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Lattice dynamics workflow using Pheasy #1063

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0775785
Add pheasy branch for phonon calculation using LASSO
leslie-zheng Sep 9, 2024
7891554
pheasy_phonons
leslie-zheng Sep 9, 2024
d643fc1
add_pheasy_to_vasp_folder
leslie-zheng Sep 10, 2024
93219ce
Add_pheasy_to_vasp_file
leslie-zheng Sep 10, 2024
f4b59c6
Merge branch 'main' into atomate2_jz_pheasy
JaGeo Sep 16, 2024
e514969
Merge branch 'main' into atomate2_jz_pheasy
JaGeo Sep 20, 2024
11d546b
Modified some parts based on Janine's comments.
leslie-zheng Sep 23, 2024
13acf5a
Merge branch 'atomate2_jz_pheasy' of https://github.com/leslie-zheng/…
leslie-zheng Sep 23, 2024
57ab59f
directly import the class methods from phonons
leslie-zheng Sep 23, 2024
647fe49
clean up the code
leslie-zheng Sep 23, 2024
94a1acc
remove some files.
leslie-zheng Sep 23, 2024
b92e34e
minor change
leslie-zheng Sep 23, 2024
05650d0
allow the users to define the number of displacements for random-disp…
leslie-zheng Sep 23, 2024
0bf1bf8
format_adjustment
leslie-zheng Sep 23, 2024
e9cd8a6
format_adjustment
leslie-zheng Sep 23, 2024
2bacc86
small update
leslie-zheng Sep 24, 2024
4535497
clean up the code and add more comments
leslie-zheng Sep 24, 2024
eab1fe6
minor update
leslie-zheng Sep 24, 2024
36aa5b7
allow the users to control the symmetry precision
leslie-zheng Sep 24, 2024
c69df93
Lower the symmetry precision to allow pheasy to find a correct space …
leslie-zheng Sep 24, 2024
92ea25a
Minor update
leslie-zheng Sep 24, 2024
5d6f122
minor adjustment
leslie-zheng Sep 24, 2024
e17a316
minor update for flow/pheasy.py
leslie-zheng Sep 24, 2024
f46c2fd
resuse some jobs from phonons
leslie-zheng Sep 25, 2024
34a197e
clean up the job(generate_phonon_displacements)
leslie-zheng Sep 25, 2024
be89bce
finished cleaning up the pheasy jobs module
leslie-zheng Sep 25, 2024
1316b1d
finished cleaning up the shemas/pheasy
leslie-zheng Sep 25, 2024
833205a
small adjustment to pass the lint
leslie-zheng Sep 28, 2024
f741a8c
raise a error if ALM is not installed.
leslie-zheng Sep 28, 2024
30de21a
minor update
leslie-zheng Sep 28, 2024
69956d7
Merge branch 'main' into atomate2_jz_pheasy
leslie-zheng Sep 28, 2024
1726fc9
first try
leslie-zheng Sep 29, 2024
0a7018b
finished testing
leslie-zheng Sep 29, 2024
f834a6e
Extract_higher_order_FCs
leslie-zheng Sep 30, 2024
0e54a10
anharmonic FCs cals. still in experiment.
leslie-zheng Sep 30, 2024
4a0256f
minor updata for the anharmonic FCs calculations
leslie-zheng Sep 30, 2024
516a066
minor update
leslie-zheng Oct 1, 2024
79590d8
minor update
leslie-zheng Oct 1, 2024
d6713d3
minor update
leslie-zheng Oct 1, 2024
14796ea
minor update
leslie-zheng Oct 1, 2024
63db3d1
adjustment and add comments
leslie-zheng Oct 1, 2024
a64bbfc
added the missing argument mp-id
hrushikesh-s Oct 1, 2024
47b4974
added support of force field
hrushikesh-s Oct 1, 2024
ff427dc
multiply a factor of 1.89 to convert the unit of A to Borh for ALM
leslie-zheng Oct 2, 2024
63e0a1c
use filed to define fcs_cutoff_radius instead of a simple list.
leslie-zheng Oct 2, 2024
09872f8
update definition of fcs_cutoff_radius
leslie-zheng Oct 2, 2024
e2b25f9
convert Bohr radius to Å
hrushikesh-s Oct 2, 2024
a1709cd
giving a reasonable displaced distance for the anharmonic case.
leslie-zheng Oct 2, 2024
e788a9d
Merge branch 'atomate2_jz_pheasy_anharmonic' of https://github.com/le…
leslie-zheng Oct 2, 2024
2909e65
minor update
leslie-zheng Oct 2, 2024
509615c
update
leslie-zheng Oct 2, 2024
63463be
Unit tests for pheasy wf
hrushikesh-s Oct 4, 2024
d43c3ee
Test # 1
hrushikesh-s Oct 4, 2024
4e8d491
avoid circular import
leslie-zheng Oct 11, 2024
41792d4
Merge branch 'atomate2_jz_pheasy_anharmonic' of https://github.com/le…
leslie-zheng Oct 11, 2024
de6befb
update some stupid over-writing
leslie-zheng Oct 11, 2024
5e923bd
update the matrix I should use
leslie-zheng Oct 12, 2024
c7c6a5d
using phono3py for lattice thermal conductivity calculation
leslie-zheng Oct 12, 2024
b978f61
update for phono3py thermal conductivity
