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2022-10-25Replace "none" BC with Neumann for electrostatic (#3483)Gravatar David Grote 5-15/+25
* Replace "none" BC with Neumann for electrostatic * Added checking for Neumann boundaries * Updated documentation regarding Neumann BCs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-10-25Diagnostics: print when writing openPMD/Ascent/Sensei and BTD ↵Gravatar Ryan Sandberg 23-64/+174
plotfile/openPMD (#3424) * print when writing openPMD, Ascent, Sensei * remove unnecesssary variables, include min_digits * print snapshot id when writing btd * fix ascent print * compile without warnings * still working on Ascent * still working Ascent * Print when BTD buffer is flushed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * print when writing openPMD, Ascent, Sensei * remove unnecesssary variables, include min_digits * print snapshot id when writing btd * fix ascent print * compile without warnings * still working on Ascent * still working Ascent * Print when BTD buffer is flushed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add warning message if BTD not full * adjust for CI, no in-situ vis BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * revert to correct plotfile naming * change warning topic to BTD * nicer format for print statements * extend examples to fill BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reset Checksums of BTD_ReducedSliceDiag * Upgrade CI Test LaserAccelerationBoost * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * improve BTD warning notes * edit final step notes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix formatting Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-10-25CI: oneAPI with `-O1` (#3478)Gravatar Axel Huebl 1-0/+6
oneAPI 2022.2.0 hangs for `-O2` and higher: #3442
2022-10-24Add reduced diagnostics to `picmi.py` (#3475)Gravatar Roelof Groenewald 7-60/+295
* add reduced diagnostics to picmi * added test of picmi reduced diagnostics * changes requested during PR review
2022-10-24AMReX: Weekly Update (#3479)Gravatar Axel Huebl 5-5/+5
2022-10-24Fix stair-case solver in 2D Cartesian (#2942)Gravatar Remi Lehe 5-9/+26
* Fix stair-case solver in 2D Cartesian * Generalization for the macroscropic solver * Update automated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update benchmark Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-10-24Do not query redundant `do_back_transformed_particles` (#3183)Gravatar Neïl Zaim 1-3/+1
* Do not query redundant do_back_transformed_particles * Only set m_do_back_transformed_particles to true if write_species is true
2022-10-21Fix unused import warnings in python analysis scripts (#3472)Gravatar Neïl Zaim 2-5/+2
* Fix unused import warnings in python analysis scripts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-10-21User-Specified Used Inputs File (#3462)Gravatar Axel Huebl 4-3/+15
Allow users to overwrite the default for the "used inputs" file that we write.
2022-10-19OLCF Jupyter: Mamba is Pre-Installed (#3471)Gravatar Axel Huebl 1-4/+1
Mamba is now pre-installed on OLCF Jupyter base images! :)
2022-10-18AMReX: Weekly Update (#3469)Gravatar Axel Huebl 10-32/+32
2022-10-17Update GCC Requirement (#3470)Gravatar Axel Huebl 1-1/+1
* NVCC generates code that tends to trigger ICEs in GCC 7.x * CTAD erratum in GCC 8: https://gcc.gnu.org/projects/cxx-status.html#cxx17
2022-10-13CI: Fix macOS OMP (#3465)Gravatar Axel Huebl 2-0/+16
