#!/usr/bin/python
import os
from molecule import get_N, get_labels, get_xyz
def E(i,j,hi,hj):
path = "x%dx%d_%d%d/output.dat" % (i,j,hi,hj)
if os.path.isfile(path):
for line in reversed( open(path).readlines() ):
if line[:18] == " Total Energy =":
return float(line[19:])
###########################
# BEGIN COMPUTING HESSIAN #
###########################
h = 0.005 # displacement size
N = get_N() # number of atoms
H = [[0.0 for i in range(3*N)] for j in range(3*N)] # Hessian matrix -- initialize with zeros
# diagonal elements
for i in range(3*N):
H[i][i] = ( E(i,0,+1,0)+E(i,0,-1,0)-2*E(0,0,0,0) ) / (h*h)
# off-diagonal elements
for i in range(3*N):
for j in range(i):
H[i][j] = ( E(i,j,+1,+1)+E(i,j,-1,-1)-E(i,0,+1,0)-E(i,0,-1,0)-E(j,0,+1,0)-E(j,0,-1,0)+2*E(0,0,0,0) ) / (2*h*h)
H[j][i] = H[i][j]
#########################
# END COMPUTING HESSIAN #
#########################
outfile = open('hessian.txt','w')
energy('scf')
"""
def make_input(dirname,labels,coords):
coordstring = ""
for a in range(len(labels)):
coordstring += ("%3s %10.7f %10.7f %10.7f\n" % (labels[a],coords[3*a+0],coords[3*a+1],coords[3*a+2]))
if not os.path.exists(dirname):
os.makedirs(dirname)
f = open(dirname+'/input.dat','w+')
f.write(template % coordstring)
print dirname + template % coordstring
h = 0.005
N = get_N()
make_input("x0x0_00",get_labels(),get_xyz())
for i in range(3*N):
disp_forward = get_xyz()
disp_backward = get_xyz()
disp_forward[i] += h
disp_backward[i] -= h
make_input("x%dx0_10"%i, get_labels(), disp_forward)
make_input("x%dx0_-10"%i, get_labels(), disp_backward)
for i in range(3*N):
for j in range(0,i):
disp_forward = get_xyz()
disp_backward = get_xyz()
disp_forward[i] += h
disp_backward[i] -= h
#!/usr/bin/python
import os
from molecule import get_N, get_labels, get_xyz
def run_input(dirname):
os.chdir(dirname)
os.system("psi4")
print "running in ... " + os.getcwd()
os.chdir("../")
run_input("x0x0_00")
for i in range(3*get_N()):
run_input("x%dx0_10" % i)
run_input("x%dx0_-10" % i)
for i in range(3*get_N()):
for j in range(i):
run_input("x%dx%d_11" %(i,j))
run_input("x%dx%d_-1-1" %(i,j))
