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[WIP] Port Lattice Dynamics workflow into main #788

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[WIP] Port Lattice Dynamics workflow into main #788

wants to merge 196 commits into from

Commits on Jun 21, 2019

  1. new directory test

    @rees-c
    rees-c committed Jun 21, 2019
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  2. new directory test

    @rees-c
    rees-c committed Jun 21, 2019
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  3. new directory test

    @rees-c
    rees-c committed Jun 21, 2019
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Commits on Jun 25, 2019

  1. new directory test

    @rees-c
    rees-c committed Jun 25, 2019
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  2. Confirmed supercell volume compares with Pymatgen's volume 

    Added functionality for constraining supercell to a min number of atoms on top of the X times NN distances.
    @rees-c
    rees-c committed Jun 25, 2019
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  3. Added handling for transformation matrices with zero columns/rows (i.… 

    …e. materials with extremely high/low angles)
    @rees-c
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  4. Handling for max_atoms

    @rees-c
    rees-c committed Jun 25, 2019
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  5. IO for ShengBTE CONTROL file V1 (needs testing)

    @rees-c
    rees-c committed Jun 25, 2019
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Commits on Jun 26, 2019

  1. V1, needs testing with csld_main

    @rees-c
    rees-c committed Jun 26, 2019
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  2. Revised script and tested for reading, updating, and writing namelist… 

    … files from a Python dict.
    @rees-c
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  3. fixed some bugs and added a working test case in main(). Imports csld… 

    …_sc_gen
    @rees-c
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  4. Made a custom IO writer from a dict to a string to a file since f90nm… 

    …l was not writing files in format that was readable by ShengBTE.
    @rees-c
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Commits on Jul 10, 2019

  1. CSLD workflow first try

    @rees-c
    rees-c committed Jul 10, 2019
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  2. quick change

    @rees-c
    rees-c committed Jul 10, 2019
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Commits on Jul 11, 2019

  1. Debugging stuff. First version that was launched on cori

    @rees-c
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Commits on Jul 16, 2019

  1. first pass local debugging

    @rees-c
    rees-c committed Jul 16, 2019
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  2. Fixed workflow generation script and added perturbed supercells as a … 

    …required param (for putting poscars inside displacement folders)
    @rees-c
    rees-c committed Jul 16, 2019
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  3. Workflow now runs without errors but with garbage results

    @rees-c
    rees-c committed Jul 16, 2019
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Commits on Jul 17, 2019

  1. IT WORKS LETS GOOOOOO

    @rees-c
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  2. Added conventional standard primitive structure from pymatgen sga

    @rees-c
    rees-c committed Jul 17, 2019
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Commits on Jul 19, 2019

  1. Added random search for csld parameters and shengbte stuff

    @rees-c
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Commits on Jul 23, 2019

  1. accounted for CSLD github and added csld random search

    @rees-c
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  2. Added dynamic fireworks for possible error handling (i.e. larger disp… 

    …lacement values)
    @rees-c
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Commits on Jul 26, 2019

  1. Added fw_spec updates to all dynamically added fireworks and wrote a … 

    …ShengBTE firetask
    @rees-c
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  2. Added optional temperature ranges for shengbte

    @rees-c
    rees-c committed Jul 26, 2019
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  3. Added optional temperature ranges for shengbte

    @rees-c
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  4. Edited shengbte t_range option and created a CSLD preset workflow

    @rees-c
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  5. Minor edits

    @rees-c
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Commits on Jul 30, 2019

  1. Added documentation and cleaned up comments

    @rees-c
    rees-c committed Jul 30, 2019
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Commits on Jul 31, 2019

  1. Updated to reflect changes in PerturbSitesTransformation and CSLD

    @rees-c
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  2. Preset runs smoothly. Waiting on Si test run scraped from MP

    @rees-c
    rees-c committed Jul 31, 2019
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Commits on Aug 1, 2019

  1. - Updated workflow to reflect changes in PerturbStructureTransformati… 

    …on and diagonal CubicSupercellTransformation
    @rees-c
    rees-c committed Aug 1, 2019
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  2. -Added a new csld analysis file to atomate 

    parse_outputs:
- Made export_sbte be the diagonal of the trans_mat rather than 5,5,5
- Added supercell structure and trans_mat to the CSLD firework DB summary
- Passed trans_mat into the sbte firetask

csld:
- Minor edits
    @rees-c
    rees-c committed Aug 1, 2019
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  3. -Only pass successful static calculations into the CSLD firework

    @rees-c
    rees-c committed Aug 1, 2019
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Commits on Aug 5, 2019

  1. Working workflow

    @rees-c
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Commits on Aug 6, 2019