Fix: ``` $ cmake -S . -B build_dp ... -- The C compiler identification is AppleClang 13.0.0.13000029 -- The CXX compiler identification is AppleClang 13.0.0.13000029 ... CMake Error at /usr/local/Cellar/cmake/3.24.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message): -- Configuring incomplete, errors occurred! Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) ``` ``` libomp 14.0.6 is already installed but outdated (so it will be upgraded). ==> Downloading https://ghcr.io/v2/homebrew/core/libomp/manifests/15.0.2 ==> Downloading https://ghcr.io/v2/homebrew/core/libomp/blobs/sha256:a4e0796616d09221e2a486c95f9aa7c12d3c617e594b1d463a8f479bd4fa45c2 ==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sha256:a4e0796616d09221e2a486c95f9aa7c12d3c617e594b1d463a8f479bd4fa45c2?se=2022-10-13T20%3A50%3A00Z&sig=a68J671xfsvWip4TqYo5%2B2E0U5AswwCQDocHLNc6XXE%3D&sp=r&spr=https&sr=b&sv=2019-12-12 ==> Upgrading libomp 14.0.6 -> 15.0.2 ==> Pouring libomp--15.0.2.big_sur.bottle.tar.gz ==> Caveats libomp is keg-only, which means it was not symlinked into /usr/local, because it can override GCC headers and result in broken builds. For compilers to find libomp you may need to set: export LDFLAGS="-L/usr/local/opt/libomp/lib" export CPPFLAGS="-I/usr/local/opt/libomp/include" ==> Summary 🍺 /usr/local/Cellar/libomp/15.0.2: 7 files, 1.7MB ==> Running `brew cleanup libomp`... Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). Removing: /usr/local/Cellar/libomp/14.0.6... (7 files, 1.6MB) Removing: /Users/runner/Library/Caches/Homebrew/libomp--14.0.6... (548.8KB) ```
2022-10-12Correct particle positions outside refined injection (#3463)Gravatar Remi Lehe 3-33/+47
* Correct particle positions outside refined injection * Improve test * Update benchmark * Update Examples/Physics_applications/laser_acceleration/analysis_refined_injection.py
2022-10-11openPMD Engines: Allow Params w/o Type (#3460)Gravatar Axel Huebl 1-10/+20
The current implementation only accepted parameters for ADIOS2 engines if the engine type was also specified. That is not necessary, the default (bp4) will usually be taken and thus the documentation did not work. This fixes it, keeping the engine type optional in the inputs.
2022-10-11Docs: Expand Debugging Workflow (#3461)Gravatar Axel Huebl 1-0/+30
Add more instructions how to debug errors seen in *Release* mode.
2022-10-10AMReX: Weekly Update (#3459)Gravatar Axel Huebl 5-5/+5
2022-10-10Add functions for reading particle id and cpu numbers correctly (#3457)Gravatar Andrew Myers 5-9/+234
2022-10-10Partial refactoring of the utils directory (#3404)Gravatar Luca Fedeli 95-1599/+1997
* initial work to clean WarpX Utils * remove AMRCore from Ionization tables * progress * refactoring of a part of the utils directory * fix bug * fixed bug * fixed bug * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * remove debug line accidentally slipped into the code * cleaning * fixed bug
2022-10-08Fix synchronization of nodal points in subcycling (#3455)Gravatar Remi Lehe 2-31/+35
* Fix synchronization of nodal points in subcycling * Update checksum
2022-10-08Updated 1D CI tests with particles because of update of yt (#3458)Gravatar David Grote 6-26/+27
* Updated 1D CI tests with particles * Updated required version of yt to 4.1.0 * Fixed CI analysis of collisionXYZ Fixed the fetching of the particle data
2022-10-06Spack Desktop: Simpler CUDA Visualization (#3337)Gravatar Axel Huebl 1-2/+8
* Spack Desktop: Simpler Visualization Reduce the dependencies for in situ vis, avoiding to build DevilRay in Ascent, which takes very long right now. We mostly use Ascent with VTK-m for now, so that works. * CUDA Ascent & VTK-M: static * ADIOS2: w/o CUDA See https://github.com/ornladios/ADIOS2/issues/3332
2022-10-05Doc: BLAS++/LAPACK++ on GitHub (#3449)Gravatar Axel Huebl 9-22/+22
* Doc: BLAS++/LAPACK++ on GitHub BLAS++ and LAPACK++ development has moved to GitHub :tada: Welcome! :) * Update bitbucket mention to GH * SLATE: Rename Missing Links Co-authored-by: Mark Gates <mgates3@icl.utk.edu>
2022-10-05openPMD: Shape of Constant Particle Records (#3451)Gravatar Axel Huebl 1-1/+4
We forgot to set the shape (particle number) of constant particle records. This violates the openPMD standard and complicates post-processing.
2022-10-03BTD: Improve Z-Slice Message (#3440)Gravatar Axel Huebl 1-1/+9
Add values that are checked to the msg, e.g., I see: ``` z-slice in lab-frame (0.049998) is outside the buffer domain physical extent (0.049998 to 0.050000). ```
2022-10-03Docs: Fix PICMI Builds (#3447)Gravatar Axel Huebl 3-5/+6
Unbreak the RTD build. We need to do this all relative to the root directory.
