print ' '
print 'Mismatch between provided temperature and temperature in the calculation'
sys.exit()
print 'The instanton mode is %s' % mode
print 'The temperature is %f K' % (temp / K2au)
if mode == 'rate':
h0 = red2comp(hessian, nbeads, natoms)
pos, nbeads, hessian2 = get_double(beads.q, nbeads, natoms, h0)
hessian = hessian2
m3 = np.concatenate((beads.m3, beads.m3), axis=0)
omega2 = (temp * nbeads * kb / hbar)**2
if not quiet:
spring = SpringMapper.spring_hessian(natoms,
nbeads,
beads.m3[0],
omega2,
mode='full')
h = np.add(hessian, spring)
print 'The full ring polymer is made of %i' % (nbeads)
print 'We used %i beads in the calculation.' % (nbeads / 2)
elif mode == 'splitting':
if input_freq == None:
print 'Please provide a name of the file containing the list of the frequencies for the minimum using "-freq" flag'
print '(You can generate that file using this script in the case reactant.)'
sys.exit()
print 'Our linear polymer has %i' % (nbeads)
pos = beads.q
m3 = beads.m3
omega2 = (temp * nbeads * kb / hbar)**2
if np.absolute(temp - temp2) / K2au > 2:
print(
"\n Mismatch between provided temperature and temperature in the calculation"
)
sys.exit()
if mode == "rate":
h0 = red2comp(hessian, nbeads, natoms)
pos, nbeads, hessian2 = get_double(beads.q, nbeads, natoms, h0)
hessian = hessian2
m3 = np.concatenate((beads.m3, beads.m3), axis=0)
omega2 = (temp * nbeads * kb / hbar) ** 2
if not quiet:
spring = SpringMapper.spring_hessian(
natoms, nbeads, beads.m3[0], omega2, mode="full"
)
h = np.add(hessian, spring)
elif mode == "splitting":
if input_freq is None:
print(
'Please provide a name of the file containing the list of the frequencies for the minimum using "-freq" flag'
)
print(" You can generate that file using this script in the case reactant.")
sys.exit()
print(("Our linear polymer has {}".format(nbeads)))
pos = beads.q
m3 = beads.m3
omega2 = (temp * nbeads * kb / hbar) ** 2
# spring = SpringMapper.spring_hessian(natoms,nbeads,beads.m3[0],omega2,mode='half')
if np.absolute(temp - temp2) / K2au > 2:
print ' '
print 'Mismatch between provided temperature and temperature in the calculation'
sys.exit()
print 'The instanton mode is %s' % mode
print 'The temperature is %f K' % (temp / K2au)
if mode == 'rate':
h0 = red2comp(hessian, nbeads, natoms)
pos, nbeads, hessian2 = get_double(beads.q, nbeads, natoms, h0)
hessian = hessian2
m3 = np.concatenate((beads.m3, beads.m3), axis=0)
omega2 = (temp * nbeads * kb / hbar) ** 2
if not quiet:
spring = SpringMapper.spring_hessian(natoms, nbeads, beads.m3[0], omega2, mode='full')
h = np.add(hessian, spring)
print 'The full ring polymer is made of %i' % (nbeads)
print 'We used %i beads in the calculation.' % (nbeads / 2)
elif mode == 'splitting':
if input_freq == None:
print 'Please provide a name of the file containing the list of the frequencies for the minimum using "-freq" flag'
print '(You can generate that file using this script in the case reactant.)'
sys.exit()
print 'Our linear polymer has %i' % (nbeads)
pos = beads.q
m3 = beads.m3
omega2 = (temp * nbeads * kb / hbar) ** 2
# spring = SpringMapper.spring_hessian(natoms,nbeads,beads.m3[0],omega2,mode='half')
if not quiet: