement * Changed BL_USE_MPI to AMREX_USE_MPI * Added test to verify correct passing of MPI communicator to amrex * Added ability to pass mpi_comm to sim.step * Change test to check for differeing outputs when passed different inputs * Removed obsolete comments refactored program to use more shared code * Refactored comments * Updated description to match test * Removed unecessary imports and updated comments
2021-07-06Add possibility to start and stop moving window (#2027)Gravatar thomas clark 1-2/+2
* Add possibility to start and stop moving window * Update Benchmark laserInjection_2d * Update Source/Diagnostics/BTDiagnostics.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * modification of the MoveWindow function in the python interface * False to True for move j in python function Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-06-24Use "Include What You Use" on WarpX (#1947)Gravatar Luca Fedeli 1-4/+21
* 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>
2021-06-07Call function ReadBCParams() during python execution (#1972)Gravatar roelof-groenewald 1-0/+5
* 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
2021-01-21Define: _OPENMP -> AMREX_USE_OMP (#1520)Gravatar Axel Huebl 1-3/+2
* 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
2020-12-02Fix python wrapper (#1532)Gravatar David Grote 1-16/+23
* Fixes to the Python interface for accessing field and particle data * In Python wrapper, cleaned up how ngrow is handled
2020-10-23Fix Warning for SigmaBox FabFactory (#1466)Gravatar Weiqun Zhang 1-1/+1
2020-10-16New reduced diag: number of macroparticles (#1414)Gravatar NeilZaim 1-5/+5
* New reduced diag: number of macroparticles * Add parentheses in header line * Apply suggestions from code review Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com> * Add some consts * Fuse some lines with std::ofstream Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
2020-09-30removed extra ; (#1397)Gravatar Luca Fedeli 1-34/+34
2020-07-30Add input parameter to control Galerkin-scheme gather (#1191)Gravatar danielbelkin 1-2/+2
* Rename l_lower_order_in_v to galerkin_interpolation * Changed galerkin_interpolation from int to bool * ... and same for member versions. * Add input parameter to control galerkin_interpolation * Update documentation * semicolon * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Docs/source/running_cpp/parameters.rst Resolve ambiguity Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix doc * Add references to documentation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-07-20Overwrite AMReX Defaults: Python (#1177)Gravatar Axel Huebl 1-2/+3
Forgot to also overwrite the initialization defines for Python with my last PR.
2020-06-22Added check of gridding for RZ spectral solver (#1005)Gravatar David Grote 1-0/+5
* Added CheckGriddingForRZSpectral * Bug fix in check gridding for RZ Spectral, fixing handling of refinement ratio * Change numprocs=2 for python reg tests and reset benchmarks (#1075) * changing nprocs to 2 for Python_PlasmaAcceleration test * Resetting benchmark for Python_PlasmaAcceleration test case due to change in nprocs=2 in reg test * resetting benchmarks for Python test-cases except Python_Langmuir due to change in numprocs in WarpX-tests.ini * changing numprocs=2 for Python tests * resetting python reg test benchmarks after updating pywarpx Co-authored-by: Revathi Jambunathan <revanathan@pop-os.localdomain> Co-authored-by: Tools <warpx.lbl.gov> Co-authored-by: Tools <warpx@lbl.gov> * Updates to picmi, mostly related to fields, and add psatd (#1077) * Fixed bad arguments in PICMI_inputs_laser_acceleration.py (#1074) Note that polarization_angle was changed to 0 since that was the value being used because the polarization_argument was bad. * Fix typo for pml_ncell in parameters doc (#1071) * remove #line wp_parser.l because it causes issues with AMReX make system (#1078) * remove amrex namespace from diag functor cpp files and use amrex:: prefic (#1093) * For RZ spectral, updated documentation regarding blocking factor and max grid size Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Co-authored-by: Revathi Jambunathan <revanathan@pop-os.localdomain> Co-authored-by: Tools <warpx@lbl.gov> Co-authored-by: NeilZaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: WeiqunZhang <WeiqunZhang@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-05-01Do not rely on nodal flags (#931)Gravatar Edoardo Zoni 1-16/+17
* 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
2020-05-01Delete old diagnostics (#933)Gravatar MaxThevenet 1-27/+0
* 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>
2020-03-23Updated Python interface for Python_Langmuir_rz_multimode test (#810)Gravatar David Grote 1-0/+29
* Added nodal and cell size data to the Python interface and updates the Python_Langmuir_rz_multimode regression test * Cleanup of PICMI_inputs_langmuir_rz_multimode_analyze.py
2020-03-16Added Python wrapper of charge density arrays (#783)Gravatar David Grote 1-0/+20
2020-02-25Includes: Clean Up (#743)Gravatar Axel Huebl 1-5/+6
- 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.
2020-02-10Python Compile in Single PrecisionGravatar Axel Huebl 1-4/+6
2020-01-28Merge pull request #661 from MaxThevenet/copyrightGravatar Remi Lehe 1-0/+8
Add Copyright header in all source files
2020-01-28Simplify Plot OptionsGravatar Axel Huebl 1-0/+9
Remove the `dump_plotfile` switch and only control via interval value in `plot_int` for plotfiles. Remove the `dump_openpmd` switch and only control via interval value in `plot_openpmd` for openPMD data dumps. openPMD: pick first available backend if unspecified.
2020-01-27Automatically add copyright header with update_copyright.shGravatar Tools 1-0/+8
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