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2021-01-22Fix number of guard cells in PML with 2D PSATD (#1648)Gravatar NeilZaim 1-2/+13
2021-01-21Start: PerformanceHints After Init (#1630)Gravatar Axel Huebl 2-0/+38
Start a helper routine that gives performance hints after initialization of the simulation.
2021-01-21Define: _OPENMP -> AMREX_USE_OMP (#1520)Gravatar Axel Huebl 43-111/+110
* Define: _OPENMP -> AMREX_USE_OMP Replace the define check of `_OPENMP` with the explicit backend control of `AMREX_USE_OMP` for parallel constructs. Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency pulls it in for linear algebra, I/O, etc. This can led to confusion if the user explicitly requested a serial build. Also, we might want to use OpenMP functionality here and there for auxiliary functions w/o having to use the AMReX OpenMP backend, i.e. because we compile for GPUs. * Add missing amrex::Gpu::notInLaunchRegion
2021-01-20openPMD: Particle Filter (Container) (#1632)Gravatar Axel Huebl 4-62/+147
* openPMD: Particle Filter (Container) A fresh implementation of particle filters for openPMD diagnostics using the generalized `PhysicalParticleContainer` approach that we also use in plotfiles :tada: * Ion Example: Filter & Coarsen Test diagnostics filter & coarsen functions in CI. Test reduced diagnostics (histograms).
2021-01-20openPMD: ionizationLevel (#1622)Gravatar Axel Huebl 2-63/+118
* openPMD: ionizationLevel Write out the ionizationLevel with openPMD. * openPMD Record Repetitions: Use Lambdas
2021-01-20Fix FilterFunctor in non-3D (#1633)Gravatar Axel Huebl 1-3/+3
Fix an out-of-bounds access to positions in 2D & RZ for filter functors.
2021-01-20Fix 2D: ParticleHistogram (#1635)Gravatar Axel Huebl 1-3/+3
Fix out-of-bounds access in particle histogram in non-3D.
2021-01-20SpeciesProperties: C, N, O, Cu (#1638)Gravatar Axel Huebl 4-68/+146
* SpeciesProperties: C, N, O, Cu Add more ionic species as pre-defined particle species. * Cu: Add to Ionization Energies
2021-01-19Distribution mapping and cost plotting (#1444)Gravatar Michael E Rowan 7-0/+440
* Distribution mapping and cost plotting Cleanup Cleanup Cleanup EOL Unused import * Cost initializes to 0.0 * plot slices of 3D * WIP * WIP docs * docs * docs * docs * docs * docs * docs * docs * docs * EOL
2021-01-19Add Superparticle version of getParticlePosition. (#1640)Gravatar Andrew Myers 1-7/+34
* Add Superparticle version of GetParticlePosition. * move unpack_particle to a free function and rename * no longer need SuperPType * Update Source/Particles/Pusher/GetAndSetPosition.H * remove templating from get_particle_position * remove template * Add missing include Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-15Unused Params: Check after Step 0 (#1596)Gravatar Axel Huebl 1-0/+9
An early check for unused parameters after the first step.
