Change Log

2024.10.16

  • Add a update_incar option in VaspJob which updates parameters from a previous vasprun.xml.

2024.10.15

  • Bug fix for pip installation.

2024.10.14

  • PR #342 from @esoteric-ephemera (#342) Minor update to the logic of the auto_nbands check for VaspErrorHandler. This check sees if the number of bands has been updated by VASP, and currently it only checks to see if that updated number is very large. However, there are cases where the user specifies an NBANDS that is incompatible with their parallelization settings, as NBANDS must be divisible by $(\mathrm{ranks}) / (\mathrm{KPAR} \times \mathrm{NCORE})$. In these cases, VASP increases the number of bands to ensure the calculation can still proceed. This can happen in MP’s band structure workflows with uniform $k$-point densities. However, since the current auto_nbands handler applies no corrections to the job, these otherwise successful runs are killed. This PR adds logic to ensure that the calculation is rerun with a higher number of bands appropriate to the parallelization setting. This is kinda redundant, since VASP already does this. But I think it has to occur this way because VaspErrorHandler is monitoring the job and flags it for an auto_nbands error. Another implementation concern: it’s generally safer to decrease the number of bands since this requires a lower energy cutoff to converge each band. It might be safer to decrease NBANDS as a fix

2024.6.24

  • Improved handling of ISMEAR for NKPT<4 (@Andrew-S-Rosen, @esoteric-ephemera)

2024.4.18

  • Enable export of environment variables plus lobster run as a command enhancement lobster (@JaGeo)
  • New Gaussian plugin (@rashatwi)
  • Add missing directory kwarg on QCJob run() method (@Andrew-S-Rosen)
  • Add support for directory for Q-Chem (@Andrew-S-Rosen)

2024.3.12

  • Make Custodian threadsafe with explicit file paths (@zulissimeta).

v2024.2.15

🐛 Bug Fixes

  • Fix KspacingMetalHandler triggering on runs that don’t use KSPACING by @janosh in https://github.com/materialsproject/custodian/pull/298
  • Fixed a small issue with the erroneous attribute call on a Structure object in AMIN handler by @fyalcin in https://github.com/materialsproject/custodian/pull/297
  • Move TEST_DIR + TEST_FILES from custodian/__init__.py to tests/conftest.py by @janosh in https://github.com/materialsproject/custodian/pull/312

🛠 Enhancements

  • Rewrite handler tests by @janosh in https://github.com/materialsproject/custodian/pull/299
  • Fix AliasingErrorHandlerTest modifying test files by @janosh in https://github.com/materialsproject/custodian/pull/301
  • Caching parsed output files by @gpetretto in https://github.com/materialsproject/custodian/pull/273

🧹 House-Keeping

  • Move tests to their own root-level directory by @janosh in https://github.com/materialsproject/custodian/pull/305
  • Refactor test file copying by @janosh in https://github.com/materialsproject/custodian/pull/306
  • Move _clear_tracked_cache fixture by @gpetretto in https://github.com/materialsproject/custodian/pull/307
  • Don’t needlessly inherit from unittest.TestCase by @janosh in https://github.com/materialsproject/custodian/pull/308

🧪 Tests

  • Add new error handlers, add tests for NonConvergingErrorHandler by @esoteric-ephemera in https://github.com/materialsproject/custodian/pull/313

🏥 Package Health

  • Merge setup.py into pyproject.toml by @janosh in https://github.com/materialsproject/custodian/pull/304
  • Fix release CI by @janosh in https://github.com/materialsproject/custodian/pull/314

🤷‍♂️ Other Changes

  • Add eddiag error handling and fix AMIN error handling in VaspErrorHandler by @esoteric-ephemera in https://github.com/materialsproject/custodian/pull/302

New Contributors

  • @esoteric-ephemera made their first contribution in https://github.com/materialsproject/custodian/pull/302

Full Changelog: https://github.com/materialsproject/custodian/compare/v2023.10.9…v2024.2.15

2023.10.9

  • PR #293 from @samblau (#293) A bug was introduced during the recent Minor Q-Chem updates PR:

      - os.mkdir(local_scratch, exist_ok=True)
  + os.makedirs(local_scratch, exist_ok=True)

    I would appreciate it if a new version could please be released after this PR is merged. Thanks!

