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2021-10-27Fix Doxygen: Particles (#2486)Gravatar Axel Huebl 15-152/+146
* Fix Doxygen: Particles Fix doxygen errors & warnings. * Apply suggestions from code review Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Apply suggestions from code review * Document ForwardIterator * Fix tparam and comma Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2021-10-27Fix Doxygen: Utilities (#2485)Gravatar Axel Huebl 2-13/+37
* Fix Doxygen: Utilities Fix doxygen errors & warnings. * Review: Add doxygen title & brief body
2021-10-27Doxygen: Add Landing (Main) Page (#2509)Gravatar Axel Huebl 2-1/+61
Add a main page for Doxygen, to guide users/developers that land there. Heavily inspired by AMReX' landing page.
2021-10-27Apply damping BC to any direction (#2503)Gravatar David Grote 2-91/+96
* Apply damping to all directions * Fixed error when damped BC is not used on both sides * Bug fix - forget a brace
2021-10-27Doxygen: Tagfile on RTD (#2497)Gravatar Axel Huebl 2-3/+7
Publish the doxygen tagfile on readthedocs. Clean temporary tagfiles in `make clean`.
2021-10-27CI: Draft Do Not Skip Source (#2500)Gravatar Axel Huebl 1-2/+0
Source tests are fast and check that documentation builds successfully.
2021-10-27Python Module for Analysis of Restart Tests (#2493)Gravatar Edoardo Zoni 4-92/+64
* Python Module for Analysis of Restart Tests * Remove Unused Import
2021-10-27Fix BinaryCollision on GPU (#2504)Gravatar Neïl Zaim 1-4/+6
2021-10-27More fixes for the Python fields module (#2502)Gravatar David Grote 1-60/+64
Fixed indexing for PML fields. Add all of the fixes to the setitems routines.
2021-10-26Fix Doxygen: BTD (#2487)Gravatar Axel Huebl 3-48/+56
* Fix Doxygen: BTD Fix doxygen errors & warnings. * Add Reva's Parameter Updates :) * Document leftover params Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
2021-10-26Revert latest amrex updates in order to fix CI (#2494)Gravatar Remi Lehe 4-4/+4
* Revert "Update AMReX to include EB solver fix (#2484)" This reverts commit 105e127b95db5707d17cadc77fe68f1d68453d06. * Revert "AMReX/PICSAR: Weekly Update (#2478)" This reverts commit 7341fa0eda39368b1c6f2cf6d6dc20462fd6c3fc.
2021-10-26gitignore: add WarpX tagfile (#2490)Gravatar Axel Huebl 1-0/+1
Temporarily created during documentation build
2021-10-26Fix Doxygen: Embedded Boundaries (#2489)Gravatar Axel Huebl 1-1/+1
Fix doxygen errors & warnings.
2021-10-25Fix Doxygen: FieldSolver/QED (#2488)Gravatar Axel Huebl 2-8/+15
Fix doxygen errors & warnings.
2021-10-25PICMI: Add PML div(E),div(B) Cleaning Options (#2480)Gravatar Edoardo Zoni 3-2/+5
2021-10-25Raise an exception if an MultiFab was not intialized (#2476)Gravatar David Grote 2-75/+97
2021-10-25Update AMReX to include EB solver fix (#2484)Gravatar Kevin Z. Zhu 4-4/+4
2021-10-25Bugfixes for ref_ratio = 4 in the moving window direction. (#2452)Gravatar Andrew Myers 5-14/+31
* Bugfixes for ref_ratio = 4 in the moving window direction. * == should be <= * only adjust guard cells for moving window by ref_ratio if nlevs > 1 * restore logic to always have at least 2 grow cells if moving window is on * remove comment about this not being needed on level 0 - it does.
