[WIP] Lattice dynamics workflow using hiPhive #1062
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1. using replace instead of add in hiphive_static_calcs job 2. ensuring that the given structure. in primitive, if not then converting to prim structure. 3. updated logic to write the FC_3rd order file 4. ruff fixes 5. added support of amabte, shengbte, and phono3py in LTC calculation 6. updated logic to only use lambda=0 for TI, when imag_modes_bool = False
1. ruff fixes 2. updated class attributes 3. added bulk modulus to the metadata 4. #TODO: Implement Quality Control Job 5. updated fireworks config for each job 6. updated definition to extract phonon dispersion 7. updated definition to extract LTC, depending upon whether or not renormalization was performed. 8. updated name of the flow
using tags in accordance with atomate LD workflow
1. supports shengBTE, almaBTE & phono3py as of now. 2. before running any of these calculators, make sure to successfully compile them as explained on their respective websites. 3.Also, remember to put the execution command for each of these calculators in atomate2.yaml file
the decision is now made based on whether n_imaginary > 0 from the fitting_data.json @ 0K
1. largest displacement is based on the avg row (periodic table) number of the compound. 2. displacements are skewed towards the large displacement 3. # of displaced structures to generate depends on the n_structures, which depends upon the symmetry of the primitive structure 4. smallest displacement is fixed at 0.01 Å
1. added a job that creates multiples sub jobs for each hiphive fitting and then collects the fitting data & the fcs. fcp, cluster space and other properties corresponding to the best cutoff! 2. setting the min # of displ to 4 & max # of displ to 60
Trying different strategies for perturbing the atoms in the supercell -- 1. Fixed displacement 2. MC Rattle 3. MD informed displacements Adding a penalty to the displacements that are generated out of the distribution.
1. selects cutoffs based on target DOFs for 2nd, 3rd and 4th order.
2. all the functions have doctrings. 3. modified the function that generates perturbed structures 4. updated def get_cutoffs -- generates a grid of cutoffs that satisfy the given # of required DOFs for 2nd, 3rd and 4th order interaction. 5. sequentially performs the linear regression for each cutoff. 6. modified the files that are saved during the execution of workflow
2. removed files that are not required to be saved during the workflow execution.
* Bump monty from 2024.2.2 to 2024.2.26 Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2024.2.2 to 2024.2.26. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.md) - [Commits](materialsvirtuallab/monty@v2024.2.2...v2024.2.26) --- updated-dependencies: - dependency-name: monty dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> * bump pymatgen>=2024.3.1 to fix deprecation removal CI errors --------- Co-authored-by: Janosh Riebesell <[email protected]>
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.0.2 to 8.1.0. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.0.2...8.1.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: utf <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
Bumps [ipython](https://github.com/ipython/ipython) from 8.22.1 to 8.22.2. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@8.22.1...8.22.2) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [chgnet](https://github.com/CederGroupHub/chgnet) from 0.3.4 to 0.3.5. - [Release notes](https://github.com/CederGroupHub/chgnet/releases) - [Commits](CederGroupHub/chgnet@v0.3.4...v0.3.5) --- updated-dependencies: - dependency-name: chgnet dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.6.3 to 2.6.4. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.6.3...v2.6.4) --- updated-dependencies: - dependency-name: pydantic dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [custodian](https://github.com/materialsproject/custodian) from 2024.2.15 to 2024.3.12. - [Release notes](https://github.com/materialsproject/custodian/releases) - [Changelog](https://github.com/materialsproject/custodian/blob/master/docs/changelog.md) - [Commits](materialsproject/custodian@v2024.2.15...v2024.3.12) --- updated-dependencies: - dependency-name: custodian dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.21.2 to 2.22.0. --- updated-dependencies: - dependency-name: phonopy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…t#1051) Updates the requirements on [versioningit](https://github.com/jwodder/versioningit) to permit the latest version. - [Release notes](https://github.com/jwodder/versioningit/releases) - [Changelog](https://github.com/jwodder/versioningit/blob/master/CHANGELOG.md) - [Commits](jwodder/versioningit@v1.0.0...v3.1.2) --- updated-dependencies: - dependency-name: versioningit dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Added the Materials Virtual Lab GW Set to the repo and implemented the MVLGWSetGenerator * add a Materials Virtual Lab GW band structure maker * fix bug * rename MVLGWMaker * created a Flow that does all three stages (static, diag, gw) for a GW band structure calculation * fixed bug * update the mvl gw yaml file and explicity copy the magmon in it * update the gw workflow * Revert line 37 to original state and fixed a typo * update the class doc of MVLGWSetGenerator * rewrite job name * rewrite job name * make job and flow names short * update job name * change the method names to adjust for recent updates on the main branch * explicitly specify files to copy * copied all data files for gw test case * add testcase for running MVL GW workflow * modified the files needed to copy between jobs * fixed wrong assertation * added missing data files to run the tests * add a warning in the GW workflow * removed MVL GW set yaml file, instead, import from pymatgen * reorganize the mvl jobs * reorganize the mvl gw workflow * update test case for mvl gw workflow and update the test data * update the mvl gw workflow * update test case for mvl gw workflow and corresponding test data * Bump emmet-core from 0.84.2 to 0.84.3rc3 * updated test data for mvl g0w0 * removed MVLGWSetGenerator class; use MVLGWSet directly instead * removed deprecate comments * remove CONTCAR.gz, use CONTCAR instead
Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2024.7.30 to 2024.10.21. - [Release notes](https://github.com/materialsvirtuallab/monty/releases) - [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.md) - [Commits](https://github.com/materialsvirtuallab/monty/commits/v2024.10.21) --- updated-dependencies: - dependency-name: monty dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add trajectory reporter to openmm workflow * respond to janosh review * fix test * slightly stricter asserts in test_trajectory_reporter --------- Co-authored-by: Janosh Riebesell <[email protected]>
input & output VASP files
added the testing python file for hiphive
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1062 +/- ##
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- Coverage 4.32% 3.85% -0.48%
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Files 178 193 +15
Lines 12911 14710 +1799
Branches 1278 1476 +198
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+ Hits 559 567 +8
- Misses 12321 14112 +1791
Partials 31 31
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hrushikesh-s
changed the title
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Oh I see. Thanks for sharing that info!
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