def get_fmo_energy(self):
"""
get H**O, LUMO and their gap
"""
f = self.f
cmd1 = "awk '/^ The electronic state is/{print NR}' %s | tail -n 1" % f
Ln1 = int(io2.cmdout2(cmd1)) + 1
cmd2 = "awk '/^ Condensed to atoms \(all electrons\)/{print NR}' %s | tail -n 1" % f
Ln2 = int(io2.cmdout2(cmd2)) - 1
cmd = "sed -n '%d,%dp' %s | grep Beta" % (Ln1, Ln2, f)
cont0 = io2.cmdout2(cmd)
if self.isp:
print(' ## spin polarised!')
h**o = None
lumo = None
else:
cmd = "sed -n '%d,%dp' %s | grep ' Alpha virt. eigenvalues --' | head -n 1" % (
Ln1, Ln2, f)
ct = io2.cmdout2(cmd)
lumo = eval(ct.split()[-5]) * self.uo.h2e
cmd = "sed -n '%d,%dp' %s | grep ' Alpha occ. eigenvalues --' | tail -1" % (
Ln1, Ln2, f)
ct = io2.cmdout2(cmd)
h**o = eval(ct.split()[-1]) * self.uo.h2e
return h**o, lumo
def get_mulliken_population(self):
# note that the output Mulliken charge starting line may be different
# for different versions of Gaussian, i.e., with or without `atomic` in between
# "Mullike" and "charges:", so a "robust" regular expression is used
cmd1 = "awk '/^ Mulliken [a-zA-Z]*\s?charges:/{print NR}' %s | tail -1" % self.f
Ln1 = int(io2.cmdout2(cmd1)) + 2
cmd2 = "awk '/^ Sum of Mulliken [a-zA-Z]*\s?charges =/{print NR}' %s | tail -1" % self.f
Ln2 = int(io2.cmdout2(cmd2)) - 1
cmd = "sed -n '%d,%dp' %s" % (Ln1, Ln2, self.f)
cs = io2.cmdout2(cmd).split('\n')
pops = np.array([eval(ci.split()[2]) for ci in cs])
return pops
def get_polarizability(self):
cmd = "awk '/Isotropic polarizability/{print $6}' %s" % self.f
a = None
try:
a = eval(io2.cmdout2(cmd))
except:
print(' * WARNING: no Isotropic polarizability found')
return a
def get_force(self):
iou = io2.Units()
const = iou.h2e / iou.b2a # from hartree/bohr to eV/A
#cmd = "grep '^\s*[XYZ][0-9]* ' %s | awk '{print $3}'"%self.f #
cmd1 = "awk '/^ Variable Old X -DE/{print NR}' %s | tail -1" % self.f
Ln1 = int(io2.cmdout2(cmd1)) + 2
cmd2 = "awk '/^ Item Value Threshold Converged/{print NR}' %s | tail -1" % self.f
Ln2 = int(io2.cmdout2(cmd2)) - 1
cmd = "sed -n '%d,%dp' %s" % (Ln1, Ln2, self.f)
#print cmd
cs = io2.cmdout2(cmd).split('\n')
vals = [eval(ci.split()[2]) for ci in cs]
#print vals
#print len(vals)
forces = np.array(vals).reshape((self.na, 3)) * const
#abs_forces = np.linalg.norm( forces, axis=1 )
#self.forces = abs_forces[:, np.newaxis]
return forces
def get_cf_and_chg(self):
""" cf: chemical formula
chg: charge """
cmdi = "grep Stoichiometry %s | tail -1" % f
ct = io2.cmdout2(cmdi)
info = ct.split()[-1]
if ('(' in info) and (info[-1] == ')'):
# charged mol
cf, c0_ = info.split('(') # cf: chemical formula;
if c0_[-2] == '-':
chg = -int(c0_[:-2]) # negatively charged
elif c0_[-2] == '+':
chg = int(c0_[:-2]) # positively charged
else:
#print 'c0_ = ', c0_, ', ct = ', ct
#sys.exit(2)
chg = 0 # spin-polarized case, e.g., C4H9O(2)
else:
chg = 0
cf = info
return cf, chg
def get_dipole_moment(self):
cmd = "grep -A1 ' Dipole moment (field-independent basis, Debye):' %s | tail -1 | awk '{print $NF}'" % self.f
mu = eval(io2.cmdout2(cmd))
return mu
def get_task(self):
task = 'e'
if io2.cmdout2('grep -i " opt[(\s]" %s' % (self.f)):
task = 'optg'
return task