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2022-02-24Updated documentation for predefined_profile_params for parabolic_channel ↵Gravatar David Grote 1-3/+3
(#2880)
2022-02-24Add mesh refinement for electrostatic solver and scraping (#2728)Gravatar Yinjian Zhao 10-59/+161
* Modify in ElectrostaticSolver.cpp. * Apply suggestions from code review Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Can compile. * Apply suggestions from code review Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * compiling error * Can compile. * Fix compileing error for 3D. * Can pass test Examples/Tests/ElectrostaticSphereEB/analysis_rz.py with mesh refinement added. * Initial modification. * Remove an assert. * Add new test. * Update WarpX.cpp * Debuging. * Add print for debuging. * Remove prints. * reset benchmark for ElectrostaticSphereEB_RZ_MR * Fix compilation * Fix number of guard cell for coarse patch * Update Source/WarpX.cpp * Correct inverse cell side when interpolating EB distance * Cleaning up * Fix unused variable call * Partition: copy all compile-time attributes * Fix compilation * Update Regression/WarpX-tests.ini * Fix bug * reset benchmark for scarping 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>
2022-02-23Re-order all particle quantities when doing MR partition (#2888)Gravatar Remi Lehe 3-34/+13
* Re-order all particle quantities when doing partition * Fix compilation
2022-02-23Bug fix. (#2887)Gravatar Yinjian Zhao 1-1/+3
2022-02-22fix sign error in refine plasma option (#2883)Gravatar Andrew Myers 1-2/+2
2022-02-22GCC 11: Silence Warning in ShapeFactors (#2857)Gravatar Axel Huebl 1-2/+2
Silence a warning about a missing return type when building with GCC 11.2. First seen on Perlmutter (NERSC).
2022-02-17openPMD: Add ADIOS2 Engine Parameter Control (#2872)Gravatar Kshitij Mehta 4-17/+100
* Adds support for ADIOS engines #2866 Input file can now have lines like diag1.adios2_engine.parameters.NumAggregators=2 * Docs for ADIOS engine type and parameters #2866 * Aesthetic edit in adios2 engine documentation #2866 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed debug print statement #2866 * Style Updates Co-authored-by: Mehta, Kshitij V <kshitij-v-mehta@github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-17Fix number of guard cell for coarse patch (#2869)Gravatar Remi Lehe 1-4/+3
2022-02-17Do Not Fill PML Guard Cells w/ Inverse FFTs (#2854)Gravatar Edoardo Zoni 1-2/+4
2022-02-17Update parsing of FieldProbe in 2D and 1D (#2818)Gravatar Neïl Zaim 3-7/+30
* Update parsing of FieldProbe in 2D and 1D * Fix unused variables * Allow plane probe in 2D and line probe in 1D * doc update
2022-02-17Add warning to FieldProbe re: Boosted Frame (#2868)Gravatar Tiberius Rheaume 2-0/+13
* Add warning to FieldProbe re: Boosted Frames Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-16Rotate momentum for RZ flux injection (#2867)Gravatar Remi Lehe 2-3/+2
2022-02-16Refactor Current Correction Functions (#2839)Gravatar Edoardo Zoni 23-212/+89
* Refactor Current Correction Functions * Clean Up, Reset Benchmark
2022-02-16Lassen: Fix Chunked HDF5 with MPI (#2863)Gravatar Axel Huebl 1-0/+4
Try to work-around segfaults with HDF5 when running on more than one node.
2022-02-16Provide `t_min` and `t_max` for flux injection (#2842)Gravatar Remi Lehe 10-10/+22
* Implement injection orthogal to plane * Generalize momentum distribution for flux injection * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks" This reverts commit b0cd1891771a4c49c14abb7cb9df7374cee4458c. * Revert "Generalize momentum distribution for flux injection" This reverts commit 0a22b1d8fa68a3a5705d8f4824f757b6dee497f0. * Rotate momentum initialization * Correct flux number when the direction is normal to plane * Update distribution of particles within a cell * Clean-up injection code * Add more documentation * Add more comments * Handle 1D case * Only do the rotation for Gaussian flux profile * Fix compilation error * Correct compilation for GPU * Start adding automated test * Correct sign of velocity * Update to add continuous injection * Finalize test * Correct processing of flux_normal_axis * Add checksum * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix bug * Update script * Implement maximum injection time * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add parameter tmin * Make parameter optional ; update documentation * [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>
2022-02-16ABLASTR: Refactor `deposit_charge` API (#2856)Gravatar Axel Huebl 2-40/+79
Simplified and re-ordered interface for `ablastr::particles::deposit_charge`.
