class TurbomoleResults(Results):
def __init__(self, controlfile='control', coordfile='coord', outname=None):
self.mol = VibToolsMolecule()
self.coordfile = coordfile
if outname:
print "WARNING: normal modes are read from aoforce output file"
self.aoforceoutput = AOForceOutputFile(filename=outname)
else:
self.aoforceoutput = None
self.controlfile = TMControlFile(filename=controlfile)
def _get_modes(self):
if self.aoforceoutput:
return self.aoforceoutput.modes
else:
return self.controlfile.modes
modes = property(_get_modes)
def read(self):
self.mol.read_from_coord(filename=self.coordfile)
self.controlfile.read(self.mol)
if self.aoforceoutput:
self.aoforceoutput.read(self.mol)
else:
self.controlfile.read_hessian(self.mol)
def get_tensor_deriv_c(self, tens, ncomp=None):
if tens == 'dipole':
return self.controlfile.dipgrad
else:
raise Exception('Not implemented for Turbomole')
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 __init__(self, controlfile='control', coordfile='coord', outname=None):
self.mol = VibToolsMolecule()
self.coordfile = coordfile
if outname:
print "WARNING: normal modes are read from aoforce output file"
self.aoforceoutput = AOForceOutputFile(filename=outname)
else:
self.aoforceoutput = None
self.controlfile = TMControlFile(filename=controlfile)
def __init__(self,
outname='snf.out',
restartname='restart',
coordfile='coord'):
self.mol = VibToolsMolecule()
self.snfoutput = SNFOutputFile(filename=outname)
self.snfcontrol = SNFControlFile()
self.restartfile = SNFRestartFile()
self.restartname = restartname
self.coordfile = coordfile
self.intonly = False
def __init__(self, output='full-output.vasp', coordfile='coord'):
"""
Constructor for VASPResults
All arguments are optional, leaving out an argument will choose default settings.
@param coordfile: path to Turbomole formated coordinates file (default: pwd/coord)
@type coordfile: str
@param output: path to VASP output file (OUTCAR) (default: full-output.vasp)
@type output: str
"""
self.mol = VibToolsMolecule()
self.coordfile = coordfile
self.output = VASPoutput(filename=output)
class VASPResults(Results):
"""
Class that reads in and contains VASP results.
"""
def __init__(self, output='full-output.vasp', coordfile='coord'):
"""
Constructor for VASPResults
All arguments are optional, leaving out an argument will choose default settings.
@param coordfile: path to Turbomole formated coordinates file (default: pwd/coord)
@type coordfile: str
@param output: path to VASP output file (OUTCAR) (default: full-output.vasp)
@type output: str
"""
self.mol = VibToolsMolecule()
self.coordfile = coordfile
self.output = VASPoutput(filename=output)
def _get_modes(self):
return self.output.modes
modes = property(_get_modes)
def read(self):
"""
Reading the results.
"""
self.mol.read_from_coord(filename=self.coordfile)
self.output.read(self.mol)
self.output.read_hessian(self.mol)
def get_tensor_deriv_c(self, tens, ncomp=None):
if tens == 'dipole':
return self.output.dipgrad
else:
raise Exception('Not implemented')
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 __init__(self):
self.mol = VibToolsMolecule()
self.modes = None # instance of class VibModes
self.lwl = None
class SNFResults(Results):
def __init__(self,
outname='snf.out',
restartname='restart',
coordfile='coord'):
self.mol = VibToolsMolecule()
self.snfoutput = SNFOutputFile(filename=outname)
self.snfcontrol = SNFControlFile()
self.restartfile = SNFRestartFile()
self.restartname = restartname
self.coordfile = coordfile
self.intonly = False
def _get_modes(self):
if self.snfoutput.intonly:
return self.snfcontrol.modes
else:
return self.snfoutput.modes
modes = property(_get_modes)
lwl = property(lambda self: self.snfoutput.lwl)
def read(self):
