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2022-02-16Refactor Current Correction Functions (#2839)Gravatar Edoardo Zoni 16-163/+17
* Refactor Current Correction Functions * Clean Up, Reset Benchmark
2022-02-03Rename PSATD Classes (#2805)Gravatar Edoardo Zoni 12-79/+79
* Rename PSATD Classes * Rename PsatdAlgorithmJLinear as PsatdAlgorithmJLinearInTime
2022-01-31Separate Class for Multi-J PSATD Algo (#2748)Gravatar Edoardo Zoni 6-188/+610
* Separate Class for Multi-J PSATD Algo * Cleaning * X1,...,X6 Real, not Complex * Cleaning * Improve Comments, Rename Jx as Jx_old (etc.)
2022-01-20Implement PML for the outer RZ boundary with PSATD (#2211)Gravatar David Grote 4-0/+251
* Initial version of RZ PSATD PML BCs * Cleaned up some bugs * Add support of do_pml_in_domain option * Cleaned up stuff for building * Fix PMLPsatdAlgorithm macro * Removed unneeded variable from SpectralSolverRZ * Change length 3 arrays to length 2 (for 2D) * Cleanup around DampPML * Added more checks of pml[lev] * Added CI test for RZ PML * Added code to update the corner guard cells * Further updates * Added CI test * Fixed EOL space * Updated CI benchmarks, removing round off fields * Changes to CI missed on previous commit * Various fixes for clean up * More fixes for clean up * Further cleanup * Updated benchmark * Fixed benchmarks file * Minor cleanup * Added round off benchmark values * Fixed testname in analysis_pml_psatd_rz.py * Update comment in analysis file * Put pml_rz code in RZ and PSATD macro blocks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add geometry.dims input to CI test input file, inputs_rz * Cleanup to match recent changes Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-01-09Multi-J: J Always Linear in Time (#2679)Gravatar Edoardo Zoni 4-31/+32
* 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
2021-12-16Doxygen: Fix Diags, FieldSolver, Parallelization & Particles (#2662)Gravatar Axel Huebl 7-0/+17
* Doxygen: Fix Diags, FieldSolver, Parallelization & Particles * Apply suggestions: Remi Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions: Roelof Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Apply suggestions: Luca Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Andrew * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Neil Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Apply suggestions: Roelof * Apply suggestions: Weiqun Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-12-08Replace AMREX_SPACEDIM: Evolve & FieldSolver (#2642)Gravatar Prabhat Kumar 7-40/+40
* AMREX_SPACEDIM : Boundary Conditions * AMREX_SPACEDIM : Parallelization * Fix compilation * AMREX_SPACEDIM : Initialization * Fix Typo * space * AMREX_SPACEDIM : Particles * AMREX_SPACEDIM : Evolve and FieldSolver
2021-12-02div(E,B) Cleaning Options for PSATD (#2403)Gravatar Edoardo Zoni 1-23/+29
* Implement div(E)/div(B) Cleaning with Standard PSATD * Cleaning * Update Benchmark * Add Nodal Synchronization of F,G * OneStep_multiJ: Nodal Syncs, Damp PML * OneStep_multiJ: Push PSATD Fields in PML * div Cleaning Defaults (Domain v. PML) * Include Fix of #2429 until Merged * Reset Benchmark of Langmuir_multi_psatd_div_cleaning * Multi-J: Remove PML Support * Include Fix of #2474 Until Merged * Exchange All Guard Cells for F,G * Fix Defaults * Update Test, Reset Benchmark * Fix Defaults * Cleaning * Default update_with_rho=1 if do_dive_cleaning=1 * Update CI Test pml_psatd_dive_divb_cleaning * Replace Warning with Abort
2021-11-22Added abort error message to prevent using averaged Galilean PSATD with ↵Gravatar Olga Shapoval 1-0/+4
psatd.update_with_rho=0 (#2571)
2021-10-21Div(B) Cleaning: Change Normalization of G (#2429)Gravatar Edoardo Zoni 2-14/+14
* 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
2021-10-11Use parser for more input parameters (#2386)Gravatar Neïl Zaim 6-9/+9
* Use parser for more input parameters * Fix PSATD compilation and apply suggestions from code review * Avoid out of bound array access for num_particles_per_cell_each_dim * Fix few input files with respect to num_particles_per_cell_each_dim * Fix get that incorrectly became query
2021-08-05RZ PSATD: Time Averaging for Multi-J Algorithm (#2141)Gravatar Edoardo Zoni 2-3/+125
* RZ PSATD: Time Averaging for Multi-J Algorithm * Fix Wrong Signs in Bm * Use Time Averaging in CI Test, Update Benchmark * Minor Fix
