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Add supercell to UEP clustering #78 #79

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Jun 9, 2023
Merged

Add supercell to UEP clustering #78 #79

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2de985a
Add supercell to UEP clustering #78
patrick-austin Apr 11, 2023
99575d7
Flake8 line length in test_utils.py #78
patrick-austin Apr 11, 2023
01f87ae
Refactor write_cell and use to save clusters #78
patrick-austin Apr 11, 2023
94deccc
Merge branch 'main' into uep_supercell_78
patrick-austin Jun 9, 2023
baf2ec8
Remove unused import following merge
patrick-austin Jun 9, 2023
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83 changes: 51 additions & 32 deletions pymuonsuite/io/castep.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
import numpy as np
import scipy.constants as cnst

from ase import io
from ase import Atoms, io
from ase.calculators.castep import Castep
from ase.io.castep import read_param, write_param
from ase.io.magres import read_magres
Expand Down Expand Up @@ -177,48 +177,67 @@ def write(self, a, folder, sname=None, calc_type="GEOM_OPT"):
| calc_type (str): Castep task which will be performed:
| "GEOM_OPT" or "MAGRES"
"""
if calc_type == "GEOM_OPT" or calc_type == "MAGRES":
if sname is None:
sname = os.path.split(folder)[-1] # Same as folder name
if sname is None:
sname = os.path.split(folder)[-1] # Same as folder name

self._calc = deepcopy(self._calc)
self.write_cell(a, folder, sname, calc_type)

# We only use the calculator attached to the atoms object if a calc
# has not been set when initialising the ReadWrite object OR we
# have not called write() and made a calculator before.
write_param(
os.path.join(folder, sname + ".param"),
a.calc.param,
force_write=True,
)

if self._calc is None:
if isinstance(a.calc, Castep):
self._calc = deepcopy(a.calc)
self._create_calculator(calc_type=calc_type)
else:
self._update_calculator(calc_type)
a.calc = self._calc
with silence_stdio():
io.write(
os.path.join(folder, sname + ".cell"),
a,
magnetic_moments="initial",
)
write_param(
os.path.join(folder, sname + ".param"),
a.calc.param,
force_write=True,
)
if self.script is not None:
stxt = open(self.script).read()
stxt = stxt.format(seedname=sname)
with open(os.path.join(folder, "script.sh"), "w", newline="\n") as sf:
sf.write(stxt)

if self.script is not None:
stxt = open(self.script).read()
stxt = stxt.format(seedname=sname)
with open(os.path.join(folder, "script.sh"), "w", newline="\n") as sf:
sf.write(stxt)
else:
def write_cell(
self, a: Atoms, folder: str, sname: str, calc_type: str = "GEOM_OPT"
):
"""Writes only the cell file for an Atoms object, but includes settings
from the Castep calculator.

| Args:
| a (ase.Atoms): Atoms object to write. Can have a Castep
| calculator attached to carry cell/param
| keywords.
| folder (str): Path to save the input files to.
| sname (str): Seedname to save the files with. If not
| given, use the name of the folder.
| calc_type (str): Castep task which will be performed:
| "GEOM_OPT" or "MAGRES"
"""
if calc_type != "GEOM_OPT" and calc_type != "MAGRES":
raise (
NotImplementedError(
"Calculation type {} is not implemented."
" Please choose 'GEOM_OPT' or 'MAGRES'".format(calc_type)
)
)

self._calc = deepcopy(self._calc)

# We only use the calculator attached to the atoms object if a calc
# has not been set when initialising the ReadWrite object OR we
# have not called write() and made a calculator before.
if self._calc is None:
if isinstance(a.calc, Castep):
self._calc = deepcopy(a.calc)
self._create_calculator(calc_type=calc_type)
else:
self._update_calculator(calc_type)
a.calc = self._calc

with silence_stdio():
io.write(
os.path.join(folder, sname + ".cell"),
a,
magnetic_moments="initial",
)

def _create_calculator(self, calc_type=None):
with silence_stdio():
if self._calc is not None and isinstance(self._calc, Castep):
Expand Down
132 changes: 68 additions & 64 deletions pymuonsuite/io/output.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,11 @@


import os
from ase import io
from ase import Atoms, io
import numpy as np
from datetime import datetime
from scipy.constants import physical_constants as pcnst

from pymuonsuite.utils import safe_create_folder
from pymuonsuite.utils import make_muonated_supercell, safe_create_folder
from pymuonsuite.io.castep import ReadWriteCastep
from pymuonsuite.io.dftb import ReadWriteDFTB

