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path: root/Source/FieldSolver/SpectralSolver/SpectralAlgorithms/PsatdAlgorithmRZ.cpp (follow)
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2023-08-14Clang-tidy: add more misc-* checks to clang-tidy CI test (#4170)Gravatar Luca Fedeli 1-2/+0
* Clang-tidy: add more misc-* checks to clang-tidy CI test * address issues found with clang-tidy
2023-08-01Clang tidy CI test: add several readability checks to clang tidy CI test ↵Gravatar Luca Fedeli 1-2/+2
(#4124) * add few readability checks to clang-tidy CI test * address all the issues found with clang-tidy * fix bug * fixed bug * fix residual issue * fix issue found with clang-tidy
2023-05-09Do not duplicate protected member of base class (#3915)Gravatar Edoardo Zoni 1-1/+0
2023-05-01Use WARPX_ABORT_WITH_MESSAGE("msg") instead of ↵Gravatar Luca Fedeli 1-8/+8
amrex::Abort(Utils::TextMsg::Err("msg")) (#3879) * use WARPX_ABORT_WITH_MSG instead of amrex::Abort(Utils::TextMsg::Err(msg)) [WIP] * use WARPX_ABORT_WITH_MESSAGE * fix typo * fix missing parenthesis * remove spaces to prevent automatic text wrapping * remove wrong parenthesis
2023-03-28Fix bugs related to azimuthal modes for multi-J algo in RZ geometry (#3764)Gravatar Olga Shapoval 1-5/+5
* Bug fix: loop over all azimuthal modes taking into account the shift `mode*n_fields` * Bug fix: added missing speed of light factor in coefficient `c2` * Bug fix: added missing `mode` as fourth optional component in `X5(i,j,k,mode)` and `X6(i,j,k,mode)` coefficients, used only with RZ multi-J averaged PSATD * Reset benchmark of `multi_J_rz_psatd`
2023-03-09New user input for grid type (collocated, staggered, hybrid) (#3683)Gravatar Edoardo Zoni 1-2/+2
* Introduce `warpx.grid_type` parameter * Replace `or` with `||` * Update examples with new user input syntax * Fix `if` condition * Improve error message * Fix `if` condition * Fix bugs * Fix warning * Fix RZ * Debugging * Fix RZ * Fix bug * Clean up * More changes: - set default algo parameters with hybrid grid - all hybrid input parameters under warpx name * Set default field gathering algo for hybrid grids * Update documentation
2022-12-07PSATD: Implement First-Order Equations (#3466)Gravatar Edoardo Zoni 1-12/+15
* Implement First-Order PSATD Equations * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Unused Parameter Warning * Fix RZ Build * Fix Normalization of G to Match PML * Add CI Test: 3D Uniform Plasma * Cleaning * Update 2D CI Checksums * Update 3D CI Checksums * Add F,G to CI Checksums of `uniform_plasma_multiJ` * Allow User to Choose First-Order v. Second-Order * Add WARPX_ALWAYS_ASSERT_WITH_MESSAGE * Rename New Class `PsatdAlgorithmFirstOrder` * Remove Inline Comment * Update RZ CI Checksums * Fix inline comment * Use auxiliary variables to avoid divisions * Use auxiliary variables to avoid divisions * Make `nci_psatd_stability` dir and merge inputs * Move all Galilean tests to `nci_psatd_stability` * Fix CI * Fix index for backward FFT of J Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-09-20PSATD: More Options for Time Dependency of J, Rho (#3242)Gravatar Edoardo Zoni 1-15/+18
* Rename PsatdAlgorithm as PsatdAlgorithmJConstantInTime * Add New Inputs: psatd.J_in_time, psatd.rho_in_time * Update PSATD Classes * Fix Bug for FDTD Build * Fix Warning for RZ PSATD Build * Fix Multi-J Loop w/ J Constant in Time * Clean up * Fix Error Message * Fix Time of Charge Deposition for Rho Linear * Add 3D Langmuir CI Tests w/ Multi-J Algo * Fix Checksums of New CI Tests * Remove Extra CI Tests (added in #3363) * Fix CI Tests w/ Multi-J PSATD * Add Docs for New Input Parameters * Galilean/Comoving PSATD Not Compatible w/ J Linear
2022-05-30Use Utils::TextMsg::Err and WARPX_ALWAYS_ASSERT_WITH_MESSAGE in more files ↵Gravatar Luca Fedeli 1-4/+9
(#3117) * use formatted error messages * fixed bug * fixed bug * fixed bugs * fixed bug
2022-03-03Refactor Vay Deposition Functions (#2885)Gravatar Edoardo Zoni 1-3/+1
* Refactor Vay Deposition Functions * Use rho Index Type for FFT of D * Improve Doxygen Strings
2022-02-16Refactor Current Correction Functions (#2839)Gravatar Edoardo Zoni 1-19/+1
* Refactor Current Correction Functions * Clean Up, Reset Benchmark
2022-01-09Multi-J: J Always Linear in Time (#2679)Gravatar Edoardo Zoni 1-15/+15
* Remove WarpX::J_linear_in_time * Fix Bug * Implement Deposition of Rho at Half Time * Implement New Equations for E * Fix New Equations for E * Cleaning * Fix Limits of X2, X3, X7 * Implement New Equations for F * Implement New Equations for F * Revert E Equations to Avoid Roundoff Changes * Remove Quadratic Equations * Remove Deposition of Rho at Half Time Step
