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2023-02-27Change plotfile RZ allowed diags to r,t from x,y (#3663)Gravatar Ryan Sandberg 2-19/+45
* change plotfile RZ allowed diag to r,t from x,y * Change labeling in checksums * add rz silver mueller analysis script * make analysis_silver_mueller_rz.py executable * change x,y fields to r,t in more tests * x->r in MR RZ checksums * correct analysis for plotfiles saved as 'boxlib' * add self to creator list * change rz diags in PICMI * correct PICMI changes * another y->t in an rz test * update picmi plotfile rz btd names * review suggestion to condense analysis * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-22Reduced diagnostics: charge on the embedded boundary (#3648)Gravatar Remi Lehe 6-2/+268
* Prepare structure to compute charge inside boundary * Add calculation without embedded boundaries * Use EB area fraction * Skip cells that are not cut-cells * Choose point outside of the EB * Skip covered or regular boxes * Only compile with EB and 3D support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test for charge on EB * Add automated test * Add automated Python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Avoid compilation error * Enable PICMI test * Rename ChargeInsideBoundary to ChargeOnEB * Update comments * Add parser for weighting * Call weighting function * Call weighting function * Add documentation * Update Python test * Add Python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix compilation errors * Fix access of attribute on GPU * Use difference in surface area * Pick smaller radius in test This is in order to avoid the influence of the boundaries * Update benchmark * Update benchmark * Properly add diagnostic * Update radius in analysis * Update analysis script * Relax tolerance * Fix tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Python tests * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Test one-eighth from Python * Add one-eighth charge in tests * Handle ChargeOnEB * Remove bug when handling charge on eb * Fix Python errors * Fix Python issues * Use more natural setting of tilebox --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-22Fix getBulkMomentum for Maxwellian distributions (#3705)Gravatar David Grote 1-20/+21
* Fix getBulkMomentum for Maxwellian distributions * Add more "_rt" to real literals * More cleanup
2023-02-22Add option to increase `max_step` or `stop_time` to fill BTD (#3693)Gravatar Ryan Sandberg 3-7/+39
* add option to increase max_step to fill BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make sure code compiles locally * allow for unspecified max step if setting by BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clarify docs, match default max_step value * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review shortening flag name * add example input script, fix bugf * check stop_time and max_step * account for stop time * Fix logic, improve 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>
2023-02-21Fix Silver-Mueller boundary condition in 1D (#3703)Gravatar Remi Lehe 1-5/+2
* Fix Silver-Mueller boundary condition in 1D * Use WARPX_ZINDEX * Add automated test * Add benchmark
2023-02-21Renamed "particle_vel" to "particle_mom" (#3672)Gravatar Davide Terzani 4-27/+55
* Renamed particle_vel to particle_mom * Changed vel to u * Updated gitignore with vscode-specific folder * Updated docs for single particle * Revert "Updated gitignore with vscode-specific folder" This reverts commit cb44ef8d66c123daa93d6a13d5a1d88416e866bb. * Fixed typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed other typo * Add species indication in warning --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-02-21Add warning message in RZ for < 2 azimuthal modes (#3655)Gravatar Davide Terzani 1-0/+13
* Add warning message in RZ for < 2 azimuthal modes * Simplify if statements C++ operator precedence doesn't require double parenthesis in `if` statements Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-02-21GetExternalEBField: Use AMReX's CompileTimeOption ParallelFor (#3696)Gravatar Weiqun Zhang 4-14/+56
This greatly improves the performance on AMD and Intel GPUs when GetExternalEBField is not used.
2023-02-09Pass seed for gpu in ResetRandomSeed (#3682)Gravatar David Grote 1-4/+8
2023-02-08CI & Bug Fixes: 1D & 2D Compile (#3680)Gravatar Axel Huebl 2-10/+30
* CI: 1D & 2D Compile Add a modern CI entry that compiles 1D and 2D with `-Werror` and many warnings enabled. * Fix: 1D Field Init in z * Fix 1D: filterCreateTransformFromFAB * CI Job: Rename * CI: 1D/2D EB Off Not yet working.
