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2021-10-11Reduced diagnostics: fix calculation of particle energy in single precision ↵Gravatar Luca Fedeli 3-8/+33
(#2397) * fix kinetic energy calculation in single precision * really fix the issue... * add missing _rt * we don't need m2 now * remove unused variable * always perform kinetic energy calculation in double precision * put w where it was * fixed bug * fixed bug * use threshold for kinetic energy * fix bug * increase order of Taylor expansion * increase order of Taylor expansion * reduce classical/relativistic threshold for kinetic energy * reset threshold to 1.005 * improve test
2021-10-11Remove unused pusher_algo parameter (#2388)Gravatar Neïl Zaim 2-2/+0
2021-10-11Allow Neumann domain boundary conditions for the electrostatic potential (#2345)Gravatar Roelof Groenewald 6-23/+94
* initial commit for adding a spatially varying potential for EBs * refactored logic to set the boundary conditions and boundary values for the electrostatic solver * style change * removed extra semi-colon * fixed issue causing oneAPI DPC++ build failure * fixed issue that led to CI test failure * fixed incorrect placement of definePhiBCs() call from previous commit * avoid the more expensive function to set the EB potential if it does not vary spatially * have to make a new parser when phi EB is only a function of time * fixed typo in previous commit * added option to use Neumann boundary conditions with the electrostatic solver * cleaned up logic for whether or not boundary potential values should be set * avoid using reference to __host__ variable * added CI test for mixed boundary conditions for the electrostatic solver * added documentation
2021-10-11Azure: Ubuntu 20.04 (#2302)Gravatar Axel Huebl 1-6/+9
Update to the latest Ubuntu LTS release (20.04) on our Azure CI tests. The sytem compiler updates from 7.4.0 to 9.3.0
2021-10-11Add Python Analysis for CI Test uniform_plasma_restart (#2393)Gravatar Edoardo Zoni 3-0/+27
2021-10-11Multi-J & Galilean RZ PSATD: Serialize RNG (#2404)Gravatar Axel Huebl 1-2/+2
* multi-J RZ PSATD: Serialize RNG This test uses: - RZ particles (default: random theta angle) - a temperature for the driver which are all RNG dependent. Serialize the RNG to avoid discrepancies with varying compile/runtime environments. * Fix: galilean_rz_psatd Uses a temperature on particles and thus should serialize the RNG.
2021-10-11Docs: serialize_ics (#2405)Gravatar Axel Huebl 2-2/+3
- slightly more user-facing info / context - add doxygen string to member variable
2021-10-11AMReX/PICSAR: Weekly Update (#2402)Gravatar Axel Huebl 4-4/+4
Weekly update to latest AMReX. Weekly update to latest PICSAR (no changes). ``` ./Tools/Release/updatePICSAR.py ./Tools/Release/updateAMReX.py ```
2021-10-08correct_misprint (#2395)Gravatar Luca Fedeli 1-1/+1
2021-10-08Fix checkpoint with runtime components through the Python interface. (#2332)Gravatar Andrew Myers 6-9/+308
* add component names to checkpoint * read in particle components and add the missing ones on restart * do not add components if one by the name already exists * sign error * Better warning messages * Update Source/Diagnostics/ParticleIO.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add CI test for restarting particles with runtime-added attributes * remove unused module Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-10-07Improve Python Analysis of Restart Tests (#2384)Gravatar Edoardo Zoni 5-40/+41
* Check All Particle Species, All Directions * Check also Particle Momenta * Add Check on Particle Weight, Fields * Smaller Field Tolerance (1e-12) * Single Loop over Particles and Fields * Cleaning * Add ds.force_periodicity() for yt-4.0
2021-10-07Remove unused fftw_plan_measure parameter (#2387)Gravatar Neïl Zaim 6-34/+19
2021-10-07Interpolate mu to B-location when computing H (#2252)Gravatar Revathi Jambunathan 8-182/+264
* interpolate mu to B-location when computing H * add comments * modify comment to reflect interpolation * eol * add struct to compute macroparameters at x,y,z, and util function to compute cellcoordinates * fix eol * remove unused variables, multifabs, and initialization of macro multifabs * host device function * fix typo * doxygen comments
2021-10-07Fix memory leak in I/O in rz mode (#2391)Gravatar Weiqun Zhang 1-6/+5
A temporary MultiFab was not properly deleted.
2021-10-07Implement Higginson's nuclear fusion algorithm (#2290)Gravatar Neïl Zaim 5-20/+343
* Implement Higginson's nuclear fusion algorithm * Fix uninitialized variable * Typo fix and compute probability in a more robust way numerically * Set mask to false when no fusion * Update NuclearFusionFunc Doxystring
2021-10-06Python Analysis of Restart Tests: Small Cleanup (#2368)Gravatar Edoardo Zoni 1-9/+1
* Python Analysis of Restart Tests: Small Cleanup * Remove Unused Import
2021-10-06FillBoundaryG: Add PML Exchange (#2381)Gravatar Edoardo Zoni 3-2/+31
2021-10-06CI: Groups Include Branch (#2378)Gravatar Axel Huebl 7-7/+7
On pushes to mainline, if mainline contains multiple branches, these branches cancelled each other. This should fix this.
