def nuclear_dipole_moment(atomlist):
rcc=['CC', 0.0, 0.0, 0.0]
for atom in atomlist:
rcc[1] += atomic_data.charge(atom[0])*atom[1]
rcc[2] += atomic_data.charge(atom[0])*atom[2]
rcc[3] += atomic_data.charge(atom[0])*atom[3]
for i in range(1,4):
if rcc[i]<1e-10:
rcc[i]=0.0
return rcc[1:]
def nuclear_repulsion(atomlist):
nucrep=0.0; total_charge=0.0
for i in range(len(atomlist)):
if atomlist[i][0] in ecp_atoms:
qi = atomic_data.ecp_charge(atomlist[i][0])
else:
qi = atomic_data.charge(atomlist[i][0])
total_charge += qi
for j in range(i+1,len(atomlist)):
if atomlist[j][0] in ecp_atoms:
qj = atomic_data.ecp_charge(atomlist[j][0])
else:
qj = atomic_data.charge(atomlist[j][0])
nucrep += qi*qj / atomdist(atomlist[i],atomlist[j])
return nucrep, total_charge
def get_atoms(filename,verbose=False):
import sys
from utils import atomic_data
from utils.conversion import au2ang
try:
dalinp=open(filename,'r')
except:
print 'file not found:', filename
sys.exit(2)
atomlist=[]
symgenlist=[]
fact = 1.0
ntypes_count=0
line=dalinp.readline()
while line:
if line.find('Atomtypes')>-1:
pos=line.find('Atomtypes')+len('Atomtypes')+1
ntypes=int(line[pos:pos+2])
if line.find('Angstrom')>-1:
fact=1.0/au2ang
if line.find('Generators')>-1:
if line.find(' X ')>0:
symgenlist.append([-1, 1, 1])
if line.find(' Y ')>0:
symgenlist.append([1, -1, 1])
if line.find(' Z ')>0:
symgenlist.append([1, 1, -1])
if line.find(' XY ')>0:
symgenlist.append([-1, -1, 1])
if line.find(' XZ ')>0:
symgenlist.append([-1, 1, -1])
if line.find(' YZ ')>0:
symgenlist.append([1, -1, -1])
if line.find('XYZ')>0:
symgenlist.append([-1, -1, -1])
if line.find('Atoms')>-1:
ntypes_count+=1
pos=line.find('Atoms')+len('Atoms')+1
natoms=int(line[pos:].split()[0])
pos=line.find('Charge')+len('Charge')+1
charge=float(line[pos:pos+4])
label=''
for l in atomic_data.labels:
if not label:
if atomic_data.charge(l)==charge:
label=l
if not label:
print 'atomic label not found for charge=',charge
sys.exit()
for i in range(0,natoms):
line=dalinp.readline()
field=line.split()
atom=[label,\
float(field[1])*fact,\
float(field[2])*fact,\
float(field[3])*fact]
atomlist.append(atom)
line=dalinp.readline()
if verbose:
if fact == 1.0:
print 'Input file coordinates were given in a.u.'
else:
print 'Input file coordinates were given in Angstrom'
print 'Atoms specified in input file:'
for atom in atomlist:
print atom
print 'Symmetry generators specified in input file:'
for symgen in symgenlist:
print symgen
if ntypes!=ntypes_count:
print 'Incorrect specification of number of atom types.'
sys.exit(2)
return atomlist,symgenlist
