class AOForceOutputFile(object):
def __init__(self, filename='aoforce.out'):
self.filename = filename
self.modes = None
def read(self, mol):
natoms = mol.natoms
self.modes = VibModes(3 * natoms, mol)
f = file(self.filename, 'r')
lines = f.readlines()
f.close()
start = -1
end = -1
for i, l in enumerate(lines):
if 'NORMAL MODES and VIBRATIONAL FREQUENCIES' in l:
start = i
elif (start > -1) and ('zero point VIBRATIONAL energy' in l):
end = i
break
if start == -1:
raise Exception('dipole gradients not found in control file')
lines = lines[start + 1:end]
freqlines = [
l[14:] for l in lines if l.strip().startswith('frequency')
]
freqs = ' '.join(freqlines).replace('i', '-')
freqs = numpy.array([float(f) for f in freqs.split()])
self.modes.set_freqs(freqs)
masslines = [
l[22:] for l in lines if l.strip().startswith('reduced mass')
]
redmass = ' '.join(masslines)
redmass = numpy.array([float(f) for f in redmass.split()])
lines = [l[18:] for l in lines]
lines = [
l[2:] for l in lines
if l.startswith('x') or l.startswith('y') or l.startswith('z')
]
normalmodes = numpy.zeros((3 * natoms, 3 * natoms))
ncol = len(lines[0].split())
icol = -ncol
for i, l in enumerate(lines):
irow = i % (3 * natoms)
if irow == 0:
icol += ncol
else:
line = [float(fl) for fl in l.split()]
normalmodes[icol:icol + ncol, irow] = line
self.modes.set_modes_c(normalmodes)
def read_hessian(self, mol):
"""
Reading in the hessian martix.
"""
natoms = mol.natoms
self.hessian = numpy.zeros((natoms * 3, natoms * 3))
self.modes = VibModes(3 * natoms, mol)
f = open(self.filename, 'r')
line = f.readline()
while line != '':
if 'SECOND DERIVATIVES' in line:
break
line = f.readline()
if line == '':
raise Exception('hessian not found in output file')
line = f.readline()
line = f.readline()
line = f.readline()
tmp = [] #temporary list for the lines
while line != '':
if line != ' \n':
tmp.append(line)
line = f.readline()
else:
break
for i, l in enumerate(tmp):
l = l.split()
l.pop(0)
tmp[i] = map(float, l)
self.hessian = numpy.array(tmp)
#symmetrizing the hessian
self.hessian = -(self.hessian + self.hessian.transpose()) / 2.0
f.close()
for i, atmass in enumerate(mol.atmasses):
self.hessian[:,
3 * i:3 * i + 3] = self.hessian[:, 3 * i:3 * i +
3] / math.sqrt(atmass)
self.hessian[3 * i:3 * i +
3, :] = self.hessian[3 * i:3 * i +
3, :] / math.sqrt(atmass)
evals, evecs = numpy.linalg.eigh(self.hessian)
# evals are in eV/Angs**2 *amu
# convert to cm^-1 [evals are in Hartree / (Bohr**2 * amu) ]
evals = evals * eV_in_Joule / (1e-10**2 * amu_in_kg
) # in J/(m*m*kg) = 1/s**2
#print numpy.sqrt(abs(evals))/(2.0*math.pi)/cvel_ms*1e-2
#print '-'*30
for i in range(evals.size):
if evals[i] > 0.0:
evals[i] = math.sqrt(evals[i])
else:
evals[i] = -math.sqrt(-evals[i])
evals = evals / (2.0 * math.pi) # frequency in 1/s
evals = evals / cvel_ms * 1e-2 # wavenumber in 1/cm
#numpy.set_printoptions(precision=4)
#print evals
self.modes.set_freqs(evals)
self.modes.set_modes_mw(evecs.transpose())
def read_hessian(self, mol):
natoms = mol.natoms
self.hessian = numpy.zeros((natoms * 3, natoms * 3))
self.modes = VibModes(3 * natoms, mol)
f = open(self.filename, 'r')
lines = f.readlines()
f.close()
start = -1
end = -1
for i, l in enumerate(lines):
if l.startswith('$hessian'):
start = i
elif (start > -1) and l.startswith('$'):
end = i
break
if start == -1:
raise Exception('dipole gradients not found in control file')
lines = lines[start + 1:end]
ncol = len(lines[0].split()) - 2
lines = [l[6:] for l in lines]
nrow = 3 * natoms / ncol
if 3 * natoms % ncol: nrow = nrow + 1
for i in range(3 * natoms):
row = ' '.join(lines[i * nrow:(i + 1) * nrow])
row = numpy.array([float(f) for f in row.split()])
self.hessian[i, :] = row
# mass-weight Hessian
for i, atmass in enumerate(mol.atmasses):
self.hessian[:,
3 * i:3 * i + 3] = self.hessian[:, 3 * i:3 * i +
3] / math.sqrt(atmass)
self.hessian[3 * i:3 * i +