2021-10-25Modernize field access in yt scripts (#2455)Gravatar Luca Fedeli 10-36/+36
* increase tolerance for single precision test * reset checksum * change ad['field'] into ad[('mesh','field')] or ad['boxlib','field'] in yt script * update field access in several files * Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi_rz.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi_2d.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi.py * Update Examples/Tests/Langmuir/analysis_langmuir_multi.py * Update Examples/Modules/boosted_diags/analysis_3Dbacktransformed_diag.py * Update Examples/Modules/boosted_diags/analysis_3Dbacktransformed_diag.py Co-authored-by: Tools <warpx@lbl.gov>
2021-10-25Spatially vary temperature in momentum initialization (#2357)Gravatar Hannah Klion 13-69/+394
* Add GetTemperature class - Object that can be called with signature GetTemperature(x,y,z) to get temperature at coordinates x,y,z - Can take either a constant temperature or a parser, to be passed in from the input param file * Further develop GetTemperature - Rename GetTemperature to TemperatureInit - TemperatureInit is a union of TemperatureInitParser and TemperatureInitConstant, modeled after the InjectorMomentum class - InjectorMomentum will take a TemperatureInit object where it needs a temperature, rather than a constant value. It will be able to call TemperatureInit->getTemperature(x,y,z), regardless of the temperature type * finish renaming GetTemperature to TemperatureInit * InjectorMomentum now takes TemperatureInit object - For Maxwell-Boltzmann and Maxwell-Juttner distributions, InjectorMomentum takes a pointer to TemperatureInit rather than a single amrex::Real * Pass TemperatureInit to InjectorMomentum by reference - Pass TemperatureInit to InjectorMomentum by reference - Removed copy constructor deletion - Fixed some other compilation errors * Prevent copy constructors for TemperatureInit * Add PlastmaInjector::parseTemperature - parseTemperature reads temperature parameters and creates a TemperatureInit object that contains the information - parseTemperature returns a unique pointer to the TemperatureInit object, which is then passed directly to the InjectorMomentum constructor * InjectorMomentum takes unique pointer to TemperatureInit - Boltzmann and Juttner InjectorMomentum types take a unique pointer to Temperature Init - Adjusted initializers to move instead of copy, where required - Added a blank destructor for Object, which may not actually be necessary, but currently needed for compilation. * Fix bug and pass TemperatureInit by reference - Fixed bug where the parser in TemperatureInit was going out of scope before we were done using the executor. This has been fixed by making the parser a member of the PlasmaInjector class so it won't be prematurely garbage collected. This should be temporary until the refactor of TemperatureInit - TemperatureInit is no longer a union, and is instead just a struct whose first member indicates the type - The PlasmaInjector method that reads the temperature parameters is now void. It takes a TemperatureInit object by reference and does the real initialization. * Restructure how temperature data are stored - TemperatureInit renamed to TemperatureProperties - Temperature data is stored in an instance of TemperatureProperties, a smart pointer to which is owned by PlasmaInjector. - TemperatureProperties is initialized with a reference to parameters, and owns the temperature function parser, if used. - GetTemperature is a functor that takes three doubles (x, y, and z coordinates) and returns the initial temperature at that location. This is either a constant or a parser evaluated at (x,y,z), depending on input parameters. - InjectorMomentum takes a const reference to GetTemperature in its constructor when needed and stores a copy. The compiled parser will remain in scope because it is owned by TemperatureProperties, which is in turn owned by PlasmaInjector. * Fix compilation bugs - Fix some include file names - Add TemperatureProperties.cpp to CMake - Fix some class names * update list of .cpp files in Make.package * Split GetTemperature implementations implementations into .cpp * update include statements * fix default constant temperature * add documentation for new runtime params * add further documentation * added test for spatially varying temeperature * update comments on tests * remove empty destructor for Object in InjectorMomentum * reset benchmark for initial_distribution because added check for spatially-varying temp * Moved GetTemperature::operator() to header file since that seems to help GPU compilation on my local machine * make position arguments to GetTemperature const * LaTeXify new documentation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add const where applicable Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * renamed TemperatureInitType members to avoid collisions with MacroparameterInitType * Update Examples/Tests/initial_distribution/analysis_distribution.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add comment to document why h_mom_temp is a PlasmaInjector member * Add warning/abort messages if temperature is out of MJ or MB range * Theta is now mandatory * update documentation * negative theta values not allowed * Remove theta>0.01 warning in getMomentum and fix GPU compile issues Co-authored-by: Hannah Klion <hannah.klion@gmail.com> Co-authored-by: Tools <warpx@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-10-25AMReX/PICSAR: Weekly Update (#2478)Gravatar Axel Huebl 4-4/+4
Weekly update to latest AMReX. Weekly update to latest PICSAR (no changes). ``` ./Tools/Release/updatePICSAR.py ./Tools/Release/updateAMReX.py ```
2021-10-25Make tests `pml_x_psatd` and `pml_x_yee` also restart tests. (#2444)Gravatar Yinjian Zhao 5-6/+75
* Test will crash for some reasons. * Modify more. * Debuging. * Fix a bug. * Change interval back to 50. * Apply suggestions from code review * Add more careful restart tests. Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-10-25Increase EB coarsening level for linear solvers (#2457)Gravatar Weiqun Zhang 1-2/+9
* Increase EB coarsening level for linear solvers * Apply suggestions from code review Add comments.
2021-10-25Fix Bug with Python Wrappers for F,G (#2474)Gravatar Edoardo Zoni 2-8/+8
2021-10-23Add automated test of refined injection feature. (#2473)Gravatar Andrew Myers 3-0/+116
* 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
2021-10-23PICMI: Add div(E),div(B) Cleaning Options (#2477)Gravatar Edoardo Zoni 3-2/+4
* PICMI: Add div(E),div(B) Cleaning Options * Update PICMI Version: 0.0.15
2021-10-22Fix average wall time per step (#2475)Gravatar Weiqun Zhang 1-1/+2
It should be computed using the number of steps in this run, otherwise the number is incorrect for restart runs.
