def mddata(self, inf='md.in', outf='md.out'):
if self.md_init is None:
try:
return md.Md(inf, outf)
except FileNotFoundError:
print("No MD data found in {}".format(os.get_cwd()))
return self.md_init
def main():
dest_dir='./scfs'
try:
os.mkdir(dest_dir)
except FileExistsError:
pass
x=md.Md('md.in','md.out')
traj = x.get_trajectory1()
for i in range(len(traj)):
pos = ''
for line in traj[i]:
pos += line+'\n'
scfinput = fstring.format(i,pos)
f=open('{}/scf.{}.in'.format(dest_dir,i),'w')
f.write(scfinput)
f.close()
def main():
dest_dir = './scfs'
try:
os.mkdir(dest_dir)
except FileExistsError:
pass
x = md.Md('md.in', 'md.out')
nat = x.nat
ntyp = x.ntyp
traj = x.get_trajectory1()
latvex = x.latvex_string
for i in range(len(traj)):
positions = ''
for line in traj[i]:
positions += line + '\n'
scfinput = fstring.format(i, nat, ntyp, latvex, positions)
f = open('{}/scf.{}.in'.format(dest_dir, i), 'w')
f.write(scfinput)
f.close()
#!/usr/bin/env python3
import md as md
import datafile as d
import matrix as m
import matplotlib.pyplot as plt
nat = 24
x = md.Md('md.out')
positions = x.get_trajectory2()
latvecs = m.get_pwi_latvecs('md.in')
positions.pop()
#xyzpositions = []
#for i in positions:
# xyz = []
# for j in range(nat):
# xyz.append(latvecs @ i[j])
# xyzpositions.append(xyz)
# getting Cl1-C2 bondlengths
# must subtract 1 due to zero indexing
Cl_ind = 1 - 1
C_ind = 2 - 1
distances = []
"""
Generate x-hetero modes for Cl libration in pcl2phi.
usage: ./xhet.py arg1
arg1 is the angle by which
Cl12 and Cl11 will be rotated
about the point at the nearest carbon.
"""
if len(sys.argv) > 1:
theta_y = int(sys.argv[1])*np.pi/180
# We attempt to roate the molcule to correct orientation
# by roating the molecule about the z axis
x = md.Md('best.origin.crystal.works.pwi')
pos = x.get_trajectory2()[0]
rc1 = pos[0]
rc11 = pos[10]
rc4 = pos[3]
rcl12 = pos[11]
# these two R's should be identical
# but due to OCD we will define both
# R412: the distance from c4 to cl12
# R111: the distance from c1 to cl11
R412 = m.norm(rc4-rcl12)
R111 = m.norm(rc1-rc11)