3, :] = self.hessian[3 * i:3 * i +
3, :] / math.sqrt(atmass)
evals, evecs = numpy.linalg.eigh(self.hessian)
# convert to cm^-1 [evals are in Hartree / (Bohr**2 * amu) ]
evals = evals * Hartree_in_Joule / (Bohr_in_Meter**2 * amu_in_kg
) # in J/(m*m*kg) = 1/s**2
for i in range(evals.size):
if evals[i] > 0.0:
evals[i] = math.sqrt(evals[i])
else:
evals[i] = -math.sqrt(-evals[i])
evals = evals / (2.0 * math.pi) # frequency in 1/s
evals = evals / cvel_ms * 1e-2 # wavenumber in 1/cm
self.modes.set_freqs(evals)
self.modes.set_modes_mw(evecs.transpose())
def read(self, mol):
f = file('snf_control', 'r')
lines = f.readlines()
f.close()
for i, l in enumerate(lines):
if l.startswith('$nummodes'):
nmodes = int(l.split()[-1])
start = i + 1
natoms = mol.natoms
self.modes = VibModes(nmodes, mol)
normalmodes = numpy.zeros((nmodes, 3 * natoms))
freqs = numpy.zeros((nmodes))
for imode in range(nmodes):
freqs[imode] = float(lines[start + imode * natoms].split()[0])
for i in range(natoms):
x, y, z = lines[start + imode * natoms + i].split()[-3:]
normalmodes[imode, 3 * i:3 * i + 3] = [x, y, z]
self.modes.set_modes_c(normalmodes)
self.modes.set_freqs(freqs)
def read(self, mol):
f = file(self.filename, 'r')
lines = f.readlines()
f.close()
for l in lines:
if 'intensities-only-mode' in l:
self.intonly = True
first = 0
last = 0
for i, l in enumerate(lines):
if (first == 0) and ('root no.' in l):
first = i
if 'Generate fake outputs for' in l:
last = i
break
if 'W A R N I N G' in l:
last = i - 1
break
if 'Raman Optical Activity properties for freq.' in l:
self.lwl = float(l[46:57])
if not self.intonly:
natoms = mol.natoms
self.modes = VibModes(3 * natoms - 6, mol)
lines = lines[first:last]
lines = [l for l in lines if not len(l.strip()) == 0]
lines = [l for l in lines if not l.startswith('1')]
normalmodes = numpy.zeros((3 * natoms - 6, 3 * natoms))
freqs = numpy.zeros((3 * natoms - 6))
ncol = len(lines[2][10:].split())
icol = -ncol
for i, l in enumerate(lines):
irow = i % (3 * natoms + 2) - 2
if irow == -2:
if not ('root' in l):
raise Exception(
'wrong number of lines for normal modes')
icol += ncol
else:
line = [float(fl) for fl in l[10:].split()]
if irow == -1:
freqs[icol:icol + ncol] = line
else:
normalmodes[icol:icol + ncol, irow] = line
self.modes.set_modes_mw(normalmodes)
self.modes.set_freqs(freqs)
class AKIRAResults(Results):
def __init__(self,
iterationsfile='akira_iterations.out',
coordfile='coord'):
self.mol = VibToolsMolecule()
self.iterationsfile = iterationsfile
self.coordfile = coordfile
self.modes = None
self.irints = None
def read(self):
import numpy, re
self.mol.read_from_coord(filename=self.coordfile)
#read akira iterations
f = open(self.iterationsfile)
lines = f.readlines()
f.close()
for i, l in enumerate(lines):
if re.search('Final results from module Davidson', l):
start = i
nbas = int(lines[start + 3].split()[-1])
lines = lines[start + 8:start + 8 + nbas]
modes = []
for l in lines:
spl = l.split()
if spl[10] == 'YES':
modes.append([float(spl[2]), float(spl[8])])
self.modes = VibModes(len(modes), self.mol)
self.modes.set_freqs(numpy.array([m[0] for m in modes]))
self.irints = numpy.array([m[1] for m in modes])
def get_ir_intensity(self):
return self.irints
def read(self):
import numpy, re
self.mol.read_from_coord(filename=self.coordfile)
#read akira iterations
f = open(self.iterationsfile)
lines = f.readlines()
f.close()
for i, l in enumerate(lines):
if re.search('Final results from module Davidson', l):
start = i
nbas = int(lines[start + 3].split()[-1])
lines = lines[start + 8:start + 8 + nbas]
modes = []
for l in lines:
spl = l.split()
if spl[10] == 'YES':
modes.append([float(spl[2]), float(spl[8])])
self.modes = VibModes(len(modes), self.mol)
self.modes.set_freqs(numpy.array([m[0] for m in modes]))
self.irints = numpy.array([m[1] for m in modes])
class VASPoutput(object):
"""
Class that handles VASP output (OUTCAR) file.
