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2020-11-11Fix error with nested MFIter loop in Schwinger (#1509)Gravatar NeilZaim 1-3/+3
2020-11-09sx_node_galerkin: fix access to uninitialized memory (#1500)Gravatar Luca Fedeli 1-2/+3
* fix a possibly uninitialized variable warning * adopted alternative solution following dpgrote suggestion
2020-11-06Fix check of m_do_scale in ScaleFields (#1505)Gravatar David Grote 1-1/+1
2020-11-06ParticleNumber reduced diag: also output total number of physical particles ↵Gravatar NeilZaim 2-22/+65
(#1502)
2020-11-05Fix includes in RhoFunctor.cpp (#1498)Gravatar David Grote 1-1/+1
2020-11-03Use the parser for more input parameters (#1481)Gravatar MaxThevenet 3-10/+42
* option to smart-query input arguments using the parser * modify one example to illustrate * cleaner naming * cleaner call to the parser, no need to go through a pointer * better naming and more doc for queryWithParser * update the documentation
2020-11-02fixed calls to amrex::Random() to enable HIP compilation (#1487)Gravatar Luca Fedeli 7-15/+28
2020-11-02[mini-PR ] Fix an "unused variable" warning (#1488)Gravatar Luca Fedeli 1-2/+1
* fixed unused variable * eliminate superfluous include
2020-10-30In Situ Vis.: Fix Rho Contouring (#1482)Gravatar Axel Huebl 1-2/+10
Fill the boundaries up to one cell after calculating fields such as `rho`/`rho_<species>` on the fly. This is necessary for properly initialized boundary cells as we pass the data on to in situ visualization libraries.
2020-10-28deleted some useless end-of-line ';' (#1478)Gravatar Luca Fedeli 3-8/+8
2020-10-26Filter diagnostic rho (#1295)Gravatar David Grote 3-8/+50
* First cut of adding filtering of rho diagnostic - not yet working * Fixed the handling of parallel transfers in RhoFunctor when filtering is turned on * Fixed end of line space * In RhoFunctor, only do kspace filter with RZ and PSATD * PICMI analytic applied fields (#1306) * PICMI Added applied fields * PICMI fixed typo in Constants * Change picmistandard version requirement to 0.0.9 * Increment required picmi version Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Updated checksums with filter of diagnostic rho * Fix comment in rho diagnostic * Updated LaserIonAcc2d benchmark after filtering rho * Update galilean_rz_psatd benchmark with filtering of rho Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-10-26FieldMaximum reduced diag: average all components to cell centers (#1411)Gravatar NeilZaim 1-58/+98
* FieldMaximum reduced diag: average all components to cell centers * Remove read_raw_data.py in reduced diag automated test * No longer output raw fields in reduced diags tests * Modify a comment
2020-10-26PSATD: only deposit charge if needed (#1428)Gravatar NeilZaim 2-7/+19
* PSATD: only deposit charge if needed * Update Source/FieldSolver/WarpXPushFieldsEM.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2020-10-26Explicit choice of `max_iters` for MLMG solver (#1471)Gravatar Igor Andriyash 4-3/+8
* added an option to set explicitely `max_iters` for MLMG solver * fix EOL white spaces * fix EOL white spaces 2
2020-10-26Initialize last element of PML sigma_star arrays (#1460)Gravatar NeilZaim 1-3/+3
2020-10-26Fix warning related to external laser binary file (#1470)Gravatar Luca Fedeli 1-39/+33
* fix read of binary file * removed useless include
2020-10-26Ascent: Fix Contour Plots (#1469)Gravatar Axel Huebl 2-5/+5
Fix the missing ngrow of one cells for Ascent, which guarantees that the `FillBoundary` calls after centering field data provide an extra cell for contouring. Also fix a few doc typos and unused variable warnings.
2020-10-24Update a couple of asserts if warpx.numprocs is used (#1440)Gravatar NeilZaim 3-7/+41
* Update a couple of asserts if warpx.numprocs is used * Set blocking factor to 1 when warpx.numprocs is used * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-10-24fix 'comparison of integer expressions of different signedness' warning in ↵Gravatar Luca Fedeli 4-483/+653
parser (#1463) fix 'comparison of integer expressions of different signedness' warning in parser Co-authored-by: Tools <warpx@lbl.gov>
2020-10-23Fix Warning message <pmap.resize> (#1461)Gravatar Lígia Diana Amorim 1-1/+2
2020-10-23Fix Warning for SigmaBox FabFactory (#1466)Gravatar Weiqun Zhang 6-33/+55
2020-10-22Fix NVCC Regression in Parser (#1458)Gravatar Axel Huebl 6-777/+488
* Fix NVCC Regression in Parser Fix a regression with the recompilation of the parser that shows up with NVCC and GNUmake on Summit. * Modify Parser's makefile to remove #line and rename bison's output file to .cpp Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
2020-10-22Remove a few segfaults when there is zero particle species (#1449)Gravatar NeilZaim 2-16/+73
* Remove a few segfaults when there is zero particle species * Docs: Update Example * We don't have `part_per_proc` so exemplify with something else. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-10-22Fix warning with openPMD (#1452)Gravatar Edoardo Zoni 1-1/+1
2020-10-22[mini-PR, even if it does not look "mini"]Fix unused function warning in ↵Gravatar Luca Fedeli 5-271/+377
parser (#1448) When compiling WarpX I got this warning message: `wp_parser.lex.c:1356:17: warning: ‘void yyunput(int, char*)’ defined but not used [-Wunused-function]` This can be fixed by adding `%option nounput` option to `wp_parser.l` and re-generating the parser with `make`.