2021-01-15Fix bug in momentum-conserving interpolation function with MR (#1624)Gravatar Edoardo Zoni 2-15/+20
* Fix bug in momentum-conserving interpolation function * Reset checksum benchmark for CI test momentum-conserving-gather
2021-01-15Handle units properly in the particle filter function. (#1598)Gravatar Andrew Myers 2-10/+29
* Handle units properly in the particle filter function * have the particle filter func work in normalized units. * need to convert units before * Apply suggestions from code review
2021-01-15openPMD: 0.13.1 (#1620)Gravatar Axel Huebl 1-1/+1
2021-01-15Lassen (LLNL): HDF5 (#1629)Gravatar Axel Huebl 1-1/+2
2021-01-15LLNL: Newer CMake (#1625)Gravatar Axel Huebl 2-2/+2
2021-01-14Unify intervals notation (#1485)Gravatar NeilZaim 71-133/+178
* Unify intervals notation * Fix diagnostic intervals with PICMI * Use new syntax in updated Larmor test * Update PICMI to comply with the standard * Update new hybrid test * Update particles_in_PML test input files
2021-01-14replace some naked new with unique_ptr (#1627)Gravatar Luca Fedeli 2-7/+8
2021-01-14minor: fix typo in Juwels doc (#1628)Gravatar MaxThevenet 1-1/+1
2021-01-14fix warning raised by clang-tidy (#1626)Gravatar Luca Fedeli 1-2/+1
2021-01-12update CoriGPU build instruction in docs (#1617)Gravatar Revathi Jambunathan 1-1/+1
2021-01-12Remove unused functions "ExchangeWithPml..." (#1616)Gravatar Edoardo Zoni 2-42/+0
2021-01-12Fix some other warnings (#1618)Gravatar Luca Fedeli 10-69/+81
* fix warnings * fixed bug
2021-01-12Parser: Flex Prefix (#1615)Gravatar Axel Huebl 9-172/+691
* Parser: Flex Prefix Add a prefix to all flex symbols in the parser. This ensures that in builds with complex dependencies, which might also use flex for their own purposes, no symbol collisions occur. * Parser: Flex Rebuild * Flex Prefix: Update Parser Usage * Parser: Fix prefixes * Parser: Flex Rebuild Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
2021-01-12Fix some double-->float warnings in NCIGodfrey table (#1610)Gravatar Luca Fedeli 2-431/+445
* fix double-->float warnings in NCIGodfrey table * Revert "fix double-->float warnings in NCIGodfrey table" This reverts commit f094c12d0208439d141161eeb1f5cb5829472193. * fix double-->float warnings in NCIGodfrey table * add missing header * bugfixing * now using literal _rt instead of amrex::Real * fixed bug
2021-01-11New reduced diag: maximum charge densities (#1535)Gravatar NeilZaim 16-35/+286
* New reduced diag: maximum charge densities * Apply suggestions from code review Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com> * Update benchmark and apply suggestions from review Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
2021-01-11For python regression tests, fix the setup step (#1611)Gravatar David Grote 2-9/+9
The option "--prefix=" was added to the setup since on some systems "--prefix" is set by default and this conflicts with "--user".
2021-01-11Add electrostatic to picmi (#1548)Gravatar David Grote 2-5/+28
* Update ElectrostaticSolver in picmi * Added relativistic option to picmi ElectrostaticSolver * Update PICMI version * Fix electrostatic with picmi Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-01-11Fix some warnings (#1612)Gravatar Luca Fedeli 13-146/+165
* fixed some warnings * add missing files * fixed bug * fix several other warnings * add missing include * fixed bug * fixed bug * fixed bug * fixed bug
2021-01-08Avoid stringent assert statement on GPU (#1597)Gravatar Remi Lehe 1-2/+22
* Avoid stringent assert statement on GPU * Fix Pointer Member Access * fix nGrow with Vector * Update Source/Particles/WarpXParticleContainer.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-01-08Set laser initiation in RZ to be 3D (#1550)Gravatar Igor Andriyash 3-57/+57
* set diffraction in gaussian laser initiation in RZ to be 3D instead of 2D * fix whitespace * added proper conditions for RZ geometry in LaserProfileFromTXYEFile * reset benchmark for LaserAccelerationRZ because better laser initialization Co-authored-by: Igor Andriyash <igor.andriyash@ensta-paris.fr> Co-authored-by: Tools <warpx@lbl.gov>
2021-01-07Implemented update without rho in RZ spectral solver (#1569)Gravatar David Grote 9-32/+71
* Implemented update without rho in RZ spectral solver * Updated documentation for update_with_rho for RZ * Tiny fix in GalileanPsatdAlgorithmRZ reordering declarations * In Langmuir_multi_rz_psatd, set update_with_rho = 1
2021-01-07fix some unused variables (#1606)Gravatar Luca Fedeli 2-0/+6
2021-01-07CI: Intel ICX/ICPX (#1608)Gravatar Axel Huebl 1-0/+38
* CI: Intel ICX/ICPX Add coverage for Intels icx/icpx compilers. Those are the next-gen intel compilers, while icc/icpc are considered "classic" (read as: legacy). * Manually work-around dependency * Explicit release selection * remove unnecessary newline * remove unnecessary newlines (more) * Add moar random dpcpp packages * Start-over: assume it's in dpcpp * Fix C Compiler Detection * fix eol whitespace * More C Compiler Maskerading * Typos in default std * Fix backend selection (copy-pasted)
2021-01-07Cleaned calculation of current time in analysis scripts (#1609)Gravatar David Grote 3-3/+3
2021-01-04openPMD-api: 0.13.0 (#1601)Gravatar Axel Huebl 3-3/+3
2021-01-04LGTM: Fix & Modernize C++ Build (#1603)Gravatar Axel Huebl 1-14/+14
Modernize and fix LGTM analysis.
