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2020-06-12Docs: Summit Restructure (#1090)Gravatar Axel Huebl 3-48/+76
* Docs: Summit Restructure Restructures the instructions for Summit (OLCF). This loads all software that might be needed to reduce the "if then else" logic a user has to understand during install. Everything is now required or optional, but everything is compatible or simply ignored. Uses new conventions for downloaded source and manually built software to structure things in a simpler, scalable manner. * Summit Docs: Fix Typos
2020-06-12update doc on ionization (#1068)Gravatar MaxThevenet 1-2/+2
2020-06-12Stop mailing errors from Battra (#1079)Gravatar MaxThevenet 1-1/+1
* stop mailing errors from Battra * remove Axel from Battra mails * Battra mails: remove Diana & Edoardo Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-06-10[Mini] Z Offset to loaded openPMD particles (#1070)Gravatar L. Diana Amorim 6-6/+15
* Added description of singleparticle particle injection style * Revert "Added description of singleparticle particle injection style" This reverts commit f02d842c935311458024da6e661950742de24f63. * Added use_q_shift and q_shift variables * Removed use_q_shift * Added description of q_shift to the Docs * Replaced q_shift by z_shift as suggested by @ax3l * Added recommendation to PWFA example * z_shift should be optional (used query instead of get) * Fix compile problem Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-06-09CI Inputs Check: Fix Silent Abort (#1081)Gravatar Axel Huebl 1-1/+1
If a file is missing at all then it is not being tested. This currently did abort and fail the test without a hint to the developer. Now it still fails as it should but it also gives a nice hint.
2020-06-09Cori: ADIOS2 (#1067)Gravatar Axel Huebl 1-2/+1
- ADIOS2 2.5.0 is available on Cori - ADIOS1 is no longer needed - Dynamic library support is now the default
2020-06-09Doc: document time staggering in output file (#1076)Gravatar MaxThevenet 1-0/+19
* add doc table for time staggering of output quantities * clarify * Update Docs/source/visualization/visualization.rst
2020-06-06remove #line wp_parser.l because it causes issues with AMReX make system (#1078)Gravatar WeiqunZhang 1-52/+0
2020-06-05Fix typo for pml_ncell in parameters doc (#1071)Gravatar NeilZaim 1-1/+1
2020-06-05Fixed bad arguments in PICMI_inputs_laser_acceleration.py (#1074)Gravatar David Grote 1-3/+2
Note that polarization_angle was changed to 0 since that was the value being used because the polarization_argument was bad.
2020-06-05Updates to picmi, mostly related to fields, and add psatd (#1077)Gravatar David Grote 4-5/+40
2020-06-05Change numprocs=2 for python reg tests and reset benchmarks (#1075)Gravatar Revathi Jambunathan 7-41/+41
* changing nprocs to 2 for Python_PlasmaAcceleration test * Resetting benchmark for Python_PlasmaAcceleration test case due to change in nprocs=2 in reg test * resetting benchmarks for Python test-cases except Python_Langmuir due to change in numprocs in WarpX-tests.ini * changing numprocs=2 for Python tests * resetting python reg test benchmarks after updating pywarpx Co-authored-by: Revathi Jambunathan <revanathan@pop-os.localdomain> Co-authored-by: Tools <warpx.lbl.gov> Co-authored-by: Tools <warpx@lbl.gov>
2020-06-03In picmi.py, convert the diagnostics to write into a sorted list (#1069)Gravatar David Grote 1-14/+29
2020-06-03Add checksum regression tests (#1065)Gravatar MaxThevenet 120-40/+3367
* add a checksum module for regtests * All capabilities to checksum tests * update tests to generate a clean benchmark * call checksum tests from analysis scripts * Add checksum json benchmarks * add missing script, better printing and increase tol * eol * fix permission, and bump tolerance * chmod +x checksumAPI.py * update benchmarks, probably old ones were wrong due to parallelization * remove unused variable, thanks lgtm * special handling when the benchmark is 0 * non-zero but very small CFL for 1 step for init tests * reset erroneous Python benchmarks * slightly bump tolerance for initial distribution test * too small dr results in nans * improve prints, tolerance handling, and fix tests * typo * enable tolerance and fields/particles optional comparison to fix tests * more minor cleaning in space charge initialization tests * update Python benchmarks for serial runs * Run Python tests with 1 rank instead of 2 * fields that are zero should not be in reg tests * Add developer documentation on checksum regression tests Co-authored-by: Tools <warpx@lbl.gov>
2020-06-01update release number everywhere in repo (#1064)Gravatar MaxThevenet 3-3/+3
2020-05-30Delete more deprecated code after in-situ uses new diagnostics format (#1041)Gravatar MaxThevenet 6-463/+23
* move ascent to new diagnostics * move Sensei to the new diagnostics * minor cleaning in new diagnostics * Delete more deprecated code after in-situ uses new diags * remove deprecated input options from subcycling test * Finish updating the doc for Sensei and Ascent with the new diags
2020-05-29Move sensei to new diagnostics (#1040)Gravatar MaxThevenet 18-167/+199
* move ascent to new diagnostics * move Sensei to the new diagnostics * minor cleaning in new diagnostics * oops, had forgotten some files * fix typo * another typo introduced when merging master into this branch * FlushFormat::WriteToFile takes Vector<MultiFab>& instead of Vector<const MultiFab*> * IO output multifab has 1 guard cell when using sensei * updates to FlushFormatSensei * add some documentation to the class * add refrence to AmrMesh instance needed by the adaptor * add some error output in the case WarpX was not compiled w/ SENSEI * tested with SENSEI 3.2.0 Co-authored-by: Burlen Loring <bloring@lbl.gov>