  1. Updated doc strings and comments for CSLD firetasks and moved code ou… 

    …tside the grid search loop
    @rees-c
    rees-c committed Aug 6, 2019
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  2. Updated trans_mat doc string

    @rees-c
    rees-c committed Aug 6, 2019
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  3. docstring

    @rees-c
    rees-c committed Aug 6, 2019
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Commits on Aug 7, 2019

  1. Cleaned up code (made functions for CSLD firetask, adhered to PEP gui… 

    …delines, etc.)
    @rees-c
    rees-c committed Aug 7, 2019
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  2. Delete

    @rees-c
    rees-c committed Aug 7, 2019
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  3. Delete

    @rees-c
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  4. Delete

    @rees-c
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  5. Delete

    @rees-c
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  6. Added csld_main to csld analysis file. Add beginnings of testing files

    @rees-c
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  7. Merge branch 'CSLD' of https://github.com/rees-c/atomate into CSLD

    @rees-c
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Commits on Aug 8, 2019

  1. updated script for creating workflows

    @rees-c
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Commits on Aug 9, 2019

  1. More unit tests and minor bug fixes

    @rees-c
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  2. Junsoo's

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  3. debug

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  4. last cleanup of the term

    @rees-c
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Commits on Feb 19, 2020

  1. Merge with master

    @utf
    utf committed Feb 19, 2020
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  2. Remove optional requirements

    @utf
    utf committed Feb 19, 2020
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Commits on Feb 25, 2020

  1. Begin refactoring workflow

    @utf
    utf committed Feb 25, 2020
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  2. Remove old firetasks

    @utf
    utf committed Feb 25, 2020
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  3. Add ShengBTE command to config

    @utf
    utf committed Feb 25, 2020
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  4. Update requirements

    @utf
    utf committed Feb 25, 2020
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  5. Add first pass at lattice_dynamics firetasks

    @utf
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  6. Add first pass at lattice_dynamics fireworks

    @utf
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  7. Add methods for fitting force constants

    @utf
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  8. Add methods for generating phonon band structure & DOS

    @utf
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  9. Rewrite lattice dynamics workflow

    @utf
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  10. Add optional requirements

    @utf
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  11. Refactor firetasks to not rely on wf_uuid

    @utf
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  12. Refactor lattice dynamics fireworks to remove wf_uuid

    @utf
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  13. Rewrite lattice dynamics workflow with chaining in mind

    @utf
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  14. Add pymongo to requirements

    @utf
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  15. Remove circular imports

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Commits on Feb 26, 2020

  1. Use proper name for 3rd order fc

    @utf
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  2. Refactor lattice dynamics fireworks

    @utf
    utf committed Feb 26, 2020
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  3. Use latest fireworks in LD workflow

    @utf
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  4. Run isort and black

    @utf
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  5. Update docstrings

    @utf
    utf committed Feb 26, 2020
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  6. Rewrite preset workflow

    @utf
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  7. Move most phonopy functions to pymatgen

    @utf
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  8. Tidy polarization tests

    @utf
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  9. FIX: Use proper phonon function name

    @utf
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  10. Finish tidying polarization tests

    @utf
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  11. Add lattice dynamics test files

    @utf
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  12. Remove parents options from ld fireworks

    @utf
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  13. BUG: Fixes for lattice dynamics workflow

    @utf
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  14. Add lattice dynamics workflow test

    @utf
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Commits on Feb 28, 2020

  1. BUG: Fix bugs in lattice dynamics firetasks

    @utf
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  2. Fix bugs in lattice dynamics workflow

    @utf
    utf committed Feb 28, 2020
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  3. Update firetasks

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  4. Update lattice dynamics workflow test

    @utf
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  5. Merge branch 'CSLD' into lattice-dynamics

    @utf
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Commits on Apr 1, 2020

  1. Merge branch 'master' of github.com:hackingmaterials/atomate into lat… 

    …tice-dynamics
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Commits on Apr 7, 2020

  1. Add powerup for updating any firetask

    @utf
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  2. Tidy docstrings

    @utf
    utf committed Apr 7, 2020
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  3. Tweak lattice dynamics settings

    @utf
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  4. Change imaginary mode requirements

    @utf
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  5. Lattice dynamics settings tweaks

    @utf
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  6. Copy vasp outputs

    @utf
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  7. Fix bug in lattice dynamics wf

    @utf
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Commits on Apr 10, 2020

  1. Tweak VaspToDb params

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Commits on Apr 11, 2020

  1. Handle prior structural relaxations

    @utf
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  2. optimize drone parsing

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Commits on Apr 12, 2020

  1. fix typo in hiphive analysis

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Commits on Oct 30, 2020

  1. Merge branch 'master' of github.com:hackingmaterials/atomate into lat… 

    …tice-dynamics
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Commits on May 24, 2021