Expand All @@ -34,7 +33,6 @@ def write_cluster_report(args, params, clusters):
)

with open(params["name"] + "_clusters.txt", "w") as f:

f.write(
"""
****************************
Expand Down Expand Up @@ -62,11 +60,9 @@ def write_cluster_report(args, params, clusters):
)

for name, cdata in clusters.items():

f.write("Clusters for {0}:\n".format(name))

if params["clustering_save_min"] or params["clustering_save_type"]:

if params["clustering_save_folder"] is not None:
clustering_save_path = safe_create_folder(
params["clustering_save_folder"]
Expand All @@ -79,7 +75,6 @@ def write_cluster_report(args, params, clusters):
raise RuntimeError("Could not create folder {0}")

for calc, clusts in cdata.items():

# Computer readable
fdat = open(
params["name"] + "_{0}_{1}_clusters.dat".format(name, calc),
Expand All @@ -94,7 +89,6 @@ def write_cluster_report(args, params, clusters):
min_energy_structs = []

for i, g in enumerate(cgroups):

f.write(
"\n\n\t-----------\n\tCluster "
"{0}\n\t-----------\n".format(i + 1)
Expand All @@ -111,6 +105,7 @@ def write_cluster_report(args, params, clusters):
f.write(
"\t{0:.2f}\t\t{1:.2f}\t\t{2:.2f}\n".format(Emin, Eavg, Estd)
)
structure = coll[np.argmin(E)].structures[0]

fdat.write(
"\t".join(
Expand All @@ -122,9 +117,9 @@ def write_cluster_report(args, params, clusters):
Emin,
Eavg,
Estd,
coll[np.argmin(E)].structures[0].positions[-1][0],
coll[np.argmin(E)].structures[0].positions[-1][1],
coll[np.argmin(E)].structures[0].positions[-1][2],
structure.positions[-1][0],
structure.positions[-1][1],
structure.positions[-1][2],
],
)
)
Expand All @@ -133,66 +128,26 @@ def write_cluster_report(args, params, clusters):

f.write(
"\n\tMinimum energy structure: {0}\n".format(
coll[np.argmin(E)].structures[0].info["name"]
structure.info["name"]
)
)

# update symbol and mass of defect in minimum energy structure
min_energy_struct = coll[np.argmin(E)].structures[0]
csp = min_energy_struct.get_chemical_symbols()[:-1] + [
params.get("mu_symbol", "H:mu")
]
min_energy_struct.set_array("castep_custom_species", np.array(csp))
masses = min_energy_struct.get_masses()[:-1]
masses = np.append(
masses,
params.get("particle_mass_amu", pcnst["muon mass in u"][0]),
)
min_energy_struct.set_masses(np.array(masses))

# Save minimum energy structure
if (
params["clustering_save_type"] == "structures"
or params["clustering_save_min"]
):
# For backwards-compatability with old pymuonsuite
# versions
if params["clustering_save_min"]:
if params["clustering_save_format"] is None:
params["clustering_save_format"] = "cif"

try:
calc_path = os.path.join(clustering_save_path, calc)
if not os.path.exists(calc_path):
os.mkdir(calc_path)
fname = "{0}_{1}_min_cluster_" "{2}.{3}".format(
params["name"],
calc,
i + 1,
params["clustering_save_format"],
)

with silence_stdio():
io.write(
os.path.join(calc_path, fname),
min_energy_struct,
)

except (io.formats.UnknownFileTypeError) as e:
print(
"ERROR: File format '{0}' is not "
"recognised. Modify 'clustering_save_format'"
" and try again.".format(e)
)
return
except ValueError as e:
print(
"ERROR: {0}. Modify 'clustering_save_format'"
"and try again.".format(e)
)
success = write_structure(
params,
clustering_save_path,
calc,
f"{params['name']}_{calc}_min_cluster_{i+1}",
structure,
)
if not success:
return

min_energy_structs.append(min_energy_struct)
min_energy_structs.append(structure)

f.write("\n\n\tStructure list:")