2020-05-29Improve documentation to compile with openPMD support on Summit (#1057)Gravatar Luca Fedeli 1-0/+5
* updated documentation to build with openPMD support on Summit * CXX et al: Move to Modules Prep for general CMake niceness. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-05-29update link to APOSMM (#1052)Gravatar MaxThevenet 1-1/+1
2020-05-29Encapsulate FFTs (#1055)Gravatar MaxThevenet 7-243/+311
* wrap fft libraries * implementation in cpp to avoid duplicate symbole * delete some fftw code * further cleaning * typo * pass fft plans by reference * fix bug due to typo. Dammit, macros sometimes make it hard * FFT wrapper also support cuFFT (not tested yet) * eol * further cleaning * fix cuFFT, tested on Summit * clean WarpX Complex checks * pass directly the IntVect instead of the components (what were you thinking?) * add some amrex prefix * add a few const * Should not need an FFT library to compile FDTD * gather all FFT header files into one. * eol * minor changes in code comments. * let dimension be chosen at runtime instead of at compile-time * fix compilation on GPU * add description to the wrapper namespace
2020-05-29Macroscopic EvolveE with constant properties (#991)Gravatar Revathi Jambunathan 13-1/+365
* Adding macro-E Push and new file * Add macroEvolveE, call it, and include algo selection in utils * fix eol * Fixing bug in macroE for sigma method 1 * changing MacroEvolveE to MacroscopicEvolveE * add class for macroscopicproperties and an object in WarpX class * fix eol * adding templated ckc call with comment that EvolveE is same for yee and ckc * add header file pointing to ckc algorithm * adding obejct m_macroscopic_properties to access sigma,eps,mu * some cleaning * Adding comments * adding documentation * spelling wandroff to wendroff * fixing eol * eol * const in the right place. Thanks bot! * profiler for macroscopic evolveE * re-introduced deleted line when fixing conflict to declare templated EvolveBPMLCartesian function * fixing if-else statement for RZ in MAcroscopicEvolveE.cpp * adding suggestions and corrections made in PR review. * fixing grammar in docs * fix eol whitespace * fix typo
2020-05-29Set particular modified wavenumbers to 0 for spectral (nodal). (#1030)Gravatar Olga Shapoval 1-0/+18
* Set particular modified wavenumbers to 0 for spectral (nodal). * Add comments Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-05-29CI: DPC++ (#1054)Gravatar Axel Huebl 1-3/+48
* CI: oneAPI (DPC++) * shell: bash * sudo install preserve env vars... export (LD_)LIBRARY_PATH * openPMD: Manual Install * DPC++: Cleanup CI
2020-05-29Docs: 3D Define (#1060)Gravatar Axel Huebl 1-0/+1
Add the macro that is defined in 3D3V to our developer docs.
2020-05-29CI: Fix Brew Install (#1061)Gravatar Axel Huebl 1-0/+2
Brew is weeeird. "Already installed (all good)" is not a reason to return a non-zero exit code. Urgh.
2020-05-27Add Schwinger in developers doc (#1001)Gravatar NeilZaim 3-1/+48
* Add Schwinger in developers doc * Add newline at end of file * Add doxygen doc into qed sphinx doc
2020-05-26specify _rt in the particle pushers (#1049)Gravatar Andrew Myers 5-27/+36
* specify _rt in the particle pushers * EOL
2020-05-26[tiny] Docs Summit CPUs + PSATD (#1018)Gravatar L. Diana Amorim 1-0/+14
* Added description of singleparticle particle injection style * Revert "Added description of singleparticle particle injection style" This reverts commit f02d842c935311458024da6e661950742de24f63. * Added tip note in Docs Summit with PSATD + CPUs
2020-05-26[mini] Clean EB field initialization using parser (#1017)Gravatar Revathi Jambunathan 2-71/+35
* fixing bug to initialize CellCenterFunctor for Bx * removing unnecessary indextype determination since it is already passed as an argument * Adding precision extensions * adding amrex:: prefix in the part of code being cleaned * fixing error that came up with tiling by correctly defining Box using nodal flags * obtaining nodal flag in the kernel instead of sending in as argument. * amrex prefix for IntVect
2020-05-26Implement intervals parser for plot_int (#1009)Gravatar NeilZaim 4-12/+15
2020-05-25Merge particle push (#1036)Gravatar Andrew Myers 6-157/+274
* add functor for doing the tmp particles copy for the back-transformed diagnosti * merge the particle push options into one kernel * EOL * fix assertion * allow this functor to be constructed even it we aren't doing the back transformed diagnostics * EOL * init this val to 0.0 * put the push type selection in a device function so it can be reused * EOL * add docstring for the pusher selector function * EOL
2020-05-23Esirkepov rt (#1044)Gravatar Andrew Myers 1-28/+28
* use _rt for literals in esirkepov current deposition * fix tabs * fix indentation
2020-05-22Dpcpp (#1045)Gravatar WeiqunZhang 7-15/+28
* Make changes to be able to compile with DPC++. Parser is disabled for DPC++ because it does not work. amrex::Math::abs instead of std::abs is used in device functions. * std::isnan not supported on device with DPC++
2020-05-22Summit: jsrun in CMake (#1043)Gravatar Axel Huebl 1-1/+1
Just in case someone wants to run `ctest`: this is how one sets the right `mpiexec` wrapper on Summit.