  1. Merge branch 'main' of github.com:hackingmaterials/atomate into latti… 

    …ce-dynamics
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Commits on May 26, 2021

  1. gruneisen and CTE

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  2. gruneisen

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  3. gruneisen

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  4. gruneisen

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Commits on May 27, 2021

  1. imports

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  2. FW

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Commits on May 29, 2021

  1. VASP runs successfully

    @jsyony37
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  2. no DEFAULT TEMPERATURE

    @jsyony37
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  3. T_KLAT

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  4. T_RENORM

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  5. import renormalization

    @jsyony37
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  6. parameters to best_fit

    @jsyony37
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  7. cluster_space to best_fit

    @jsyony37
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  8. get_cutoffs

    @jsyony37
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Commits on May 31, 2021

  1. cutoff vs cell_size

    @jsyony37
    jsyony37 committed May 31, 2021
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Commits on Jun 2, 2021

  1. bulk_mod input

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    jsyony37 committed Jun 2, 2021
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Commits on Jun 6, 2021

  1. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  2. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  3. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  4. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  5. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  6. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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  7. separate fitting

    @jsyony37
    jsyony37 committed Jun 6, 2021
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Commits on Jun 9, 2021

  1. presets + other things

    @jsyony37
    jsyony37 committed Jun 9, 2021
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  2. presets

    @jsyony37
    jsyony37 committed Jun 9, 2021
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  3. preset

    @jsyony37
    jsyony37 committed Jun 9, 2021
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  4. preset

    @jsyony37
    jsyony37 committed Jun 9, 2021
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Commits on Jun 18, 2021

  1. update

    @jsyony37
    jsyony37 committed Jun 18, 2021
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  2. update

    @jsyony37
    jsyony37 committed Jun 18, 2021
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  3. update

    @jsyony37
    jsyony37 committed Jun 18, 2021
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  4. update

    @jsyony37
    jsyony37 committed Jun 18, 2021
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Commits on Jul 2, 2021

  1. fixed cutoff

    @jsyony37
    jsyony37 committed Jul 2, 2021
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Commits on Jul 8, 2021

  1. update

    @jsyony37
    jsyony37 committed Jul 8, 2021
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  2. disp_cut

    @jsyony37
    jsyony37 committed Jul 8, 2021
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  3. disp_cut fix

    @jsyony37
    jsyony37 committed Jul 8, 2021
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  4. disp_cut in FitForceConstantsFW

    @jsyony37
    jsyony37 committed Jul 8, 2021
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Commits on Oct 27, 2022

  1. renormalization

    Junsoo Park authored and Junsoo Park committed Oct 27, 2022
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Commits on Nov 1, 2022

  1. any changes?

    Junsoo Park authored and Junsoo Park committed Nov 1, 2022
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  2. workflow name

    Junsoo Park authored and Junsoo Park committed Nov 1, 2022
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Commits on Nov 2, 2022

  1. firetask error fix

    Junsoo Park authored and Junsoo Park committed Nov 2, 2022
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Commits on Nov 4, 2022

  1. T_qha

    Junsoo Park authored and Junsoo Park committed Nov 4, 2022
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Commits on Nov 7, 2022

  1. T_qha

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    jsyony37 committed Nov 7, 2022
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  2. T_qha

    Junsoo Park authored and Junsoo Park committed Nov 7, 2022
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  3. max cutoff

    Junsoo Park authored and Junsoo Park committed Nov 7, 2022
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Commits on Nov 15, 2022

  1. file copy

    Junsoo Park authored and Junsoo Park committed Nov 15, 2022
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Commits on Nov 21, 2022

  1. clusterspace

    Junsoo Park authored and Junsoo Park committed Nov 21, 2022
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Commits on Nov 23, 2022

  1. calc_loc

    Junsoo Park authored and Junsoo Park committed Nov 23, 2022
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Commits on Dec 1, 2022

  1. renormalization calc_loc

    Junsoo Park authored and Junsoo Park committed Dec 1, 2022
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Commits on Feb 27, 2023

  1. copy_files

    @jsyony37
    jsyony37 committed Feb 27, 2023
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  2. add_attiaional_fields_to_taskdocs

    Junsoo Park authored and Junsoo Park committed Feb 27, 2023
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Commits on Feb 28, 2023

  1. RunHiPhiveRenorm

    Junsoo Park authored and Junsoo Park committed Feb 28, 2023
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Commits on Mar 1, 2023

  1. revert to structure container for fitting

    Junsoo Park authored and Junsoo Park committed Mar 1, 2023
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Commits on Mar 8, 2023

  1. fit_data parallel

    Junsoo Park authored and Junsoo Park committed Mar 8, 2023
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  2. typo

