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[WIP] MPMorph Flows #818

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BryantLi-BLI wants to merge 206 commits intomaterialsproject:mainmaterialsproject/atomate2:mainfrom BryantLi-BLI:feature/mpmorphBryantLi-BLI/atomate2:feature/mpmorphCopy head branch name to clipboard

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Commits

Commits on Oct 12, 2023

• Added EOS and MP-compat EOS workflows

  

  Aaron Kaplan

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Commits on Oct 13, 2023

• Add EOS jobs, fix broken wf

  

  Aaron Kaplan

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• Merge branch 'materialsproject:main' into EOS_workflows

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• fix broken mp eos flow

  

  Aaron Kaplan

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• Merge branch 'EOS_workflows' of https://github.com/esoteric-ephemera/atomate2 into EOS_workflows

  

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• fix update_user_incar_settings

  

  Aaron Kaplan

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• rewrite TransmuterMaker in vasp.EOS.jobs to allow changing transformations on the fly (TransmuterMaker has transformations only as class attr)

  

  Aaron Kaplan

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• typo defomration --> deformation

  

  Aaron Kaplan

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• fix accession of output reference objects

  

  Aaron Kaplan

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Commits on Oct 16, 2023

• Merge branch 'materialsproject:main' into EOS_workflows

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• Add postprocessing step to EOS flow

  

  Aaron Kaplan

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• Merge branch 'EOS_workflows' of https://github.com/esoteric-ephemera/atomate2 into EOS_workflows

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Commits on Oct 18, 2023

• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Oct 19, 2023

• Add statics to MP-GGA EOS WFs, add MP-Meta-GGA compat WFs

  

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• Merge branch 'materialsproject:main' into EOS_workflows

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• bug fix r2SCAN EOS WF

  

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• precommit fixes

  

  Aaron Kaplan

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• fix ISMEAR/SIGMA in EOS relax

  

  Aaron Kaplan

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• Pop KSPACING from MP Meta-GGA INCAR tags

  

  Aaron Kaplan

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Commits on Oct 20, 2023

• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Oct 23, 2023

• Fix EOS input sets - incorrectly assumed inheritance of base class get_incar_updates params

  

  Aaron Kaplan

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Commits on Nov 3, 2023

• overhaul legacy GGA and modern GGA sets/jobs/flows

  

  esoteric-ephemera

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• refactor flow / postprocess

  

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• fix typo in EOS flow

  

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• Add tiered double-relaxation (coarse --> fine) for GGA EOS

  

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Commits on Nov 8, 2023

• Add failsafe for when EOS fitting fails

  

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Commits on Nov 17, 2023

• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Nov 21, 2023

• Finished tests for MP EOS jobs and flows

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• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Nov 22, 2023

• Edits for maintainer comments: change EOS --> eos, pare down test files

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• renaming EOS --> eos (why does MacOS have to be case-insensitive)

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• renamed EOS --> eos (why does MacOS have to be case-insensitive)

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• more case insensitive values why oh why oh why

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Commits on Dec 14, 2023

• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Dec 15, 2023

• Generalization of EOS routines to make common template for flow; remaining to add forcefield flow

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Commits on Jan 18, 2024

• Refactor generalized EOS wfs, ignore pre-commit

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• Refactor generalized EOS wfs, ignore pre-commit

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Commits on Jan 19, 2024

• Merge branch 'materialsproject:main' into EOS_workflows

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• Refactor to ensure correct flow

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• remove key from jobs

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Commits on Jan 22, 2024

• fix postprocess dict update

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• Fix linting

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• fix init

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• Add MLFF EOS workflows and tests for these

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• remove mystery vasp docs

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• Merge branch 'materialsproject:main' into EOS_workflows

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• Clean up ML FF EOS test

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• Trying to suss why CHGNet and M3GNet tests pass locally but fail in CI

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• Ensure consistent ML FF dtype in tests