2021-10-21Div(B) Cleaning: Change Normalization of G (#2429)Gravatar Edoardo Zoni 1-7/+7
* 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
2021-08-05RZ PSATD: Time Averaging for Multi-J Algorithm (#2141)Gravatar Edoardo Zoni 1-3/+124
* RZ PSATD: Time Averaging for Multi-J Algorithm * Fix Wrong Signs in Bm * Use Time Averaging in CI Test, Update Benchmark * Minor Fix
2021-07-26RZ PSATD: Multi-J Algorithm (#2111)Gravatar Edoardo Zoni 1-13/+88
* RZ PSATD: Implement Multi-J Algorithm * Implement J_linear_in_time Option * Reduce Style Changes * Move Copy/Zero/Scale Functions to SpectralFieldDataRZ * Remove Unused Member m_n_rz_azimuthal_modes from SpectralSolverRZ * Fix CI -Werror Warnings * Implement Same Changes of #2116, Cleaning * Fix Bug: Pass Correct dt to SpectralSolverRZ * Add CI Test * CI Test: Set random_theta = 0, Update Benchmark * Remove random_theta from Inputs * Update Benchmark of multi_J_rz_psatd
2021-07-15Spectral Index: Replace `struct`s of `enum` with Class (#2062)Gravatar Edoardo Zoni 1-28/+30
* Add New Spectral Index Class * Cleaning * Use New Spectral Index Class in PML * Cleaning * Reuse Available Data for divE * Allocate Rho Data Only when Necessary * Cleaning * Fix Bug in RZ Geometry * Revert Commits for Allocation of Rho Data * Cleaning * Update Forward Declaration Header * Do Not Include Unnecessary Header Files * Doxygen * Do Not Use Separate div() Cleaning Flags * SpectralFieldIndex: Add Missing param to Doxygen * Remove Unused getRequiredNumberOfFields
2021-06-24Use "Include What You Use" on WarpX (#1947)Gravatar Luca Fedeli 1-1/+1
* 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>
2021-03-19Warnings: PSATD+RZ & More (#1814)Gravatar Axel Huebl 1-1/+1
* PSATD+RZ: Fix Warnings Fix a couple of warnings in PSATD + RZ. * BesselRoots: Missing Include & using * Kernel & Util: Unused Code & Var
2021-03-16Add timers in routines that depend on cell-related work (#1692)Gravatar Michael E Rowan 1-8/+13
* Add timers * eol * AtomicAdd * lev argument for getCosts * style * style * wip * eol * .ipynb * passing down lev * eol * passing lev * eol * Update Source/Particles/Collision/PairWiseCoulombCollision.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add for QED and ionization routines * eol * remove unneeded * mfi-->pti * move cost * eol Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-07Implemented update without rho in RZ spectral solver (#1569)Gravatar David Grote 1-5/+20
* Implemented update without rho in RZ spectral solver * Updated documentation for update_with_rho for RZ * Tiny fix in GalileanPsatdAlgorithmRZ reordering declarations * In Langmuir_multi_rz_psatd, set update_with_rho = 1
2020-10-02Fix some warnings for PSATD builds (#1401)Gravatar Edoardo Zoni 1-5/+3
* Fix warnings for 2D/3D PSATD builds * Fix warnings for RZ PSATD builds * Update FIXME comment: no known bug * Fix remaining warning for RZ PSATD builds
2020-09-24RZ spectral current correction and Galilean (#1216)Gravatar David Grote 1-17/+93
* Added stub for current correction in RZ spectral solver * Fixed comments in RZ spectral for current correction stub * Modified automated test for Galilean PSATD (#1033) * Impemented current correction in RZ spectral * Implementation Galilean version of RZ spectral solver * For RZ spectral, do forward and backward transform with current correction * Big fix in DivEFunctor.cpp for RZ spectral * Added RZ rho diagnostic for saving the modes * Implemented fft_periodic_single_box for RZ spectral * Moved routines from SpectralSolverRZ.H to .cpp * Added hook for VayDeposition in GalileanPsatdAlgorithmRZ * Bug fix in DivEFunctor * Fixes and cleanup for GalileanPsatdAlgorithmRZ * Fix line spacing in SpectralSolverRZ.H * Fix factor 1/2 in update of Ep_m * Fix factor 1/2 in update of Em_m * Fix sign error in current correction in GalileanPsatdAlgorithmRZ.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Add Langmuir RZ PSATD test with current correction * Add Galilean tests with/without current correction * For RZ psatd, simplified copy for forward transform * Added GalileanPsatdAlgorithmRZ.cpp to CMakeLists * Minor cleanup in RZ spectral solver * In GalileanPsatdAlgorithmRZ.cpp use member initialization for m_v_galilean Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Added some _rt to GalileanPsatdAlgorithmRZ.cpp Co-authored-by: Olga Shapoval <30510597+oshapoval@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2020-08-06Galilean PSATD: current correction and rho-free formulation (#1151)Gravatar Edoardo Zoni 1-2/+2
