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2022-07-18[pre-commit.ci] pre-commit autoupdate (#3246)Gravatar pre-commit-ci[bot] 1-1/+1
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>
2022-07-18AMReX: Weekly Update (#3244)Gravatar Axel Huebl 5-5/+5
2022-07-14Remove Unused Allocations of Averaged MultiFabs (#3237)Gravatar Edoardo Zoni 1-18/+30
2022-07-14CMake: 3.20+ (#3196)Gravatar Axel Huebl 5-12/+6
We already use this version in ImpactX. The main reason is a severe simplifcation of CMake CUDA search logic that we can rely on. X-Ref.: https://github.com/AMReX-Codes/amrex/blob/2d931f63cb4d611d0d23d694726889647f8a482d/Tools/CMake/AMReXParallelBackends.cmake#L55
2022-07-13Refactor code in fusion module to avoid machine-precision issues (#3229)Gravatar Remi Lehe 3-14/+16
* Refactor code in fusion module to avoid machine-precision issues * Update formula
2022-07-12Fix: Write Used Inputs Once (#3234)Gravatar Axel Huebl 1-4/+6
Ooopsi, nearly killed a PFS again :D Only the IO processor should write this and not every rank on the planet.
2022-07-12Update 2D nuclear fusion test input file (#3230)Gravatar Neïl Zaim 2-65/+65
* Update 2D nuclear fusion test input file * Update Benchmarks
2022-07-12[pre-commit.ci] pre-commit autoupdate (#3226)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v1.3.5 → v2.0.1](https://github.com/hadialqattan/pycln/compare/v1.3.5...v2.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-07-12Add 2D tests for proton boron fusion (#2540)Gravatar Neïl Zaim 4-5/+391
* Add 2D tests for proton boron fusion * Apply suggestions from review * Fix WarpX-tests.ini * Update benchmarks
2022-07-11Docs: Update WarpX Reference (#3223)Gravatar Edoardo Zoni 1-2/+2
2022-07-09Cleanup how fields_to_plot = none is handled (#3219)Gravatar David Grote 7-21/+15
* For fields_to_plot=none, do allocation with ncomp=0 * Update AMReX Via ``` ./Tools/Release/updateAMReX.py ``` Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-07-09Release 22.07 (#3211)Gravatar Axel Huebl 12-18/+17
* AMReX: 22.07 * PICSAR: 22.07 * WarpX: 22.07 * SENSEI: Update to 4.0.0 * AMReX: 22.07-4-gcbdc6580ee Include SENSEI build fixes.
2022-07-08Improve Docs on max_grid_size/blocking_factor for RZ (#3221)Gravatar Edoardo Zoni 1-1/+2
2022-07-07Parse the quantity `zmax_plasma_to_compute_max_step` in PICMI (#3217)Gravatar Remi Lehe 1-0/+3
* Parse the quantity `zmax_plasma_to_compute_max_step` * Apply review comments
2022-07-06Initialize multi-physics module (ionization, QED) when restarting ↵Gravatar Remi Lehe 5-16/+29
simulations from checkpoints (#3194) * Move the initialization of multi-physics module earlier * Fix syntax error * Initialize multi-physics modules also when restarting the simulation
2022-07-05Add new entries in Physical Species properties (+ refactoring of the ↵Gravatar Luca Fedeli 23-362/+549
SpeciesPhysicalProperties file) (#3090) * initial work * fixed bugs and added species * update documentation * delete unused file * Add neutron * Fix nuclear fusion * Reset benchmarks * 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 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>
2022-07-05[pre-commit.ci] pre-commit autoupdate (#3213)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.2.0 → v1.3.0](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.2.0...v1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-07-05Merge `FillBoundary` and `NodalSync` (`OneStep_multiJ`) (#3169)Gravatar Edoardo Zoni 5-109/+53
* Merge `FillBoundary` and `NodalSync` (`OneStep_multiJ`) * `NodalSync` Not Needed Anymore
2022-07-02Use amrex::RandomNormal in Maxwell-Boltzmann momentum injection (#3209)Gravatar Neïl Zaim 6-172/+167
* Use amrex::RandomNormal in Maxwell-Boltzmann momentum injection * Remove factor sqrt(2) in std calculation * Update benchmarks * Increase relative tolerance for Python_background_mcc checksum * Update Source/Initialization/InjectorMomentum.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-06-28[pre-commit.ci] pre-commit autoupdate (#3205)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v1.3.3 → v1.3.5](https://github.com/hadialqattan/pycln/compare/v1.3.3...v1.3.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-06-27AMReX: Weekly Update (#3204)Gravatar Axel Huebl 5-5/+5
2022-06-24Added `none` as an option for fields_to_plot (#2419)Gravatar David Grote 8-11/+92
* Added `none` as an option for fields_to_plot * Added CI test case * Further updates, for picmi and CI tests * Skip the call to amrex::WriteMultiLevelPlotfile when writing no fields * Now clears m_varnames_fields * Don't allocate m_mf_output if no varnames * Updated WarpX-tests.ini
2022-06-23Remove Unused Function `getcurrent` (#3197)Gravatar Edoardo Zoni 1-1/+0
2022-06-22AMReX/PICSAR: Weekly Update (#3192)Gravatar Axel Huebl 7-44/+44
* AMReX: Weekly Update * Reset: `reduced_diags_single_precision` * Reset: `background_mcc_dp_psp`
2022-06-21fix missing newline in documentation (#3193)Gravatar Luca Fedeli 1-0/+1
2022-06-20Remove temporary copy of MultiFab (#3190)Gravatar Marco Garten 1-10/+1
Use template specification of amrex::FillBoundary directly with comm_float_type in case of single-precision communication. Leave out FillBoundaryAndSync for now because it requires AMReX changes.