2022-10-03Doc: Dev FAQ Pinned Memory (#3437)Gravatar Axel Huebl 1-0/+17
* Doc: Dev FAQ Pinned Memory Since I spoke to two devs in 24hrs about the topic, let us document it. Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> Co-authored-by: David Grote <dpgrote@lbl.gov>
2022-10-03Release 22.10 (#3444)Gravatar Axel Huebl 11-13/+13
* AMReX: Weekly Update One commit after 22.10 release, to fix oneAPI DPC++ 2022.02: 22.10-1-g13aa4df0f5 * PICSAR: 22.10 * WarpX: 22.10
2022-10-02Use parser for input parameters of type long (#2506)Gravatar Neïl Zaim 5-24/+67
* Use parser for input parameters of type long * Revert "Use parser for input parameters of type long" This reverts commit 9573bb3f693f1247e77faa433fd96dc294e68361. * Use parser for inputs of type long * add safeCasttoLong function * Fix typo in comment
2022-10-02Major update of the Python/picmi documentation (#3329)Gravatar David Grote 15-145/+776
* Include WarpX specific documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Undo the precommit change of import in __init__.py * Docs: Install Pure Python WarpX PICMI Allows to use these classes in our Sphinx autodocs in the manual. * Sphinx: Add Napoleon Extension https://sphinxcontrib-napoleon.readthedocs.io * PICMI Doc Strings: Fix Some Warnings * Removed the DocumentedMetaClass since it was moved to picmistandard * Defined the languate in Docs/source/conf.py * Cleaned up minor issues in the rst files * Updated existing doc strings in picmi.py * Reformatted doc strings in Regression/Checksum/checksumAPI.py * Reformatted doc strings in Regression/Checksum * First set of WarpX specific documentation * Updated to picmistandard version 0.0.20 * Cleaned up the Python document page Fixed up the text to be more clear. Added section headers for each picmi class (for easy reference). * Further updates to picmi.py doc strings Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-10-02Sphinx Extension: Sphinx-Design (#3361)Gravatar Axel Huebl 3-0/+3
2022-10-02Lassen (LLNL): HDF5 1.12.2 (#3378)Gravatar Axel Huebl 1-1/+1
The HDF5 1.10.4 module on Lassen (LLNL) has severe performance issues. We saw that 1.10.5+ fixed those. We now have a new module, 1.12.2, that we can use.
2022-10-02Docs: BELLA MVA PoP & Ion PRAB Published (#3435)Gravatar Axel Huebl 1-5/+6
* Docs: BELLA MVA PoP Published Update the science hightlights with the final, published paper. * Levy et al. PRAB published, too
2022-09-30Implement tridiag solver for 1D (#3431)Gravatar David Grote 5-50/+280
* Added tridiag solve for 1D * Added tridiag solver to WarpX.H * Updated PICMI_inputs_1d.py to use float64 This was done so that it will compare to the tridiag to machine precision * Updated 1D capacitive_discharge test, adding pythonsolver flag * Update capacitive_discharge analysis_1d.py file with updated reference data * Add periodic boundary conditions, plus other fixes * Added CI test Python_background_mcc_1d_tridiag * Fix for parallel * Fixed CI test file prefix for PICMI_inputs_1d.py * Fixed comments
2022-09-29Add quiet option to Summit post-proc. docs (#3434)Gravatar Marco Garten 1-1/+5
The quiet option drastically reduces the in-cell output of package installation with mamba but does not completely silence.