self.mol.read_from_coord(filename=self.coordfile)
self.snfoutput.read(self.mol)
self.intonly = self.snfoutput.intonly
if self.snfoutput.intonly:
self.snfcontrol.read(self.mol)
if self.restartname:
self.restartfile.read(filename=self.restartname)
else:
self.snfoutput.read_derivatives(self.mol)
self.dipole_deriv_c = self.snfoutput.dipole
self.pollen_deriv_c = self.snfoutput.pollen[:, :, :
6] / Bohr_in_Angstrom**2
self.polvel_deriv_c = self.snfoutput.polvel[:, :, :
6] / Bohr_in_Angstrom**2
self.gtenlen_deriv_c = self.snfoutput.gtenlen
self.gtenvel_deriv_c = self.snfoutput.gtenvel
self.aten_deriv_c = self.snfoutput.aten
def get_tensor_mean(self, tens, ncomp=None):
tensor = eval('self.restartfile' + '.' + tens)
ncalcsets = tensor.shape[0]
nval = tensor.shape[1] / 2
if (ncomp == None):
ncomp = tensor.shape[2]
displ = self.restartfile.displ
mean = numpy.zeros((ncalcsets, nval, ncomp))
for i in range(nval):
mean[:, i, :] = (tensor[:, 2 * i, :ncomp] +
tensor[:, 2 * i + 1, :ncomp]) / 2.0
return mean
def get_tensor_deriv_c(self, tens, ncomp=None):
if hasattr(self, tens + '_deriv_c'):
return eval('self.' + tens + '_deriv_c')
if not (self.restartfile.iaus == 2):
raise Exception('Differentiation only implemented for iaus = 2')
if self.intonly:
raise Exception(
'Cartesian derivatives not available in intensities only mode')
tensor = eval('self.restartfile' + '.' + tens)
natoms = tensor.shape[0]
if (ncomp == None):
ncomp = tensor.shape[2]
displ = self.restartfile.displ
deriv = numpy.zeros((natoms, 3, ncomp))
for i in range(3):
deriv[:, i, :] = (tensor[:, 2 * i, :ncomp] -
tensor[:, 2 * i + 1, :ncomp]) / (2.0 * displ)
setattr(self, tens + '_deriv_c', deriv)
return deriv
def get_tensor_deriv_nm(self, tens, ncomp=None, modes=None):
if modes == None:
if hasattr(self, tens + '_deriv_nm'):
return eval('self.' + tens + '_deriv_nm')
elif self.intonly:
raise Exception(
'Argument modes of get_tensor_deriv_nm must be None in intensities-only mode'
)
if self.intonly:
tensor = eval('self.restartfile' + '.' + tens)
nmodes = tensor.shape[0]
if (ncomp == None):
ncomp = tensor.shape[2]
displ = self.restartfile.displ
deriv_nm = numpy.zeros((nmodes, ncomp))
deriv_nm[:, :] = (tensor[:, 0, :ncomp] -
tensor[:, 1, :ncomp]) / (2.0 * displ)
modes = self.get_c_normalmodes()
for i in range(nmodes):
deriv_nm[i, :] = deriv_nm[i, :] * math.sqrt(sum(modes[i, :]**
2))
else:
deriv_nm = Results.get_tensor_deriv_nm(self, tens, ncomp, modes)
if modes == None:
setattr(self, tens + '_deriv_nm', deriv_nm)
return deriv_nm
def check_consistency(self):
print
print "Checking consistency of SNF restart file "
print " Large numbers mean that the change of the polarizabilities deviates from linear behavior."
print
def check(ten):
if ten.startswith('pol'):
mean_pol = self.get_tensor_mean(ten, 6)
else:
mean_pol = self.get_tensor_mean(ten)
ncalcsets = mean_pol.shape[0]
nval = mean_pol.shape[1]
ncomp = mean_pol.shape[2]
mean_pol = mean_pol.reshape((ncalcsets * nval, ncomp))
for icomp in range(ncomp):
print " %14.8f min: %3i max: %3i" % \
(mean_pol[:,icomp].max()-mean_pol[:,icomp].min(),
mean_pol[:,icomp].argmin(), mean_pol[:,icomp].argmax() )
print
wrong = {}
for i in range(ncalcsets):
if (max(abs(mean_pol[3 * i:3 * i + 3, 0] - mean_pol[0, 0])) >
0.001):
wrong[i + 1] = [
abs(mean_pol[3 * i, 0] - mean_pol[0, 0]) > 0.001,
abs(mean_pol[3 * i + 1, 0] - mean_pol[0, 0]) > 0.001,
abs(mean_pol[3 * i + 2, 0] - mean_pol[0, 0]) > 0.001
]
print i + 1, mean_pol[3 * i:3 * i + 3, 0] - mean_pol[0, 0]
return wrong
print " Dipole moment "
return check('dipole')
return
print " Polarizability (length) "
check('pollen')
print " Polarizability (vel) "
check('polvel')
print " G-tensor (len) "
check('gtenlen')
print " G-tensor (vel) "
check('gtenvel')
print " A-tensor "
check('aten')