2021-10-22Fix damped BC when running with a single box (#2407)Gravatar David Grote 2-63/+79
* Fix damped BC when running with a single box * Cleanup of comments and code
2021-10-22Docs: Tagfile (Doxygen) (#2463)Gravatar Axel Huebl 3-5/+13
* Docs: Tagfile (Doxygen) Generate a tagfile. Used as anchor in external projects. * Doxygen Interlink: External AMReX Tagfile Link AMReX objects to the AMReX doxygen page via its latest Doxygen tagfile.
2021-10-22Fix fields indexing (#2469)Gravatar David Grote 1-30/+31
* Fix fields indexing * Added additional documentation * Fixed comment
2021-10-22Added documentation for the Python interface (#2465)Gravatar David Grote 2-0/+73
* Added documentation for the Python interface * Clean up EOL space
2021-10-21CI: Test Windows + openPMD (#2440)Gravatar Axel Huebl 1-6/+8
* CI: Windows + openPMD * Windows: Work-Around <variant> mismatch Build openPMD-api in C++17 as well, so we consistently use `<variant>` over `<mpark/variant.hpp>`. * Test Fix for 0.14.3 (openPMD-api 1128) Test PR in https://github.com/openPMD/openPMD-api/pull/1128 * Finalize CI for now
2021-10-21Add Python Wrappers for F,G (#2460)Gravatar Edoardo Zoni 4-0/+254
2021-10-21Raw Diagnostics: Plot rho,F Automatically (#2456)Gravatar Edoardo Zoni 16-77/+31
2021-10-21Div(B) Cleaning: Change Normalization of G (#2429)Gravatar Edoardo Zoni 6-26/+28
* PSATD with div(B) Cleaning: Change Normalization of G * Use New Normalization also in RZ * Use New Normalization also in FDTD * Reset Benchmark of Test divb_cleaning_3d
2021-10-21Add 2D Langmuir Test with MR (#1716)Gravatar Edoardo Zoni 2-0/+63
* Add first Langmuir test with MR and clean up 2D analysis script * Cleaning, Remove Unused Import * Revert Changes to Python Analysis Script * Reset Benchmark of Langmuir_multi_2d_MR
2021-10-20⚠️ Add warning logger (#2113)Gravatar Luca Fedeli 32-90/+2218
* improve error msg * eliminate final dot * initial layout of the main classes * progress * progress with warnings * print local errors * progress with warning logger * improved MsgLogger * added file to test warnings * added method to read debug warnings from inputfile * progress towards collective gather of warnings * add missing blank line in warning message * move misplaced file * refactoring * fixed bugs * progress * fixed bugs * fixed some bugs * it finally works! * add comments in WarpX.H * add missing comment * added comments to WarpX.cpp * add profiler to WarpX.cpp * expose option to enable 'warn immediately' feature in cmake * Add comment to main.cpp * add missing comment in WarpX.cpp * add copyright and include guards to WarnManager_fwd.H * cleaning and added comments to WarnManager.H * updated test * added fwd file for MsgLogger * cleaning * Added copyright in WarnManager.cpp * Cleaning * cleaning * Add missing copyright * cleaning * clean and add comments to MsgLoggerSerialization.H * cleaning MsgLogger_fwd.H * cleaning * continue cleaning MsgLogger * added comments & bugfixing * removed test file * fixed bugs * Update Source/Utils/MsgLogger/MsgLogger.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/WarpX.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLogger.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLogger.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLogger.cpp Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLoggerSerialization.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLoggerSerialization.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLoggerSerialization.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLoggerSerialization.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/MsgLogger/MsgLoggerSerialization.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/WarnManager.cpp Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/WarnManager.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/WarnManager.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Update Source/Utils/WarnManager.cpp Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * fixed bugs * Update Source/Utils/MsgLogger/MsgLogger.cpp Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Added comment to explain rotation * use last value computed by partial_sum * fix bug * now use error stream * using anonymous namespace for helper functions * print on both stderr and stdout * now using runtime parameter to always print warnings * added documentation * using long int for counter * sort affected warnings list * add doc entry * removed doc * added documentation * fixed bug * fixed bug * removing unnecessary text * reformatting * reformatting * fixed bug * fixed bug * correction * add warning_logger.rst to toctree in developers.rst Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2021-10-20Increase tolerance for single precision test & reset checksums (#2454)Gravatar Luca Fedeli 2-31/+31
* increase tolerance for single precision test * reset checksum Co-authored-by: Tools <warpx@lbl.gov>
2021-10-19Simplify momentum initialization in example input files (#2309)Gravatar Neïl Zaim 46-661/+609
* 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>
2021-10-19BinaryCollision: implement particle creation functor (#2315)Gravatar Neïl Zaim 6-103/+313
* BinaryCollision: implement particle creation functor * Apply suggestions from code review (restrict keyword) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Don't restrict the particle pointers * Use atomicSetID * Use more restricts * Don't use auto restrict Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-10-19Add reduced diag test in single precision (#2398)Gravatar Luca Fedeli 5-305/+392
* fix kinetic energy calculation in single precision * really fix the issue... * add missing _rt * we don't need m2 now * remove unused variable * initial work to add reduced diags test in single precision * updated tests * add back accidentally deleted comment * reduced tolerance in single precision * increase tolerance in single precision * always perform kinetic energy calculation in double precision * put w where it was * fixed bug * fixed bug * add json file for new test * use threshold for kinetic energy * fix bug * increase order of Taylor expansion * increase order of Taylor expansion * reduce classical/relativistic threshold for kinetic energy * reset threshold to 1.005 * improve test Co-authored-by: Tools <warpx@lbl.gov>
2021-10-19Added --detach to the updating scripts (#2447)Gravatar David Grote 3-3/+3
2021-10-19Simplify Esirkepov formula even more (#2374)Gravatar Remi Lehe 2-20/+26
* Simplify formulas for Esirkepov deposition * Simplify Esirkepov formulas even more * Update Source/Particles/Deposition/CurrentDeposition.H
2021-10-18Use os.path.join in picmi.py for portability (#2400)Gravatar Andrew Myers 1-4/+5
* Use os.path.join in picmi.py for portability * Apply suggestions from code review
2021-10-18GH Action CI Builds: Ninja (#2428)Gravatar Axel Huebl 11-26/+87
* GH Action CI Builds: Ninja Use Ninja for most builds to compile faster than using the GNU Makefile generator. * oneAPI: w/o Ninja Seems to be 10% slower for these compilers, so we keep the default. * NVHPC: w/o Ninja Seems to be 10% slower for `nvcc -ccbin=nvc++`, so we keep the default. * macOS: w/o Ninja Seems to be 20% slower, so we keep the default. * Clang pywarpx: w/o Ninja Seems to be 20% slower, so we keep the default.
2021-10-18Docs: Nsight-Systems (#2436)Gravatar Axel Huebl 1-2/+53
* Docs: Nsight-Systems How to use Nsight-Systems. Tested on Cori DGX. * Profiling: Link TinyProfiler Script Co-authored-by: Michael Kieburtz <michaelkieburtz@gmail.com> Co-authored-by: Michael Kieburtz <michaelkieburtz@gmail.com>
2021-10-18Fix typo: code-blockGravatar Axel Huebl 2-2/+2
2021-10-18OLCF/NERSC: Post-Processing (Jupyter) (#2443)Gravatar Axel Huebl 4-0/+80
Doc pages to get started with post-processing using Python and Jupyter at OLCF and NERSC.
2021-10-18Option to do single precision mesh communication. (#2294)Gravatar Andrew Myers 23-138/+581
* option to use single precision guard cell exhanges * add missing files * fix namespace issue * change precision of comms to float * ParmParse the single_precision_comms flag * set back to real * test * make sure dst is filled * nGrow -> nGrowVect * restore float * don't override valid cells * single precision mesh * whitespace * wrap SumBoundary * Wrap additional uses of FillBoundary. * catch missing copies of ParallelCopy * missing OverrideSyncs * add wrapper for iMultifab * fix typo * moar typos * typo * strip single_precision_mesh option * fix original copy * update fusible syntax Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> * Fix: Single Precision Builds Should not copy around data for `do_single_precision_comms` * Docs: warpx.do_single_precision_comms * initialize this tmp multifab to 0.0 * fix tiny profile label * remove orig copies, they are only correct for FillBoundary * loosen tolerance for space charge tests for single precision * missing some setVal * another missing setVal * missing setVal * add wrapper for new version of sumboundary * add explicit cast to silence compiler warning * add a test for single precision comms * revert change to test precision * add benchmark for single precision comms test * restore tolerance I removed by mistake * tolerance * copyright headers * drop tolerance for single precision tests in default analysis script * missing python module * bump tol again * fix bad merge * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-10-18AMReX/PICSAR: Weekly Update (#2442)Gravatar Axel Huebl 4-4/+4
Weekly update to latest AMReX. Weekly update to latest PICSAR (no changes). ``` ./Tools/Release/updatePICSAR.py ./Tools/Release/updateAMReX.py ```
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