2022-02-16ParticleBuffer: Generalize & Move (#2860)Gravatar Axel Huebl 12-52/+18
* ParticleBuffer: Generalize & Move - move the `ParticleBuffer` to ABLASTR - generalize the API - remove `amr_core` argument - use more semantic naming - add docs * Use `amrex::ParticleContainer::make_alike` * Update AMREX to include https://github.com/AMReX-Codes/amrex/pull/2630
2022-02-16Gaussian particle beam: add error message when using y_rms = 0 in 2D (#2862)Gravatar Neïl Zaim 1-0/+15
2022-02-16Correct typo in the relativistic Poisson solver (#2853)Gravatar Remi Lehe 2-6/+7
* Correct typo in the relativistic Poisson solver * Fix unused variable * Update benchmark
2022-02-15update CI to use ascent 0.8.0 release container (#2858)Gravatar Cyrus Harrison 1-2/+2
* use ascent 0.8.0 release container * try again * restore * use new install loc
2022-02-15AMReX/PICSAR: Weekly Update (#2849)Gravatar Axel Huebl 5-5/+5
* AMReX: Update latest commit * AMReX: Update to 76d08651adb987e3fba6b232e806c5e7c365a8d9
2022-02-15Allow flux injection in the out-of-plane direction for RZ/2D geometry (#2788)Gravatar Remi Lehe 9-21/+257
* Implement injection orthogal to plane * Generalize momentum distribution for flux injection * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks" This reverts commit b0cd1891771a4c49c14abb7cb9df7374cee4458c. * Revert "Generalize momentum distribution for flux injection" This reverts commit 0a22b1d8fa68a3a5705d8f4824f757b6dee497f0. * Rotate momentum initialization * Correct flux number when the direction is normal to plane * Update distribution of particles within a cell * Clean-up injection code * Add more documentation * Add more comments * Handle 1D case * Only do the rotation for Gaussian flux profile * Fix compilation error * Correct compilation for GPU * Start adding automated test * Correct sign of velocity * Update to add continuous injection * Finalize test * Correct processing of flux_normal_axis * Add checksum * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix bug * Update script * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update checksum Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-02-15Only set modified k to 0 for even number of points (#2852)Gravatar Remi Lehe 1-1/+1
* Only set modified k to 0 for even number of points * Update Source/FieldSolver/SpectralSolver/SpectralKSpace.cpp
2022-02-14Use parser to read laser spatio-temporal couplings direction (#2843)Gravatar Neïl Zaim 1-1/+1
2022-02-14[pre-commit.ci] pre-commit autoupdate (#2851)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.11 → v1.1.12](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.1.11...v1.1.12) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-02-14Don't cut all particles in a Gaussian beam when x_rms=0 (#2844)Gravatar Neïl Zaim 1-3/+3
2022-02-11User-defined integer and real particle attributes (#2735)Gravatar Revathi Jambunathan 14-43/+192
* define user attributes, parse them, initialize with respective parsers * fix warning by using static_cast for int attribute as parser returns real * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clean-up from self-review * adding dimensionless velocity, gamma*v/c and time to parser argument * add documentation * typo in comment * unused var * device vector for kernels * particle attribute in developer doc * data ptr for device vector * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ignore_unused * Docs: Describe all particle attributes including pre-defined ones :) * Docs: Fix formatting (user params) * Add: 1D and RZ Support * Docs: Fix Typo in Function Declaration * Laser-Ion Example: User-Defined Attrib. Add two user-defined attributes to the laser-ion acceleration example. This is a 2D test. Documents the name in the table of commonly used, user-defined attribute names. The attribute added is the original position of particles, which I like to plot in "potential" plots that correlate original position in the target with final energy. * changing user-interface API with .attribute. and no need for separate 1D 2D 3D RZ code for parser. pos.x/y/z returns the right values * Adding 1D, 3D, and rz tests * attribute in inputs * at(i) * refinining names for inputs for laser ion and acceleration tests * typo in input * reset benchmarks for test-cases that included attributes Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-11Add amrex REPO and BRANCH flags for python builds (#2845)Gravatar Peter Scherpelz 2-0/+8
* Add WarpX_amrex_repo and _branch options to Python In python setup, environment variables WARPX_AMREX_REPO and WARPX_AMREX_BRANCH will now set these variables * Update documentation with new compile envvars
2022-02-11Fix some offsets with the gather buffers (#2847)Gravatar Neïl Zaim 3-30/+28
2022-02-11Rename ngE as ngEB (used for E,B) (#2841)Gravatar Edoardo Zoni 19-91/+91
2022-02-10ABLASTR: particle weights `const` (#2838)Gravatar Axel Huebl 4-5/+5
* ABLASTR: particle weights `const` We can declare the particle weights `const` because we don't change values in them during deposition. * DepositCharge: `const`-ify usage
2022-02-10BackTransformParticleFunctor: Unused Counter (#2840)Gravatar Axel Huebl 1-3/+1
Remove an unused counter in BTD particle filtering. Seen first with a HIP diagnostics.
