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2021-04-01PSATD: use number of guard cells from input file in PMLs (#1451)Gravatar Neïl Zaim 1-13/+14
2021-04-01set default value for BTD buffer to 0 (#1862)Gravatar Revathi Jambunathan 1-0/+1
2021-04-01add buffer as input parameter (#1858)Gravatar Revathi Jambunathan 6-14/+36
max box size in virtual function define max box size add max box size as argument Update Source/Diagnostics/BTDiagnostics.cpp add buffer size to old BTD set max box size to buffer size only if it is small define buffer size and max box size correctly fix compilation error
2021-03-31paraview.pmd: write on close (#1860)Gravatar Axel Huebl 2-15/+29
Initially we wrote those on open. The problem was that writing this file depends on an existing directory structure, which is first created on earlierst on the first `flush()` and in case of extensive ADIOS buffering actually latest on `close()`. Since in backtransformed diagnostics (BTD) this flush happens very late. The directory did not exist and thus the creation of the helper file early on did fail (silently).
2021-03-31FlushFormatOpenPMD: Cleanup (#1861)Gravatar Axel Huebl 2-15/+14
2021-03-31Add Time-Averaged Fields To Raw Fields Output (#1859)Gravatar Edoardo Zoni 2-0/+26
2021-03-31Move KernelTimer to Parallelization (#1856)Gravatar Michael E Rowan 2-1/+1
2021-03-31fix bx used in amrexPArallelFor (#1855)Gravatar Revathi Jambunathan 2-12/+2
2021-03-30Remove the avg_aux fields (#1849)Gravatar Remi Lehe 16-87/+25
* Remove the avg_aux fields * Update 3D benchmark * Update benchmark in 2D * Initialize Bfield_avg_cp * Fix two whitespaces left out * Fix two more whitespaces left out Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-03-30we dont need warpx do_back_transformed_daig for field =1 (#1848)Gravatar Revathi Jambunathan 1-2/+0
2021-03-29openPMD: QED Attributes as scalars (#1777)Gravatar Axel Huebl 1-8/+8
Avoid writing QED particle attributes as scalars. Needs testing.
2021-03-29Regrid spectral solver during load balance (#1815)Gravatar Michael E Rowan 3-37/+210
* add PSATD support when remaking level * eol * update_with_rho * Update WarpXRegrid.cpp * Upate WarpXRegrid.cpp * Update WarpXRegrid.cpp * WIP * Cleanup * Remove * Add function to allocate spectral solver * EOL * spaces * Remove comment * Update documentation * eol * Remove function arguments * fix * Move lines into function * eol * amrex::Real * args
2021-03-29Add option for finite-order centering of currents (nodal to staggered) (#1763)Gravatar Edoardo Zoni 6-158/+407
* Start adding centering of current * Implement arbitrary order centering and split inputs * No need to define a brand new interpolation function * Update input file of hybrid CI tests * Clean up * Clean up more * Fix bug and clean up * Use current centering in two existing CI tests * Update documentation * Move Calls To UpdateCurrentNodalToStag Into SyncCurrent * Add Doxygen For New Function UpdateCurrentNodalToStag * Add Doxygen For New Functions Used For Stencil Coefficients * Finite-Order Centering of Currents Not Implemented With MR
2021-03-29Silver Mueller in RZ (#1804)Gravatar Lígia Diana Amorim 1-4/+81
* Added RZ Er, Et, Ez and Br, Bt and Bz * Answered my own question * Making Yee and cells domain check for RZ too * Added relevant coefficients * Derivative in z requires coefsz and n_coefsz * Bt computed with UpwardDz * UpwardDz might require CylindricalYeeAlgorithm.H * Added mode 0 Bz * Added higher-order modes for Bt * Added higher-order modes for Bz * Fix to EOLs * Fix typo * Added cylindrical specific parameters * Fix error of #endif * rmin also needed in RZ parameters * T_Algo needed for RZ -> different initialization in .H * Fix private / public function * Replacing T_Algo by CylindricalYeeAlgorithm * Fix typo * ParallelFor for Br, Bt and Bz separated * Compiled after removing unecessary Br * Changes suggested by reviewer * No need to compute r before if() * Corrected real and imaginary parts of Bz * Remove vscode file Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-03-29Class `PsatdAlgorithm`: Simplify Initialization of Coefficients (#1819)Gravatar Edoardo Zoni 2-616/+432
* Split Initialization Functions of Spectral Coefficients * Simplify Initialization of Coefficients Without Averaging * Do Not Store Coefficients C1,S1,C3,S3 With Averaging * Simplify Initialization of Coefficients With Averaging * Add amrex:: Prefix Following WarpX Style Guidelines * Match Names Of Coefficients With/Without Averaging * 'pow' Cannot Be Used in a Constant Expression * Update Doxygen Documentation
2021-03-23Disable charge deposition for photons (#1825)Gravatar Remi Lehe 1-0/+12
2021-03-22CMake: Print Version (#1820)Gravatar Axel Huebl 3-6/+6
Print the WarpX and PICSAR version to the terminal. Fetched from `git` as usual. Will use a proper tag-prefixed description as soon as we add tags in the git history.
