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2021-08-26Improvement in electrostic field solve when using EB & a small refactoring ↵Gravatar Roelof Groenewald 1-0/+1
of the Electrostatic solver (#2143) * refactored parts of the electrostatic solver to allow an outside Poisson solver to be installed * added callback to install a Poisson solver that can be used instead of the MLMG solver * added call to the poissonsolver callback if one is installed and updated ElectrostaticSolver.cpp to calculate the electric field directly in amrex if EBs are used * fixed issue causing ElectrostaticSphereEB test to crash * fixed the logic for when to call computeE * added function to allow charge density to be deposited in rho_fp from outside WarpX * fixed inconsistency between labframe and relativistic electrostatic simulation setup * fixed typo * fixed issue that caused ElectrostaticSphere test to fail and removed unnecessary call to multiply E_y by -1 when doing a 2d simulation * revert edit to error handling string * changes requested during PR review * additional change requested during PR review * fixed typo * revert unnecessary changes
2021-08-26Laser-Ion Example: Fix Histogram Functs (#2232)Gravatar Axel Huebl 1-4/+4
Avoid `sqrt(0)` and `1/sqrt(0)` operations in the inputs for the 2D3V Laser-Ion Acceleration example. Those can raise floating point exceptions and NaN's for resting particles.
2021-08-26Particle Unit Conversion: Generalize (#2223)Gravatar Axel Huebl 5-74/+121
Generalize the member to convert the internal proper velocity to SI momentum and back. This is needed for BTD diagnostics, where we have a less specialized but pinned AMReX particle container, which does not have this method.
2021-08-26add include to fix compiler error (#2237)Gravatar Corey Wetterer-Nelson 1-0/+1
2021-08-26Update AMReX: Parser, SENSEI (#2236)Gravatar Axel Huebl 4-4/+4
Update AMReX to pull in new changes about: - local variables in the parser are not reported as undefined - SENSEI fixes on AMRLevel (now truly opt-in)
2021-08-26Fix SENSEI & Ascent component in AMReX.cmake (#2235)Gravatar Corey Wetterer-Nelson 1-2/+2
* fix sensei component name in AMReX.cmake * CMake: Fix Ascent/Conduit Component Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-25Multi-J: Optimize Allocations of rho MultiFabs (#2224)Gravatar Edoardo Zoni 6-19/+22
* OneStep_multiJ: Always Deposit rho in Component 0 * For Multi-J Algo Allocate only 1 Component Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-08-25GetPosition 2D3V: y=0 (#2233)Gravatar Axel Huebl 2-9/+16
In 2D3V, we currently assigned the y position a signaling NaN in `GetPosition`, so that it cannot be used accidentially in functions. When we call parser functions, this value is copied even if it is not used, raising the signaling NaN. Rethinking the strategy, we can write more general inputs files if we instead write a sensible default for `y` in 2D3V: `y=0`. So this PR changes the default, which also fixes the issue.
2021-08-25rearranging the loops (#2231)Gravatar Lorenzo Giacomel 1-22/+15
2021-08-25Avoid Unnecessary FFTs of rho (#2234)Gravatar Edoardo Zoni 1-2/+6
2021-08-25Fix: Missing Include Guards (FWD) (#2226)Gravatar Axel Huebl 19-20/+112
* Fix: Missing Include Guards (FWD) All header files need include guards to avoid double definitons. * Fix copy-paste guard
2021-08-24Alphabetized and added PR to glossary (#2228)Gravatar Tiberius Rheaume 1-2/+3
2021-08-24WarpXComm.cpp: Fix Bug (Uninitialized MultiFabs) (#2230)Gravatar Edoardo Zoni 1-0/+6
2021-08-24Docs: Fix Summit Python (#2227)Gravatar Axel Huebl 1-1/+1
We cannot use an anaconda base package, since anaconda ships its own libstdc++ for its compiler stack, which is not compatible with our compiler choice.