2023-02-08Fix bug in mirror with F,G fields (#3681)Gravatar Edoardo Zoni 1-24/+41
2023-02-07Bug fix: retain particles in boundary buffer during Redistribute() (#3679)Gravatar Roelof Groenewald 1-1/+2
2023-02-03 Bug fix : Coarse patch dx for external field init (#3674)Gravatar Revathi Jambunathan 2-9/+16
* fix coarse patch dx for external field init * rename var * Update Source/Initialization/WarpXInitData.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * reset benchmark for PEC_mr test case --------- Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-02-03Clean warning on unused function (#3656)Gravatar Remi Lehe 1-2/+0
2023-02-03Add all the elements from Z=87 (Fr) to Z=100 (Fm) to the ionization table ↵Gravatar Luca Fedeli 2-6/+1786
(#3670) * add elements between Z=87 and Z=100 to the ionization table * update documentation
2023-02-03Fix a bug in 1D PEC (#3669)Gravatar Prabhat Kumar 1-0/+26
* Fix a bug in 1D PEC * remove print statement used for debugging * reset benchmark for LaserInjection_1d because a bug was fixed in 1D pec * use correct data file in last commit for LaserInjection_1d * update benchmark for LaserAcceleration_1d since it uses pec * use data at correct time step * fix yt version to get nonzero particle output in LaserAcceleration_1d.json * fix yt version to get nonzero particle output in LaserAcceleration_1d.json
2023-02-03fix some issues in WarpX 1D (#3671)Gravatar Luca Fedeli 3-16/+32
2023-02-02RZ: abort if warpx.numprocs[0] > 1 with PSATD (#3615)Gravatar Olga Shapoval 1-0/+6
* RZ: added abort message if warpx.numprocs[0] > 1 is set. * Clean-up. * More clean-up. * Clean up alignment * Narrow down domain decomposition abort message to spectral solvers with RZ --------- Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-02add elements from Z=55 to Z=85 to the ionization table (#3666)Gravatar Luca Fedeli 2-6/+2978
2023-02-02ADIOS2: Fix BTD Particle Resize w/ Empty Ranks (#3657)Gravatar Axel Huebl 1-0/+55
* ADIOS2: Fix BTD Resize w/ Empty Ranks For ADIOS2 BP4 and BP5 writes, setting an update of a variable's (openPMD record's) shape is not sufficient to drop all meta-data on disk. In situations where the last write to a BTD stage only adds further particles from a few ranks, we need to pad with zero-block writes so ADIOS2 `Put` gets called. Backend details: - BP4 (as of ADIOS 2.8): last MPI rank's `Put` meta-data wins - BP5 (as of ADIOS 2.8): everyone has to write an empty block * [Draft] Start Duplicating All Put Logic Jeeeeeze. * Better Work-Around Compact and general, including MR situations.