  • PR #292 from @samblau (#292) This PR fixes a few bugs in the Q-Chem error handlers, adds one new handler, adds some additional tests, and slightly extends post processing scratch file handling.
  • PR #285 from @janosh (#285) 7b0c061a fix MeshSymmetryErrorHandler treating ISYM=-1 as symmetry ON 72ac1213 PositiveEnergyErrorHandler don’t decrease POTIM for static calcs
  • PR #284 from @janosh (#284) 225a1e8d UnconvergedErrorHandler only set algo to normal if ISMEAR>=0 608530b2 mv custodian/feff/tests/test_handler{,s}.py c11ab49e tweak bravais error handling in VaspErrorHandler 283fe9d2 improve den-/tet error handling in case of not using kspacing bc022852 fix VaspErrorHandlerTest.test_bravais
  • PR #283 from @janosh (#283) When running VASP with INCAR tag kspacing instead of a KPOINTS file and encountering brmix 2 or 3 times. Reported by @esoteric-ephemera in atomate2 r2SCAN workflow.

v2023.7.22

  • Fix for LargeSigmaHandler. Now defaults to ISMEAR=1 and fallback to ISMEAR=0 if SIGMA has been modified three times from 0.2 (@Andrew-S-Rosen, @janosh)
  • More robust VASP job termination (@fyalcin)

v2023.6.5

  • New VASP error handler for invalid INCAR parameter (@Andrew-S-Rosen)
  • Change VASP terminate function to be sensitive to execution directory (@MichaelWolloch)
  • Add handler for invalid WAVECAR when going from vasp_gam to vasp_std (@Andrew-S-Rosen)

v2023.5.12

  • Add back kwargs to VaspHandler to maintain backward compatibility (@Andrew-S-Rosen)

v2023.5.7

  • VASP Handler: Better error checking for too_few_nbands (@Andrew-S-Rosen)
  • VASP Handler: General clean up and mitigating unnecessary INCAR swaps (@Andrew-S-Rosen)
  • VASP Handler: Remove deprecated handlers and kwargs (@Andrew-S-Rosen)
  • VASP Handler: Add a new correction for the ZPOTRF ZTRTRI error that is specific to small structures (@Andrew-S-Rosen)
  • VASP Handler: Add a new handler for the SET_CORE_WF error (@Andrew-S-Rosen)
  • VASP Handler: Only apply the algo_tet handler if SCF convergence failed (@Andrew-S-Rosen)
  • VASP Handler: AMIN handler should only be applied if SCF is not converged (@Andrew-S-Rosen)
  • VASP Handler: Do not set ADDGRID to True (@Andrew-S-Rosen)

v2023.3.8

  • Updates for QChem6 support (@samblau)
  • Updates for CP2K support (@nwinner)

v2022.5.26

  • PR #219 from @samblau. Q-Chem updates to NBO, new geometry optimizer, revamped SCF error handling.

v2022.5.17

  • PR #220 from @yury-lysogorskiy. Fix for NBANDS when NBANDS is very small.
  • PR #211 from @Andrew-S-Rosen. Handler for error in reading plane wave coeff.
  • PR #214 from @Andrew-S-Rosen. Handler for ZHEGV error by reducing number of cores.
  • PR #215 from @Andrew-S-Rosen. Fix for new ZPOTRF error phrasing.
  • PR #210 from @nwinner. CP2K support.

v2022.2.13

  • Support for new Lobster versions (@naik-aakash)
  • Bug fix for termination of gamma VASP runs.