* Introduce option to update E with/without rho * Clean up * Implement current correction for Galilean PSATD (needs bug fix) * Include equations in docs * Fix EOL whitespaces error * Small clean-up * Implement Galilean PSATD update without rho * Clean up * Fix bug in current correction * Fix EOL whitespaces * Clean up * Fix unused import * Remove unused variable * [skip CI] Improve docs * Clean up style * Fix EOL whitespaces * Fix EOL whitespaces * Clean up style * Revert analysis script to old status * [skip CI] Clean up style * Make equations more human-readable and improve comments * 2D test with current correction works * Temporary build fix as in #1197 * 3D test with current correction works * Rename th and th_star as theta and theta_star * Fix a couple of wrong comments * Add vertical spaces to improve readability * Improve documentation * Function CurrentCorrection is now pure * 2D benchmark fields data are now correct * Add limits of coefficients for nu=-1 * Change default of update_with_rho for Galilean PSATD
2020-07-20Vay current deposition (#1051)Gravatar Edoardo Zoni 1-0/+7
* Added stub for current correction in RZ spectral solver * Start implementation of Vay deposition * Continue implementation of Vay deposition * Correct deposition of D * Add phase shift for staggered currents * Small clean-up * Fix units in deposition of D * Implement average of cumulative sum (needs bug fix) * Start fixing bug in average of cumulative sum * Still debugging * Cumulative sums should be correct now * Subtract averages of cumulative sums: - current implementation: cumulative sums, inverse Fourier transform, subtraction of averages - needs to be tested (including units of D after Vay deposition) - needs to be shortened (too many loops over boxes and ParallelFors) * [skip CI] Clean up and fix units * Still fixing units * [skip CI] Remove temporarily averages of cumulative sums * [skip CI] Remove distinction between staggered and nodal * Vay and Esirkepov similar results on periodic single box: TODO: - debug (charge not conserved); - try using compute_shifted_shape_factor as in Esirkepov deposition; - clean up; - try on multiple boxes and with correction of mode at 0 frequency. * [skip CI] Clean up * Fix bug in 3D deposition * [skip CI] Clean up * Fix 2D and 3D implementation: - simulation results agree between direct and Vay deposition in both 2D and 3D - Travis CI tests should pass except for check of charge conservation (debug) * Small clean-up * Fix bug when compiling in RZ geometry * Add benchmark json files (will be reset later) * Do not set zero current at zero frequency * [skip CI] Revert last commit and clean up * Fix small bug after reverting commit * Set nodal test first on Travis * Fix benchmark for nodal test in 3D * Fix particle output for nodal test in 3D * Fix bugs due to staggering * Rename current nodal Travis tests * Add Travis tests staggered in 2D and 3D * Further clean-up after bug fix * Abort when using Vay deposition with domain decomposition * Add optional argument of index type to forward FFT * Fourier shifts can be private members as before * Small clean-up * Clean up and improve Doxygen documentation * Fix small bug in analysis script for 2D tests * Fix tests (remove E and B fields from particle diags) * Add option to fill guard cells and docs * Fix value of last guard cell by enforcing periodicity * Revert changes merged from #1121 * Clean up style * Improve docs * Fix forgotten alignment * Improve docs * Make base class functions VayDeposition pure Co-authored-by: Dave Grote <dpgrote@lbl.gov>
2020-07-14Fix bug in RZ PSATD rho terms (#1172)Gravatar David Grote 1-2/+2
2020-05-22Added stub for current correction in RZ spectral solver (#1007)Gravatar David Grote 1-0/+8
* Added stub for current correction in RZ spectral solver * Fixed comments in RZ spectral for current correction stub * Modified automated test for Galilean PSATD (#1033) Co-authored-by: Olga Shapoval <30510597+oshapoval@users.noreply.github.com>
2020-04-14Implementation of the RZ spectral solver (#816)Gravatar David Grote 1-0/+198
