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2020-05-01openPMD: Fix no-MPI build (#968)Gravatar Axel Huebl 2-2/+12
2020-04-30Update Python docs (#960)Gravatar David Grote 3-7/+26
* Update Python docs Added more info for Cori. Added recommendation of using virtual environments. * Update Docs/source/running_python/how_to_run.rst Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov> Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
2020-04-30openPMD: Binary Suffix (#966)Gravatar Axel Huebl 1-0/+1
Add the binary suffix `.OPMD` to WarpX binaries.
2020-04-30Fix bug when compiling OpenPMD + 2D (#963)Gravatar MaxThevenet 1-4/+4
* WARPX_DIM_2D doesn't exist, this should be WARPX_DIM_RZ * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov> Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
2020-04-29CI: macOS Single Precision (#964)Gravatar Axel Huebl 4-48/+11
* CI: macOS Single Precision Add another compile with single precision on AppleClang. * AMReX' complex for everything This is nice and compliant and works on all platforms.
2020-04-29use direct deposition for nodal tests also on Garuda (#962)Gravatar MaxThevenet 1-2/+2
2020-04-29[Mini]Fix Langmuir_multi_nodal test case (#961)Gravatar David Grote 1-2/+2
* Fix Langmuir_multi_nodal test case Current deposition was changed from esirkepov to direct * Also use direct deposition for PSATD nodal Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
2020-04-28Style change to match the standard (#957)Gravatar Michael E Rowan 15-52/+52
2020-04-28Add checkpoint capability to new diags (#951)Gravatar MaxThevenet 7-15/+172
* Move checkpoint capability to new diagnostics * error if user asks custom output for checkpoint * eol * Apply suggestions from code review Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/WarpX.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-04-28Reduce size of test output (#857)Gravatar MaxThevenet 7-104/+50
* reduce size of qed_breit_wheeler_opt_depth_evolution * Update analysis_3d_optical_depth_evolution.py * Update analysis_3d_optical_depth_evolution.py * reduce size of Langmuir_multi and delete Langmuir_{x,y,z} * reduce ppc and filter fields dumped * finalize cartesian Langmuir tests * minor changes to python rz multimode * smaller restart test * reduce size of TwoParticle_electrostatic * smaller laser_injection test * revert changes in QED 3D BW test as it is done in another PR
2020-04-26minor code changes to remove warnings when compiling with gcc DEBUG=TRUE (#950)Gravatar MaxThevenet 7-87/+89
2020-04-24Read species distribution from OPMD - part 3 (#883)Gravatar L. Diana Amorim 5-37/+114
* Added <species>.profile=external_file and .profile_file * Added description of input parameters to Docs * Changed from profile to injection option for external file * Fix typo in amrex abort message (due to copy paste) * Added the OpenPMD use amrex abort message * Minor fix - not sure how to remove EOL issue * Tried to add AddExternalFileBeam functon to PhysicalParticleContainer * Trued to fix EOL white space issue * Added read/print species name from OPMD file * Fixed OpenPMD charge and mass read * Added number of particles in species * Added nparts and converted charge/mass units to SI * Fix to nr of particles * Added q_tot parameter to determine part weight * Added macroparticle's weight * Fixed std::int typo - use only int * Added read x,y and z + ifdef 3D * Added velocity of particles and stored in container * Converted velocities to SI * No need to specfy momentum distribution if external file is used * Update Source/Initialization/PlasmaInjector.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.H Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Particles/PhysicalParticleContainer.cpp Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * No need to include openPMD header yet * Fixed const in AddExternalFileBeam * Fix compatibility with read_opmd and read_opmd_2 * Corrected position and charge units/sign * Added Doc note and abort message for RZ * Fix typo and EOL * Minor fixes * Fixed details. Added fix to EOL - testing * Changed to physical_charge and explained it in Docs * Fix header extra openPMD include files * Removed additional debugging comments * Try doxygen again * Fix plasmainjector physical_q_tot * Change apart to auto (not long as in gaussian beam injection style) Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Correct for new type of npart Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja> * Removed Geant4 renormalization * Read openPMD file and checked its units * Trying to correct momentum information in plotfiles * Compilation error - > SegFault 11 * Added unitSI() to each position/momentum direction. Compilation SegFault * Re-structured code to use only once series.flush() * Commented out amrex::Print() s * Path to fix issue * Update after review * Chanegd <physical_q_tot> to <q_tot> and made it optional * Fixed documentation typo and re-organized it * Added const to npart as per reviewer recommendation * Fixed issue with velocity - which became momentum * Fixed 2D and 3D options + documentation * Implemented fixes from past reviewsand fixed duplicate entry in Docs * Fix auto in iterator in for loop * Added fixes according to reviewer * Revert "Added fixes according to reviewer" This reverts commit 0a485d83c28014c8b6f53a30f26719f23f89bad5. * Fixed IO block and reordered logic with Axel * Fix spaces Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2020-04-24Re-initialize diag functors after LoadBalance (#943)Gravatar Revathi Jambunathan 7-56/+89
* fixing bug to initialize CellCenterFunctor for Bx * new function to initialize diag functors called from regrid * add comments and clean * more cleaning * use of unique_ptrs to prevent memory leak * fixing eol * Apply suggestions from code review Co-Authored-By: MaxThevenet <mthevenet@lbl.gov> * rho_new in PSATD defined using unique_ptr * initialize field functor per level * adding a comment for input lev * more comments * clearning * comments * space in function when called * fix eol Co-authored-by: MaxThevenet <mthevenet@lbl.gov>