2020-10-20Gpu::Atomic::Add -> Gpu::Atomic::AddNoRet (#1447)Gravatar Weiqun Zhang 2-64/+64
For HIP, AddNoRet for float is much faster because it has hardware support.
2020-10-19RZ PSATD, in forward transforms, initialize the copies to zero if needed (#1445)Gravatar David Grote 1-0/+11
2020-10-19Replace wherever possible '.reset(new' with '= make_unique' (#1429)Gravatar Luca Fedeli 30-246/+282
* replace wherever possible .reset(new with = make_unique * fixed bug * fixed bug * revert WarpXOpenPMD.cpp to the original version * removed another .reset(new
2020-10-16New reduced diag: number of macroparticles (#1414)Gravatar NeilZaim 19-49/+183
* New reduced diag: number of macroparticles * Add parentheses in header line * Apply suggestions from code review Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com> * Add some consts * Fuse some lines with std::ofstream Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
2020-10-14[mini-PR] Flag to diable all diagnostics. (#1427)Gravatar Revathi Jambunathan 1-3/+7
* turn off diagnostics * document input to enable/disable diagnostics * Update Docs/source/running_cpp/parameters.rst
2020-10-13fix bug in CMakeLists.txt (#1431)Gravatar Luca Fedeli 1-1/+1
2020-10-13[mini-PR] Fix warnings in QED module (#1433)Gravatar Luca Fedeli 3-1/+7
* fix warning concerning comparison of int and unsigned int * fix warning concerning unused variables
2020-10-12[mini-PR] Flag to turn off species output in diags (#1426)Gravatar Revathi Jambunathan 1-0/+12
* write species flag to toggle particle output * document write_species * Update Source/Diagnostics/Diagnostics.cpp * write species flag to toggle particle output * document write_species * Update Source/Diagnostics/Diagnostics.cpp
2020-10-12Separate rho per species diagnostics from particle output (#1407)Gravatar Edoardo Zoni 3-70/+55
* Separate rho per species diagnostics from particle output * Update input file of CI test dumping rho per species * Update documentation * Use m_output_species_names and m_all_species_names * Use std::string::rfind and improve error message * Rename m_all_species to m_output_species for consistency
2020-10-09fix a couple of unused variables warnings (#1423)Gravatar Luca Fedeli 2-0/+5
2020-10-09Fix error with Schwinger in 2D (#1424)Gravatar NeilZaim 1-1/+1
2020-10-08Add laser phase to gaussian profile (#1155)Gravatar Igor Andriyash 2-1/+3
* added the phase argument for the gaussian laser * removed signature * added laser phase to picmi api * added doc string for phi0 * Update parameters.rst typo fix Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-10-07RZ + single precision fix (#1417)Gravatar Michael E Rowan 3-15/+29
* RZ_SP fix * RZ SP fix * Fix cufft for single precision RZ. Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
2020-10-07rocFFT support (#1410)Gravatar Weiqun Zhang 8-27/+270
* rocFFT support * rocfft in 2d rz PSATD solver
2020-10-07Do not store first Fornberg coefficient (#1419)Gravatar Edoardo Zoni 2-31/+36
2020-10-05Add option to do collisions every # time steps (#1251)Gravatar Yinjian Zhao 5-10/+20
* Update inputs_3d * Update inputs_2d * Add ndt * Doc * Doc * Update inputs_3d * Update inputs_2d Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-10-05Replace some ".reset(new )" with " = make_unique" (#1398)Gravatar Luca Fedeli 1-79/+79
* replace some reset(new ) with make_unique * fixed bug
2020-10-02Split resampling TinyProfiler entry into 2 (#1390)Gravatar NeilZaim 2-2/+13
2020-10-02Fix some warnings for PSATD builds (#1401)Gravatar Edoardo Zoni 12-53/+39
* 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
2020-10-02[Tiny] use_fdtd_nci_corr set to false for RZ (#1405)Gravatar Lígia Diana Amorim 1-1/+4
* Made particles.use_fdtd_nci_corr false for RZ * Added AMREX ALWAYS ASSERT * Fixed AMREX ASSERT * Revert "Fixed AMREX ASSERT" This reverts commit 902fcaabbf0c01b75cd7b38e7fd198e75cf1703d. * Revert "Added AMREX ALWAYS ASSERT" This reverts commit 7c56270730d0e1e4c9a2ab705cc0027e7ecc1a79. * Fixed confusion between commits
2020-10-02Plot raw fields: fix bugs for rho and F data (#1392)Gravatar Edoardo Zoni 2-15/+38
* Plot raw fields: fix bug for rho data * Add query for <diag_name>.plot_raw_rho * Check if MultiFabs are allocated and fix bug for coarse patch * Add same check for raw F data
2020-10-02[mini] Add clean error message when user makes a typo in fields to output ↵Gravatar NeilZaim 1-0/+3
(#1409) * Add clean error message when user makes a typo in fields to output * Add a space
2020-10-02[mini-PR] Fix a couple of warnings (#1408)Gravatar Luca Fedeli 2-1/+4
* fixed unused variable warning * fixed unwanted copy
2020-10-01RZ spectral: add default value of i_comp in scalar transforms (#1404)Gravatar David Grote 1-2/+2
2020-09-30Use fewer guard cells for deposition (#1368)Gravatar Edoardo Zoni 5-35/+75
* Use fewer guard cells for deposition * Update some CI benchmarks * Revert "Update some CI benchmarks" This reverts commit 2f40062557d75e3f6b2d3ba284332b8a92a0d404. * Check if shapes and guard cells are compatible only for rho * Do not allocate one extra guard cell for J * Add more relaxed check on shapes and guard cells for J
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