| Age | Commit message (Collapse) | Author | Files | Lines |
|---|
|
* Add pre-commit
Add basis for automated pre-commit checks.
Install locally via:
```bash
python3 -m pip install -U pre-commit
pre-commit install
```
See: https://pre-commit.com
* Cleanup: Whitespaces
* Cleanup: requirements.txt order
|
|
* added functionality to picmi.py to initialize MCC collisions from python runscripts
* bug fix and copyright declaration change
* add Boltzmann's constant to picmi.py
* added test for picmi MCC setup
* set diagnostic output name for test and cleaned up analysis.py
* fixed style issue with EOL white space after merge
|
|
* Added functionality to pass mpi comm from python script to amrex during initialization
* Fixed missing _ in MPI._sizeof()
* Added functions to get the current processor's rank and total number of processors
* Renamed MPI_Comm to _MPI_Comm_type and defined _MPI_Comm_type in except statement
* Updated comment to explain why mpi4py needs to be imported before loading libwarpx
* Removed ifdef flags that prevent amrex_init_with_inited_mpi from being declared when MPI is off
* Changed amrex_init_with_inited_mpi to be declared even when not using mpi, but will be defined to be functionally the same as amrex_init
* Defined MPI = None to signify whether MPI is used, to add another check when initializing amrex
* Changed ifdef blocks in WarpXWrappers.cpp/h to fix compile errors.
Added ifdef block to conditionally declare amrex_init_with_inited_mpi in WarpXWrappers.h to prevent compile error when not using MPI. Removed ifdef block to declare/define same function in WarpXWrappers.cpp since function needs to be declared even when MPI is not used, but will never be called in that case.
* Changed BL_USE_MPI to AMREX_USE_MPI and removed incorrect MPI=None statement
* Changed BL_USE_MPI to AMREX_USE_MPI
* Added test to verify correct passing of MPI communicator to amrex
* Added ability to pass mpi_comm to sim.step
* Change test to check for differeing outputs when passed different inputs
* Removed obsolete comments refactored program to use more shared code
* Refactored comments
* Updated description to match test
* Removed unecessary imports and updated comments
|
|
simulations (#1761)
* Update copyright notices
* allow specification of boundary potentials at runtime when using Dirichlet boundary conditions in the electrostatic solver (labframe)
* added parsing to boundary potentials specified at runtime to allow time dependence through a mathematical expression with t (time)
* updated to picmistandard 0.0.14 in order to set the electrostatic solver convergence threshold
* update docs
* various changes requested during PR review
* fixed issue causing old tests to break and added a new test for time varying boundary potentials
* possibly a fix for the failed time varying boundary condition test
* changed permission on the analysis file for the time varying BCs test
* switched to using yt for data analysis since h5py is not available
* made changes compatible with PR#1730; changed potential boundary setting routine to use the ParallelFor construct and set all boundaries in a single call
* fixed typo in computePhiRZ
* updated docs and fixed other minor typos
* fixed bug in returning from loop over dimensions when setting boundary potentials rather than continuing
* changed to setting potentials on domain boundaries rather than tilebox boundaries and changed picmi.py to accept boundary potentials
* now using domain.surroundingNodes() to get the proper boundary cells for the physical domain
* fixed typo in variable name specifying z-boundary potential
* changed boundary value parameter for Dirichlet BC to boundary.field_lo/hi and changed setPhiBC() to only loop over the grid points when a boundary value has changed
* switched specifying potential boundary values though individual inputs of the form boundary.potential_lo/hi_x/y/z and incorporated the new BC formalism through FieldBoundaryType::Periodic and FieldBoundaryType::PEC rather than Geom(0).isPeriodic(idim)
* removed incorrect check of whether the potential boundary values are already correct, also had to change the input to test space_charge_initialization_2d to comply with the new boundary condition input parameters and finally changed permissions to analysis_fields.py file for the embedded boundary test since it was failing
* remove line from WarpX-tests.ini that was incorrectly added during upstream merge
* changed input file for relativistic space charge initialization to new boundary condition specification