2020-05-22Move ascent to new diagnostics (#1038)Gravatar MaxThevenet 6-89/+151
* move ascent to new diagnostics * minor: this should not be there. * pass bp_mesh to WriteParticles in FlushFormatAscent * need import in header file * udpate documentation
2020-05-22Use C++ templates for the PML field pusher (#808)Gravatar Remi Lehe 10-787/+525
* Allow to pass component in stencil templates * Define and use enum to address PML components * Start implementing PML equations * Implement EvolveEPML * Implemented EvolveBPML * Added interface for pml_has_particles * Added interface for pml_has_particles * [skip ci] Add update expressions for E * [skip ci] Fix compilation * Call new PML pusher for B field * Fix compilation errors * Fix more typos * Abort code if `do_pml` is used in cylindrical geometry * Add contribution from F in EvolveEPML * Remove unused function for CKC coefficients * Remove unneeded ExchangeF * Add damping for J * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Revert "Apply suggestions from code review" This reverts commit 08f262a676ba5e5b44b9118b8daba1b03c08b64b. * Remove sanity checks for nodal * Implement dive cleaning in PML * Implement push F in the PML * Clean-up unused code Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-05-22minor bugfix for photon push (#1042)Gravatar Andrew Myers 1-2/+2
2020-05-22Fix DivE diagnostic in RZ (#1034)Gravatar David Grote 5-9/+64
* Added dump_rz_modes to picmi field diagnostic * Fixed DivEFunctor for RZ * In Diagnostics, write out RZ components of divE if requested * Fix RZ component names in diagnostic files * Fixed RZ spectral back transform, fixing DivE calculation * In SpectralSolverRZ.H changed BL_PROFILE to WARPX_PROFILE * Undid change of BL_PROFILE to WARPX_PROFILE in SpectralSolverRZ.H
2020-05-22Added stub for current correction in RZ spectral solver (#1007)Gravatar David Grote 4-0/+55
* 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>
2020-05-20Modified automated test for Galilean PSATD (#1033)Gravatar Olga Shapoval 2-3/+3
2020-05-19Bug fix in picmi field diagnostics with picmistandard.0.0.8 (#1032)Gravatar David Grote 2-2/+3
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2020-05-19Assign the external E and B inside the field gather kernel (#1029)Gravatar Andrew Myers 5-113/+155
* Assign the external E and B inside the field gather kernel * EOL * actually add new file * EOL * cannot do this yet * update comments * put shared code in base class * EOL * make clear in the name that these are external fields
2020-05-18Fix 2D3V Particle Position openPMD (#1019)Gravatar Axel Huebl 1-15/+77
* Fix 2D3V Particle Position openPMD Correct the labels for 2D3V particle positions in 2D3V. We previously labeled "z" as "y". Also, avoid writing the "positionOffset" constant record component for "y" in 2D3V, which confuses reading a series back. * Coordinates: Re-arrange `#ifdef`s * Typo: missing "t"
2020-05-18Require Python 3.6+ (#1021)Gravatar David Grote 3-2/+5
* Added specification of the version picmistandard * Set the requirement of Python version >= 3.6 * Add Python version requirement to the docs * Add comment about Python version to docs
2020-05-18Mention the use of amrex:: prefix in CONTRIBUTING (#1024)Gravatar MaxThevenet 1-5/+17
* mention the use of amrex:: prefix in CONTRIBUTINH * forgot eol * incorporate review suggestions. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-05-15better doc on how to make a release (#1028)Gravatar MaxThevenet 2-7/+19
2020-05-15replace release number 20.04 by 20.05 in the repo (#1027)Gravatar MaxThevenet 3-3/+3
2020-05-15Minor updates to Schwinger tests (#1003)Gravatar NeilZaim 3-18/+31
* Minor updates to Schwinger tests * Update Examples/Modules/qed/schwinger/analysis_schwinger.py Co-authored-by: MaxThevenet <mthevenet@lbl.gov> * Set tests in parallel with 2 threads and 2 procs Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
2020-05-15Crash if deprecated input parameters are used. (#981)Gravatar MaxThevenet 5-0/+58
* crash for deprecated input parameters * typo
2020-05-15Summit: ADIOS2 Usage (#1026)Gravatar Axel Huebl 1-1/+2
Document how to use ADIOS2 (new module) on Summit with openPMD.
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