2021-08-24Avoid an NaN in collision module (#2225)Gravatar Yinjian Zhao 1-2/+7
* Update inputs_3d * Update inputs_2d * Update inputs_2d * Update inputs_3d * fix nan
2021-08-23Use the function `SyncRho` and the array `rho_fp` in the Electrostatic ↵Gravatar Remi Lehe 2-16/+8
solver (#1811) * Use `SyncRho` in Electrostatic solver * Reuse rho_fp arrays * Allocate arrays for rho * Fix unused variable * Fix bug in rho deposition * Only use rho_fp in lab-frame Poisson solver * Update test cases * Incorporate PR comments
2021-08-23Enable restart with PSATD (#1367)Gravatar Remi Lehe 6-9/+98
* Enable restart with PSATD * Add new restart test * Add new input file * New CI Test: Fix Inputs, Fix Analysis Script * Reuse input for Restart with FDTD * Read time_of_last_gal_shift from Checkpoint * Upload Benchmark for restart_psatd * Update Benchmark for restart_psatd Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2021-08-23Ascent/SENSEI: Add Profiler (#2204)Gravatar Axel Huebl 2-0/+15
* Ascent/SENSEI: Add Profiler Add overall write profilers to Ascent & SENSEI. Add detailed profile for sub-operaions (blueprint, publish, execute) to Ascent as well. * Simplify One-Time Profiler Vars
2021-08-23Check for unused WarpX environment variables when compiling (#2208)Gravatar Michael Kieburtz 1-21/+27
* Added check for unused 'WarpX' environment variables * Changed the approach of this - Go through environment variables as they are used to set cmake flags, and then check any remaining if they start with warpx. * Improved the warning message Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-23Scalar field interpolator from grid to particle position (#2221)Gravatar Roelof Groenewald 4-80/+133
* refactored distance to EB calculation to have a more general function to interpolate from a scalar field on the grid to a given position * changed RZ error message to general interpolation function * changed function names to specify that scalar field interpolation is for a nodal field only
2021-08-23AMReX/PICSAR: Weekly Update (#2222)Gravatar Axel Huebl 4-4/+4
Weekly update to latest AMReX. No changes in PICSAR.
2021-08-23No particle resorting when no species (#2136)Gravatar Revathi Jambunathan 1-16/+21
* default sort interval for particles if there are not species * declare parmparse Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * fix eol * define and set sort_interval default to -1 and then reset them to 4 for GPU, -1 for CPU if there are species/lasers in the input Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-08-23Docs: Cori PICMI Instructions (#2219)Gravatar Axel Huebl 1-24/+94
* Docs: Cori PICMI Instructions Too tricky to get right to just cross-link - add documentation how to build & run PICMI interfaces on Cori. * Link: Jupyter Instructions
2021-08-23Evolve: Reorder py_afterstep and cur_time break (#2213)Gravatar Peter Scherpelz 1-10/+13
2021-08-20Added transform of fields from lab to boosted frame (#2201)Gravatar David Grote 3-8/+58
2021-08-20Allow Silver-Mueller boundary conditions to only be applied in certain ↵Gravatar Remi Lehe 6-66/+57
directions (#2220) * Apply Silver-Mueller boundary only in requested direction * Include a test with independent Silver-Mueller boundary conditions * Correct typo in implementation
2021-08-20Docs: OLCF ADIOS2 Currently BrokenGravatar Axel Huebl 1-1/+1
Tickets open: - OLCFHELP-3319 - https://github.com/ornladios/ADIOS2/issues/2836
2021-08-20Updated the installation instructions (#2218)Gravatar Michael Kieburtz 1-1/+1
2021-08-20Particle boundary scrape (#2124)Gravatar Andrew Myers 18-28/+462
* Some prelimary refactoring. * missing header * implement scraping particles that leave the domain boundaries into buffers * fix tabs * missing return * merging * remove redefinition * functor to work around cuda bug. * handle 2D * Add support for EB buffer * protect for AMREX_USE_EB, static_assert that EB and RZ aren't both on. * fix unused * add inputs file * add test * fix bugs, remove print * fix test * fix test path. * remove no-op code * adding clear particles method * attempt at adding time stamp * Use integer step number instead of physical time to timestamp particles; also put shared code into named functor. * move call to before apply boundary conditions * use more descriptive inputs parameter * Update Source/Particles/ParticleBoundaryBuffer.cpp * fix comp bug * move CopyAndTimestamp to cpp file * also move IsOutsideProblemDomain functor * Rename to m_particle_boundary_buffer - Name: currently only used for boundary scraping - Singular: only one instance * Fix missing EOF newline * Typo: author * Param Read / Init: Cleanup For Simplify Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-20Improved error handling when the libwarpx shared object library can't be ↵Gravatar Michael Kieburtz 1-2/+7
loaded (#2215) * Improved error handling when the libwarpx shared library can't be loaded * Removed extra newline * Improved check and ended program on error
2021-08-20Docs: Summit with RHEL8 (#2216)Gravatar Axel Huebl 1-16/+13
Summit has undergone a major software update to RHEL8. The default compilers and CUDA version have been modernized, among others providing C++17 support by default. Also, our scientific I/O stack is now system-provided, thanks to our Spack and E4S efforts :tada: Please update your `warpx.profile` on Summit, re-build your Python virtual environment and re-compile your executables.