2021-07-29PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (#2142)Gravatar Edoardo Zoni 1-0/+10
2021-07-26RZ PSATD: Multi-J Algorithm (#2111)Gravatar Edoardo Zoni 2-14/+97
* 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
2021-07-21Multi-J Algo: Make div(E)/div(B) Cleaning Optional (#2116)Gravatar Edoardo Zoni 2-35/+70
* Multi-J Algo: Make div(E)/div(B) Cleaning Optional * Remove Unnecessary Newlines
2021-07-19Fix Bug in Multi-J PSATD Equations (#2106)Gravatar Edoardo Zoni 1-3/+3
2021-07-15Spectral Index: Replace `struct`s of `enum` with Class (#2062)Gravatar Edoardo Zoni 14-371/+371
* 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
2021-07-08Do Not Fill Guard Cells with Inverse FFTs, Unless for Field Damping (#2045)Gravatar Edoardo Zoni 8-16/+35
* Do Not Always Fill Guard Cells with Inverse FFTs * Query psatd.fill_guards from Inputs * Clean Up and Reduce Style Changes * Fix Bug for Periodic Single Box * Clean Up and Reduce Style Changes * Fix Bug for RZ PSATD * Remove Input Parameter, Default 0 Unless Damping * Fix CI Tests (2D) * Fix CI Tests (3D)
2021-07-06remove extra semicolon (#2052)Gravatar Luca Fedeli 1-1/+1
2021-06-28Multi-J scheme (#1828)Gravatar Remi Lehe 2-22/+219
* Introduce new option skip_deposition * Properly implement the option to skip deposition * Skip deposition for electrostatic solver * Correct typo * Add Index Enumerator and Equations for F/G Without Averaging * Define new functions for current deposition and charge deposition * Disable interpolation between levels * Correct compilation error in RZ mode * Add argument for relative time * Add Index Enumerator and Equations for F/G With Averaging * [skip ci] Add new OneStep function * Fix compilation errors * Correct more compilation errors * [skip ci] Fix compilation * Split the PSATD push into separate functions * Add guards for rho field * [skip ci] Use new functions in OneStep * [skip ci] Separate the inverse transform of E_avg, B_avg * Add deposition of rho * [skip ci] Prevent deposition of rho if unallocated * Fix error in deposition function * Add subcycling of current deposition * [skip ci] Add inverse transform of averaged fields * [skip ci] Move component of rho * Add function to copy J * Temporarily deactivate contribution from F * [skip ci] Implement call to linear in J * Add psatd time averaging for multiJ * [skip ci] Fix implementation of averaging * [skip ci] Implement divE cleaning * Fix Bug for RZ Builds * Fix Bug for RZ Builds * Fix Bug in Init of PML Spectral Solvers * Cleaning * Cleaning * Add div(B) Cleaning (G Equation) * Multi-J Not Implemented with Galilean PSATD or PMLs * Add 2D CI Test Using Multi-J Scheme * Add More Inline Comments * Add More Inline Comments & Doxygen * Add Doxygen for Constructor of SpectralSolver * More Doxygen in Class SpectralSolver * Add Doxygen for New Functions in WarpXPushFieldsEM.cpp * Add Doxygen for New Functions in WarpX/MultiParticleContainer * do_dive/b_cleaning Must Be True With linear_in_J Option * Cast multij_n_depose to Real in Divisions * New Input Syntax * Add const where Possible, Fix Warnings * Docs for New Input Syntax, Fix Abort Messages * Consistent Use of Idx, IdxAvg, IdxLin * Improve Documentation of psatd.J_linear_in_time * Use const Type Qualifier whenever Possible * Simplify Initialization of Pointer ion_lev * Improve Doxygen * Update documentation * Add Note on NCI to Docs * Make warpx.do_multi_J_n_depositions Not Optional * Simplify Logic in getRequiredNumberOfFields * Use More const Type Qualifiers Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2021-06-24Use "Include What You Use" on WarpX (#1947)Gravatar Luca Fedeli 10-24/+135
* 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>
2021-05-10NVCC: Fix PSATD+RZ Build Error (#1950)Gravatar Axel Huebl 1-1/+2
Work-around for: ``` Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.cpp(145): error #2985: identifier "PhysConst::ep0" is undefined in device code ```
2021-04-19Divergence cleaning for PSATD in PML (#1600)Gravatar Edoardo Zoni 2-69/+232