2021-10-06Documentation: add link to AMReX doc that lists available parser functions ↵Gravatar Neïl Zaim 1-1/+2
(#2380)
2021-10-06Docs: Simplify Release Log (#2372)Gravatar Axel Huebl 1-1/+1
Way easier :D
2021-10-06NodalSync: Less Duplicate Code (#2375)Gravatar Edoardo Zoni 3-89/+21
2021-10-06Simplify formulas for Esirkepov deposition (#2373)Gravatar Remi Lehe 1-12/+11
2021-10-05CI: mpi4py NVHPC work-around (#2379)Gravatar Axel Huebl 1-5/+8
Compiling Python modules with NVHPC again after work-arounding the mpi4py build issue.
2021-10-05Capitalize python environment variables in CI workflows (#2376)Gravatar Neïl Zaim 6-14/+16
* Capitalize python environment variables in CI workflows * Python Envs: Update Cori/Summit Docs * NVHPC: Disable MPI4PY https://github.com/mpi4py/mpi4py/issues/114 Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-10-05CU: NVHPC (CUDA) (#2371)Gravatar Axel Huebl 2-0/+70
Add NVHPC (21.9) CUDA builds to CI. Uses the `nvcc -cbin nvc++` compiler combination, as currently set by Cray systems with the `PrgEnv-nvidia` environment (e.g., Perlmutter at NERSC).
2021-10-04Fix my_constants being cast to float in single precision (#2369)Gravatar AlexanderSinn 2-8/+42
* Parse my_constants always as double * remove debug print out * add comment * fix comment * add additional comment
2021-10-04Electrostatic boundary condition handling refactor (#2303)Gravatar Roelof Groenewald 4-168/+162
* initial commit for adding a spatially varying potential for EBs * refactored logic to set the boundary conditions and boundary values for the electrostatic solver * style change * removed extra semi-colon * fixed issue causing oneAPI DPC++ build failure * fixed issue that led to CI test failure * fixed incorrect placement of definePhiBCs() call from previous commit * avoid the more expensive function to set the EB potential if it does not vary spatially * have to make a new parser when phi EB is only a function of time * fixed typo in previous commit
2021-10-04Add structure for proton-boron fusion module (#2217)Gravatar Neïl Zaim 22-60/+450
* Add structure for proton-boron fusion module * Fix clang compile error * Generalize structure for other nuclear fusion types * Workaround: try to use std::vectors to fix clang compile error * Simplify workaround for clang * Rebase on 2245 and add empty particle creation functor * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add couple of consts and runtime assert * Add another const Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-10-04Release 21.10 (#2370)Gravatar Axel Huebl 10-12/+12
* Update: AMReX/PICSAR to 21.10 * WarpX: 21.10
2021-10-04Implement Checkpoint / Restart for Laser Particles (#2360)Gravatar Andrew Myers 12-112/+174
* Initialize lasers when restarting + recalculate z position at each iteration * Fix restart for rigid-injected particles * Fix laser injection box at restart * Use correct positions for the moving window of the BTD * implement restart for laser particles * add CI test for laser acceleration restarting * writespace * Revert "Fix restart for rigid-injected particles" This reverts commit 33bf3a60126539b9566ead3115ff2bcdf4b80516. * don't add lasers to all full diags, only checkpoints * fix unused parameter warning * move the call to reset the m_laser_injection_box into PostRestart * bugfix for non-boosted frame simulations * Read the mean velocity of the injected species * Remove unused line * Revert "Initialize lasers when restarting + recalculate z position at each iteration" This reverts commit 322634c35aa996649d0e8fff9fb683d04f2ee121. * Add new ReadHeader / WriteHeader functions * Add WriteHeader/ReadHeader for laser particles * Revert "add CI test for laser acceleration restarting" This reverts commit 6ba0fb3c121027eecf8b5845f55080e5b187375d. * Fix merge commit * Correct reading of updated position * Add laser in restart test * Remove unused parameters * Update regression tests * Add benchmark files * Update boundary conditions for restart_psatd Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-10-01Docs PoP: Fix Co-Authors (#2367)Gravatar Axel Huebl 1-1/+1
2021-10-01Fix restart for rigid injected particles (#2363)Gravatar Remi Lehe 5-100/+106
* Activate rigid injected species in restart tests * Fix reading of injection position and velocity * Update checksum * Update Examples/Tests/restart/analysis_restart.py
2021-09-30Style: Old BTD Definitions (#2352)Gravatar Axel Huebl 2-58/+58
Add spaces before definitions in the old BTD. Was just adding them as we looked for a solution to fix restarts with the old particle BTD.