* fixed outdated comment and updated documentation to reflect that the Dirichlet BCs can also be specified when using the relativistic electrostatic field solver
* moved call to get domain boundaries inside the loop over levels
* cleaned up the code some by using domain.smallEnd and domain.bigEnd rather than lbound and ubound
* added check that a box contains boundary cells before launching a loop over that box cells to set the boundary conditions
Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com>
|
|
|
|
* Implemented new particle diagnostics in picmi
* Cleaned up picmi adding new particle diagnostics
* In PICMI examples, use name option for diagnostics
* For travis, update ubuntu version to bionic
|
|
* Create subsection for diags documentation in input parameters list
* Replace old diags with new ones IN DOC ONLY
* eol whitespace
* Check first CI test with new diags, before changing all of them
* use diags in all CI
* oops, had forgotten all examples except Tests/
* Updated picmi interface to use the new diagnostics
* fix bug in how field functors are initialized for diags
* fix bug: should always dump output at the end of simulation
* eol
* update test parameters in ini file
* Further fixes to picmi for new diagnostics
* Updates PICMI input files to use the new diagnostics
* avoid dumping final plotfile twoce
* update test to run with new diags
* fix typo introduced when fixing merge conflicts
* had accidentally removed the max_step here, so the run never ended on TravisCI
* Add Diagnostics.py for picmi with new diagnostics
* Adding m_ for member variables in new diags (#934)
* fixing bug to initialize CellCenterFunctor for Bx
* diag_name renamed to m_diag_name
* some more diag members made m_
* renaming member variable mf_avg to m_mf_output
* fixing m_mf_output to mf_dst in comments
* Python documentation updates (#936)
* Update Python documentation
* Added numpy as a requirement for the Python installation
* Cleaned EOL white space in Python documentation
* Add periodictable to the Python packages required
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Added periodictable to required packages for pure Python version
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add hostname to LoadBalanceCosts reduced diagnostic (#902)
* Add hostname to reduced diags
EOL
Fix rd loadbalancecosts test
AMREX_USE_MPI
EOL
move macro to source file
Review changes
eol
add GPU ID if running on GPU
eol
Typo in comment
use vectors to get rid of C-style memory management
Fix for test
eol
* Compute number of unique box data fields in analysis script
* analysis script
* Use amrex Tokenize to split string
* Update WarpXUtil.cpp
* Update WarpXUtil.H
* [mini] Add contact us section to documentation (#941)
* add contact us section to doc
* Update Docs/source/contact_us.rst
Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov>
* Update Docs/source/contact_us.rst
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
* stop calling the old WritePlotFile functions
* fix new diags, problem with rho and PSATD and particle output variables
* remove more deprecated code for old diags
* Move checkpoint capability to new diagnostics
* error if user asks custom output for checkpoint
* eol
* some more old diags code deleted
* further cleaning
* eol
* further cleaning, make sure that WarpX compiles with USE_OPENPMD
* remove old diags parameters
* use new option to change the plotfile name
* typo
* do not need checkpoint files
* adapt to new option for checkpoint
* removed unread options as they make tests crash
* remove warpx_checkInt from the Python layer
* remove some more python wrappers
* add checkpoint capability with 2 diags in new output
* fix bug in MultiDiagnostics, and (should) fix checkpoint-restart test
* fix restart CI test
* avoid issue when writing the last plotfile twice
* dpgrote's fix for the Python tests
* update doc for diagnostics
* stop requesting ndiags, this is read from the list of diags
* awk to remove ndiags from all example input files
* Removed diagnostics.ndiags from picmi interface
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
A pure Python version can be installed when only writing input files is reguired.
|
|
|
|
Fixed handling species with same name as predefined species.
Removed dependency on six
|
|
|
|
|
|
|
|
|
|
|
|
particle injection from Python.
|
|
|
|
|
Axel Huebl
Roelof Groenewald
KZhu-ME
David Grote
MaxThevenet
Tools
Andrew Myers
Grote
Remi Lehe