2023-02-01Use a simpler expression for particle energy for reduced diagnostics. (#3650)Gravatar David Grote 1-18/+8
2023-02-01Fix NUniformPerCell for 1D (#3659)Gravatar David Grote 1-1/+1
* Fix NUniformPerCell for 1D * Fix CI benchmarks
2023-01-31Add Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe to the ↵Gravatar Luca Fedeli 2-63/+1075
ionization table (#3652) * add Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe to the ionization tables * fix bug
2023-01-30Implement linear interpolation for both cell-centered and nodal data types ↵Gravatar Prabhat Kumar 1-14/+16
(#3638) * use two points and correct weights for higher order interpolation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * better alignment * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Parallelization/WarpXComm_K.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Reset CI benchmarks * apply review suggestion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * white space --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2023-01-30add K,Ca,Sc,Zn,Ga,Ge,As,Se,Br to ionization tables (#3646)Gravatar Luca Fedeli 2-12/+593
2023-01-29Clean loadbalance params (#3632)Gravatar Hannah Klion 1-5/+9
* add tables for heuristic weights to documentation * re-format tables * only read in load balancing parameters when used
2023-01-28Add ionization support for Titanium (#3645)Gravatar Marco Garten 2-11/+43
* Add ionization support for Titanium This commit adds ionization support for Titanium as asked for in WarpX Issue 3641. * [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>
2023-01-25Fix few includes in WarpXAMReXInit.cpp/H and TextMsg.cpp using IWYU tool (#3627)Gravatar Luca Fedeli 3-1/+6
* Fix a couple of include directives * fix bug * Update Source/Initialization/WarpXAMReXInit.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * remove unnecessary AMReX.H include Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-01-24Fix bug with PML in 2D when compiling with EB (#3637)Gravatar Remi Lehe 2-4/+9
* Fix condition to update PML in 2D * Add automated test: PML with EB compiled * Pass correct cell sizes * Update automated test * Update benchmark
2023-01-23added space to warning message when too many boxes per GPU (#3633)Gravatar Hannah Klion 1-1/+1
2023-01-17replaced vector.insert with std::copy to avoid issues with g++ 12 (#3625)Gravatar Luca Fedeli 1-2/+2
2023-01-13Fix segfault in interpolation with anisotropic ref ratio (#3613)Gravatar Prabhat Kumar 2-2/+8
* Fix segfault in interpolation with anisotropic ref ratio * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/ablastr/coarsen/average.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/ablastr/coarsen/average.cpp Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2023-01-13EB potential python interface (#3624)Gravatar David Grote 4-1/+24
* Add Python routine set_potential_EB to modify eb_potential * Add CI test
2023-01-12Fix Doxygen Warnings (#3616)Gravatar Axel Huebl 7-8/+10
2023-01-09Correct typo in PML+PSATD warning message (#3608)Gravatar Luca Fedeli 1-1/+1
2023-01-09Vay deposition not implemented with multi-J algorithm (#3606)Gravatar Edoardo Zoni 1-0/+6
2023-01-06add local flag to ParticleBoundaryBuffer::getNumParticlesInContainer (#3586)Gravatar Roelof Groenewald 5-7/+7
2023-01-06For the tridiag, remove the guard cells since they are not needed (#3604)Gravatar David Grote 1-45/+30
* Removed the guard cells since they are not needed for the tridiag * Clean up the copy into the 1d array * For the upper boundary, use explicit indices instead of temporaries to make the code more clear
2023-01-04Generalize interpolation routines in diags for anisotropic ref ratio (#3603)Gravatar Prabhat Kumar 4-15/+17
* Correct particle positions outside refined injection * Improve test * Update benchmark * Modifications for vector refinement ratio * Update getPosition function * Update code for anisotropic injection * Correct compilation * Correct code for RZ and 1D * Correct indentation * Correct integer overflow, as suggested by Weiqun * Generalize interpolation routines in diagnostics for anisotropic ref ratio * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Utils/Interpolate.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Utils/Interpolate.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Utils/Interpolate_K.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Utils/Interpolate.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * apply review suggestion Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-01-04Refined injection with anisotropic mesh refinement ratio (#3464)Gravatar Remi Lehe 2-21/+31
* Correct particle positions outside refined injection * Improve test * Update benchmark * Modifications for vector refinement ratio * Update getPosition function * Update code for anisotropic injection * Correct compilation * Correct code for RZ and 1D * Correct indentation * Correct integer overflow, as suggested by Weiqun
2023-01-04Fix bug for intra-species Coulomb collisions (#3526)Gravatar Yinjian Zhao 2-3/+15
* Correct density * update * Add test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Regression/WarpX-tests.ini * update * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review * update * Fix shadowing of variables * Simplify code * Correct density * Update checksum * Update exponential fit * Remove unused global variable * Add comment on exponential fit * Cleaning * Cleaning * [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> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-01-02fix two issues with unchecked possibly null pointer found with CodeQL (#3582)Gravatar Luca Fedeli 1-4/+5
2023-01-02Fix a Bug in 1D ES (#3597)Gravatar Weiqun Zhang 1-4/+3
After the tri-diagonal solve, the data in the special single-box MultiFab need to be copied back to the normal MultiFab. However, when there was a bug for periodic boundary. The issue is the special MultiFab is really special. It has a nodal Box that grows the original nodal Box by 1 node in the lower boundary and 2 (why 2?) nodes in the upper boundary and these grown nodes are considered valid nodes, even though they do not have valid data. Therefore amrex::ParallelCopy with periodicity does not work in this case. For example, for a domain with 96 cells, the data at nodes 1 and 2 of the normal MultiFab could be written with the invalid data at nodes 97 and 98 of the special MultiFab. This bug is fixed by replacing it with a ParallelCopy without periodicity followed by a FillBoundary.