2022-06-20Use ablastr::utils::communication::FillBoundary instead of ↵Gravatar David Grote 1-2/+4
amrex::FillBoundary in PML_RZ (#3191)
2022-06-16Docs: Move LPI Experiment Citation (#3187)Gravatar Axel Huebl 1-5/+5
Moving a citation down to LPI.
2022-06-16Extract function for two-particle fusion reaction (#3175)Gravatar Remi Lehe 2-100/+192
* Extract function for fusion reaction between 2 particles * Extract function for two-particle momenta in fusion reaction * Apply suggestions from code review Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Remove obsolete comment * Update Source/Particles/Collision/BinaryCollision/NuclearFusion/TwoProductFusionUtil.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-06-15ABLASTR: Compute Phi (#2994)Gravatar Axel Huebl 7-267/+473
* ABLASTR: Compute Phi Expose the computation of the electro-static potential for relativistic beams via ABLASTR for ImpactX. * Add `ablastr::fields::computePhi` Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Cleanup: Old Comments Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2022-06-14CMake: Generalize `CMAKE_INSTALL_CMAKEDIR` (#3180)Gravatar Axel Huebl 2-7/+10
* CMake: Generalize `CMAKE_INSTALL_CMAKEDIR` Generalize the control of the global `CMAKE_INSTALL_CMAKEDIR` variable. This way, we can control the variable in superbuilds that include ABLASTR, e.g., in ImpactX. * WarpXFunctions: Remove Unused Python Not (yet) used.
2022-06-14AMReX/PICSAR: Weekly Update (#3177)Gravatar Axel Huebl 5-5/+5
* AMReX: Weekly Update * AMReX: Bump Once More to 1a2fc3dbee1ce0c168cdb66710458757e92a0605
2022-06-14CMake: AMReX_PIC (`-fPIC`) for ABLASTR (#3181)Gravatar Axel Huebl 1-1/+1
Make sure that AMReX is also built with position independent code if the corresponding ABLASTR option is set.
2022-06-14openPMD-api: 0.14.5 (#3171)Gravatar Axel Huebl 1-1/+1
Automatically pull the lastet openPMD-api release, 0.14.5.
2022-06-14[pre-commit.ci] pre-commit autoupdate (#3178)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pre-commit/pre-commit-hooks: v4.2.0 → v4.3.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.2.0...v4.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-06-13Extend MCC to accurately treat relativistic particles (#3118)Gravatar Roelof Groenewald 15-227/+541
* initial commit for MCC to support relativistic particles * proper calculation of collision energy when target mass is not much greater than projectile mass * fix bug with scattered velocity rotation to lab frame * refactor the MCC sequence for clarity * use cross-section input to determine energy limits when calculating the maximum collision frequency * code cleanup * updated CI tests * added Collisions section to Implementation Details in docs * reset benchmark for mixed precision MCC test and other more code cleanup * fix issue with single precision and simplified implementation * use `double` for particle mass and energy calculations in MCC * added comment to ImpactIonization.H explaining why `double`s are used for `energy` and `mass` * switch to round off safe version of energy calculation and switched to using u instead of v for gamma*v in ParticleUtils.H * update documentation * simplified expression for collision energy, updated docs * Add comment that the direct solver can be replaced for the MLMG solver once the issue with that solver is fixed (in the 1d MCC test)
2022-06-10Update glossary.rst (#3174)Gravatar Marco Garten 1-0/+6
Add *Ascent, IPO, LTO, PICMI, PICSAR, SENSEI*
2022-06-09Summit: Fix BLAS++/LAPACK++ Modules (#3172)Gravatar Axel Huebl 1-2/+2
These modules are by default using GPU support, which points to CUDA 11.0. Due to C++17 compiler bugs in that early CUDA release, we cannot use that version and pull in circular dependencies to two different CUDA toolkit versions as soon as we use BLAS++ & LAPACK++: when compiling PSATD+RZ. Nonetheless, we do not use BLAS++/LAPACK++ on GPU yet anyway. Thus, we can simply use the CPU versions of those modules.