v2022.1.17

  • New NBANDS not sufficient handler in VASP (@Andrew-S-Rosen)
  • New VASP error handling for VASP 6.2.1 HNFORM error (@Andrew-S-Rosen)
  • Improve zbrent handler by trying to get IBRION = 2 to succeed before switching to IBRION = 1 (@Andrew-S-Rosen)
  • Updates to ALGO handling with grad_not_orth and algo_tet (@Andrew-S-Rosen)

v2021.12.2

  • Address new VASP6 inconsistent Bravais lattice error (@Andrew-S-Rosen)
  • Don’t check for drift if NSW = 1 (@Andrew-S-Rosen)
  • [VASP] Switch from IBRION = 1 –> 2 if the BRIONS error occurs more than once (@Andrew-S-Rosen)
  • Handle finite difference ncore error (@utf)
  • [VASP] More robust zbrent fix (@Andrew-S-Rosen)
  • [VASP] Increase posmap error count (@Andrew-S-Rosen)
  • [VASP] Update real_optlay logic to avoid LREAL = True (@Andrew-S-Rosen)
  • [VASP] More appropriate grad_not_orth fix and new algo_tet error handler (@Andrew-S-Rosen)
  • [VASP] Adjust SCF Ladder for meta-GGAs/hybrids (@Andrew-S-Rosen)
  • Refactor VaspErrorHandler.check() (@janosh)
  • Fix VaspErrorHandler not handling “tetrahedron method fails” (@janosh)

v2021.2.8

  • Allow static calculations with ISMEAR = -5 for metals (@MichaelWolloch).

v2021.1.8

  • New handlers for VASP6 (@mkhorton, @rkingsbury)

v2021.1.7

  • Improved handling of scratch directories and update for QChem.

v2019.8.24

  • Cleanup codestyle, which is now enforced.
  • Py3k support only, in line with pymatgen.
  • Update dependencies.
  • Sentry support (@mkhorton).
  • Complete qchem overhaul (frequency flattening optimization, refined error handlers) (@samblau)

v2019.2.10

  • Improved slow convergence handling. (@shyamd)

v2019.2.7

  • Improved error logging.
  • Improved handling of frozen jobs and potim errors.
  • Improved Exceptino handling. (Guido Petretto)

v2017.12.23

  • cstdn command line tool is now official with docs.
  • Fine-grained control of VaspErrorHandler is now possible using errors_subset_to_catch.
  • Switched to date-based versioning for custodian like pymatgen.

v1.1.1

  • DriftErrorHandler (Shyam)

v1.1.0

  • Improved error handling for Qchem calculations.

v1.0.4

  • Improved handling of non-zero return codes.

v1.0.2

  • Interrupted run feature. (Shyam Dwaraknath)

v1.0.1

  • Pymatgen 4.0.0 compatible release.

v1.0.0

  • Custodian now comes with a “cstdn” script that enables the arbitrary creation of simple job sequences using a yaml file, and the running of calculations based on these yaml specifications.

v0.8.8

  1. Fix setup.py.

v0.8.5

  1. Refactoring to support pymatgen 3.1.4.

v0.8.2

  1. Made auto_npar optional for double relaxation VASP run.

v0.8.1

  1. Misc bug fixes (minor).

v0.8.0

  1. Major refactoring of Custodian to introdce Validators, which are effectively post-Job checking mechanisms that do not perform error correction.
  2. Backwards incompatibility BadVasprunXMLHandler is now a validator, which must be separately imported to be used.
  3. Miscellaneous cleanup of Py3k fixes.

v0.7.6

  1. Custodian is now Python 3 compatible and uses the latest versions of pymatgen and monty.

v0.7.5

  1. Major Custodian now exits with RuntimeError when max_errors or unrecoverable_error is encountered.
  2. Added BadVasprunXMLHandler.

v0.7.4

  1. auto_npar option in VaspJob now properly handles Hessian calculations.
  2. WalltimeHandler now supports termination at electronic step (David Waroquiers).
  3. Improved handling of BRMIX fixes.

v0.7.3

  1. Improved backwards compatibility for WallTimeHandler.
  2. Improvements to VaspErrorHandler. No longer catches spurious BRMIX error messages when NELECT is specified in INCAR, and pricel and rot_mat errors are now fixed with symmetry precision and gamma centered KPOINTS instead.
  3. Improved Qchem error handler (Xiaohui Qu).