2022-02-09Adding documentation for lxplus (#2756)Gravatar Lorenzo Giacomel 4-0/+256
* Adding documentation for lxplus * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding the new documentation * Apply suggestions from code review Some suggestions from the code review. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Removing suggestion about miniconda * Switched to using anonymous environment * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixing the architecture * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Tools/machines/lxplus-cern/spack.yaml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Updating env to use pre-installed openmpi * Moving a file * Docs: Now using GCC 11.2.0 * Add OpenMPI Version in Spec * Add CPU target architecture note * One more GCC 9.2.0->11.2.0 Update * Finalize Spack Stack Setup Notes * Move AFS Spack Config to Environment File * Comment on Variations of the Spack Env * Improve git clone and spack activation * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Fixing ncurses Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix: Spack Concretization (CUDA/Python) Somehow, this concretizes the variants not properly otherwise. * Not using the preinstalled openmpi anymore * updated lxplus.rst * added lxplus_warpx.profile.example * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Updated documentation * Added a precisation about warpx.profile * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add missing empty newline Co-authored-by: lgiacome <lorenzo.giacome@cern.ch> 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>
2022-02-08NCIGodfreyFilter: Fix Int Division (#2837)Gravatar Axel Huebl 5-90/+90
* NCIGodfreyFilter: Fix Int Division `m_cdtodz` is between 0 and 1, and we interpolate a set of coefficients from a table. * reset benchmarks Co-authored-by: Tools <warpx@lbl.gov>
2022-02-07Crusher: CMake 3.22.1 (#2835)Gravatar Axel Huebl 1-1/+1
Update to the lastest available CMake on Crusher. This one includes https://gitlab.kitware.com/cmake/cmake/-/merge_requests/6264 in case we need to build directly with `hipcc` to work-around some internal compiler errors with the Cray wrappers.
2022-02-07Implement some clang-tidy suggestions (#2826)Gravatar Luca Fedeli 8-33/+23
* implement some clang-tidy suggestions * Update loop Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-02-07Binary Collisions: Const & Restrict (#2829)Gravatar Axel Huebl 4-5/+9
`const`-ifying and `restrict`-ing pointers to index arrays for binary collision routines. This should allow the compiler to do more optimizations.
2022-02-07AMReX/PICSAR: Weekly Update (#2836)Gravatar Axel Huebl 6-6/+6
* AMReX: Update latest commit * PICSAR: Update latest commit
2022-02-07replace deprecated header ctype.h with cctype (#2831)Gravatar Luca Fedeli 2-2/+2
2022-02-07fix issues found with performance-for-range-copy clang-tidy check (#2833)Gravatar Luca Fedeli 2-2/+2
2022-02-07simplify WarpXUtil::is_in (#2834)Gravatar Luca Fedeli 1-10/+3
2022-02-05Fixes removing implicit double to float conversions (#2687)Gravatar David Grote 18-90/+102
* Fixes removing implicit double to float conversions * Minor fix in Evolve * Removed comments * Reverted amrex::second to original version. This change will be made in a separate PR * More fixes * Performance: pow2 & pow3 * One more pow2 * Cleaning: auto where types are repetitive std::pow(float, int): see comments and https://stackoverflow.com/a/5627278/2719194
2022-02-04added `local` flag to `warpx_getNumParticles` (#2828)Gravatar Roelof Groenewald 3-5/+8
2022-02-04Updated documentation regarding MCC collisions (#2827)Gravatar David Grote 1-1/+6
2022-02-04Apply clang-tidy suggestions to MsgLogger and WarnManager (#2823)Gravatar Luca Fedeli 4-63/+62
* Add misc suggestions from clang-tidy for MsgLogger and WarnManager * add [[maybe_unused]] to private member variable * fixed issue with unused variable * fix bug
2022-02-04CMake: Add More Pip Helpers (#2822)Gravatar Axel Huebl 5-55/+141
* CMake: Add More Pip Helpers Add and document more helpers to quickly and iteratively install our PICMI Python bindings with a one-liner from CMake. This should accelerate development cycles. * CI tests: Changed CMake target name * Update `.gitignore`: Python Workflows
2022-02-04Docs: NERSC Jupyter ipympl==0.8.6 (#2825)Gravatar Axel Huebl 1-1/+1
NERSC rolled out a new base environment, we now need to pin `ipympl` in version `0.8.6`.
2022-02-03Fix typo in laser assert (#2824)Gravatar Neïl Zaim 1-1/+1
2022-02-03Fixing the computation of ECT Rho Field (#2711)Gravatar Lorenzo Giacomel 8-112/+219
* Fixed computation of ECT Rho * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding a missing preprocessor directive * Updated contributors list * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fixed an abort message * Fix in Source/Initialization/WarpXInitData.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Added some comments * Made EvolveRhoCartesianECT not static Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: lgiacome <lorenzo.giacome@cern.ch> 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>
2022-02-03Rename PSATD Classes (#2805)Gravatar Edoardo Zoni 15-90/+90
* Rename PSATD Classes * Rename PsatdAlgorithmJLinear as PsatdAlgorithmJLinearInTime
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