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Commits on Jan 24, 2024

• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Feb 2, 2024

• mpmorph features: added equilibrate.py in atomate2.common.jobs, amorphous.py in atomate2.common.flows, amorphous.py in atomate2.vasp.flows; still in progress md.py in atomate2.forcefields.sets, job…

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• small edits

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• fixed some dataclasses that were not defined with Maker prorperly

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• fixed some dataclasses that were not defined with Maker prorperly v2

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Commits on Feb 3, 2024

• Merge remote-tracking branch 'aaron/EOS_workflows' into feature/mpmorph

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• Merge branch 'materialsproject:main' into EOS_workflows

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• added EquilibriumVolumeMaker in atomate2.common.flows.amorphous.py to include eos functionality. However the dynamic response is still a work in progress

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Commits on Feb 5, 2024

• modified beta version of EquilibriumVolumeMaker

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• Merge branch 'materialsproject:main' into EOS_workflows

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Commits on Feb 6, 2024

• debug EquilibriumVolumeMaker, modified eos.py in both flows and jobs dir fyi

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• modified logic of equilibriumvolumemaker

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• current version of EVM (equilibriumvolumemaker) is stuck in an infinite loop. Trying to debug it now

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• test

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• added job decorator to make function in EVM

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Commits on Feb 7, 2024

• refactor postprocessing step to be MSONable class, preparation for MPMorph PR

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• Merge remote-tracking branch 'atomate2/EOS_workflows' into feature/mpmorph

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• Slight refactor / typo cleanup

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• Merge remote-tracking branch 'atomate2/EOS_workflows' into feature/mpmorph

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• Refactor equilibration flow, add docstr

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• correct typo

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• Merge branch 'materialsproject:main' into feature/mpmorph

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Commits on Feb 12, 2024

• Merge branch 'feature/mpmorph' of https://github.com/BryantLi-BLI/atomate2 into feature/mpmorph

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• Rebased the feature/mpmorph branch on top of the latest master branch. This is a good practice to keep the feature branch up to date with the latest changes in the master branch.

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Commits on Feb 13, 2024

• modified EVM to streamline some bugs; first if statement can produce correct things, but else statement hit

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• tests with postprocessor maker for EquilVolMaker

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Commits on Feb 14, 2024

• Clean up equilibrate volume wf, add atomate2.vasp.flows.test_mpmorph

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• resolve merge conflicts

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Commits on Feb 15, 2024

• updates to pytest for test_mpmorph.py; seems like the flow works properly now

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• Cleanup, remove unneeded jobs

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• fix equilibration and mpmorph wflows

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• added tests and tes data for recursion and mpmorph maker test in test_mpmorph.py

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• fix pressure updating in recursive equilibration

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• cleaned up test_mpmorph.py, tests should work now

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• FF MD fully implemented

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• change MD defaults to be NVT + Langevin dynamics

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Commits on Feb 16, 2024

• added docstring to amorphous.py in common dir and cleaned up some files

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• add md defaults that are as consistent with vasp implementation as possible

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• Merge branch 'materialsproject:main' into mlff_md

  esoteric-ephemera

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• correct typing of langevin friction coeff

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• Add option to ForceFieldTaskDocument to store trajectory information as pmg object

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• Merge branch 'materialsproject:main' into mlff_md

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• Add tests, remove dependence on pickle for trajectory i/o

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Commits on Feb 17, 2024

• fix tests, update matgl dependence

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Commits on Feb 20, 2024

• rename MD forcefield class vars to be consistent with VASP MDSetGenerator

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Commits on Feb 22, 2024

• Merge branch 'materialsproject:main' into mlff_md

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• Add option to explicitly specify thermostat as ASE MolecularDynamics object

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Commits on Feb 23, 2024

• refactoring and add T/P schedule

  

  Yuan Chiang

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Commits on Feb 24, 2024

• implement T/P schedule and attach callback func

  

  Yuan Chiang

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• np.nan

  

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• np.nan

  

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• Merge branch 'mlff_md' of github.com:esoteric-ephemera/atomate2 into mlff-md

  