2022-12-22Feature magnetostatic solver (#3551)Gravatar S. Eric Clark 18-10/+900
* Initial working Magnetostatic solver integration into warpx. Includes hooks in Python library, and a test problem. Build files updates. New solver algorithm and inputs. * Fixed indexing to allow Magnetostatic solver to work in RZ and 3D. * Removing trailing whitespace. * Adding basic regression testing with benchmarks. * Updated Regression test ini * Augmented test scripts to compare to analytical results for uniform beam. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updating CI tests for magnetostatic solver. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated magnetostatic CI tests to pass locally in regression testing framework. * Adjusting tolerance on magnetostatic_rz regression test to allow for noise in near zero fields. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Converted particle layout to Gridded instead of PsedupRandom to improve reproducibility of particle deposition for regression testing. * Dropped benchmark field comparisons with fields near zero. Dropped particle benchmark for magnetostatic_eb_rz regression test due to randomized particle theta adding noise to fields after a timestep. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Found and fixed a bug in syncronization of MultiFabs when interpolating between grids in the magnetostatic solver. Added Python output for nodal current and vector potential. Updated the CI tests to disable dynamic scheduling and enbale serialization of initial conditions. Updated benchmarks fro tests. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Adding random_theta flag to PICMI interface and updating RZ CI test and benchmark with change to disable randomized theta. * Added documentation to parameters.rst for relativistic-magnetostatic flag. Documentation corrections. Removal of commented source. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removing need to use do_current_centering. Updated current density inverse scaling support for nodal Jr in radius. Added flag to check for m_rz_random_theta when laying down particles in RZ. * Remove dA/dt term to decouple electrostatic and magnetostatic solvers. * Remove update of auxiliary fields * Adding non-Python test case for magnetostatic solver. Updating benchmarks. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Diagnostics/Diagnostics.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Evolve/WarpXEvolve.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.H Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Refactor names of functions for magnetostatic solver implementation. Remove current_fp_nodal python interface. Drop extraneous ghost cell exchanges. * Adding radial weighting at r=0 for Jr if nodal. * Splitting off Amrex bucket and adjustments to RZ radial weighting into different branches to be merged. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Switch name to labfame-electromagnetostatic * Update example scripts Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2022-12-22Adding radial weighting at r=0 for Jr if nodal. (#3589)Gravatar S. Eric Clark 1-17/+22
2022-12-21Avoid touching device memory on host in FieldProbe (#3579)Gravatar Weiqun Zhang 1-16/+23
The implementation here can be optimized by using shared memory. However, instead of doing it here, I am going to add a helper function to AMReX. Also removed an unnecessary synchronization, because there is a synchronization in the destructor of the particle iterator.