Expand Down Expand Up @@ -270,10 +225,60 @@ def write_cluster_report(args, params, clusters):
f.write("\n==========================\n\n")


def write_phonon_report(args, params, phdata):
def write_structure(
params: dict, clustering_save_path: str, calc: str, seedname: str, structure: Atoms
) -> bool:
"""Writes the minimal energy structure in a cluster to file.

| Args:
| params (dict): PyMuonSuite MUAIRSS parameters.
| clustering_save_path (str): Directory to save the clusters in.
| calc (str): Calculator used for the optimisation.
| seedname (str): Seedname for the saved structure files.
| structure (Atoms): ASE Atoms to save.
|
| Returns:
| (bool): Whether the structure was written to file successfully.
"""
# For backwards-compatibility with old pymuonsuite versions
if params["clustering_save_min"]:
if params["clustering_save_format"] is None:
params["clustering_save_format"] = "cif"

try:
calc_path = os.path.join(clustering_save_path, calc)
if not os.path.exists(calc_path):
os.mkdir(calc_path)

with silence_stdio():
if calc == "uep":
structure = make_muonated_supercell(
structure, params["supercell"], params["mu_symbol"]
)

with open(params["name"] + "_phonons.txt", "w") as f:
if params["clustering_save_format"].lower() == "cell":
# Account for CASTEP calc settings
read_write_castep = ReadWriteCastep(params)
read_write_castep.write_cell(structure, calc_path, seedname)
else:
filename = f"{seedname}.{params['clustering_save_format']}"
io.write(os.path.join(calc_path, filename), structure)

return True

except io.formats.UnknownFileTypeError as e:
print(
f"ERROR: File format '{e}' is not recognised. "
"Modify 'clustering_save_format' and try again."
)
return False
except ValueError as e:
print(f"ERROR: {e}. Modify 'clustering_save_format' and try again.")
return False


def write_phonon_report(args, params, phdata):
with open(params["name"] + "_phonons.txt", "w") as f:
f.write(
"""
****************************
Expand Down Expand Up @@ -322,7 +327,6 @@ def write_phonon_report(args, params, phdata):


def write_symmetry_report(args, symdata, wpoints, fpos):

print("Wyckoff points symmetry report for {0}".format(args.structure))
print("Space Group International Symbol: " "{0}".format(symdata["international"]))
print("Space Group Hall Number: " "{0}".format(symdata["hall_number"]))
Expand Down
11 changes: 2 additions & 9 deletions pymuonsuite/muairss.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,14 @@
from spglib import find_primitive

from ase import Atoms, io
from ase.build import make_supercell
from soprano.utils import customize_warnings, silence_stdio
from soprano.collection import AtomsCollection
from soprano.collection.generate import defectGen
from soprano.analyse.phylogen import PhylogenCluster, Gene
from soprano.rnd import Random

from pymuonsuite.utils import (
make_3x3,
make_supercell,
safe_create_folder,
get_element_from_custom_symbol,
)
Expand Down Expand Up @@ -64,13 +63,7 @@ def generate_muairss_collection(struct, params):
)

# Make a supercell
sm = make_3x3(params["supercell"])
# ASE's make_supercell is weird, avoid if not necessary...
smdiag = np.diag(sm).astype(int)
if np.all(np.diag(smdiag) == sm):
scell0 = struct.repeat(smdiag)
else:
scell0 = make_supercell(struct, sm)
scell0 = make_supercell(struct, params["supercell"])

reduced_struct = find_primitive_structure(struct)

Expand Down