"""
def __init__(self, filename='full-output.vasp'):
"""
The constructor of VASPoutput.
"""
self.filename = filename
self.dipgrad = None
self.hessian = None
########## UPDATE below
def read(self, mol):
"""
Reading in the output file
"""
natoms = mol.natoms
self.dipgrad = numpy.zeros((natoms, 3, 3))
f = open('full-output.vasp', 'r')
line = f.readline()
while line != '':
if 'BORN EFFECTIVE CHARGES' in line:
break
line = f.readline()
if line == '':
raise Exception('Born effective charges not found in output file')
line = f.readline()
line = f.readline()
line = f.readline()
bec = []
ion = []
while line != '' and line != '\n':
if 'ion' not in line:
line = map(float, line.split()[1:])
ion.append(line)
line = f.readline()
else:
bec.append(ion)
ion = []
line = f.readline()
bec.append(ion)
ion = []
self.dipgrad = numpy.array(bec)
print self.dipgrad.shape
f.close()
#dipgrad = ' '.join(lines[start+1:end]).replace('D', 'E').replace('d', 'E').split()
#self.dipgrad = numpy.array([float(d) for d in dipgrad])
#self.dipgrad.shape = (natoms,3,3)
#### up to here
def read_hessian(self, mol):
"""
Reading in the hessian martix.
"""
natoms = mol.natoms
self.hessian = numpy.zeros((natoms * 3, natoms * 3))
self.modes = VibModes(3 * natoms, mol)
f = open(self.filename, 'r')
line = f.readline()
while line != '':
if 'SECOND DERIVATIVES' in line:
break
line = f.readline()
if line == '':
raise Exception('hessian not found in output file')
line = f.readline()
line = f.readline()
line = f.readline()
tmp = [] #temporary list for the lines
while line != '':
if line != ' \n':
tmp.append(line)
line = f.readline()
else:
break
for i, l in enumerate(tmp):
l = l.split()
l.pop(0)
tmp[i] = map(float, l)
self.hessian = numpy.array(tmp)
#symmetrizing the hessian
self.hessian = -(self.hessian + self.hessian.transpose()) / 2.0
f.close()
for i, atmass in enumerate(mol.atmasses):
self.hessian[:,
3 * i:3 * i + 3] = self.hessian[:, 3 * i:3 * i +
3] / math.sqrt(atmass)
self.hessian[3 * i:3 * i +
3, :] = self.hessian[3 * i:3 * i +
3, :] / math.sqrt(atmass)
evals, evecs = numpy.linalg.eigh(self.hessian)
# evals are in eV/Angs**2 *amu
# convert to cm^-1 [evals are in Hartree / (Bohr**2 * amu) ]
evals = evals * eV_in_Joule / (1e-10**2 * amu_in_kg
) # in J/(m*m*kg) = 1/s**2
#print numpy.sqrt(abs(evals))/(2.0*math.pi)/cvel_ms*1e-2
#print '-'*30
for i in range(evals.size):
if evals[i] > 0.0:
evals[i] = math.sqrt(evals[i])
else:
evals[i] = -math.sqrt(-evals[i])
evals = evals / (2.0 * math.pi) # frequency in 1/s
evals = evals / cvel_ms * 1e-2 # wavenumber in 1/cm
#numpy.set_printoptions(precision=4)
#print evals
self.modes.set_freqs(evals)
self.modes.set_modes_mw(evecs.transpose())
class SNFOutputFile(object):
def __init__(self, filename='snf.out'):
self.modes = None
self.lwl = None
self.filename = filename
self.intonly = False
def read(self, mol):
f = file(self.filename, 'r')
lines = f.readlines()
f.close()
for l in lines:
if 'intensities-only-mode' in l:
self.intonly = True
first = 0
last = 0
for i, l in enumerate(lines):
if (first == 0) and ('root no.' in l):
