def center_of_mass(atomlist):
total_mass=0.0
rcm=['CM', 0.0, 0.0, 0.0]
for atom in atomlist:
total_mass += atomic_data.mass(atom[0])
rcm[1] += atomic_data.mass(atom[0])*atom[1]
rcm[2] += atomic_data.mass(atom[0])*atom[2]
rcm[3] += atomic_data.mass(atom[0])*atom[3]
for i in range(1,4):
rcm[i] = rcm[i]/total_mass
if rcm[i]<1e-10:
rcm[i]=0.0
return rcm
def get_gaussian_results(filename):
"""Reads information from Gaussian formatted checkpoint files."""
input = open(filename,'r')
s=input.readline()
while s:
if s.find('Number of atoms')!=-1:
natoms=int(s.split()[4])
N=3*natoms
if s.find('Atomic numbers')!=-1:
atom_l=[]
mass_l=[]
nrows=int( (natoms+5)/6 )
for irow in range(nrows):
for Z in input.readline().split():
atom_l.append(label(int(Z)))
mass_l.append(mass(label(int(Z))))
if s.find('Current cartesian coordinates')!=-1:
cart_l=[]
nrows=int( (N+4)/5 )
for irow in range(nrows):
cart_l+=map(float,input.readline().split())
cart_l=array(cart_l)
if s.find('Cartesian Force Constants')!=-1:
h=zeros((N,N))
r=0; c=0
nrows=int( (N*(N+1)/2+4)/5 )
for irow in range(nrows):
hessian_elements=input.readline().split()
for j in hessian_elements:
if c<r:
h[r,c]=float(j)
h[c,r]=h[r,c]
c+=1
elif c==r:
h[r,r]=float(j)
c=0;r+=1
s=input.readline()
return h, atom_l, mass_l, cart_l