    Junsoo Park authored and Junsoo Park committed Mar 8, 2023
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  3. BTE.KappaTotalTensorVsT_CONV

    Junsoo Park authored and Junsoo Park committed Mar 8, 2023
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Commits on Mar 10, 2023

  1. small fix for cutoffs and fit_method

    Zhuoying Zhu authored and Zhuoying Zhu committed Mar 10, 2023
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Commits on Mar 14, 2023

  1. construct_fit_data

    Junsoo Park authored and Junsoo Park committed Mar 14, 2023
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Commits on Mar 17, 2023

  1. fit_data unpack :

    Junsoo Park authored and Junsoo Park committed Mar 17, 2023
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  2. debug

    Junsoo Park authored and Junsoo Park committed Mar 17, 2023
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  3. debug

    Junsoo Park authored and Junsoo Park committed Mar 17, 2023
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Commits on Mar 18, 2023

  1. sc

    @jsyony37
    jsyony37 committed Mar 18, 2023
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  2. phonopy_orig.yaml

    Junsoo Park authored and Junsoo Park committed Mar 18, 2023
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Commits on Mar 20, 2023

  1. phonopy_orig

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  2. anharmonic properties return

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  3. changes

    @jsyony37
    jsyony37 committed Mar 20, 2023
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  4. Merge branch 'lattice-dynamics' of https://github.com/jsyony37/atomate … 

    …into lattice-dynamics
    @jsyony37
    jsyony37 committed Mar 20, 2023
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  5. anharmonic properties return

    @jsyony37
    jsyony37 committed Mar 20, 2023
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  6. nconfig0 nconfig

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  7. parallel renormalization fireworks for each T

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  8. parallel renormalization fireworks for each T

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  9. parallel renormalization fireworks name

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  10. renormalization klat dir link

    Junsoo Park authored and Junsoo Park committed Mar 20, 2023
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  11. TE iter fix

    @jsyony37
    jsyony37 committed Mar 20, 2023
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  12. anything?

    @jsyony37
    jsyony37 committed Mar 20, 2023
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  13. ToDB

    @jsyony37
    jsyony37 committed Mar 20, 2023
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  14. error fix

    @jsyony37
    jsyony37 committed Mar 20, 2023
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Commits on Mar 21, 2023

  1. renormalization works

    @jsyony37
    jsyony37 committed Mar 21, 2023
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  2. anything?

    @jsyony37
    jsyony37 committed Mar 21, 2023
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  3. renorm data push

    @jsyony37
    jsyony37 committed Mar 21, 2023
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Commits on Mar 23, 2023

  1. renorm_thermal_data

    @jsyony37
    jsyony37 committed Mar 23, 2023
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  2. dependencies

    Junsoo Park authored and Junsoo Park committed Mar 23, 2023
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  3. len(temperature)=1

    @jsyony37
    jsyony37 committed Mar 23, 2023
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Commits on Apr 4, 2023

  1. everything works?

    @jsyony37
    jsyony37 committed Apr 4, 2023
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  2. cleanup

    @jsyony37
    jsyony37 committed Apr 4, 2023
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Commits on May 19, 2023

  1. fixed random displacements

    Junsoo Park authored and Junsoo Park committed May 19, 2023
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Commits on May 24, 2023

  1. T diff

    Junsoo Park authored and Junsoo Park committed May 24, 2023
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Commits on May 25, 2023

  1. syntax errors

    Junsoo Park authored and Junsoo Park committed May 25, 2023
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Commits on Jun 9, 2023

  1. remove separate_fit

    Junsoo Park authored and Junsoo Park committed Jun 9, 2023
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  2. remove separate_fit

    @jsyony37
    jsyony37 committed Jun 9, 2023
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Commits on Jun 14, 2023

  1. separate harmonic

    Junsoo Park authored and Junsoo Park committed Jun 14, 2023
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Commits on Jun 21, 2023

  1. small fix

    Zhuoying Zhu authored and Zhuoying Zhu committed Jun 21, 2023
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  2. clean-up

    @Zhuoying
    Zhuoying committed Jun 21, 2023
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Commits on Jan 5, 2024

  1. PhonopySupercellTransformation

    @jsyony37
    jsyony37 committed Jan 5, 2024
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Commits on Jan 12, 2024

  1. ARC AIMD

    Junsoo Park committed Jan 12, 2024
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Commits on Mar 2, 2024

  1. TI_IFC + clean-up

    @jsyony37
    jsyony37 committed Mar 2, 2024
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Commits on Mar 4, 2024

  1. Merge branch 'jsyony37:lattice-dynamics' into lattice-dynamics

    @Zhuoying
    Zhuoying committed Mar 4, 2024
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