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2021-01-14Unify intervals notation (#1485)Gravatar NeilZaim 1-4/+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
2021-01-11Add electrostatic to picmi (#1548)Gravatar David Grote 1-4/+27
* Update ElectrostaticSolver in picmi * Added relativistic option to picmi ElectrostaticSolver * Update PICMI version * Fix electrostatic with picmi Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-12-11PSATD Runtime Control (#1300)Gravatar Axel Huebl 1-3/+2
* Docs: PSATD Runtime Option * Tests: PSATD Runtime Option Add new runtime option to PSATD regression test matrix. * PICMI: PSATD runtime option * Source: PSATD Runtime Option
2020-12-01Update and fix to picmi.py (#1539)Gravatar David Grote 1-2/+5
2020-11-17use_filter now controls physical and k-space filtering (#1516)Gravatar David Grote 1-7/+2
* use_filter now controls physical and k-space filtering * Added backward compatibility error if use_kspace_filter is set
2020-11-16Update picmi constants to match the values in PhysConst (#1483)Gravatar David Grote 1-6/+12
* Update picmi constants to match the values in PhysConst * In picmi, use string q_e for charge instead of float with charge_state = +-1 * Updated benchmarks of picmi tests
2020-10-22picmi - minor cleanup, removing unneeded input quantities (#1446)Gravatar David Grote 1-9/+0
2020-10-12picmi - do name mangling on expression variables to ensure their uniqueness ↵Gravatar David Grote 1-30/+58
(#1361) Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-10-08Add laser phase to gaussian profile (#1155)Gravatar Igor Andriyash 1-0/+1
* added the phase argument for the gaussian laser * removed signature * added laser phase to picmi api * added doc string for phi0 * Update parameters.rst typo fix Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-10-05PICMI: read flag for laser continuous injection (#1358)Gravatar Edoardo Zoni 1-1/+3
* PICMI: read flag for laser continuous injection * Simplify assignment of do_continuous_injection * Update PICMI version Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-09-22Initial version of use_damp_fields_in_z_guard option (#1304)Gravatar David Grote 1-0/+3
* Initial version of use_damp_in_z_guard option * Fix typo in WarpX.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Changed use_damp_in_z_guard to use_damp_fields_in_z_guard * Added documentatin for use_damp_fields_in_z_guard * Clean up for use_damp_fields_in_z_guard * Added use_damp_fields_in_z_guard to picmi interface, and moved it to the psatd input group * For RZ spectral, damping of the fields is on by default when not periodic * Updated documentation for use_damp_fields_in_z_guard Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2020-09-17picmi - implemented rigid advance species option (#1338)Gravatar David Grote 1-2/+16
2020-09-15For PICMI, expect length 2 args for 2D solver (#1326)Gravatar David Grote 1-4/+8
* picmi - For 2D, changed arguments to expect length 2 lists * picmi - For 2D, guard_cells should be length 2
2020-09-14picmi: replaced warpx_n[xyz]_guard with grid.guard_cells (#1317)Gravatar David Grote 1-6/+4
2020-09-14PICMI analytic applied fields (#1306)Gravatar David Grote 1-0/+59
* PICMI Added applied fields * PICMI fixed typo in Constants * Change picmistandard version requirement to 0.0.9 * Increment required picmi version Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-09-14picmi: use kspace filter automatically for RZ PSATD (#1318)Gravatar David Grote 1-5/+4
2020-08-31[mini]Bug fix in ParticleListDistribution (#1252)Gravatar David Grote 1-1/+1
This fixes a small bug in the `picmi.ParticleListDistribution` class.
