Age | Commit message (Collapse) | Author | Files | Lines |
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* use bibtex citations in collisions theory section
* use keyprefix b for collisions citations
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Remove label prefix.
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* AMReX: Weekly Update
* Reset: `reduced_diags_single_precision`
* Reset: `background_mcc_dp_psp`
* Added docs for NCU
* Fixed script to run on perlmuttert
* quick typo fix
* ran space fixer
* Update Docs/source/developers/profiling.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/developers/profiling.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* A little more description about why compute slow
---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: kaplannp <kaplannp@whitman.edu>
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* Squashed commit of the following:
commit 5452b0a818e952fc8ac989a306b0ea83738243f1
Merge: a21dda0f 90b72e80
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Sep 23 13:22:03 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
commit a21dda0f1bad8ee8601104c3322631d5f385ffdd
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Sep 23 13:13:23 2022 -0700
Update
commit 3394416cc0f7dc1e4742249b469957bedbfd5e84
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 24 13:37:30 2022 -0700
Update Examples/Tests/LoadExternalField/*
commit f0650b02e2f2d8d9719163ed5d4fd932a9d62a5b
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 24 12:41:11 2022 -0700
parameters.rst added
commit a96a3eb3a181d6e1a649a43bc9eb2e00e4e0ef57
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 15:15:43 2022 -0700
Add 3D test
commit caf213cdff02213cf0ff7389b399898bc76951b5
Merge: e85a7105 2b60afe8
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:02:35 2022 -0700
Merge branch 'add_external_fields' of https://github.com/Yin-YinjianZhao/WarpX into add_external_fields
commit e85a7105dceb80bc8769062a306248f57ac0939d
Merge: d00ce279 642f6c0f
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:01:59 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
commit 2b60afe876b6e4400e9f2676824ec94a4728c468
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu Aug 18 19:01:58 2022 +0000
[pre-commit.ci] auto fixes from pre-commit.com hooks
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commit d00ce2790ae56148bd717baa7c8e074a2d12a6bf
Merge: fbaf5226 c21244d1
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:01:42 2022 -0700
minor
commit fbaf5226ee92444b618029ad56722f8e54918448
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 11:57:46 2022 -0700
The automated test of RZ passed, cleaning up needed.
commit c21244d103e3eb245ebb1d3b9d2c4b016afd8671
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed Aug 17 20:51:59 2022 +0000
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commit 0a52f2976b58cdbb48673387decce61aabf61561
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 17 13:51:40 2022 -0700
Add RZ test, but has a bug.
commit 2c6e1537e9fa1f630134e64800b2d509088481b8
Merge: d3b6b0cd b4686616
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 13:37:01 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
commit d3b6b0cd8eb34a5832bc8b439e96744f7a01a2ce
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 13:36:36 2022 -0700
Do not use WARPX_EXTERNAL_FIELD
commit a32207ab2c4476feab0cb4b1e9a65a6181c7bf81
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 10:50:18 2022 -0700
In the middle of clean up.
commit dcfcb02b9e053391c59cef50c692e84cf379fb8a
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 9 11:08:42 2022 -0700
RZ OpenPMD bug fixed, but code is messy, and chunk load is not done.
commit dec17c35d025ac4d40dcaca4b68853959e176782
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 9 10:43:58 2022 -0700
Has bug using RZ OpenMPD
commit b32e6efdd766f5986d66b213479d7c84587fca7e
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Aug 5 13:17:04 2022 -0700
Add OpenPMD 3D.
commit 7b7f48e2ae751d0393703c912116f5cb4d4dffbc
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 4 15:50:00 2022 -0700
Revert "minor"
This reverts commit 01e022958bad3057737e57fda4ecfaed22778b51.
commit 01e022958bad3057737e57fda4ecfaed22778b51
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 2 15:03:24 2022 -0700
minor
commit 774e591959fce76f94dcb96ae17f43c71ee7b931
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Jul 29 11:13:14 2022 -0700
Make 1d work
commit 5db4e862104459e5511dad9869764866dc88e62d
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Fri Jul 29 10:27:03 2022 -0700
Make xz working
commit 03c3d0062e301c1dd525a50f7ea84c2ccad6d679
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Fri Jul 29 09:38:43 2022 -0700
Make rz workiong
commit 8864a1780606bfa68e842d6902d28a34da659dc8
Merge: 0c1c7b7b a514e793
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed Jun 22 14:02:05 2022 -0700
Merge branch 'add_external_fields' of https://github.com/Yin-YinjianZhao/WarpX into add_external_fields
commit 0c1c7b7bda98549559d44125bb48e78ac6af24aa
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed Jun 22 14:01:42 2022 -0700
Fix a bug.
commit a514e793cb5e30591debc475082cc48f9172ee25
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed Jun 15 19:47:43 2022 +0000
[pre-commit.ci] auto fixes from pre-commit.com hooks
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commit dd3c3749e2793c8c489652a8152c166def995514
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed Jun 15 12:47:23 2022 -0700
Use txt file.
