XspectraCalculation+XspectraParser: Add Features for Restarts and Other Updates
#837
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Added CalcJob implementations of the xspectra.x executable and upf2plotcore.sh shell script from the Quantum ESPRESSO library
Added Parser classes for the xspectra.x executable and upf2plotcore.sh shell script from the Quantum ESPRESSO library
Added entry points for both CalcJob and Parser classes required for XSpectra post-processing calculations
Change 'spectra_data' output to 'spectra' Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Change the caplitalization for XSpectraCalculation to XspectraCalculation Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Correct the capitalization of XSpectraParser to XspectraParser Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Correct the capitalization of XSpectraCalculation to XspectraCalculation Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Correct the capitalization of XSpectraParser to XspectraParser Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
…ved redundant file loop, and added new error code
Fixed the terms used in the XSpectra-specific error codes in order to make them easier to read.
Changed filename assigned to `_Plotcore_FILENAME` from `plotcore.out` to `stdout` in order to work properly with the `aiida-shell` plugin.
Made corrections to the parsing of various output parameters (e.g. energy levels and associated units) in both spin-polarised and unpolarised cases. An additional parameter `lsda` is also added to report explicitly the case of spin polarisation.
Adds tests of the `XspectraParser`, covering spin-polarised and non-spin-polarised cases, interrupted calculations, and XSpectra-specific error codes 313 and 314.
Adds the following features to the `XspectraCalculation` and
`XspectraParser` classes:
- A save file ('xanes.sav') is now reserved by default and is printed
at the end of each calculation run or after a designated time limit.
The file can then be used for re-starting halted calculations or
re-plotting spectra from previously-finished calculations.
- The `XspectraCalculation` class now copies the save file from a
parent calculation if the calculation type is itself an
XspectraCalculation, thus re-starts and re-plot runs are handled
automatically.
- An error code has been added (315) for calculations which safely exit
after reaching their time limit, thus enabiling a restart.
- Additional information is now included in the `output_parameters`
node (e.g. the polarisation vectors used and whether the calculation was
set to "xonly_plot").
Updates `XspectraParser` tests to work with changes made in a previous commit (commit 875fa58) and adds a new test for error code 315 (job exceeded time limit)
sphuber
requested changes
Sep 5, 2022
There was a problem hiding this comment.
Thanks @PNOGillespie . Just some minor comments but overall the changes look good.
Addresses aiidateam#837 Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Addresses PR aiidateam#837 Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Addresses PR aiidateam#837 Changes error code from 315 to 400 to match conventions Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Addresses PR aiidateam#837 Required for commit aiidateam@746770e Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Addresses PR aiidateam#837 Required with commit aiidateam@746770e Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Addresses PR aiidateam#837 Cleans-up the code for detecting if the parent calculation was an `XspectraCalculation` Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
|
Thank you @sphuber for the review, I will put out a new commit after my meetings today to shorten the out-of-walltime test file. Regarding the discussion here: #837 (comment) - The original formulation included FolderData as a means to provide a parent calculation for the calculation run, however the use of this wasn't tested before and I'm not familiar with the procedure for retrieving the files required in order to use the FolderData node properly for this purpose. I have opted to simply remove the option from the inputs for now and then add it back in via a later commit once I understand how this process works. |
Addresses comment for PR aiidateam#837: aiidateam#837 (review) Safely trims down the file length of the stdout file for `failed_timeout` test of `XspectraParser`
…umespresso into local develop
sphuber
requested changes
Sep 27, 2022
There was a problem hiding this comment.
Thanks @PNOGillespie . Just one minor mistake in the test docstring and one outstanding comment. If you can address those, this can be merged.
Edit: never mind, I see you addressed that comment regarding the FolderData in a separate post. Just the docstring then and I will merge this.
Correct text of docstring for `test_xspectra_failed_timeout` Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
|
Thank you for the reply @sphuber (and for spotting that mistake). I've addressed the requested change, so I'll leave the rest to you. |
sphuber
approved these changes
Sep 27, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adds features necessary for restarting XSpectra calculations:
xanes.sav) in thecodeinfoobject.xanes.savin thelocal_copy_listif the parent calculation is anXspectraCalculation(taken from the parent folder), thus simplifying the setup for calculation restarts.Other additions included in the PR:
XspectraParser(code 315) to detect if the code has cleanly exited after reaching a set maximum time limit (including an accompanying test).output_parameterscollected: adds the polarisation vectors chosen for the calculation and whether the calculation was set to re-plot (i.e.xonly_plot = .true./.false.in the inputs).gamma_file(SinglefileDataformat) required to run calculations using an external file for applying spectral broadening to the final spectrum (usinggamma_mode = "file").