def term_setup(self):
"""Setup function that makes sure all keywords are properly defined and
defaulted.
"""
# check coefficient
if not 'coeff' in self.term:
self.term['coeff'] = 1.0
# check units
if not 'units' in self.term:
self.term['units'] = 'au'
# do unit conversions for the coefficients
self.term['units'] = self.term['units'].lower()
self.term['coeff'] *= units.convert_to(self.term['units'])
# default electronic operator to 1
if not 'elop' in self.term:
self.term['elop'] = '1'
if 'modes' in self.term:
# if there are modes make sure it's a list
if not isinstance(self.term['modes'], list):
self.term['modes'] = [self.term['modes']]
if not isinstance(self.term['ops'], list):
self.term['ops'] = [self.term['ops']]
minv = 1.43e-3
E0 = 0.0
E1 = 2.00
W0 = 2.3
W1 = 1.50
lamda = 0.19
hterms = []
# electronic energy shifts
hterms.append({'coeff': E0+0.5*W0, 'units': 'ev', 'elop': '0,0'})
hterms.append({'coeff': E1-0.5*W1, 'units': 'ev', 'elop': '1,1'})
## coupling mode harmonic oscillator potential
hterms.append({'coeff': wc, 'units': 'ev', 'modes': 0, 'ops': 'KE'})
hterms.append({'coeff': 0.5*wc, 'units': 'ev', 'modes': 0, 'ops': 'q^2'})
hterms.append({'coeff': kappa1, 'units': 'ev', 'modes': 0, 'elop': '1,1', 'ops': 'q'})
hterms.append({'coeff': lamda, 'units': 'ev', 'modes': 0, 'elop': 'sx', 'ops': 'q'})
# torsional mode plane wave potential
hterms.append({'coeff': -0.5*minv, 'units': 'ev', 'modes': 1, 'ops': 'KE'})
hterms.append({'coeff': -0.5*W0, 'units': 'ev', 'modes': 1, 'elop': '0,0', 'ops': 'cos'})
hterms.append({'coeff': 0.5*W1, 'units': 'ev', 'modes': 1, 'elop': '1,1', 'ops': 'cos'})
ham = Hamiltonian(nmodes, hterms, pbfs=pbfs)
dt = 1.0
times = np.arange(0.0,4000.,dt)*units.convert_to('fs')
#wf = vmfpropagate(times, ham, pbfs, wf, 'rhodopsin_diabatic_pops_test.txt')
#wf = vmfpropagate(times, ham, pbfs, wf, 'rhodopsin_diabatic_pops.txt')
#wf = vmfpropagate(times, ham, pbfs, wf, 'rhodopsin_diabatic_pops_small.txt')
wf = vmfpropagate(times, ham, pbfs, wf, 'rhodopsin_diabatic_pops_really_small.txt')