commit 61fb96d9219598d10dab6a729eb4db7278583d2e
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Thu May 26 13:51:58 2022 -0700
Now the loaded external field does not match the provided external field data.
commit 7354a1abcd3b36e97d2145eff0c4b1da0a3aca27
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed May 18 15:21:15 2022 -0700
Try to add new arguments in the doGatherShapeN function, such that external fields can be added.
commit 3a0db5fcbaf4298c7cf59ba4443f3cdf7a21094b
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Tue May 10 14:35:53 2022 -0700
Changed to mfi.growntilebox() to include the guard cells.
commit 33e3393eb6bf769a2d92043c1012796b8212e653
Merge: 53201644 32fe8aac
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local.dhcp.lbl.gov>
Date: Thu May 5 13:37:24 2022 -0700
A bug needs to be fixed related to the growth of cells.
commit 53201644322ae2a65c121a6f0559cda874edd98d
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local.dhcp.lbl.gov>
Date: Thu May 5 13:35:39 2022 -0700
A bug needs to be fixed related to the growth of cells.
commit 32fe8aacc16a749910956e28120e31f1807f3bc1
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue May 3 22:54:42 2022 +0000
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commit f434bff0e12643ba03fc76b1693c4875ef799fc6
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Tue May 3 15:54:25 2022 -0700
In the middle.
commit 698e8f3e69dac5945b332c67570272bf2f4ae168
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local.dhcp.lbl.gov>
Date: Tue May 3 09:32:54 2022 -0700
In the middle.
commit 9d9f88d59820e00eed0e962c8c8905d3f1964083
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed Apr 27 14:07:31 2022 -0700
In the middle of reading data.
commit 3640e134fa0970b6b4ec0bf7f1c7f779c730b9a1
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Thu Apr 21 09:43:06 2022 -0700
Draft.
commit 85e16cafbf65cf502b82943d5bae98c4e1d750df
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Mon Apr 18 15:15:22 2022 -0700
Minor: change tag.
commit 0b7d2723c225cc4eed09eb58ad7f049d6baa650a
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Mon Apr 18 15:04:19 2022 -0700
Allocate MultiFabs for the external E and B fields.
* Conditionalize compilation on openPMD support
* Switch bit-flag integer configuration to separate booleans
* Clean up and modernize allocation and reading logic
* Roll back addition of external fields in all calls down to doGatherShapeN
* Do away with separate MultiFABs for file-read field values, and just read into the main ones
* Check that solved and externally-prescribed fields are mutually exclusive
* Clean up compilation issues
* Support GPUs
* Correct data sets URLs
* Fix compilation for 1D
* Fix some GPU issues
* Extract elements of various random little types that aren't GPU-friendly
* Run RZ test along with the others, not with the 2D tests
* Fix complaint about unused variable
* Fix complaints about unused variable from 1D
* Clean up 1D warning issues harder
* Clone the example dataset repository directly, like warpx-data
* Allow composition of external and internal fields
* Go back to reading external field into a separate MultiFAB
* Vaguely working for lab frame electrostatic case
* Fix copy-paste errors
* Replace magic constants by enumerators
* Get indexing order right for RZ
* Put external field contribution in the right place
* Fix GPU and unused variable issues
* Match renamed input variable
* Update input parameters
* reset benchmark for LoadExternalField3D because data actually get loaded now
* reset benchmark for LoadExternalFieldRZ because data actually get loaded now
* Drop unused includes
* Read data once for all boxes
* Guard against unimplemented mesh refinement support
* Rename function to slightly better reflect substance
* Use existing linear interpolation routines
* Specify type argument for interpolation to avoid mixture
* Account for Array4 indexing in Fortran order
* Address Edoardo's review comments
* Support load balancing
* Add assertions of assumptions about input file format
* Move assertion about max levels to earlier in initialization
* Error in XZ case since it's untested
* Don't pretend implementation covers XZ
* Name variables to correspond to dimensionality
* Reword comment per request
* Correct typos
* Add issue numbers for different unimplemented bits, and guard 1D case
* Fix comment about RZ ParallelFor
* Fix reStructuredText syntax
* Shift 2D case to the unimplemented path to avoid unused parameter/variable warnings
* Use 2020+ Curl Command
* Support older curl
---------
Co-authored-by: Tools <warpx@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* added onbreaksignal python callback
* added documentation
* fixed bug executing onbreaksignal callbacks at stoptime
* applied suggestion from code review.
* updated doc-strings
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* Update of the Perlmutter documentation page
The last paragraph of the page has been modified
* Apply suggestions from code review
Doc: Update of the Perlmutter Filesystem Note
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Document to use libmamba for conda workflows.
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* Doc: add instructions to use Fugaku supercomputer
* Update Docs/source/install/hpc/fugaku.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/install/hpc/fugaku.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add fugaku page to toc
---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* move KernelTimer to ablastr
* add missing folder
* fixed bug
* fixed bug
* really fixed the bug
* kernelTimer -> KernelTimer
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* use_powi
* fix bug
* fix bug
* fix bug
* fix bug
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Add more docs and examples on how to use VisualPIC with WarpX openPMD
data.