* Add div(E)/div(B) cleaning options for PSATD in PMLs * Pass missing flags to spectral solver in PML * Duplicate MPI exchange and communication functions for G * Use separate parameters for div cleaning in PMLs * Add asserts for features that are not implemented * Do not need to duplicate MPI exchange functions for G * Add short documentation for new input parameters * Set new parameters true by default with PSATD solver * Add CI test for PML div cleaning with PSATD * Use new syntax <diag_name>.intervals in new input file * Reset benchmark of new CI test * Always synchronize nodal points of G MultiFab * Fix few warnings in 2D build * Update Benchmark of pml_psatd_dive_divb_cleaning * Improve Documentation of warpx.do_pml_dive_cleaning Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Improve Documentation of warpx.do_pml_divb_cleaning Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Improve Abort Message * Clean Up Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2021-04-07Remove Unused Variable in ComovingPsatdAlgorithm (#1879)Gravatar Luca Fedeli 2-3/+3
2021-03-29Class `PsatdAlgorithm`: Simplify Initialization of Coefficients (#1819)Gravatar Edoardo Zoni 2-616/+432
* Split Initialization Functions of Spectral Coefficients * Simplify Initialization of Coefficients Without Averaging * Do Not Store Coefficients C1,S1,C3,S3 With Averaging * Simplify Initialization of Coefficients With Averaging * Add amrex:: Prefix Following WarpX Style Guidelines * Match Names Of Coefficients With/Without Averaging * 'pow' Cannot Be Used in a Constant Expression * Update Doxygen Documentation
2021-03-19Warnings: PSATD+RZ & More (#1814)Gravatar Axel Huebl 3-4/+4
* 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 14-63/+95
* 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>
2021-03-10Spectral Solver: Remove Unused Header Files (#1778)Gravatar Edoardo Zoni 2-138/+0
2021-03-04Implement averaged algo on staggered grids & merge spectral classes (#1544)Gravatar Edoardo Zoni 6-1153/+915
* Refactor and clean up some spectral classes * Abort when current correction or Vay deposition are not implemented * Implement general equations for averaged Galilean * Allocate averaged MultiFabs also when aux_is_nodal=1 and do_nodal=0 * Allocate +ngextra guard cells also for averaged MultiFabs * Make alias MultiFabs for averaged aux data * With averaging, interpolate from avg_fp (not fp) to aux * Fix some limits of the coefficients * Fix bug causing NaNs in spectral coefficients * Add 2D CI test with same analysis as nodal test * Add 3D CI test with same analysis as nodal test * Add limit that was not covered (knorm=0 && knorm_c!=0 && nu=0) * Allocate T2_coef only if Galilean algorithm is used * Allocate X4_coef only if Galilean algorithm is used * Remove extra ghost cell from 'avg_fp' MultiFabs
2021-02-11Spectral solver: remove extra semicolons (#1709)Gravatar Luca Fedeli 3-3/+3
2021-01-07Implemented update without rho in RZ spectral solver (#1569)Gravatar David Grote 4-15/+60
* 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
2020-12-02Improve spectral solver on staggered grids (#1468)Gravatar Edoardo Zoni 6-74/+786
* Implement Galilean PSATD equations on staggered grids * Implement high-order interpolation in 2D/3D * Include missing header file and small clean-up * Fix bug for FDTD build * Small clean-up * Modify current correction for staggered grids * Implement comoving PSATD scheme (formulation with rho) * Fix single-precision builds * Do not implement rho-free formulation for comoving PSATD yet * Invert sign of comoving velocity to match Galilean convention * Fix two bugs in comoving PSATD algorithm * Update benchmark of CI test momentum-conserving-gather * Update benchmark of CI test PlasmaAccelerationMR * Update documentation * Clean up comoving PSATD class * Clean up comoving PSATD class (more) * Clean up comoving PSATD class (more) * Implement changes requested in PR review * Add 2D regression test for staggered Galilean PSATD * Add 2D regression test for staggered comoving PSATD * Unify input files for new CI tests to avoid duplication * Fully rebase benchmarks changes on development * Update benchmark of Galilean hybrid test after #1536
2020-11-16Fix PSATD equations used with PML (#1513)Gravatar Edoardo Zoni 2-60/+130
* Implement new PML PSATD equations * Update CI test and benchmark * Compute coefficients C1,...,C22 on the fly * Add check on initial energy from diagnostics
2020-10-02Fix some warnings for PSATD builds (#1401)Gravatar Edoardo Zoni 7-48/+25