2021-09-30CMake: More Robust git STRIP (#2358)Gravatar Axel Huebl 1-1/+1
Sometimes a `git` executable can be found but is unusable. Quoting the result for empty strings makes the build logic more robust in such scenarios. Mitigates: ``` CMake Error at cmake/WarpXFunctions.cmake:289 (string): string sub-command STRIP requires two arguments. Call Stack (most recent call first): CMakeLists.txt:256 (get_source_version) ``` Provoked via: Mixing of brew and Spack (git from brew + Spack env with `export DYLD_LIBRARY_PATH=/Users/axel/src/spack/var/spack/environments/warpx-dev/.spack-env/view/lib`)
2021-09-30Remove array of ints `done_injecting` (#2365)Gravatar Remi Lehe 3-17/+1
2021-09-30Rigid injected species: Remove unused function and variables (#2350)Gravatar Remi Lehe 14-136/+0
* Remove unused function * Remove `focused` and `projected` for rigid particles
2021-09-30Update AMReX (#2362)Gravatar Axel Huebl 5-6/+8
Update pulls in: - Intel DPC++ 2021.4.0 support (SYCL) - Nvidia NVHPC 21.9 support (CUDA)
2021-09-29CI: Update HIP Repo URL (#2359)Gravatar Axel Huebl 1-1/+1
Thanks to @wyphan in https://github.com/AMReX-Codes/amrex/pull/2366 > This updates the repo line for HIP to the latest version as documented on https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#installing-a-rocm-package-from-a-debian-repository > Notably, `xenial` is now `ubuntu`.
2021-09-28Use correct positions for the moving window of the BTD (#2356)Gravatar Remi Lehe 1-2/+3
2021-09-27Update read_raw_data to RZ (with multiple modes) (#2313)Gravatar David Grote 1-2/+10
2021-09-28Stencil: Fix non-3D Compiles on GPU (#2353)Gravatar Axel Huebl 2-2/+51
* CI: HIP 2D Add a HIP 2D Test to compilation. * Stencil: Fix non-3D Compiles on GPU Overlooked the `#else` branch severely. * CI: HIP 2D DP
2021-09-27Comoving PSATD: New Input psatd.use_default_v_comoving (#2304)Gravatar Edoardo Zoni 2-2/+23
2021-09-27SumBoundary: Use Fewer Guard Cells for J/rho (#2323)Gravatar Edoardo Zoni 2-21/+65
* SumBoundary: Use Fewer Guard Cells for J/rho * Account for Stencil of Bilinear Filter * Revert Last Commit, Replace SumBoundary/Copy With ParallelAdd * Account for Stencil of Bilinear Filter * Reset Benchmarks of Averaged Galilean Hybrid Tests * Revert Last Commit This reverts commit 7963176b46708eb08e7c41e67a3b0a6fe6cb2147. * Account for Stencil of Current Centering
2021-09-27Summit: Known Issues Since RHEL8 (#2349)Gravatar Axel Huebl 1-0/+60
* Summit: Known Issues Since RHEL8 Document all known issues and work-arounds for Summit users. * Summit: libfabric developer notes
2021-09-27Allow more work for OpenMP threads in `WarpX::UpdateAuxilaryData` (#2342)Gravatar Remi Lehe 1-7/+7
* Allow more work for OpenMP threads in AuxilaryData * Better parallelization in stagger-to-nodal current interpolation
2021-09-27AMReX: Weekly Update (#2348)Gravatar Axel Huebl 4-4/+4
``` ./Tools/Release/updateAMReX.py ```
2021-09-27Doc: Disable CCache (#2339)Gravatar Axel Huebl 2-0/+5
Document on how to disable CCache. Add CCache control to Python builds.
2021-09-24ParticleIO: Fix All Container Restart (#2341)Gravatar Axel Huebl 2-36/+48
* ParticleIO: Fix All Container Restart * Fix comment
2021-09-24Restart: Handle Header File Read Errors (#2335)Gravatar Axel Huebl 6-19/+17
* Restart: Handle Read Errors `std::istringstream` does not throw automatically if errors occur. This leads to silently skipped reads. Enable throwing on all errors to avoid hard to debug follow-up errors. * Fix: Write All Particle Containers Forgot to write laser particle containers but then tried to read them in. The mass & charge of those are not essential for us to restore, but it avoids confusion and extra logic if we just write them properly at the general location.
2021-09-24DPC++: Disable -fPIC (#2338)Gravatar Axel Huebl 1-1/+4
Sporadic segfaults in `dpcpp` with shared objects since last release. Needs to be triaged. Disabled to unblock community devs.
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