def get_extremal_mode_vectors(self, save2file=True):
"""
This function gets the values of the displacements of the irreducible
sites of the structures between which we are interpolating.
"""
if self.modeValues is not None:
print("Extremal modes have already been extracted.")
return None
if 'modevals_dict.npy' in os.listdir("."):
if self.verbose:
print("Reading end-member mode values from .npy file.")
self.modeValues = list(
np.load('modevals_dict.npy', allow_pickle="TRUE"))
else:
# Initialise Isodistort instance with HTT
iso = isodistort(self.HS, silent=self.silent)
self.modeValues = []
for lsFile in [self.LS1, self.LS2]:
iso.load_lowsym_structure(lsFile)
iso.get_mode_labels()
self.modeValues.append(iso.modevalues)
iso.close()
if self.verbose:
return self.modeValues
elif save2file:
#Save to binary file if requested
np.save('modevals_dict.npy', self.modeValues)
def print_interp_cif(self, extent='all'):
# Launch ISODISTORT class instance
# Load HS and starting-point LS structures
itp = isodistort(self.HS, silent=self.silent)
itp.load_lowsym_structure(self.LS1)
itp.get_mode_labels()
if extent == 'all':
for key in self.interpList:
if self.verbose:
print(key)
# Define filename
fname = "La2MgO4_interpolated_{:.3f}_{:.3f}.cif".\
format(key[0], key[1])
# Pass if filename already in directory
if fname in os.listdir('.'):
continue
assert 'subgroup_cif(1).txt' not in os.listdir('.'),\
"New structure 'subgroup_cif.txt' downloaded " + \
"before previous one was converted."
# Set the mode values for this interpolation
# Iterate over interpolation entries
itp.modevalues = self.interpList[key]
itp.set_amplitudes()
itp.save_cif(fname=fname)
elif extent in self.interpList:
key = extent
if self.verbose:
print(key)
# Set the mode values for this interpolation
# Iterate over interpolation entries
itp.modevalues = self.interpList[key]
itp.set_amplitudes()
fname = "La2MgO4_interpolated_{:1.3f}_{:1.3f}.cif".\
format(key[0], key[1])
itp.save_cif(fname=fname)
# Close ISODISTORT page instance.
time.sleep(2)
itp.close()
return None
def reduce_common_subgroup(self):
"""
This function reduces the two low-symmetry files to a common subgroup
with common lattice parameters.
Parameters:
----------
subgroup: int
The number corresponding to the space group of the common subgroup
to both low-symmetry structures.
cellparams: int
The lattice parameters to use for the common reduction of both
low-symmetry structures. 0: high-symmetry file, 1: low-symmetry
file 1, 2: low-symmetry file 2.
Returns:
--------
LS#file_"subgroup".cif: file
Two CIF files in the same directory for the two reduced structures
"""
for sfile in [self.LS1, self.LS2]:
# Initialise ISODISTORT and get reduced structure
iso = isodistort(sfile, silent=self.silent)
iso.choose_by_spacegroup(self.subgroup)
iso.select_space_group()
# Save CIF file and get new name
sfile = sfile.replace('.cif', '_{}.cif'.format(self.subgroup))
iso.save_cif(fname=sfile, close=True)
count = 0
while sfile not in os.listdir("."):
time.sleep(1)
assert count < 10, "Printing CIF file took too long."
return None
def check_mode_vector(self, filename, mode):
"""
This function checks whether the mode amplitude of the generated file
has the expected angle and magnitude.
Parameters:
-----------
filename: str
CIF file given as interpolated_rho_theta.cif
Returns:
"""
seed = filename.strip("interpolated_").strip(".cif")
(rho, theta) = (float(seed.split("_")[0]), float(seed.split("_")[1]))
isocheck = isodistort(self.HS, silent=self.silent)
isocheck.load_lowsym_structure(filename)
isocheck.get_mode_labels()
modevalues = isocheck.modevalues[mode]
isocheck.close()
N = len(modevalues)
norm = round(la.norm(modevalues), 3)
try:
thetas = (180 / np.pi)*np.array([np.arctan(modevalues[i]/\
modevalues[i+1]) for i in range(0, N, 2)])
except ZeroDivisionError:
thetas = np.array([0.0, 0.0, 0.0])
#assert abs(rho - norm) < 1e-3, "The magnitudes of the modes are not"+\
# "the same as what is expected. The expected norm is" + str(rho) + \
# " and the calculated norm is " + str(norm)
#assert abs(thetas[0] - theta) > 1e-3, "The angles are not the same "+\
#"The expected angle is {.1f} and the calculated angle is {.1f}." % \
#(theta, thetas[0])
return modevalues, rho, theta, norm, thetas
import sys
from isodistortfile import isodistort
"""
Script for representing a cif file as a lower symmetry space group by
inputing zero amplitude distortions using isodistort
e.g.
./iso_index_as.py input.cif output.cif 31
To make an output file that is space group 31 from input.cif
or ./iso_index_as.py input.cif output.cif 31 2
If you know that the particular SG 31 cell you want is the third option.
"""
HSfile = os.getcwd()+'/'+sys.argv[1]
outputfile = sys.argv[2]
SG = int(sys.argv[3])
if len(sys.argv) > 4:
list_id = int(sys.argv[4])
else:
list_id = 0
iso = isodistort(HSfile, silent=True)
iso.choose_by_spacegroup(SG)
iso.select_space_group(list_id=list_id)
iso.set_amplitudes(outputfile, {})
iso.close()