leslie-zheng Oct 12, 2024
5875952
update phonon energy renomralization
leslie-zheng Oct 13, 2024
ffcbbdd
phonon renormalization
leslie-zheng Oct 13, 2024
7a6a0ad
Auto stash before rebase of "atomate2_jz_pheasy_anharmonic" onto "ori…
hrushikesh-s Oct 13, 2024
572ede4
test files for pheasy
hrushikesh-s Nov 21, 2024
30cab3f
added 1 extra disp
hrushikesh-s Nov 21, 2024
91481a0
ruff fixes to schemas/pheasy.py
hrushikesh-s Nov 21, 2024
905c8ac
ruff fixes to flows/pheasy.py
hrushikesh-s Nov 21, 2024
dc89ca6
ruff fixes to jobs/pheasy.py
hrushikesh-s Nov 21, 2024
4ec42ad
pre-commit vasp/flows/pheasy
hrushikesh-s Nov 22, 2024
4370a64
updated pyproject.toml
hrushikesh-s Nov 22, 2024
9ebcaec
Merge branch 'remote-main' into atomate2_jz_pheasy_anharmonic
hrushikesh-s Nov 22, 2024
6453445
updated the way to install pheasy for testing purposes
hrushikesh-s Nov 22, 2024
1708153
removed pheasy from [strict]
hrushikesh-s Nov 22, 2024
3f3a01a
added hiphive dependency
hrushikesh-s Nov 22, 2024
e56a6fb
added max_length argument
hrushikesh-s Nov 22, 2024
32d5523
removed forcefields/test_pheasy.py
hrushikesh-s Nov 22, 2024
294a787
add conda install steps for alamode
hrushikesh-s Nov 22, 2024
6ba11d5
updated conda command for alamode
hrushikesh-s Nov 22, 2024
efd1480
adding f90nml to strict
hrushikesh-s Nov 22, 2024
cae1727
adding further installation steps for alamode
hrushikesh-s Nov 22, 2024
dd5ec21
alamode installation -- bug fix 1
hrushikesh-s Nov 22, 2024
5a410d4
alamode installation -- bug fix 2
hrushikesh-s Nov 22, 2024
a8f805a
alamode installation -- bug fix 3
hrushikesh-s Nov 22, 2024
f1c5ee5
alamode installation -- bug fix 4
hrushikesh-s Nov 22, 2024
fc5901d
alamode installation -- bug fix 5
hrushikesh-s Nov 22, 2024
9880778
alamode installation -- bug fix 6
hrushikesh-s Nov 22, 2024
6a6c2aa
added tol to test_phonons.py
hrushikesh-s Nov 22, 2024
35ac961
bug fix for linear strain passing in qha (#1061)
JaGeo Nov 22, 2024
6fd44f1
Fix `generate_phonon_displacements` magmom removal side effect (#1064)
janosh Nov 22, 2024
3d22e6a
Bump emmet-core from 0.84.3rc3 to 0.84.3rc4 (#1065)
dependabot[bot] Nov 25, 2024
bc11904
Bump jobflow from 0.1.18 to 0.1.19 (#1067)
dependabot[bot] Nov 25, 2024
2189373
add openmm description to docs (#1069)
JaGeo Nov 25, 2024
6eca446
fix minor code formatting issues + typos (#1070)
janosh Nov 25, 2024
8a0541a
Docs update, forcefield elastic convenience maker, forcefield enum hy…
esoteric-ephemera Nov 26, 2024
7b16765
Fix bump phonopy (#1006)
naik-aakash Nov 30, 2024
7a98a88
Bump mp-api from 0.42.2 to 0.43.0 (#1075)
dependabot[bot] Dec 2, 2024
66dfd5b
Bump pytest from 8.3.3 to 8.3.4 (#1077)
dependabot[bot] Dec 2, 2024
305bc3b
Bump ipython from 8.29.0 to 8.30.0 (#1076)
dependabot[bot] Dec 2, 2024
244da21
Bump sevenn from 0.10.1 to 0.10.2 (#1080)
dependabot[bot] Dec 9, 2024
de84bc0
Bump emmet-core from 0.84.3rc4 to 0.84.3rc6 (#1081)
dependabot[bot] Dec 9, 2024
dc9335e
update calorine version (#1083)
naik-aakash Dec 9, 2024
31474ef
soften the assert output["relax"]["EOS"]["birch_murnaghan"]["b0"]
hrushikesh-s Dec 10, 2024
a525799
further softening
hrushikesh-s Dec 10, 2024
b2493f9
providing absolute path for FC file
hrushikesh-s Dec 10, 2024
4618005
changed the location of reading FC file
hrushikesh-s Dec 10, 2024
b6964f3
changed the run_locally's attribute of create_folders to false
hrushikesh-s Dec 10, 2024
35a2c40
changed it back to True
hrushikesh-s Dec 10, 2024
0836d1e
adding some print statements for debugging
hrushikesh-s Dec 10, 2024
af27d7b
adding more logger statements for debugging
hrushikesh-s Dec 10, 2024
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12 changes: 12 additions & 0 deletions .github/workflows/testing.yml
Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,20 @@ jobs:
mkdir -p ~/.abinit/pseudos
cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
uv pip install .[strict,strict-forcefields,tests,abinit]
uv pip install -i https://test.pypi.org/simple/ pheasy==0.0.1 # Install pheasy
uv pip install torch-runstats
uv pip install --no-deps nequip==0.5.6