2020-08-24For PICMI, added more arguments for psatd solver (#1259)Gravatar David Grote 1-6/+16
2020-07-27Input: Remove n<something> options (#1217)Gravatar Axel Huebl 1-4/+3
* 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>
2020-07-27Added k-space filter for RZ spectral solver (#1006)Gravatar David Grote 1-1/+9
* Added k-space filter for RZ spectral solver * Added SpectralBinomialFilter files for RZ spectral solver * Added RZspectral binomial filter to CMakeLists.txt * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/FieldSolver/SpectralSolver/SpectralBinomialFilter.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/FieldSolver/SpectralSolver/SpectralBinomialFilter.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/FieldSolver/SpectralSolver/SpectralFieldDataRZ.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fixed literals in SpectralBinomialFilter.cpp * For RZ spectral, apply filter to rho old and new * Added SpectralBinomialFilter::InitFilterArray * For SpectralBinomialFilter, combine R and Z into one routine Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * For SpectralBinomialFilter, combine R and Z into one routine, part 2 Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * For SpectralBinomialFilter, combine R and Z into one routine, part 3 Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2020-07-02PSATD: current correction works only with global FFTs (#1131)Gravatar Edoardo Zoni 1-2/+2
* Clean up implementation of current correction: - abort when current correction runs with psatd.periodic_single_box_fft=0 - rename input parameter from psatd.do_current_correction to psatd.current_correction - add nodal tests in 2D and 3D (using direct current deposition) - change 2D test: use Esirkepov deposition, instead of direct, as in 3D test - add/update relevant checksum benchmarks * Small clean-up
2020-06-05Updates to picmi, mostly related to fields, and add psatd (#1077)Gravatar David Grote 1-5/+28
2020-06-03In picmi.py, convert the diagnostics to write into a sorted list (#1069)Gravatar David Grote 1-14/+29
2020-05-22Fix DivE diagnostic in RZ (#1034)Gravatar David Grote 1-0/+2
* Added dump_rz_modes to picmi field diagnostic * Fixed DivEFunctor for RZ * In Diagnostics, write out RZ components of divE if requested * Fix RZ component names in diagnostic files * Fixed RZ spectral back transform, fixing DivE calculation * In SpectralSolverRZ.H changed BL_PROFILE to WARPX_PROFILE * Undid change of BL_PROFILE to WARPX_PROFILE in SpectralSolverRZ.H
2020-05-19Bug fix in picmi field diagnostics with picmistandard.0.0.8 (#1032)Gravatar David Grote 1-1/+2
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-05-14Implemented new particle diagnostics in picmi (#984)Gravatar David Grote 1-28/+57
* 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
2020-05-05PICMI: Add analytic laser (#800)Gravatar David Grote 1-3/+23
* In PICMI, added AnalyticLaser * Bug fixes for PICMI AnalyticLaser * In PICMI, use laser's name input option
2020-05-01Delete old diagnostics (#933)Gravatar MaxThevenet 1-51/+54
* 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>
2020-03-30[mini-PR] Clarifying ionizable particle charge (#863)Gravatar L. Diana Amorim 1-0/+1
* Added documentation note on ionization particle charge * Added correct charge of ion to be ionized * Corrected multiplication symbol Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Testing doxygen issue * Charge correction only to ionizable species * Trying to fix doxygen url fetch issue Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
2020-03-30Added blocking factor to 2d and RZ geometries (#864)Gravatar L. Diana Amorim 1-1/+2
2020-03-19Remove costs full diagnostic (#791)Gravatar Michael E Rowan 1-2/+0
* Remove costs full diagnostic * whitespace * Remove warpx.plot_costs from PlasmaMirror test * minor * Minor * Remove plot_costs
2020-01-27Automatically add copyright header with update_copyright.shGravatar Tools 1-0/+8
2020-01-09For picmi, minor clean upGravatar Dave Grote 1-4/+1
2020-01-09For picmi, added plot_vars for speciesGravatar Dave Grote 1-3/+34
2020-01-03In picmi diagnostics, added plot_finepatch etc to listGravatar Dave Grote 1-0/+10
2020-01-03Updated handling of fields_to_plot in picmi interfaceGravatar Dave Grote 1-19/+36
2019-12-20Removed test function print()Gravatar L. Diana Amorim 1-1/+0
2019-12-20Merge remote-tracking branch 'upstream/dev' into picmi_ionGravatar L. Diana Amorim 1-1/+1
2019-12-20Fixed pywarpx class where ionization call is definedGravatar L. Diana Amorim 1-9/+8
2019-12-20Fix EOL whitespaceGravatar Remi Lehe 1-1/+1
2019-12-18Added print line to see absent interactionsGravatar L. Diana Amorim 1-9/+9
The search for ionization should only happen for particles other than elementary
2019-12-18Merge branch 'picmi_mw' into picmi_ionGravatar L. Diana Amorim 1-8/+9
2019-12-18Tried to add PICMI class for ionizationGravatar L. Diana Amorim 1-0/+9
2019-12-18moving_window_velocity does not exist in PICMI RZGravatar L. Diana Amorim 1-3/+0
2019-12-18Corrected WarpX RZ to use PICMI moving_window_zvelocityGravatar L. Diana Amorim 1-4/+7
2019-12-18Fix to RZ scalar moving windowGravatar L. Diana Amorim 1-7/+8
Tried to make exception message clearer
2019-11-07Implement space-charge initialization (non-relativistic, single-level)Gravatar Remi Lehe 1-6/+6
2019-10-25replace 'boosted frame diags' with 'back-transformed diags'Gravatar MaxThevenet 1-4/+4
2019-08-21Fixes in picmi for parsing momentum functionsGravatar Dave Grote 1-6/+6
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