2022-12-21Allow const_dt with EM and check it for ES (#3561)Gravatar David Grote 3-4/+7
* Allow const_dt with EM and check it for ES * Update PR according to comments * Fix typo * Fix invalid reference to m_const_dt * Fixed another invalid reference to m_const_dt * Remove erroneous setting of `const_dt` test * Add doc for const_dt Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2022-12-21Add accelerator lattice, starting with quadrupoles (#3063)Gravatar David Grote 25-2/+1282
* Initial version of accelerator lattice * Clean up EOL white space * Small clean up for GPU * Fixed up consts * Added hard edge fraction plus other clean ups * More clean up * Restructure to work on GPUs * Now this grabs its own copies of particle info * Updates, including adding dBdx * Small cleanup in Quad * Small fixes for GPU * More cleanup for GPU * More GPU cleanup * Rewrite of the accelerator lattice implementation to better handle GPU * Fix struct forward definition * Another forward definition fix * Bug fix * Added LatticeElementBase * Removed zcenters array * Added CI test case * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Clean up in CI analysis.py * Cleanup of coding * Added CI test hard_edged_quadrupoles_moving * Added Lorentz transform between boosted frame and lab frame * Fixes for working in the boosted frame * Added boosted CI test * Change input name, adding the prefix "lattice." * Added plasma lens lattice element This will replace the external field plasma lens * Fixed CI analysis script to look for "lattice.quad" * Added checks of lattice element input * Added documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed duplicate call to lattice finder UpdateIndices * Added extensive comments * Reworked the input to use the MAD like description This is the same as the method used in ImpactX * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove old lines from inputs_lattice_3d * Added "lattice" element type * Fixed some Real and ParticleReals * [pre-commit.ci] pre-commit autoupdate (#3246) updates: - [github.com/hadialqattan/pycln: v2.0.1 → v2.0.3](https://github.com/hadialqattan/pycln/compare/v2.0.1...v2.0.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ABLASTR: Update Poisson Solver API (#3243) Update the Poisson Solver API to be more usable. Needed for ImpactX. * Docs: New OLCF Machine (#3228) * D-T fusion (#3153) * 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 * Apply suggestions from code review * Update PR according to comments * Update benchmark * Address additional comments * Numerical Literals Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Docs: gaussian beam `q_tot` is not optional (#3249) * Fix a bug in GPU version of Hankel Transform (#3253) amrex::Array4 is a 4D array that can be accessed with three spatial indices plus an optional component index. We must always provide all three spatial indices even in 2D. * Add Python Callback Call when Checkpointing Signal is Received (#3251) * CI: Add Missing Regression Analysis (NCI corrector) (#3252) * Fixes to allow mixed precision, ParticleReal float, Real double (#3239) * Fixes to allow mixed precision, ParticleReal float, Real double * Fix for the optical depth * A different way of fixing QuantumSynchrotronEvolveOpticalDepth * In the QED code, consistently use ParticleReal * Use ParticleReal type consistently * Fix typo Docs/source/usage/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix typo Docs/source/usage/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix small error in plasma lens lattice documentation * Small addition to the documentation * Fix the residence correction to allow short elements * Updated CI benchmarks * Added check of lattice to isNoOp * Updated the hard_edged_quadrupoles CI benchmarks It is not clear why there was a change, but the difference is essentially round off in the E field. The important thing is that the particles are still correct. * Update Source/AcceleratorLattice/AcceleratorLattice.H Add include statements Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/AcceleratorLattice/LatticeElements/LatticeElementBase.H Add includes Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Renamed to README.rst and updated headers * Made d_lattice_element_finder optional type * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Include `<optional>` * Docs: Developer AccLattice Inclusion 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: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-12-19managed memory for user defined attribs in addplasma (#3576)Gravatar Revathi Jambunathan 1-25/+66
2022-12-19Clean up documentation (#3542)Gravatar David Grote 27-77/+96
* Fix comments for documentation * More fixes to comments for documentation * Fixes in the doc files * Fix typo in parameters.rst
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