* For diagnostics, added RZ modes of scalars, allowed different centerings * For RZ, generalized the centering of the inverse volume scaling of J and rho * Fixed spacing in ConstructTotalRZScalarField Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Added Python wrapper of charge density arrays * Add assert ensuring that Jr is never node-centered Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Small fixes to Python to better handle particle weights * Implementation of the RZ spectral solver * Removed k-space filtering code * Removed more k-space filter code from RZ spectral solver * For RZ spectral, added _rt for literals and cleaned up namespace use * In RZ spectral solver, cleaned up some member names * Update Docs/source/building/rzgeometry.rst Small fix for clarity. Co-Authored-By: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Evolve/WarpXEvolve.cpp Fix macro indentation Co-Authored-By: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Evolve/WarpXEvolve.cpp Fix more macro indentation Co-Authored-By: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Evolve/WarpXEvolve.cpp Fix another macro indentation Co-Authored-By: Remi Lehe <remi.lehe@normalesup.org> * New diagnostics support RZ (#836) * Start implementation of new averaging with staggering: - face-to-cell-center and edge-to-cell-center replaced so far; - TODO: node-to-cell-center and 1D behavior (AMREX_SPACEDIM=1). * first implementation of Diags base classes * add example, temporarily * Continue implementation of new averaging with staggering: - new function takes reference to single MultiFab (no vector); - TODO: node-to-cell-center still in progress. * Fix small bug and clean up * Fix bug in loop over n=0,...,ncomp-1 and clean up * add more functions * Add Doxygen documentation and clean up * Small clean-up in Doxygen documentation * Compile in single precision: add _rt suffix to avoid unnecessary conversions * Avoid accessing staggering index directly from IntVect in innermost loops * Replace do-while loop with for loop (default ncomp=1) * Remove temporary pointer and pass reference to MultiFab (instead of MultiFab*) * Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor * cleaning and initialize output mf * use general average routine * move flush in new class, and implemented the Plotfile derived class * add comments * eol * free memory in destructor * typo * typo * no need to clear MF pointers there * though shalt not break existing tests * FlushRaw doesnt have to be virtual for now * The importance of being constant * Capability to select fields in output files * EOL * revert to old inputs * const in right place * avoid brace initializer there * oops, fix logic error in is_in * user can choose flush interval, same behavior as plot_int * Add option to plot raw fields * eol * replace ter flush with dump to avoid confusion * add options * Diagnostics stores a vector of functors to compute diags on the fly * eol * Field gather from diags to sync particle quantities * New diagnostics handle RZ with same behavior as old ones * cleaning and doc * const ref for string * smarter for loop from Axel and typo fix from Reva * simplify code following Dave's comments * rename mode_avg to convertRZmodes2cartesian * Update CellCenterFunctor.H * fill varnames and vector of functors at the same time * WarpX instance not needed here * add const Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> * Add load balance options documentation (#842) * Add load balance options documentation * Add load balance options documentations * EOL * Replace tilebox by growntilebox (#849) * Updated Profiling information in running_cpp (#776) * Fixed link that was pointing to 404 error page * Added motivation for profiling and TINYPROFILERS explanation * Moved section on NERSC profiling to developers Docs * Update Docs/source/running_cpp/profiling.rst Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Update tiny profilers suggestion Docs/source/running_cpp/profiling.rst Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Fix typo Docs/source/running_cpp/profiling.rst Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Add a few additional diags (divE etc.) (#844) * Start implementation of new averaging with staggering: - face-to-cell-center and edge-to-cell-center replaced so far; - TODO: node-to-cell-center and 1D behavior (AMREX_SPACEDIM=1). * first implementation of Diags base classes * add example, temporarily * Continue implementation of new averaging with staggering: - new function takes reference to single MultiFab (no vector); - TODO: node-to-cell-center still in progress. * Fix small bug and clean up * Fix bug in loop over n=0,...,ncomp-1 and clean up * add more functions * Add Doxygen documentation and clean up * Small clean-up in Doxygen documentation * Compile in single precision: add _rt suffix to avoid unnecessary conversions * Avoid accessing staggering index directly from IntVect in innermost loops * Replace do-while loop with for loop (default ncomp=1) * Remove temporary pointer and pass reference to MultiFab (instead of MultiFab*) * Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor * cleaning and initialize output mf * use general average routine * move flush in new class, and implemented the Plotfile derived class * add comments * eol * free memory in destructor * typo * typo * no need to clear MF pointers there * though shalt not break existing tests * FlushRaw doesnt have to be virtual for now * The importance of being constant * Capability to select fields in output files * EOL * revert to old inputs * const in right place * avoid brace initializer there * oops, fix logic error in is_in * user can choose flush interval, same behavior as plot_int * Add option to plot raw fields * eol * replace ter flush with dump to avoid confusion * add options * Diagnostics stores a vector of functors to compute diags on the fly * eol * Field gather from diags to sync particle quantities * New diagnostics handle RZ with same behavior as old ones * cleaning and doc * const ref for string * smarter for loop from Axel and typo fix from Reva * Functors to compute some fields * simplify code following Dave's comments * Create subfolders and add more output options (divE etc.) * eol * rename mode_avg to convertRZmodes2cartesian * Update CellCenterFunctor.H * fill varnames and vector of functors at the same time * output rho_new, not rho_old * WarpX instance not needed here * add const * little bit more of reorganization * Apply suggestions from code review Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * add a bunch of const * make derived classes final Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add Initial Distribution Test (#735) * Add Histogram * Add normalization * Add doc * Minor * Minor * Fix a bug * Add gaussian distribution test * Fix alert and change amr.plot_int * Add maxwell-boltzmann distribution test * Add maxwell-boltzmann distribution test * Add maxwell-boltzmann distribution test * Add maxwell-juttner * Minor * Typo * Minor * Minor * Add const * Apply suggestions from code review Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Modify based on suggestions. * Add histogram name * Add bin values * Don't add histogram name * Modify read_raw_data.py * Add doc * Change ux,uy,uz units * Change ux,uy,uz units * Change if format * Save some variables * Change more * Minor * Fix a bug on GPU * Fix a bug on GPU * Add wrong species name abort * Minor doc * Change #include format * Apply suggestions from code review Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Add const * Change to member variables * revert * Change units based on changes of PR#727 * merge * Add Gaussian position distribution test * Minor * Change based on suggestions * Use read_raw_data.py * Minor * Change to no normalization * Add more in doc * doc * doc * Use relative error * Don't divide by bin_size * Change based on suggestions Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Tests: Fix Bool Switch Typo OMP (#854) useOMP is 0 (False) or 1 (True) * Costs vector of (pointer to) vector (#829) * [WIP] costs mf --> costs vector * [WIP] costs vector * [WIP] vector costs * formatting * makefile * [WIP] costs vector * [WIP] *= costs * wts do not need to divide by num cells * Tiling safety on CPU * Add tests * EOL * Remove unneeded input * Update Source/WarpX.H costs documentation Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Update timers with times only if user Timers update * warpx.-->WarpX:: * warpx.-->WarpX:: * warpx.-->WarpX:: * warpx.-->WarpX:: * warpx.-->WarpX:: * add dev synch * Update Regression/WarpX-tests.ini Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Delete inputs_loadbalance_costs_heuristic * Update and rename inputs_loadbalancecosts_timers to inputs_loadbalancecosts * Update WarpX-tests.ini Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * [mini-PR] Read species distribution from OPMD file (#847) * Added <species>.profile=external_file and .profile_file * Added description of input parameters to Docs * Changed from profile to injection option for external file * Fix typo in amrex abort message (due to copy paste) * Added the OpenPMD use amrex abort message * Minor fix - not sure how to remove EOL issue * Tried to add AddExternalFileBeam functon to PhysicalParticleContainer * Trued to fix EOL white space issue * Added read/print species name from OPMD file * Update Source/Initialization/PlasmaInjector.