2022-06-08Fix: ABLASTR CMake Build (macOS) (#3173)Gravatar Axel Huebl 1-1/+1
Fix ABLASTR `WarnManager` build target.
2022-06-08AMReX: Weekly Update (#3170)Gravatar Axel Huebl 5-5/+5
2022-06-08ABLASTR: Move Communication Utilities (#3167)Gravatar Axel Huebl 21-282/+346
* Move: WarpXCommUtils to ABLASTR * Update Usage Locations * Refactor: `WarpX::do_single_precision_comms` Do not use a global from WarpX in ABLASTR routines.
2022-06-07Merge `FillBoundary` and `NodalSync` (`OneStep_nosub`, `OneStep_sub1`) (#3013)Gravatar Remi Lehe 9-113/+122
* Add argument for synchronizing nodal points * Add the option to overridesync in FillBoundaryE / FillBoundaryB * Remove explicit synchronization * Cleanup calls to nodal synchronization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Improve const Correctness * Cleaning * Merge NodalSync and FillBoundary First Restarting the implementation from scratch. To-do: remove redundant FillBoundary calls. * Merge Only for OneStep_nosub and OneStep_sub1 * Fix Checksums of Python_wrappers * Define sync_nodal_points as WarpX Private Member Variable * Keep Calls to NodalSync for B * Keep Calls to NodalSync for F * Reset Benchmark of reduced_diags_single_precision * OneStep_sub1: Remove All Calls to NodalSync * OneStep_nosub: Remove All Calls to NodalSync * Reset Benchmark of divb_cleaning_3d Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-06-07Docs: AMReX Debug Moved (#3164)Gravatar Axel Huebl 1-1/+1
The link top the AMReX debugging section in the manual moved.
2022-06-06build image - test fix for 1D builds (#3162)Gravatar Roelof Groenewald 1-4/+9
2022-06-06Release 22.06 (#3161)Gravatar Axel Huebl 11-13/+13
* AMReX: 22.06 * PICSAR: 22.06 * WarpX: 22.06
2022-06-03Vay Deposition: Add Cumulative Sums (#2958)Gravatar Edoardo Zoni 8-0/+399
* Implement Cumulative Sum * Implement Subtraction of Average * Fix Bug, Remove Abort w/ Periodic Single Box * Enforce Consistency w/ Periodic Single Box * Cleaning * Cleaning * Fix Bugs * Cleaning * Compute Cumulative Sums Before Sync * Always Loop Over Full Boxes * MFIter without Tiling * Cleaning * Do Not Store Cumulative Sums * Add Two-Particle Test (3D) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Set 3D Velocity in CI Test * Precompute Normalization Factors * Add Two-Particle Test (2D) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-06-03Doc: adding few more references on numerical algorithms (#3158)Gravatar Olga Shapoval 1-4/+16
* Added assymetrical PSATD equations. * Fixed typos. * Added few more references on numerical algorithms implemented in WarpX. * Fix Extra Changes
2022-06-02Fix: WarnManager (#3159)Gravatar Axel Huebl 1-2/+2
Fix concurrently landing PRs while moving the warning manager.
2022-06-02Move warning logger in ablastr (#3154)Gravatar Luca Fedeli 33-308/+400
* initial work to move the Warning Logger into ablastr * progress with warn manager class * moved Warning Logger in ablastr * fixed bugs * Fix: `SpectralFieldDataRZ.cpp` Missing include for `WarpX::getCosts(lev);` Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-06-01Change Default for `psatd.current_correction` (#3092)Gravatar Edoardo Zoni 5-43/+64
* Change Default for `psatd.current_correction` * Fix CI Tests * Add Warning * Update Documentation * Current Correction Not Implemented for Multi-J
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