Initiate rebased branch for lattice dynamics #789

Merged

Zhuoying merged 207 commits intohackingmaterials:mainfrom Zhuoying:fix-ld-wf

Mar 12, 2024

Commits on Mar 5, 2024

new directory test

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new directory test

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new directory test

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new directory test

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Confirmed supercell volume compares with Pymatgen's volume

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Added handling for transformation matrices with zero columns/rows (i.e. materials with extremely high/low angles)

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Handling for max_atoms

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IO for ShengBTE CONTROL file V1 (needs testing)

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V1, needs testing with csld_main

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Revised script and tested for reading, updating, and writing namelist files from a Python dict.

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fixed some bugs and added a working test case in main(). Imports csld_sc_gen

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Made a custom IO writer from a dict to a string to a file since f90nml was not writing files in format that was readable by ShengBTE.

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CSLD workflow first try

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quick change

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Debugging stuff. First version that was launched on cori

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first pass local debugging

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Fixed workflow generation script and added perturbed supercells as a required param (for putting poscars inside displacement folders)

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Workflow now runs without errors but with garbage results

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IT WORKS LETS GOOOOOO

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Added conventional standard primitive structure from pymatgen sga

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Added random search for csld parameters and shengbte stuff

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accounted for CSLD github and added csld random search

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Added dynamic fireworks for possible error handling (i.e. larger displacement values)

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Added fw_spec updates to all dynamically added fireworks and wrote a ShengBTE firetask

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Added optional temperature ranges for shengbte

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Added optional temperature ranges for shengbte

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Edited shengbte t_range option and created a CSLD preset workflow

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Minor edits

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Added documentation and cleaned up comments

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Updated to reflect changes in PerturbSitesTransformation and CSLD

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Preset runs smoothly. Waiting on Si test run scraped from MP

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- Updated workflow to reflect changes in PerturbStructureTransformation and diagonal CubicSupercellTransformation

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-Added a new csld analysis file to atomate

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-Only pass successful static calculations into the CSLD firework

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Working workflow

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Updated doc strings and comments for CSLD firetasks and moved code outside the grid search loop

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Updated trans_mat doc string

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docstring

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Cleaned up code (made functions for CSLD firetask, adhered to PEP guidelines, etc.)

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Added csld_main to csld analysis file. Add beginnings of testing files

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Delete

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Delete

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Delete

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Delete

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updated script for creating workflows

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More unit tests and minor bug fixes

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Junsoo's

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debug

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last cleanup of the term

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Remove optional requirements

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Begin refactoring workflow

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Remove old firetasks

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Add ShengBTE command to config

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Add first pass at lattice_dynamics firetasks

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Add first pass at lattice_dynamics fireworks

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Add methods for fitting force constants

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Add methods for generating phonon band structure & DOS

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Rewrite lattice dynamics workflow

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Add optional requirements

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Refactor firetasks to not rely on wf_uuid

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Refactor lattice dynamics fireworks to remove wf_uuid

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Rewrite lattice dynamics workflow with chaining in mind

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Add pymongo to requirements

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Remove circular imports

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Use proper name for 3rd order fc

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Refactor lattice dynamics fireworks

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Use latest fireworks in LD workflow

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Run isort and black

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Update docstrings

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Rewrite preset workflow

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Move most phonopy functions to pymatgen

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Tidy polarization tests

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FIX: Use proper phonon function name

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Finish tidying polarization tests

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Add lattice dynamics test files

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Remove parents options from ld fireworks

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BUG: Fixes for lattice dynamics workflow

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Add lattice dynamics workflow test

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BUG: Fix bugs in lattice dynamics firetasks

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Fix bugs in lattice dynamics workflow

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Update firetasks

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Update lattice dynamics workflow test

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Add powerup for updating any firetask

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Tidy docstrings

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Tweak lattice dynamics settings

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Change imaginary mode requirements

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Lattice dynamics settings tweaks

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Copy vasp outputs

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Fix bug in lattice dynamics wf

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Tweak VaspToDb params

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Handle prior structural relaxations

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optimize drone parsing

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fix typo in hiphive analysis

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gruneisen and CTE

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gruneisen

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gruneisen

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gruneisen

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imports

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FW

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VASP runs successfully

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no DEFAULT TEMPERATURE

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T_KLAT

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T_RENORM

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import renormalization

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parameters to best_fit

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cluster_space to best_fit

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get_cutoffs

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cutoff vs cell_size

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bulk_mod input

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separate fitting

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separate fitting

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separate fitting

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separate fitting

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separate fitting

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separate fitting

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separate fitting

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presets + other things

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presets

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preset

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preset

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update

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update

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update

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update

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fixed cutoff

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update

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disp_cut

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disp_cut fix

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disp_cut in FitForceConstantsFW

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renormalization

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any changes?

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workflow name

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firetask error fix

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T_qha

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T_qha

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T_qha

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max cutoff

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file copy

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clusterspace

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calc_loc

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renormalization calc_loc

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copy_files

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add_attiaional_fields_to_taskdocs

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RunHiPhiveRenorm

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revert to structure container for fitting

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fit_data parallel

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typo

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BTE.KappaTotalTensorVsT_CONV

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small fix for cutoffs and fit_method

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construct_fit_data

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fit_data unpack :

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debug

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debug

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sc

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changes

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anharmonic properties return

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anharmonic properties return

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nconfig0 nconfig

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parallel renormalization fireworks for each T

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parallel renormalization fireworks for each T

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parallel renormalization fireworks name

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renormalization klat dir link

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TE iter fix

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anything?

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ToDB

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error fix

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renormalization works

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anything?

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renorm data push

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renorm_thermal_data

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dependencies

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len(temperature)=1

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everything works?

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cleanup

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fixed random displacements

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T diff

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syntax errors

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remove separate_fit

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remove separate_fit

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separate harmonic

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clean-up
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PhonopySupercellTransformation

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ARC AIMD

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TI_IFC + clean-up

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parse_output (fix conflicts and cleanup)
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cleanup imports
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Commits on Mar 7, 2024

remove __init__ for pytest 2
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Commits on Mar 12, 2024

revert back
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