run.py

from rw_xyz import read_xyz,write_xyz
from displace_coords import displace_coords 
from variables import *
from random import random

AtomList,R0,comment = read_xyz('equilibrium.xyz')  # read starting coordinates

####################################################

for j in range(N):  # loop N times
  print('Step ' + str(j+1))
  D=R0  # Starting coordinates
  for i in range(nmodes):  # Loop over modes
    if nmodes==1:
      b=a 
      imode=Modes
    else:
      b=a[i]
      imode=Modes[i]  # Mode number
    if randm==1:
      v = random()  # random value between 0 and 1
      Factor = b*(2*v-1)  # random value in range [-a,a]
    else:
      Factor = b
    D = displace_coords(D,imode,freqcm1[i],Factor)	# Displace coordinates along mode 'imode' by 'Factor'
  x=len(str(N))
  frmat="%0" + str(x) + "d"
  fname='xyz/' + str(frmat % (j+1))  + '.xyz'	# Output file name
  comment=' '  # comment on 2nd line of xyz file
  write_xyz(AtomList,D,fname,comment)  # write to xyz

####################################################