2021-03-22Applied boost to single and multiple particle input (#1800)Gravatar David Grote 2-24/+43
2021-03-19Warnings: PSATD+RZ & More (#1814)Gravatar Axel Huebl 10-12/+26
* PSATD+RZ: Fix Warnings Fix a couple of warnings in PSATD + RZ. * BesselRoots: Missing Include & using * Kernel & Util: Unused Code & Var
2021-03-18LoadBalanceCosts reduced diagnostic set spatial indices to zero depending on ↵Gravatar Michael E Rowan 1-0/+8
dims (#1785) * Fix for diff spatial dims * eol * Update LoadBalanceCosts.cpp * Update LoadBalanceCosts.cpp * Restart CI
2021-03-18Move Python Callback function (#1793)Gravatar Remi Lehe 1-4/+5
2021-03-18Add option to deposit current at arbitrary time (#1810)Gravatar Remi Lehe 6-22/+37
* Introduce relative_time for deposition * Deposit current at arbitrary time * Update documentation * Combine parameters in DepositCurrent * Explicitly show the time at which the current is deposited
2021-03-18Use Clear Naming Standard for ParmParse Variables (#1809)Gravatar Edoardo Zoni 37-453/+452
2021-03-18Remove Wrong Parser Query in MultiParticleContainer.cpp (#1808)Gravatar Edoardo Zoni 1-1/+0
2021-03-17Replaced almost all nGrow with nGrowVect (#1801)Gravatar David Grote 27-52/+78
2021-03-17openPMD: Add ParaView .pmd Helper File (#1802)Gravatar Axel Huebl 2-13/+29
ParaView 5.9+ adds initial support for openPMD files. We need the filename passed to the `openPMD::Series` constructor as a little text helper file to open the files properly, this adds this.
2021-03-17Add option to specify a0 instead of e_max for the laser (#1770)Gravatar MaxThevenet 1-1/+14
* add option to pass a0 instead of e_max for the laser e_max xor a0 must be specified * update doc for laser a0 * a0: Update Examples Using all options so they are tested. * reset benchmarks (precision E0->a0) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-17KernelTimer cleaning (#1780)Gravatar Michael E Rowan 2-11/+10
* KnlTimer cleanup * Update KernelTimer.H * minor * Update Source/Particles/Deposition/CurrentDeposition.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-16Boundary input - Periodic (#1730)Gravatar Revathi Jambunathan 7-1/+145
* Read boundary and set periodicity, enumerate BC types, added support for periodic * eol * separate particle and field boudnary structs * Update comment for particle struct * the valid values are for field/particle * adding docs * eol * remove warning * add doc only for periodic * typo
2021-03-16Move laser particle container (#1792)Gravatar Remi Lehe 7-10/+5
* Move laser particle container * Update CMake file * Fix compilation errors
2021-03-16Implement Silver Mueller boundary conditions (#1766)Gravatar Remi Lehe 8-0/+178
* Add function definitions for Silver-Mueller boundary condition * Add test file * Implement Silver-Mueller equations * Add equations for Bz * Add equation in the z direction * Add equation for Bx * Add 3D implementation * Add documentation, automated tests, and warnings * Include second automated test and evaluate benchmark * Fix unused variable warning * Fix minor bugs * Update benchmark * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Incorporate review comments * Incorporate more suggestions Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-16Add timers in routines that depend on cell-related work (#1692)Gravatar Michael E Rowan 36-237/+461
* Add timers * eol * AtomicAdd * lev argument for getCosts * style * style * wip * eol * .ipynb * passing down lev * eol * passing lev * eol * Update Source/Particles/Collision/PairWiseCoulombCollision.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add for QED and ionization routines * eol * remove unneeded * mfi-->pti * move cost * eol Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-03-15Move multi-physics module out of `OneStep` (#1790)Gravatar Remi Lehe 1-27/+21
2021-03-15Clean-up OneStep function: Move error message at initialization (#1789)Gravatar Remi Lehe 2-15/+9
2021-03-12AddPlasma: Avoid a calculation resulting in NaN when num_ppc is 0 (#1787)Gravatar Luca Fedeli 1-3/+6
* avoid a NaN when num_ppc is 0 * fix style
2021-03-12fix unused variables (#1786)Gravatar Luca Fedeli 3-2/+17
2021-03-11Spectral Solver: Fix Allocation of rho_fp and rho_cp (#1779)Gravatar Edoardo Zoni 1-4/+0
2021-03-10Minor cleanup of RZ in collisions (#1774)Gravatar Remi Lehe 1-44/+34
* Minor cleanup of RZ in collisions * Clean-up indentation * Fix white space * Further cleanup of warnings
