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Manual supercells #176

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merged 17 commits into from
Oct 25, 2024
Merged

Manual supercells #176

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f4ae0d4
add manual setable supercell_matrix to single-atom displaced supercel…
QuantumChemist Oct 23, 2024
5438847
add manual setable supercell_matrix to rattled supercell jobs
QuantumChemist Oct 23, 2024
5552845
make sure that ALGO is consitently set to Normal everywhere
QuantumChemist Oct 24, 2024
8376c3b
pass a supercell_matrix for each structure
QuantumChemist Oct 24, 2024
ca5f681
use mp_id instead of structure to pass supercell_matrix
QuantumChemist Oct 24, 2024
5dc7aae
adjust unit test to code change
QuantumChemist Oct 24, 2024
9eebac5
added a unit test and test data for manual supercells for single-atom…
QuantumChemist Oct 24, 2024
fe4c1e9
added a manual supercell_matrix test for rattled supercells
QuantumChemist Oct 25, 2024
247f719
add mock tets data
QuantumChemist Oct 25, 2024
abd5fe2
adjust mock output data
QuantumChemist Oct 25, 2024
909851c
finalize unit test
QuantumChemist Oct 25, 2024
1555529
adding comment
QuantumChemist Oct 25, 2024
23c130a
add documentation
QuantumChemist Oct 25, 2024
18d2471
switch to new MLIP PhononMaker setup
QuantumChemist Oct 25, 2024
7ee82c5
temporary adjust expected M3GNET RMSE
QuantumChemist Oct 25, 2024
17f780b
go back to old code layout for MLIP PhononMakers with adjusted Relax …
QuantumChemist Oct 25, 2024
9a0ecbb
change back the M3GNet RMSE value to the old value
QuantumChemist Oct 25, 2024
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7 changes: 6 additions & 1 deletion autoplex/auto/phonons/jobs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -327,7 +327,9 @@ def dft_phonopy_gen_data(
jobs = []
dft_phonons_output = {}
dft_phonons_dir_output = []
supercell_matrix = reduce_supercell_size(structure, **supercell_settings)
supercell_matrix = supercell_settings.get(structure, {}).get("supercell_matrix")
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if not supercell_matrix:
supercell_matrix = reduce_supercell_size(structure, **supercell_settings)

if phonon_displacement_maker is None:
phonon_displacement_maker = TightDFTStaticMaker(name="dft phonon static")
Expand All @@ -337,6 +339,7 @@ def dft_phonopy_gen_data(
run_vasp_kwargs={"handlers": {}},
input_set_generator=TightRelaxSetGenerator(
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand All @@ -360,6 +363,7 @@ def dft_phonopy_gen_data(
input_set_generator=StaticSetGenerator(
auto_ispin=False,
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand Down Expand Up @@ -488,6 +492,7 @@ def dft_random_gen_data(
run_vasp_kwargs={"handlers": {}},
input_set_generator=TightRelaxSetGenerator(
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISYM": 0, # to be changed
Expand Down
34 changes: 22 additions & 12 deletions autoplex/data/phonons/flows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ class TightDFTStaticMaker(PhononDisplacementMaker):
input_set_generator: VaspInputGenerator = field(
default_factory=lambda: StaticSetGenerator(
user_incar_settings={
"ALGO": "Normal", # not switching to Fast because it's not precise enough for the fit
"IBRION": -1,
"ISPIN": 1,
"ISMEAR": 0,
Expand All @@ -93,7 +94,6 @@ class TightDFTStaticMaker(PhononDisplacementMaker):
"EDIFF": 1e-7,
"LAECHG": False,
"LREAL": False,
"ALGO": "Normal", # not switching to Fast because it's not precise enough for the fit
"NSW": 0,
"LCHARG": False, # Do not write the CHGCAR file
"LWAVE": False, # Do not write the WAVECAR file
Expand Down Expand Up @@ -216,6 +216,7 @@ class DFTPhononMaker(PhononMaker):
run_vasp_kwargs={"handlers": {}},
input_set_generator=TightRelaxSetGenerator(
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand All @@ -239,6 +240,7 @@ class DFTPhononMaker(PhononMaker):
input_set_generator=StaticSetGenerator(
auto_ispin=False,
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand Down Expand Up @@ -329,6 +331,7 @@ class RandomStructuresDataGenerator(Maker):
run_vasp_kwargs={"handlers": {}},
input_set_generator=TightRelaxSetGenerator(
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISYM": 0, # to be changed
Expand Down Expand Up @@ -391,18 +394,23 @@ def make(
jobs.append(relaxed)
structure = relaxed.output.structure

supercell_matrix_job = reduce_supercell_size_job(
structure=structure,
min_length=self.supercell_settings.get("min_length", 12),
max_length=self.supercell_settings.get("max_length", 25),
fallback_min_length=self.supercell_settings.get("fallback_min_length", 10),
max_atoms=self.supercell_settings.get("max_atoms", 500),
min_atoms=self.supercell_settings.get("min_atoms", 50),
step_size=self.supercell_settings.get("step_size", 1.0),
supercell_matrix = self.supercell_settings.get(structure, {}).get(
"supercell_matrix"
)
jobs.append(supercell_matrix_job)

supercell_matrix = supercell_matrix_job.output
if not supercell_matrix:
supercell_matrix_job = reduce_supercell_size_job(
structure=structure,
min_length=self.supercell_settings.get("min_length", 12),
max_length=self.supercell_settings.get("max_length", 25),
fallback_min_length=self.supercell_settings.get(
"fallback_min_length", 10
),
max_atoms=self.supercell_settings.get("max_atoms", 500),
min_atoms=self.supercell_settings.get("min_atoms", 50),
step_size=self.supercell_settings.get("step_size", 1.0),
)
jobs.append(supercell_matrix_job)
supercell_matrix = supercell_matrix_job.output

random_rattle_sc = generate_randomized_structures(
structure=structure,
Expand Down Expand Up @@ -754,6 +762,7 @@ class IsoAtomStaticMaker(StaticMaker):
default_factory=lambda: StaticSetGenerator(
user_kpoints_settings={"reciprocal_density": 1},
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand Down Expand Up @@ -804,6 +813,7 @@ def make(
isolated_atom_static_input_set = StaticSetGenerator(
user_kpoints_settings={"grid_density": 1},
user_incar_settings={
"ALGO": "Normal",
"ISPIN": 1,
"LAECHG": False,
"ISMEAR": 0,
Expand Down
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