first = i
if 'Generate fake outputs for' in l:
last = i
break
if 'W A R N I N G' in l:
last = i - 1
break
if 'Raman Optical Activity properties for freq.' in l:
self.lwl = float(l[46:57])
if not self.intonly:
natoms = mol.natoms
self.modes = VibModes(3 * natoms - 6, mol)
lines = lines[first:last]
lines = [l for l in lines if not len(l.strip()) == 0]
lines = [l for l in lines if not l.startswith('1')]
normalmodes = numpy.zeros((3 * natoms - 6, 3 * natoms))
freqs = numpy.zeros((3 * natoms - 6))
ncol = len(lines[2][10:].split())
icol = -ncol
for i, l in enumerate(lines):
irow = i % (3 * natoms + 2) - 2
if irow == -2:
if not ('root' in l):
raise Exception(
'wrong number of lines for normal modes')
icol += ncol
else:
line = [float(fl) for fl in l[10:].split()]
if irow == -1:
freqs[icol:icol + ncol] = line
else:
normalmodes[icol:icol + ncol, irow] = line
self.modes.set_modes_mw(normalmodes)
self.modes.set_freqs(freqs)
def read_mat(self, id_string):
"""Read in a matrix from the snf.out file, starting with the id_string.
The matrix in the snf.out file should have the following form (only for the dipole gradients):
1 2 3
1: dmu_x / dx dmu_x / dy dmu_x / dz
2: dmu_y / dx dmu_y / dy dmu_y / dz # Atom 1
3: dmu_z / dx dmu_z / dy dmu_z / dz
4 5 6
1: dmu_x / dx dmu_x / dy dmu_x / dz
2: dmu_y / dx dmu_y / dy dmu_y / dz # Atom 2
3: dmu_z / dx dmu_z / dy dmu_z / dz
etc.
put one piece from the button to the right of the previous on and you get a 3 x 3*nr_atoms matrix
but I want to work with a 3*nr_atoms x 3
"""
f = file(self.filename, 'r')
# Little hack to assure that you find the right polarizabilities (length vs. velocity representation)
vel = False
if "velocity" in id_string:
vel = True
while (True):
line = f.readline()
if line == "":
raise Exception("Could not find " + id_string + "!!!")
if id_string in line:
# Make sure that you don't get the velocity representation instead of the length rep.
if (not vel) and ("velocity" in line):
continue
break
# Get the header
line = f.readline()
columns = int(line.split()[5])
num_rows = int(line.split()[9])
i = 0
matrix = numpy.zeros((num_rows, columns))
# How is the matrix diplayed? Usually disp_col = 3
line = f.readline()
disp_col = len(line.split())
row = 1
while (i < num_rows):
line = f.readline()
beginning = str(row) + ":"
if beginning in line:
matrix[i:(i + disp_col),
row - 1] = [float(fl) for fl in line.split()[1:4]]
if row == columns:
row = 1
i += disp_col
else:
row += 1
f.close()
return matrix
def read_derivatives(self, mol):
self.dipole = self.read_mat("gradient of dipole moments").reshape(
mol.natoms, 3, 3)
self.pollen = self.read_mat(
"gradient of polarizability tensor").reshape(mol.natoms, 3, 8)
self.polvel = self.read_mat(
"gradient of polarizability tensor (velocity representation)"
).reshape(mol.natoms, 3, 8)
self.gtenlen = self.read_mat("gradient of G/LAO tensor").reshape(
mol.natoms, 3, 9)
self.gtenvel = self.read_mat("gradient of G/AO tensor").reshape(
mol.natoms, 3, 9)
self.aten = self.read_mat("gradient of A tensor").reshape(
mol.natoms, 3, 27)