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.H Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * No need to include openPMD header yet * Fix EOL according to @ax3l's recommendation in #845 * Remove commented out AbortMessage Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Removed commented out part initialization (used only in branch for next PR) Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Added warning that this is WIP Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Changed function name to AddPlasmaFromFile * Removed AMReX warning from loop Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Ignore python build/dist and egg folders (#850) * Travis CI: set max numprocs=2 and do not overwrite (#860) * [mini-PR] Fix bug in Breit-Wheeler engine (#852) * fixed bug in BW engine * fixed bug * fixed bug * fixed bug * fixed bug * fixed bug * eliminate useless variable * updated test * updated inputfile * Updated tests * increase tolerance from .04 to .07 in QED 3D BW test * do plot pos_bw and ele_bw Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Documentation update - towards full SI (#301) * Added blank line after list. Changed characters in link to Q. H. Liu paper so hyoerlink works with sphinx-build 2.1.2. * Added line cut unintentionally. * Removed line added unintentionally. * Same as before. * Same as before, but hopefully successfully * Same as before, but hopefully successfully * Minor changes to description of PWFA example run * Revert "Minor changes to description of PWFA example run" This reverts commit a4d7fa969c906959b018efe683a3e585cbd741f9. * Revert "Profiler wrapper to allow for cudaDeviceSynchronize (#738)" This reverts commit bbefc3dad687f4370afd5bc85386d983201cb321. * Revert "Revert "Minor changes to description of PWFA example run"" This reverts commit 965982d35361ff54d0ad10101ffc31605117e5ac. * Revert "Minor changes to description of PWFA example run" This reverts commit a4d7fa969c906959b018efe683a3e585cbd741f9. * I am making a huge mess with merging * Minor changes to description of PWFA example run * Added explanation PWFA simulation section * Re-structuring. Adding sections for each choice. * Minor fix to note * Minor changes to text * Time step description + fixed line length * Added FDTD and CKC selection * Added max time step calculations * Trying to fix EOL issue * Added mesh refinement and moving window * Fixed minor issues * Fix EOL issues again * Fixed typo - auxiliary Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> Co-authored-by: Diana Amorim <diana@henrivincenti.dhcp.lbl.gov> Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Remove compiler warnings (#843) * Fix compiler warnings with DIM=2 * Fix compiler warnings with USE_RZ=TRUE * Fix compiler warnings with USE_PSATD=TRUE and DIM=2 * Fix compiler warnings with USE_PSATD=TRUE and DIM=3 * Fix bug: discard only return value when calling DefineAndReturnParticleTile * Remove unused variables not triggering warnings * [mini-PR] Fix energy calculation for photons in reduced diagnostics (#861) * fix energy calculation for photons * fixed typo and mada calculation clearer * added photon particles in reduced diags test * Update Source/Diagnostics/ReducedDiags/ParticleEnergy.cpp Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * Update Source/Diagnostics/ReducedDiags/ParticleEnergy.cpp Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Port rigid injection to the gpu (#862) * port rigid injection to the gpu * eol * Apply suggestions from code review Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * define csqi Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Added blocking factor to 2d and RZ geometries (#864) * doc: fix formatting for ascent yaml examples (#865) * [mini-PR] Clarifying ionizable particle charge (#863) * 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> * In HankelTransform, added explicit matrix multiply for GPU * In RZ spectral solver, update setval to be on device * Removed CEXE_headers from FieldSolver/SpectralSolver/Make.package * In HankelTransform, added check of the Bessel root finder * Updated includes to RZ spectral solver * Added comments on how Hankel transform matrix is calculated * Added more comments to Hankel transform calculation * For RZ spectral solver, cleaned up naming and add subdirectory for Hankel transform files * Cleaned up code in PsatdAlgorithmRZ.cpp * Updated comment for fields in SpectralFieldDataRZ.cpp * Changed HankelTransformer to MultiSpectralHankelTransformer * Updates comments in RZ spectral solver * Removed code for k-space filtering that will be added in a later PR * For RZ spectral solver, passed lev in * Fixed comment in SpectralFieldDataRZ.cpp Co-authored-by: MaxThevenet <mthevenet@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Co-authored-by: NeilZaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Yinjian Zhao <yinjianzhao@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: Diana Amorim <diana@henrivincenti.dhcp.lbl.gov> Co-authored-by: Andrew Myers <atmyers@lbl.gov> Co-authored-by: Cyrus Harrison <cyrush@llnl.gov>
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