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* Adding additional check in addPlasma and addPlasmaFlux to respect the random_theta flag, otherwise acts deterministically.
* Reset RZ benchmarks
---------
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* Add PICMI option to cover multiple cuts
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Parse flux_min, flux_tmax from PICMI
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Implement review comments
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Correct sign of the ChargeOnEB diagnostic
* Properly indent documentation
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* AMReX: Weekly Update
* Particles: Update WarpX APIs
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* Fix the reflection of velocities in RZ
* Add warpx_reflect_all_velocities to the PICMI interface
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* Doc: Tunneling Jupyter
Document how to tunnel Jupyter servers.
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add explicit headless command to workflow
* Fix quotes
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* AMReX: Weekly Update
* AMReX: Include Fix Roundoff Domain 3247
* Reset Benchmarks
* AMReX: Include PR 3248
* Update Checksums
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Document to change the default permissions of HPSS archives to be group (as in *project*) readable.
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Add AAC22 proceeding paper (preprint).
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Disable managed memory by default for performance and non-bugness.
Please disable explicitly if needed for some of the current
scripting tasks, e.g., in the current Python bindings.
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* Add callback function after the initial Esolve
* Apply suggestions from code review
* Change name of callback function
* Update PR
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Add Yin's LPA collision papers.
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Updates the installation location of software to use CFS.
HOME has only 40GB of quota, which can fill quickly when
pulling in large ML packages.
Also adds optimas for GPU including pytorch dependency.
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* refactored the charge deposition fix to be performed with the field data rather than individual particles
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* also correct current density at PEC boundary
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* corrections pointed out during code review
* fix build fails due to unused variables
* fix issue with GPU builds
* actually apply rho boundary correction in EM case
* first round of CI fixes
* second round of CI fixes
* added description of deposition logic with PEC boundaries to documentation
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* third round of CI fixing
* move J and rho boundary handling to after `SyncRho` and `SyncCurrent` calls
* properly order the application of boundary conditions on rho, for electrostatic simulations
* fourth round of CI fixing
* don't apply J field boundary in `MultiParticleContainer::DepositCurrent`
* apply changes requested during code review
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Loosen tolerance on failing CI test
* Removed unused variable
* deal with fine versus coarse patches
* move the `ApplyRhofieldBoundary` call to after `SumBoundary`
* use a uniform calculation for the number of cells a given index is from the boundary
* remove unused variable
* limit number of ghost cells updated during PEC BC application
* the number of ghost cells to consider depends on whether the field is nodal or not
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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Document Perlmutter (NERSC) CPU usage.
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* Doc: Frontier Cray HDF5 Work-Around
Document the HDF5 workaround for the current Frontier Cray
Modules.
* Frontier: Update Modules
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* Allow DD fusion products to be tritium + protium
For deuterium-deuterium (DD) fusion there are two branches:
| He-3 + n (neutronic branch, 50% probability)
d + d -> <
| t + p (anneutronic branch, 50% probability)
Currently in Warpx anneutronic DD fusion only works when the species of
the fusion products are tritium (or hydrogen3) and proton. If protium
(or hydrogen1) are specified instead of proton, the simulation aborts
with the following error message:
amrex::Abort::0::ERROR: Product species of proton-boron fusion must be of type helium3 and neutron, or tritium and proton !!!
The proposed diff allows anneutronic DD fusion to produce either protium
/ hydrogen1 or proton. It also corrects the error message.
* Shows that DD fusion cannot produce protium
Input deck that demonstrates how anneutronic DD fusion in the
development branch cannot produce protium, only proton.
Some options of the anneutronic DD branch:
1) tritium + proton (currently the only option)
2) tritium + protium (added in this branch)
3) triton + proton (another alternative)
Option 1) seems inconsistent (why include the electron mass in one
fusion product species but not in the other?). Option 2) is enabled
by the diff in this branch. Option 3) would require adding a triton
species (and deuteron and helion species for consistency).
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Remove test file
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Add message if user sets old flag `warpx.do_nodal`
* Update PICMI version
---------
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* `SyncRho`: Pass References To Charge MultiFabs
* Keep a function SyncRho for the Python interface
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Clean up calls to FillBoundary in FDTD part of `OneStep_nosub`
* Remove commented-out code
* Exchange guard cells of F,G before evolving B
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* CI: add RZ Langmuir test w/ multi-J PSATD
* Run test with 4 grids and 2 MPI procs
* Use 2 azimuthal modes in new test
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* Improve Python script to plot PSATD stencils
* Improve explanation printed to standard output
Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov>
* Fix warning, improve docstrings
* Handle exception where signal does not reach double machine precision
---------
Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov>
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* Lattice: Line Docs & Rename
Rename the `lattice` element type to `line` and add documentation
for it.
* Add `{}` for Dave :)
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'(between quotation marks)' has been removed
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ALS has been added to the glossary
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* Read particle offset when loading particles from openPMD
* Fix compilation errors
* Use loadChunk
* Use correct mass
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https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
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Only write number of retries in a single location.
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`AddSpaceChargeFieldLabFrame` (#3807)
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