2022-09-29Add 1d support to `_libwarpx.py` functions `get_particle_X` (#3421)Gravatar Roelof Groenewald 2-17/+24
* add 1d support to _libwarpx.py functions `get_particle_X` * add coverage of 1d `_libwarpx.get_particle_z` to test suite
2022-09-28AMReX/PICSAR: Weekly Update (#3412)Gravatar Axel Huebl 8-52/+52
* AMReX: Weekly Update * Roundoff Domain: Reset Checksums: - [x] 2D: `background_mcc_dp_psp` - [x] 3D: `pml_psatd_dive_divb_cleaning` - [x] SP: `reduced_diags_single_precision` * AMReX: Weekly Update Fix #3429
2022-09-26enforce 3 components for some laser parameters (#3423)Gravatar Luca Fedeli 1-0/+7
2022-09-24BTD diagnostics specified by intervals (#3367)Gravatar Ryan Sandberg 7-7/+185
* BTD diagnostics specified by intervals * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * address CI errors * refactor and test * no duplicate or out-of-order snapshots * update documentation and tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean for CI * still fighting CI * Update Source/Diagnostics/BTDiagnostics.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * refactor includes * add an explicit constexpr * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * describe algorithm for BTD intervals list * revert to old description of num_snapshots_lab * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * preserve behavior of num_snapshots_lab Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-09-23fix labels in inputfiles (#3422)Gravatar Luca Fedeli 3-3/+3
2022-09-21CI: Test New v. Legacy BTD in `BTD_ReducedSliceDiag` (#3371)Gravatar Edoardo Zoni 3-37/+102
* CI: Test New BTD in `BTD_ReducedSliceDiag` * Compare Legacy BTD vs. New BTD * Fix Bug in Loading of openPMD Array Data * Fix CI Analysis
2022-09-21Fix update of particles flushed already in BTD (#3419)Gravatar Remi Lehe 1-1/+1
2022-09-21Fix compilation of RZ version on GPU (#3418)Gravatar Remi Lehe 1-3/+0
2022-09-20Add option to deposit laser on main grid (#3235)Gravatar Remi Lehe 4-6/+32
* Add option to deposit laser on main grid * Use `deposit_on_main_grid` * Update Source/Particles/LaserParticleContainer.cpp * Add documentation * Update documentation
2022-09-20PSATD: More Options for Time Dependency of J, Rho (#3242)Gravatar Edoardo Zoni 23-97/+198
* 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
2022-09-20Correct and test fusion module in RZ geometry (#3255)Gravatar Remi Lehe 6-16/+290
* Add particle rotation in NuclearFusionFunc.H * Minor * indent * initial work * fixed bugs and added species * update documentation * delete unused file * Add properties for neutron, hydrogen isotopes, helium isotopes * Update code to be more consistent * Correct typo * Parse deuterium-tritium fusion * Start putting in place the files for deuterium-tritium * Update documentation * Prepare structures for deuterium tritium * Fix typo * Fix compilation * Add neutron * Add correct formula for the cross-section * Correct compilation error * Fix nuclear fusion * Reset benchmarks * Prepare creation functor for 2-product fusion * First implementation of momentum initialization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use utility function for fusion * Minor modification of variable names * Fix GPU compilation * Fix single precision compilation * Update types * Use util function in P-B fusion * Correct compilation errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct errors * Update values of mass and charge * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct compilation error * Correct compilation error * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reset benchmark * Use helium particle in proton-boron, to avoid resetting benchmark * Fixed proton-boron test * Revert "Fixed proton-boron test" This reverts commit 73c8d9d0be8417d5cd08a23daeebbc322c984808. * Incorporate Neil's recommendations * Reset benchmarks * Correct compilation errors * Add new deuterium tritium automated test * Correct formula of cross-section * Correct cross-section * Improve analysis script * Add test of energy conservation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test of conservation of momentum * Progress in analysis script * Fix error in the initial energy of the deuterium particles * Add check of isotropy * Clean up the test script * Rewrite p_sq formula in a way to avoids machine-precision negative numbers * Add checksum * Clean up code * Add test for fusion in RZ geometry * Update code to take into account actual timestep * Update RZ test * Update RZ test * Increase number of particles * Impart radial memory on DT particles * Correct RZ momenta * Remove unused file * Update test * Fix definition of theta * Add new test * Add checksum * Update test * Update tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Python analysis script * Remove CPU and ID from new benchmark Co-authored-by: Yinjian Zhao <yinjianzhao@lbl.gov> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-09-20More fixes for capacitive_discharge PICMI tests (#3416)Gravatar David Grote 2-3/+3
2022-09-19Add beta function to BeamRelevant (#3372)Gravatar Marco Garten 2-23/+38
* Add beta function to BeamRelevant * Beta-function: add user docs
2022-09-19Fix value of particle container m_do_back_transformed_particles when there ↵Gravatar Neïl Zaim 1-2/+4
are multiple BT diagnostics (#3184)
2022-09-19Zenodo: Add Marco Garten (#3414)Gravatar Axel Huebl 1-0/+5
Add Marco to our Zenodo file.
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