v0.7.2

  1. Improved WalltimeHandler (PBSWalltimeHandler is a subset and is now deprecated).
  2. New monty required version (>= 0.2.2).

v0.7.1

  1. Much improved qchem error handling (Xiaohui Qu).
  2. New Monty required version (>= 0.2.0).

v0.7.0

  1. **Backwards incompatible with v0.6.3. Refactoring to move commonly used Python utility functions to Monty package <https://pypi.python .org/pypi/monty>_, which is now a dependency for custodian.
  2. Custodian now requires pymatgen >= 2.9.0 for VASP, Qchem and Nwchem jobs and handlers.
  3. converge_kpoints script now has increment mode.
  4. ErrorHandlers now have a new API, where the class variables “is_monitor” and “is_terminating” are provided to indicate if a particular handler runs in the background during a Job and whether a handler should terminate the job. Some errors may not be critical or may need to wait for some other event to terminate a job. For example, a particular error may require a flag to be set to request a job to terminate gracefully once it finishes its current task. The handler to set the flag should not terminate the job.

v0.6.3

  1. Added buffer time option in PBSWalltimeHandler.
  2. Improved Qchem jobs and handlers (Xiaohui Qu).
  3. Vastly improved API docs.

v0.6.2

  1. Bug fix release to support sub dirs in run folder when using scratch.
  2. Improve handling of walltime in PBSWalltimeHander.

v0.6.1

  1. Bug fix release to address minor issue with checkpointing.
  2. Checkpointing is now turned off by default.

v0.6.0

  1. Checkpointing implemented for Custodian. Custodian can now checkpoint all files in the current working directory after every successful job. If the job is resubmitted, it will restore files and start from the last checkpoint. Particularly useful for multi-job runs.
  2. Added PBSWalltimeHandler to handle wall times for PBS Vasp Jobs.
  3. Qchem error handlers and jobs.

v0.5.0

  1. Added scratch_dir option to Custodian class as well as run_vasp and run_nwchem scripts. Many supercomputing clusters have a scratch space which have significantly faster IO. This option provides a transparent way to specify the jobs to be performed in scratch. Especially useful for jobs which have significant file IO.

v0.4.5

  1. Fix gzip of output.

v0.4.3

  1. Added handling for ZBRENT error for VASP.
  2. Minor refactoring to consolidate backup and gzip directory methods.

v0.4.2

  1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
  2. Improved VASP error handling (by Steve Dacek and Will Richards).

v0.4.1

  1. Added handling of PRICEL error in VASP.
  2. Speed and robustness improvements.
  3. BRIONS error now handled by changing ISYM.

v0.4.0

  1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
  2. Many more fixes for VASP runs, including the “TOO FEW BANDS”, “TRIPLE PRODUCT”, “DENTET” and “BRIONS” errors.
  3. VaspJob now includes the auto_npar and auto_gamma options, which automatically optimizes the NPAR setting to be sqrt(number of cores) as per the VASP recommendation for DFT runs and tries to search for a gamma-only compiled version of VASP for gamma 1x1x1 runs.

v0.3.5

  1. Bug fix for incorrect shift error handler in VASP.
  2. More robust fix for unconverged VASP runs (switching from ALGO fast to normal).
  3. Expanded documentation.

v0.3.4

  1. Added support for handlers that perform monitor a job as it is progressing and terminates it if necessary. Useful for correcting errors that come up by do not cause immediate job failures.

v0.3.2

  1. Important bug fix for VaspJob and converge_kpoints script.

v0.3.0

  1. Major update to custodian API. Custodian now perform more comprehensive logging in a file called custodian.json, which logs all jobs and corrections performed.

v0.2.6

  1. Bug fix for run_vasp script for static runs.

v0.2.5

  1. run_vasp script that now provides flexible specification of vasp runs.
  2. Vastly improved error handling for VASP runs.
  3. Improved logging system for custodian.
  4. Improved API for custodian return types during run.
  5. First stable release.

v0.2.4

  1. Bug fixes for aflow style runs assimilation.
© Copyright 2011, Materials Project