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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
2021-03-31CMake: Move CCache Message (#1853)Gravatar Axel Huebl 1-1/+3
2021-03-31More Output In `checksum.py` When Checksum Benchmarks Fail (#1845)Gravatar Edoardo Zoni 1-2/+10
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
2021-03-31Weekly Update: AMReX & PICSAR (#1843)Gravatar Axel Huebl 2-2/+2
* Weekly Update: AMReX & PICSAR ``` ./Tools/Release/updateAMReX.py ./Tools/Release/updatePICSAR.py ``` Updates AMReX to latest `devevelopment` commit (`0ab63f3f93950b5a90fb091c6eabbf3239886fcd`). No changes in PICSAR. * bump amrex again Co-authored-by: Andrew Myers <atmyers2@gmail.com>
2021-03-31Add USE_OPENPMD=TRUE To Run Test `LaserIonAcc2d` Locally (#1852)Gravatar Edoardo Zoni 1-1/+1
2021-03-30Remove the avg_aux fields (#1849)Gravatar Remi Lehe 18-121/+59
* 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
2021-03-30Tool `read_raw_data.py`: Handle Ghost Regions With Nodal/Yee Grids (#1851)Gravatar Edoardo Zoni 1-2/+9
* Read nghost as Numpy Array From String * Do Not Use non-tuple Sequence For Multidimensional Indexing
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 11-204/+459
* 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
2021-03-29CI: DPC++ apt clean (#1841)Gravatar Axel Huebl 1-2/+4
Save 1-2 GB by cleaning this out.
2021-03-26README: Project Dependencies & Communities (#1840)Gravatar Axel Huebl 1-0/+12
Add more badges to shout-out to communities & dependencies.
2021-03-25More Badges: Install, ECP (#1834)Gravatar Axel Huebl 1-3/+4
* More Badges: Install, ECP * update: funding ECP * haaands
2021-03-25CI: HIPCC as C Compiler (#1837)Gravatar Axel Huebl 1-5/+2
2021-03-24CI: HIP w/o MPI (#1836)Gravatar Axel Huebl 1-2/+5
HIP 4.1 introduces issues with C targets which break the MPI feature test in CMake's `FindMPI.cmake` for C.
2021-03-24add warning for Galerkin scheme (#1832)Gravatar Luca Fedeli 1-0/+5
2021-03-23Docs: HPC Updates (#1830)Gravatar Axel Huebl 8-49/+37
- fix minor typos in example commands - simplify/clarify `git clone` to be uniform - modernize Juwels section to CMake
2021-03-23README: More Badges, Beta (#1831)Gravatar Axel Huebl 1-3/+8
Add more badges to the README file (more badges, more creds, obviously). We will also declare the development phase from now on *beta* (21.04+) :tada:.
2021-03-23Docs: missing ::Gravatar Axel Huebl 1-1/+1
Fix a missing note.
2021-03-23Disable charge deposition for photons (#1825)Gravatar Remi Lehe 1-0/+12
2021-03-23Sphinx Documentation: Restructure (#1821)Gravatar Axel Huebl 85-897/+2738
The big restructuring & streamlining of our documentation.
2021-03-22CMake: Print Version (#1820)Gravatar Axel Huebl 6-8/+47
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.
2021-03-22CMake: Build AMReX with IPO/LTO (#1822)Gravatar Axel Huebl 2-1/+7
Add a verbose message if IPO is used and also build AMReX with IPO/LTO. WarpX binary size (default build, GCC 9.3.0 on x86_64 with Ubuntu 20.04): * no IPO: 217MiB * WarpX IPO, AMReX no IPO: 155MiB * both WarpX and AMReX with IPO: 127M
2021-03-22AMReX/PICSAR: Weekly Update (#1823)Gravatar Axel Huebl 2-2/+2
Update AMReX to 384ca2341889a8f1db78e87cb4b1735bd2d58554. No new changes in PICSAR.
2021-03-22Fix some formatting in parameters documentation (#1818)Gravatar Neïl Zaim 1-58/+58
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
2021-03-18DPC++: More Savings (#1813)Gravatar Axel Huebl 3-10/+18
- remove some binaries we do not use in CI - build shared to avoid any copies of AMReX
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
2021-03-17Docs: Sorting Defaults Changed (#1798)Gravatar Axel Huebl 2-3/+3
The sorting defaults changed to per-cell.
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 8-59/+77
* 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>
2021-03-16Add reference to WarpX slides in the acknowledge us section (#1796)Gravatar MaxThevenet 1-3/+20
* add reference to WarpX slides in the acknowledge us section * eol * replace WarpX citation with the 3-stage one in acknowledgement section
2021-03-16Boundary input - Periodic (#1730)Gravatar Revathi Jambunathan 8-1/+158
* 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 15-0/+375
* 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>
2021-03-16FFTW: CMakeConfig Support (#1765)Gravatar Axel Huebl 3-30/+95
Modern FFTW versions support CMake as an install method, which provides the legacy goodies (`.pc`) files and proper `FFTW3(f)Config.cmake` files for dependency propagation. Conda-forge uses the CMake-based method to deploy. Checking this, I realized the `.pc` files add unconditionally `libm` to the linker, which is wrong on Windows and fails the builds. Thus, forward looking we would search first for CMake based installs of FFTW and in case this search is not successful, we continue to search for the old Autotools logic and `.pc` files, which are still routinely generated by some package managers. But, due to an issue in FFTW3 3.3.9 on Linux/macOS with Autotools installs, we make `Config.cmake` file based search still opt-in for now.
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