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Commits on Feb 26, 2024

• Merge remote-tracking branch 'aaron/mlff_md' into feature/mpmorph

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Commits on Feb 27, 2024

• small fixes

  

  Yuan Chiang

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• pass ASE dynamics object instead of class, update docstring

  

  Yuan Chiang

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Commits on Feb 28, 2024

• add temp ramp test and make sure upper tria matrix cell

  

  Yuan Chiang

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• add stresses to trajeoctroy observer, add pressure schedule test

  

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Commits on Feb 29, 2024

• Merge branch 'mlff_md' of https://github.com/esoteric-ephemera/atomate2 into feature/mpmorph

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• avoid stresses key not in taskdoc bug

  

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Commits on Mar 1, 2024

• Refactory TrajectoryObserver, add option to save trajectory as either pmg or ase trajectory objects, add test for trajectory parsing

  esoteric-ephemera

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• Merge branch 'materialsproject:main' into mlff_md

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• Change decomposition to upper triangular cell only when Nose-Hoover requested

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• Merge remote-tracking branch 'upstream/main' into feature/mpmorph

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• readded MPMorphPostProcessor

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• fix on apply_strain_to_structure job in amorphous.py in common

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• un-jobbed apply_strain_to_structure

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• debug after upstream merge. Pytests work now

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• Fix failing tests

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• Change MD default TaskDoc ionic step to only store mandatory info

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• update pymatgen requirement because of CifParser deprecation

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Commits on Mar 4, 2024

• Merge branch 'materialsproject:main' into mlff_md

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Commits on Mar 6, 2024

• Significant refactor to all forcefield jobs. Use commmon ASE calc structure, allow loading via MontyDecoder. Add check in relaxation for force convergence, attr in Forcefield taskdoc

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• Merge branch 'main' into mlff_md

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• Fix forcefield utils test and lint

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• Add revert_dtype env for running forcefield relax and md jobs / undo removal

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Commits on Mar 7, 2024

• Merge branch 'main' into mlff_md

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Commits on Mar 8, 2024

• refactor nequip jobs, add md default for nequip

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• Add GAP and Nequip MD tests, fix arg / kwarg passing in MD

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• remove calculator_args / ase_calculator args, revert phonon job change

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• Merge branch 'materialsproject:main' into mlff_md

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• remove todo about adding magmoms to forcefield traj observer as that's now implemented

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Commits on Mar 13, 2024

• Remove comments, add option to seed rng for MB velocities, turn on ideal gas stress contribution only when MD trajectory outputs (temp / velocity) are stored

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• Merge branch 'materialsproject:main' into mlff_md

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Commits on Mar 25, 2024

• Merge branch 'materialsproject:main' into mlff_md

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• Ensure CHGNet and M3GNet relax / static makers convert stress to eV/A0**3; add tests for MD NVE ensemble and specifying MolecularDynamics object as input

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• fix M3GNet test related to outdated cached model

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• Merge branch 'mlff_md' of https://github.com/esoteric-ephemera/atomate2 into feature/mpmorph

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Commits on Mar 26, 2024

• refactor slightly

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Commits on Mar 27, 2024

• clean up names for files and docstrings

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• implemented SlowQuench and FastQuench and finalized version of MPMorphVASPMDMaker

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• minor updates to imports in mpmorph.py in forcefields and vasp

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• finalized format of mpmorph.py for forcefields and fixed some errors in vasp version of mpmorph

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• minor typos and errors fix in mpmorph.py of forcefields

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Commits on Mar 28, 2024

• modified post init procedure for forcefields mpmorph.py

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• cleaned up mpmorph.py in forcefields and how it calls slowquench and fastquench. removes the need to use isinstance to check maker. this format should retain the same functionality but cleaner to use

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• cleaned up mpmorph.py in vasp, similiar clean up to what was done in forcefields. Modified by slowquench and fastquench are called, and made simple cases for user friendly flows.

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• added tests; working for regular MPMorph, Slow quench, and Fast quench

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• fixed gamma k points error in test_mpmorph.py

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