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2020-06-03In picmi.py, convert the diagnostics to write into a sorted list (#1069)Gravatar David Grote 1-14/+29
2020-06-01update release number everywhere in repo (#1064)Gravatar MaxThevenet 1-1/+1
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 2-2/+3
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-05-18Require Python 3.6+ (#1021)Gravatar David Grote 1-1/+2
* Added specification of the version picmistandard * Set the requirement of Python version >= 3.6 * Add Python version requirement to the docs * Add comment about Python version to docs
2020-05-15replace release number 20.04 by 20.05 in the repo (#1027)Gravatar MaxThevenet 1-1/+1
2020-05-14Implemented new particle diagnostics in picmi (#984)Gravatar David Grote 4-34/+91
* 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 6-73/+73
* 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>
2020-04-21Python documentation updates (#936)Gravatar David Grote 1-1/+1
* 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>
2020-04-01Update release number (#875)Gravatar MaxThevenet 1-1/+1
* update release number * add message to get list of PR merged since last release * keep set -e * Update Tools/update_release.sh suggested by @ax3l
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
2020-03-23Updated Python interface for Python_Langmuir_rz_multimode test (#810)Gravatar David Grote 2-53/+257
* 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
2020-03-19Remove 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
2020-03-17Small fixes to Python to better handle particle weights (#807)Gravatar David Grote 2-6/+9
2020-03-16Added Python wrapper of charge density arrays (#783)Gravatar David Grote 2-7/+128
2020-03-12Fix misspellings of the word 'auxiliary' (#799)Gravatar Michael E Rowan 1-4/+4
2020-03-03update tag number (#764)Gravatar MaxThevenet 1-1/+1
2020-02-12update release tag in the code (#706)Gravatar MaxThevenet 1-1/+1
2020-01-28Merge pull request #661 from MaxThevenet/copyrightGravatar Remi Lehe 21-0/+134
Add Copyright header in all source files
2020-01-28Simplify Plot OptionsGravatar Axel Huebl 1-1/+3
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 21-0/+134
2020-01-16update release/tag versionGravatar MaxThevenet 1-1/+1
2020-01-09For picmi, minor clean upGravatar Dave Grote 4-11/+5
2020-01-09For picmi, added plot_vars for speciesGravatar Dave Grote 1-3/+34
2020-01-09For picmi, handle zero length list of values for outputGravatar Dave Grote 1-1/+6
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 3-21/+47
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
2019-12-20Merge pull request #574 from LDAmorim/picmi_mwGravatar Remi Lehe 1-7/+8
Fix to RZ scalar moving window
2019-12-20Merge remote-tracking branch 'upstream/dev' into picmi_ionGravatar L. Diana Amorim 2-3/+489
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
2019-12-12Added Python wrapper for the PML fieldsGravatar Dave Grote 2-0/+457
2019-12-12In Python fields wrapper, allowed multiple compoments in 3DGravatar Dave Grote 1-3/+32
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
2019-10-03Update version numberGravatar Remi Lehe 1-1/+1
2019-10-01Additional fix for single precision in Python interfaceGravatar Dave Grote 2-4/+8
2019-10-01Allowed single precision in the Python interfaceGravatar Dave Grote 1-34/+53
2019-09-06Updated Python particles interface to allow refined levelsGravatar Dave Grote 3-60/+62
2019-09-06Updated Python fields interface to work with refinementGravatar Dave Grote 2-12/+120
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