2021-08-20Add plot_raw_rho in parameters doc (#2212)Gravatar Neïl Zaim 1-0/+5
* add plot_raw_rho in parameters doc * Update Docs/source/usage/parameters.rst Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
2021-08-19Ionization.H: Fix Bug (Division by Zero) (#2214)Gravatar Edoardo Zoni 1-1/+1
2021-08-19Implemented the parsing of integer input parameters (#2138)Gravatar David Grote 5-49/+180
* Implemented the integer parser * Updated comment * Updated documentation * Fixed unused parameters * Added some additional documentation * Reworked the implementation so that expressions are evaluated as real and rounded to the nearest integer * Fixed loop type * Copied over initial value of variable to the real instance * Update Source/Utils/WarpXUtil.cpp make result const * Update Source/Utils/WarpXUtil.cpp make result const * Update Source/Utils/WarpXUtil.cpp Fix comment * Added safeCastToInt * Fixed adding of safeCastToInt * Cleaned up safe casting routine * Added parsing of more integer inputs * Cleaned up the integer parser, removing unneeded cast from int to real * Made x a const in safeCastToInt Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-18Bug fixed: looping over all species now within `OneStep_multiJ` (#2207)Gravatar Olga Shapoval 1-6/+4
* Bug fixed: looping over all species now within 'OneStep_multij' * Bug fixed: looping over all laser particles within DepositCharge in multi-J
2021-08-18Rho Diags: Do Not Allocate `rho_fp/cp`, Remove `plot_rho`, `setplot_rho` (#2203)Gravatar Remi Lehe 6-32/+7
2021-08-18update use-sensei flag (#2192)Gravatar Corey Wetterer-Nelson 15-36/+51
* update use-sensei flag also add FlushFormatSensei.cpp to CMakeLists * CMake: WarpX SENSEI Option Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-18openPMD-api: 0.14.2 (#2150)Gravatar Axel Huebl 14-27/+23
This updates our requirements to openPMD-api 0.14.2+ Among others, this release introduced resizable data sets, which we will soon use for particle backtransformed diagnostics.
2021-08-17CI: Cancel Prev. GH Action on Push (#2202)Gravatar Axel Huebl 7-0/+28
Save CI resources by canceling already running or waiting builds if a PR is updated. This was previously only done for Azure and now also for GH actions.
2021-08-16Minor fix to the documentation of the plasma lens (#2200)Gravatar Remi Lehe 1-1/+1
2021-08-16Update Scripts: .ini file (#2191)Gravatar Axel Huebl 2-0/+48
Update regression tester .ini files as well in weekly/release updates of AMReX and PICSAR.
2021-08-16Use less guard cells in ParallelCopy of refined level's UpdateAuxilaryData ↵Gravatar Neïl Zaim 1-8/+24
(#2144) * Use less guard cells in ParallelCopy of refined level's UpdateAuxilaryData * Update Source/Parallelization/WarpXComm.cpp * Add inline comments and use explicit type for ng_src Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-08-16Multi-J (Hybrid): Fix Bug with Current Centering (#2181)Gravatar Edoardo Zoni 1-2/+4
2021-08-16do_pml should not be parsed anymore. (#2183)Gravatar Revathi Jambunathan 23-61/+25
* do_pml not parsed. remove code that was added to support both types of boundary interface * add paranthesis * fix eol and move to BackwardCompatibility * missing semicolon * Update Source/WarpX.cpp * clean input files in examples * delete do_pml in performance test input * fixing an example input file in docs * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * cleaning up docs * Update Docs/source/usage/parameters.rst * fix eol Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-08-16AMReX/PICSAR: Weekly Update (#2199)Gravatar Axel Huebl 4-6/+6
Weekly update to latest AMReX. No changes in PICSAR.
2021-08-16Docs: Summit Ascent Moved (#2195)Gravatar Axel Huebl 1-1/+1
Raider is now Twix.
2021-08-16Fixed issue where GPU runs would continually print 're-sorting particles' ↵Gravatar Kevin Z. Zhu 1-1/+3
even with verbose turned off (#2197)
2021-08-13Docs: Fix Cori URL (404) (#2194)Gravatar Axel Huebl 1-1/+1
2021-08-13Implemented new style BTD in picmi (#2187)Gravatar David Grote 1-0/+87
* Implemented new style BTD in picmi * Added rho_species. Added documentation
2021-08-13WarpX::Version: Not Empty (#2193)Gravatar Axel Huebl 1-6/+12
Make sure we do not return an empty string in `WarpX::Version()`. In some situations, e.g., in CI/run_test.sh, the macro for the `WARPX_GIT_VERSION` version in GNUmake is set but empty. ` Since empty versions are problematic for HDF5 attributes and confusing anyway, we return a proper `"Unknown"` in such a situation now, too. Detected as bug in #2150 X-ref: - https://github.com/openPMD/openPMD-api/pull/1087 - https://github.com/openPMD/openPMD-api/pull/979
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