* 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 7-20/+526
* 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>
2020-09-14Clean up profiling labels (#1320)Gravatar Edoardo Zoni 1-2/+2
2020-08-24Fix some warnings (#1239)Gravatar Luca Fedeli 4-17/+22
This PR fixes the source of several compilation warnings. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-08-06Galilean PSATD: current correction and rho-free formulation (#1151)Gravatar Edoardo Zoni 12-162/+456
* 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 12-1/+200
* 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>
2020-07-17Fixing compiler warnings (#1178)Gravatar Olga Shapoval 1-13/+2
* Removed unused variables and made 'vy=v_galilean[1]' declaration conditional on 3D case (this fixes compiler warnings) * Avoid unnecessary conversion from 'double' to 'int' (this fixes compiler warnings)
2020-07-14Fix bug in RZ PSATD rho terms (#1172)Gravatar David Grote 1-2/+2
2020-07-10Fix compilation of AvgGalilean for GPU (#1159)Gravatar Remi Lehe 2-2/+18
2020-07-08Averaged Galilean PSATD (#869)Gravatar Olga Shapoval 4-0/+403
* Read Galilean velocity * Prepare structures for Galilean solver * Started implementing Galilean equations * Analytical limits for X1, X2, X3, X4 coefficients added * Slight changes added * Added Galilean position pusher * Scale galilean velocity * Remove unneeded Abort * Fix Galilean pusher * Allocate Theta2 array * Fix definition of coefficients * Increase guard cells for Galilean * Add guard cell in particle exchange * Added modifications for PICSAR galilean branch * Averaged coefficients added * Type corrected * v_gal added to warpx_current_deposition * v_gal added to WarpXParticleContainer.H * Bug fixed - update particle x-position over one time step * Fix issues with merge from dev * Averaged fileds allocated on fine patch (Ex) * Preparation for merging dev into galilean. * remove TABs by hand * Removed a tab. * Redeclared v_galilean as a vector & related changed * Added an automated test * Moved v_galilean inside WarpX constructor * Added analysis script for the automated test * Changed name of the automated test to galilean_psatd * Added InitializeSpectralCoefficients method * Removed temporary comments * Averaged fields added to FiledGather * Added infinite order k[i] * Setting kx_mod( kz_mod) = 0 for index = nx/2(-nz/2) * Adding galilean shift * Implemented galilean shift * Changed method's name from GalileanShift to ShiftGalileanBoundary * Added doxygen string for ShiftGalileanBoundary * Removed never used method LowerCornerWithCentering * Removed temporary comments * Removed dt as a variable from DepositCharge method and its dependencies * Changing type of v_galilean from amrex::Vector to amrex::Array * Changed back ng_fft to be equal nox_fft * Changed v_galilean's type from amrex::vector to amrex::array * Removed type * Removed temporary comments * Added flag 'do_time_averaging' to swith from unaveraged to averaged Galilean PSATD * Updated doxygen * Small fix on using 'do_time_averaging' flag * Remove some commented Print statements * [skip ci] Further cleanup * Fix compilation * Guard cells update of the averaged E,B fields * Corrected included header file accordingly * Removed EOL * Removed EOL * Corrected path of the included header file * Updated choice of the spectral solver. * Cleanup. * use amrex::exp instead of std::exp * no backward FFT for avg fields if avg is off * Need to shift avg fields in MoveWindow * Further cleaning * Added 2D automated test for averaged PSATD * Added automated 2D and 3D tests for averaged PSATD * Removed comments * Added specifications for averaged Galilean PSATD tests. * Bug fixed - do FillBoundary of the averaged fields only if averaged is activated * Do shiftMF of the averaged fields only if fft_do_time_averaging=true * Add checksum json benchmarks for averaged Galilean PSATD * Add missing indentation * Add missing indentation * Updated automated analysis script * Updated diags period * Fixed bug: no backtransform of the averaged fields when WARPX_DIM_RZ is set * Fixed an uninitialized variable * Clean-up * Changed permissions for analysis_avg_*d.py * Compactified variables initialization via conditional assignment * Initialized averaged E_avg, B_avg fields * Updated automated test for 2D averaged galilean PSATD * Updated benchmark for 2D averaged galilean PSATD * Updated automated 2D averaged PSATD test & benchmark * Updated automated 3D averaged PSATD test & benchmark * Fixed typo * Updated benchmark averaged_galilean_3d_psatd * Initialize the averaged fields only if the averaged Galilean PSATD algorithm is enabled * Encreased time step for automated 3D averaged Galilean PSATD (to be equal c*dt=dz while dz/dx=3) * Updated 3D automated test: specified standard deviations `.ux_th, .uy_th, .uz_th` along each direction * Typo from the previous commit: enabled the averaged algorithm * Trying out another input parameters for 3D averaged automated test with v_gal = v_plasma * Update benchmark for previously added 3D averaged automated test * Update 2D averaged automated test and corresponding benchmark * Revert "Updated diags period" This reverts commit 7334729b05e96589e020c981efdb430ca095991d. * Cleanup: removed unwanted comment. * Added descriptions of the 2D and 3D automated tests for the averaged Galilean PSATD. * Updated value calculated via standard Galilean PSATD. * Encreased relative error tolerance for 3D automated test for the averaged Galilean PSATD. * Removed to avoid duplication since it already specified in the corresponding 2D/3D input scripts. * Removed unwanted empty lines * Added spaces after function's names * Removed unwanted empty line * Removed * Fixed indentation * Cleanup: removed #include <math.h> * Cleanup: removed empty lines and fixed indentation * Added 'AvgGalileanAlgorithm.cpp' to 'CMakeLists.txt' Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
2020-07-06PSATD: add option to update E without using rho (#1128)Gravatar Edoardo Zoni 2-50/+82
* Introduce option to update E with/without rho * Clean up * Include equations in docs * Fix EOL whitespaces error * Small clean-up * Clean up
2020-07-02PSATD: current correction works only with global FFTs (#1131)Gravatar Edoardo Zoni 1-9/+9
* 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
2020-06-12Add CMake Scripts (#759)Gravatar Axel Huebl 1-0/+15
* [skip travis] CMake: Add CMake Scripts This add CMake scripts for the CMake build system generator. * CUDA Support Achieved Fastest compile via: cmake .. -DENABLE_CUDA=ON -DCUDA_ARCH=6.0 * CMake: openPMD & QED * CMake: Dimension Support WarpX_DIMS=2,3,RZ * CCache & Out-of-Source Enable CCache when found and prevent in-root builds (in-source okay-ish). * CMake: CUDA C++ Language Minimum * Add new Files * CI: Migrate macOS to CMake * Fortran: Enable Because Transitive ... for now :) * CI: Migrate Linux ICC to CMake * CI: Verbose Make * CMake: Add Missing PSATD Sources * CMake: PSATD, Compute, Precision, Clean
2020-05-22Added stub for current correction in RZ spectral solver (#1007)Gravatar David Grote 3-0/+40
* 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>
2020-05-05Current correction in Fourier space (#675)Gravatar Edoardo Zoni 3-5/+126
* Start implementing PSATD push without rho. TODO: 1) fix unit test pml_x_psatd; 2) try new PSATD push in PML; 3) avoid intro of new derived class? * Correct PSATD push to fix PML test. * Few improvements on new PSATD push: - new class name is 'PsatdAlgorithmMixed' (both rho and J are used); - new algorithm parameter to choose between available implementations: parameter name is 'psatd_push', possible values are 'standard' for old implementation using rho via Gauss law and continuity equation and 'mixed' for new implementation using rho via Gauss law and J for all remaining terms. * Fix style error (tabs vs four white spaces). * Improve comments for available PSATD algorithms. * Correct few typos in latest comments. * Implement first current correction: - new member function 'CurrentCorrection' in class SpectralSolver; - correction applied only without subcycling (in function 'OneStep_nosub'); - TODO: add correction when subcycling is used (in function 'OneStep_sub1'); - back to old implementation of PSATD push of E and B (class 'PsatdAlgorithmMixed' removed); - TODO: PML unit test 'pml_x_psatd' does not pass. * Small cleanup: - remove residual option for choice of PSATD push algorithm (only one choice now); - improve comments. * Implement div(E) diagnostics for spectral case. * split travis tests in bigger matrix * split more TravisCI tests, add electrostatic, use defaults values * typo * Move computation of div(E) to base class SpectralBaseAlgorithm. * need to split psatd too * consistent variable names and use function to avoid duplication * fix typo for qed tests * typo * also need to update run_tests.sg * Update copyright tags. * change matrix * Add test of div(E) vs rho/epsilon_0 in PML test. * Small clean-up. * Small clean-up * Remove option for current correction from input files of two new tests (not used) * Small clean-up: remove unnecessary references * More clean-up (minimize style changes to keep PR simple). * Add specific 2D/3D tests for current correction: - 'Langmuir_multi_2d_psatd_cc': same input file as 'Langmuir_multi_2d_psatd', except for current correction and output of divE; - 'Langmuir_multi_psatd_cc': same input file (3D) as 'Langmuir_multi_psatd', except for current correction and output of divE; - add corresponding Python scripts for analysis: same as previous ones, except for check on L-infinity spatial norm of rho/epsilon_0 vs div(E); - revert changes on old tests: do not use current correction in old tests (benchmarks on Battra do not need to be updated). * Improve comments. * 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). * Remove unrelated style changes (cleaner PR). * Avoid duplication of input files and analysis scripts for new tests * Improve comments for Doxygen documentation. * Improve comments for Doxygen documentation. * Small clean-up * first implementation of Diags base classes * Small clean-up * Small clean-up * Fix erroneous non-ASCII character * Small clean-up * Auxiliary function for current correction in class WarpX to keep OneStep_nosub clean * Remove unrelated style changes (cleaner PR) * Improve comments * Instrument virtual function 'CurrentCorrection' * Trying to fix build error detected by LGTM analysis only * 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 * Implement periodic-single box option for spectral * Fix out-of-bound in the periodic, single-box case * 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 * Use old name for output image of new 2D test * user can choose flush interval, same behavior as plot_int * Small clean-up in Doxygen documentation * 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 * Add documentation for periodic_single_box_fft * For periodic, single-box, apply current correction after guard cell exchange * 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 * Travis CI: force 2 MPI processes only for numprocs > 2 * Use special FFT (PR #834) and new diagnostics (PR #844) in new tests * Improve Doxygen documentation * Move option do_current_correction from warpx to psatd * Fix path to output files for tests using new diagnostics * Fix additional paths to output files for new diagnostics * Add input paramter do_current_correction to documentation * Fix test Langmuir_multi_psatd_hybrid: do not plot divE * Remove input parameter amr.plot_int in tests using new diagnostics * Trigger failing source/style checks on Travis CI * Fix build error due to public include * Add missing const keywords * Change test names and corresponding analysis scripts * Improve Python script for analysis * Do not rename output files in old CI tests (without current correction) * Fix output file name prefix for some tests * Trigger Travis CI build after AMReX bug fix * Void commit: trigger Travis CI build * Fix some tests failing due to recent changes in master * Use new diagnostics for particle output correctly Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Print tolerance and error in Python analysis Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Print tolerance and error in Python analysis Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Improve documentation Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Fix EOL white spaces * Fix name of particle output variables Co-authored-by: MaxThevenet <mthevenet@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-04-29CI: macOS Single Precision (#964)Gravatar Axel Huebl 1-3/+3
* CI: macOS Single Precision Add another compile with single precision on AppleClang. * AMReX' complex for everything This is nice and compliant and works on all platforms.
2020-04-28Style change to match the standard (#957)Gravatar Michael E Rowan 1-8/+8
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