- name: Install ALA-Mode
run: |
micromamba activate a2
micromamba install -n a2 -c conda-forge numpy scipy h5py compilers “libblas=*=*mkl” spglib boost eigen cmake ipython mkl-include openmpi --yes
git clone https://github.com/ttadano/ALM.git # do I need to modify this?
cd ALM # do I need to modify this?
cd python
python setup.py build # do I need to modify this?
uv pip install -e . # do I need to modify this?

- name: Install pymatgen from master if triggered by pymatgen repo dispatch
if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
Expand Down
3 changes: 3 additions & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ amset = ["amset>=0.4.15", "pydash"]
cclib = ["cclib"]
mp = ["mp-api>=0.37.5"]
phonons = ["phonopy>=1.10.8", "seekpath>=2.0.0"]
pheasy = ["hiphive==1.3.1"]
lobster = ["ijson>=3.2.2", "lobsterpy>=0.4.0"]
defects = [
"dscribe>=1.2.0",
Expand Down Expand Up @@ -117,6 +118,8 @@ strict = [
"seekpath==2.1.0",
"tblite==0.3.0; python_version < '3.12'",
"typing-extensions==4.12.2",
"hiphive==1.3.1",
"f90nml==1.4.4",
]
strict-forcefields = [
"calorine==3.0",
Expand Down
442 changes: 442 additions & 0 deletions src/atomate2/common/flows/pheasy.py

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1 change: 1 addition & 0 deletions src/atomate2/common/flows/phonons.py
Original file line number Diff line number Diff line change
Expand Up @@ -162,6 +162,7 @@ class BasePhononMaker(Maker, ABC):

kpath_scheme: str = "seekpath"
code: str = None
mp_id: str = None
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This can be added as metadata.

store_force_constants: bool = True
socket: bool = False

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