2021-01-03Reconfigured the collision classes to allow for generalization (#1583)Gravatar David Grote 13-166/+307
* Reconfigured the collision classes to allow for generalization * Added literals to PairWiseCoulombCollision * Minor cleanup of PairWiseCoulombCollision.cpp, removing query of ndt * Add boilerplate to CollisionBase class * Fixed white space in CollisionBase.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-03Docs: MR Ratio (#1589)Gravatar Axel Huebl 1-1/+15
Document the experimental mesh-refinement ratio option.
2021-01-02Cori: Newer CMake (#1599)Gravatar Axel Huebl 1-1/+1
Use a newer CMake on Cori. Needed by upcoming openPMD-api releases (and provides solid new `FindPython.cmake` support that goes brrrr).
2020-12-23Use PML diagonal components only with div cleaning (#1592)Gravatar Edoardo Zoni 6-57/+121
* Use PML diagonal components only with div cleaning * Apply @RemiLehe's suggestions and simplify allocations
2020-12-22Fix: PSATD + CUDA build (#1595)Gravatar Axel Huebl 3-7/+19
2020-12-21Use correct PML sigma coeffs depending on staggering (#1573)Gravatar Edoardo Zoni 2-75/+374
* Use correct sigmas for E damping * Use correct sigmas for B and F damping * Fix few compiler warnings in 2D * Use IntVect instead of GpuArray in device code
2020-12-21Fix particle injection position at restart (#1590)Gravatar Revathi Jambunathan 3-0/+5
* IO current injection position for checkpoint at restart * adding current injection position at the end of WarpXHeader file to stay compatible with yt.
2020-12-21Added phi to raw plots (#1591)Gravatar David Grote 1-0/+3
2020-12-21Generalize some interpolation functions for MR (#1585)Gravatar Edoardo Zoni 2-157/+65
* Pass refinement ratio as argument to interpolation functions * Use new general interpolation function
2020-12-21Fix: PSATD Comm. Runtime Switch (FDTD) (#1588)Gravatar Axel Huebl 3-98/+98
* Fix: PSATD Comm. Runtime Switch (FDTD) Fix a missing PSATD runtime conversion in communication. This switch could have potentially influenced FDTD simulations if PSATD was compiled but not used. Co-authored-by: David Grote <grote1@llnl.gov> * WARPX_USE_PSATD in WarpX.cpp: Fixes Fix more logic compile-time bugs that should be runtime. * Read algo.maxwell_solver early * Fix: Use-After-Free Co-authored-by: David Grote <grote1@llnl.gov>
2020-12-18CI: Fix Brew CMake (#1586)Gravatar Axel Huebl 1-1/+1
2020-12-18Fix bug in interpolation function used with MR (#1584)Gravatar Edoardo Zoni 3-6/+6
* Fix bug in interpolation function * Reset benchmarks
2020-12-17swap alpha coefficients for Ey-update (#1580)Gravatar Revathi Jambunathan 2-14/+14
* swap alpha coefficients for Ey-update * Update checksum with fixed alpha swap * Fix benchmark file name Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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