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2021-02-02Always synchronize nodal points of PML MultiFabs (#1669)Gravatar Edoardo Zoni 4-9/+63
* Always synchronize nodal points of PML MultiFabs * Reset benchmark for CI test pml_x_psatd * Use new separate functions NodalSyncPML
2021-02-02fixTypo for pml has particles parameter for docs (#1671)Gravatar Revathi Jambunathan 1-2/+2
2021-02-01remove semicolons (#1662)Gravatar Luca Fedeli 1-5/+5
2021-02-01Remove redundant "do_qed" option in inputfile (#1667)Gravatar Luca Fedeli 9-82/+21
* removed redundant do_qed option in inputfile * fixed bug
2021-01-31scipy 1.5+ (#1670)Gravatar Axel Huebl 1-1/+1
Sufficient since it was last release in december and works well. The 3.5 release series still builds wheels for Python 3.6 for Ubuntu oldstable (18.04).
2021-01-31requirements.txt: fix overspecification (#1668)Gravatar Axel Huebl 2-4/+4
I accidentally added the patch-level for version-compatible matching This removes the patch-level for `~=` matching for the packages that have a >=1 major version already.
2021-02-01parameter.rst fixes (#1663)Gravatar Michael E Rowan 1-14/+12
2021-02-01fix inconsistent formatting (#1666)Gravatar Michael E Rowan 1-2/+2
2021-02-01[mini-PR] Add particle tiling documentation (#1665)Gravatar Michael E Rowan 1-0/+4
* tiling wip * do_tiling documentation * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
2021-01-29make sure we redefine the tmp particle tiles when we load balance. (#1658)Gravatar Andrew Myers 4-6/+17
2021-01-29Reset broken benchmark for CI test initial_distribution (#1661)Gravatar Edoardo Zoni 1-7/+7
2021-01-27Updates for electrostatic solver (#1604)Gravatar David Grote 3-40/+49
* Fix electrostatic solver with momentum conservation * Fix electrostatic, adding call to FillBoundaryAux * For electrostatic, removed unneeded extra calls to UpdateAux and FillBoundary * For electrostatic, calculate fields at the end of the time step * Updated ElectrostaticSphere analysis script to use fields from end of time step
2021-01-27Modern setup.py: CMake-Driven, Multi-Dimensional (#1647)Gravatar Axel Huebl 6-2/+302
This adds a new, project-centric setup.py file. With this file, all dimensions (2D, 3D, RZ) of WarpX can be built and packaged at once, using the CMake build logic. Build & install: ```bash pip wheel -v . pip install *whl ```
2021-01-27Take time step into account to compute guard cells for J and rho (#1607)Gravatar Edoardo Zoni 10-71/+112
* Use IntVect for ng_J and ng_rho * Compute guard cells for J and rho based on dt * Reset some CI benchmarks * Fix rebase commit * Add back +1 cell for rho: fix remaining out-of-bound accesses * Simplify ASSERTS using new interface of amrex::numParticlesOutOfRange
2021-01-27Add filter for particle histogram (#1643)Gravatar NeilZaim 8-21/+86
* Add filter for particle histogram * Update benchmarks * Update benchmark again * Use serialize_ics in test + proper usage of RandomEngine * Laser-Ion Acc. (2D3V): Test Hist Filter Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-26Start Embedded Boundary development (#1641)Gravatar Weiqun Zhang 12-1/+93
* Start Embedded Boundary development Modify the build system for embedded boundary (EB) support. Currently EB is a compile time option that must be explicitly enabled. For GNU Make, one can enable it with `USE_EB=TRUE`, whereas for CMake, `-DAMReX_EB=ON`. Later we could decide to enable EB by default with all regular geometry. Add a simple geometry initialization function, WarpX::InitEB. By default, the geometry is all regular. A few basic types such as box, cylinder, plane, sphere, etc. are supported via ParmParse runtime parameters. See `amrex/Src/EB/AMReX_EB2.cpp` for more details. Later, we could build more complex geometry using constructive solid geometry (CSG). ( https://en.wikipedia.org/wiki/Constructive_solid_geometry ) See `amrex/Tutorials/EB/GeometryGeneration` for an example of CSG. There is also a STL ( https://en.wikipedia.org/wiki/STL_(file_format) ) approach under development in AMReX. Add a new member, m_factory, to WarpX class. This object can be used to obtain geometry information such as whether a cell is cut, edge centroids, etc. Currently we are not using these factories to build MultiFabs for field data to embed the geometry information into the data containers. We could do that later if it is needed or it makes things more convenient. Nevertheless, this should be sufficient to start the EB development of the field solver. It's not clear to me yet how many ghost cells are needed for the geometry information. It's currently one, and can be adjusted. In the future, when particle and embedded boundary interaction is considered, we can use `amrex::FillSignedDistance` function to obtain signed distance function on the nodes. With that information, one should be able to determine where and when a particle collides with the embedded boundary. * resize factory vector * CMake: Require AMReX_EB for embedded boundaries * Add AMReX_Config.H et al. Explicit includes are most robust to make sure defines are set with future refactorings. * rename Factory fieldFactory Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-26CI: Ubuntu-latest -> 20.04 (#1654)Gravatar Axel Huebl 2-2/+2
2021-01-26[mini-PR] Broken link to scripts (#1651)Gravatar Michael E Rowan 1-1/+1
2021-01-27Replace an always false test with an abort (#1655)Gravatar Luca Fedeli 1-3/+3
* replace always false test with abort * fix bug
2021-01-26Use pinned memory for tmp particles in diags. (#1644)Gravatar Andrew Myers 3-21/+45
* Use pinned memory for tmp particles in diags. * openPMD: pinned memory (tmp particles) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-01-22Cleaned up field diagnostic in picmi interface (#1649)Gravatar David Grote 1-11/+2
2021-01-22Add parameter for default galilean velocity (#1097)Gravatar Remi Lehe 4-8/+20
* Add parameter for default galilean velocity * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix bug in constructor of PhysicalParticleContainer * Use new input parameter in CI test Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2021-01-22Remove unused lines about particle filters (#1646)Gravatar NeilZaim 2-21/+0
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".
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