def test_Mcsqs_Caller_supercell(self):
struc = self.struc.copy()
struc.replace_species({
'Ti': {
'Ti': 0.5,
'Zr': 0.5
},
'Zr': {
'Ti': 0.5,
'Zr': 0.5
}
})
sqs = run_mcsqs(struc, {
2: 6,
3: 4
},
supercell=[2, 1, 1],
total_atoms=None,
search_time=0.01)
self.assertEqual(atat.Mcsqs(sqs).to_string() in self.pztstrings, True)
os.remove('sqscell.out')
os.remove('rndstrgrp.out')
os.remove('bestcorr.out')
os.remove('rndstr.in')
os.remove('sym.out')
os.remove('mcsqs.log')
os.remove('bestsqs.out')
os.remove('clusters.out')
def test_apply_transformation(self):
# non-sensical example just for testing purposes
self.pztstrings = np.load(os.path.join(test_dir,
"mcsqs/pztstrings.npy"),
allow_pickle=True)
self.struct = self.get_structure('Pb2TiZrO6')
trans = SQSTransformation({
2: 6,
3: 4
},
supercell=[2, 1, 1],
total_atoms=None,
search_time=0.01)
struct = self.struct.copy()
struct.replace_species({
'Ti': {
'Ti': 0.5,
'Zr': 0.5
},
'Zr': {
'Ti': 0.5,
'Zr': 0.5
}
})
sqs = trans.apply_transformation(struct)
self.assertEqual(atat.Mcsqs(sqs).to_string() in self.pztstrings, True)
os.remove('sqscell.out')
os.remove('rndstrgrp.out')
os.remove('bestcorr.out')
os.remove('rndstr.in')
os.remove('sym.out')
os.remove('mcsqs.log')
os.remove('bestsqs.out')
os.remove('clusters.out')
def test_Mcsqs_Caller_total_atoms(self):
struc = self.struc.copy()
struc.replace_species({
"Ti": {
"Ti": 0.5,
"Zr": 0.5
},
"Zr": {
"Ti": 0.5,
"Zr": 0.5
}
})
sqs = run_mcsqs(struc, {2: 6, 3: 4}, total_atoms=20, search_time=0.01)
self.assertEqual(atat.Mcsqs(sqs).to_string() in self.pztstrings2, True)
def run_mcsqs(structure,
clusters,
supercell=None,
total_atoms=None,
search_time=0.01):
"""
Helper function for calling mcsqs with different arguments
Args:
clusters (dict): dictionary of cluster interactions with entries in the form
# atoms: cutoff in angstroms
supercell (list): dimensions of the supercell in units of the original unit cell
total_atoms(int): total number of atoms in the final SQS. Choose either
this OR supercell
search_time (int): The time spent looking for the ideal SQS in minutes
Returns:
Pymatgen structure which is an SQS of the input structure
"""
num_atoms = len(structure)
if total_atoms is None:
total_atoms = num_atoms
if supercell is not None and total_atoms != num_atoms:
print("pick supercell OR number of atoms")
return
# Set supercell
cell = np.eye(3)
text_file = open("sqscell.out", "w")
text_file.write("1\n")
for i in range(len(cell)):
text_file.write("\n")
for j in range(len(cell[i])):
text_file.write(str(cell[i][j]) + " ")
text_file.close()
struccopy = structure.copy()
if supercell is not None:
struccopy.make_supercell(supercell)
struc = atat.Mcsqs(struccopy)
text_file = open("rndstr.in", "w")
text_file.write(struc.to_string())
text_file.close()
# Generate Clusters
command = ["mcsqs"]
for num in clusters:
command.append("-" + str(num) + "=" + str(clusters[num]))
p = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
)
p.communicate()
command = ["mcsqs", "-rc", "-n {}".format(len(structure))]
p = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
)
try:
p.communicate(timeout=search_time * 60)
except subprocess.TimeoutExpired:
p.kill()
p.communicate()
if os.path.exists("bestsqs.out"):
text_file = open("bestsqs.out", "r")
bestsqs = text_file.read()
text_file.close()
return atat.Mcsqs.structure_from_string(bestsqs)
else:
raise TimeoutError("Cluster expansion took too long.")
else:
struc = atat.Mcsqs(struccopy)
text_file = open("rndstr.in", "w")
text_file.write(struc.to_string())
text_file.close()
# Generate Clusters
command = ["mcsqs"]
for num in clusters:
command.append("-" + str(num) + "=" + str(clusters[num]))
p = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
)
p.communicate()
command = ["mcsqs", "-n {}".format(total_atoms)]
p = subprocess.Popen(
command,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
)
try:
p.communicate(timeout=search_time * 60)
except subprocess.TimeoutExpired:
p.kill()
p.communicate()
if os.path.exists("bestsqs.out"):
text_file = open("bestsqs.out", "r")
bestsqs = text_file.read()
text_file.close()
return atat.Mcsqs.structure_from_string(bestsqs)
else:
raise TimeoutError("Cluster expansion took too long.")