2021-03-10fix typo (#1773)Gravatar Luca Fedeli 1-2/+2
2021-03-10Spectral Solver: Remove Unused Header Files (#1778)Gravatar Edoardo Zoni 2-138/+0
2021-03-08Remove Temporary Custom Output for Reformatted BTD (#1726)Gravatar Revathi Jambunathan 4-179/+12
* add geometry object and plotfile variables for BTD * fixing buffer and snapshot definitions and emptying/refilling of buffers * Adding Plotfile capability for BTD * fix eol * add comments and remove commented line in OpnPMD * read header without bcast within io scope and modify fabname in first fabheader * remove tab * openPMD: BTD write support - open series only once - declare iteration in labframe only once - including fields & extents - use proper global lab-frame meta-data and write only once * remove TMP custom-ouput functions in reformatted BTD, clean commented-out-code
2021-03-04QEDInternals: replace amrex::Real with amrex::ParticleReal where appropriate ↵Gravatar Luca Fedeli 6-37/+48
(#1741) * Replace amrex::Real with amrex::ParticleReal where appropriate Co-authored-by: NeilZaim <49716072+NeilZaim@users.noreply.github.com>
2021-03-04RigidInjectedParticleContainer: clean duplicated code (#1752)Gravatar Luca Fedeli 1-8/+3
* avoid code duplication and implicit conversion from int* to bool * elimitate != nullptr
2021-03-04Implement averaged algo on staggered grids & merge spectral classes (#1544)Gravatar Edoardo Zoni 9-1188/+966
* Refactor and clean up some spectral classes * Abort when current correction or Vay deposition are not implemented * Implement general equations for averaged Galilean * Allocate averaged MultiFabs also when aux_is_nodal=1 and do_nodal=0 * Allocate +ngextra guard cells also for averaged MultiFabs * Make alias MultiFabs for averaged aux data * With averaging, interpolate from avg_fp (not fp) to aux * Fix some limits of the coefficients * Fix bug causing NaNs in spectral coefficients * Add 2D CI test with same analysis as nodal test * Add 3D CI test with same analysis as nodal test * Add limit that was not covered (knorm=0 && knorm_c!=0 && nu=0) * Allocate T2_coef only if Galilean algorithm is used * Allocate X4_coef only if Galilean algorithm is used * Remove extra ghost cell from 'avg_fp' MultiFabs
2021-03-04Remove extra ghost cell used with momentum-conserving gathering (#1758)Gravatar Edoardo Zoni 8-103/+80
2021-03-02ParticleContainer: Fix Unused Vars (#1756)Gravatar Axel Huebl 1-12/+0
Fix unused variable warnings in `PhyicalParticleContainer`.
2021-03-02GPU clock timer for measuring load balance costs (#1406)Gravatar Michael E Rowan 6-44/+177
* merge * wip * namespace * eol * cost * eol * fix * eol
2021-03-02CI: Always with FFTW/PSATD (#1587)Gravatar Axel Huebl 2-70/+69
* CI: Always with FFTW/PSATD Reduce build time by always building with FFTW and unifying PSATD tests. This also adds coverage for the case that we forget to make `#ifdef WARPX_USE_PSATD` runtime blocks, which can potentially be seen in FDTD runs now. * Remove worker with environment USE_WARPX_PSATD * Fix warpx_interp: Unconditional PSATD Fix the `warpx_interp` function to properly enable/disable PSATD logic based on runtime logic. 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>
2021-03-01RZ Poisson solver (#1744)Gravatar David Grote 2-5/+178
* Added RZ Poison solver * Added test case for RZ Poisson solver * Fixed intervals in RZ Poisson test case * Added RZ Poisson test to regression tests * Split ComputePhi into two routines, RZ and Cartesian * Add declaration of new functions Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-03-01Clean plotfile output for btd (#1723)Gravatar Revathi Jambunathan 1-7/+3
* add geometry object and plotfile variables for BTD * fixing buffer and snapshot definitions and emptying/refilling of buffers * Adding Plotfile capability for BTD * fix eol * add comments and remove commented line in OpnPMD * read header without bcast within io scope and modify fabname in first fabheader * remove tab * openPMD: BTD write support - open series only once - declare iteration in labframe only once - including fields & extents - use proper global lab-frame meta-data and write only once * make BTD plotfile path consistent with boosted plotfile path * same prefix code for openpmd and plotfile * Update Source/Diagnostics/WarpXOpenPMD.cpp * Update Source/Diagnostics/BTDiagnostics.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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