def test2():
from Atom import Atom
from Molecule import Molecule
from TullySurfaceHopping import TullySurfaceHopping
from Constants import fs2tau, tau2fs
from IO_MOLPRO import molpro_input_parser
from VelocityVerlet import set_random_momentum
mol, inp = molpro_input_parser("mlpinp1.com")
set_random_momentum(mol,0.1)
pot = Potential_TSH(mol,inp,now_state=0,nrange=3)
pot.override_output("mlpinp0.out_01")
read_velocity(mol,"velocity5_1")
read_coord(mol,"coord5_1")
tsh = TullySurfaceHopping(mol,pot,dt=0.5*fs2tau,nstep=100,\
tsh_times=5) # These are special fort TSH
tsh.run()
from IO_MOLPRO import molpro_input_parser
from Potential import Potential_TSH_CASSCF, Potential_MM, Potential_QMMM
from TullySurfaceHopping import TullySurfaceHopping_QMMM
from Constants import fs2tau, bohr2ang
import sys
from IO_MOLPRO import OutputMOLPRO
from MakeInitial import SetLattice, SetMaxwell, superpositioned_atoms_delete
mol_qm, inp = molpro_input_parser("template.com")
mol_qm.read_coord_from_file("coord1")
mol_qm.read_velocity_from_file("velocity1")
pot_qm = Potential_TSH_CASSCF(mol_qm, inp, now_state=2, nrange=4)
n = 500
lattice = SetLattice("Ar",n,1.77)
vlength = lattice.get_lattice_length()
mol_mm = lattice.set_molecule()
SetMaxwell(mol_mm, 300).set_velocities()
mol_mm = superpositioned_atoms_delete(mol_mm, mol_qm)
pot_mm = Potential_MM(mol_mm, rlimit = vlength / 2)
pot_qmmm = Potential_QMMM(mol_qm, mol_mm, rlimit = vlength / 2)
tsh = TullySurfaceHopping_QMMM(mol_qm, mol_mm, pot_qm, pot_mm,\
pot_qmmm, dt=0.5*fs2tau, nstep=5000,tsh_times=5)
tsh.run()
if chk and l.find('Intensities [relative]') > -1:
for _ in xrange(len(mol)*3):
l = f.readline()
trs1.append(map(float,l.split()[1:]))
if chk2:
trs = np.append(trs,trs1,axis=1)
else:
trs = trs1
trs1 = []
chk2 = True
if chk and l.find('Wavenumbers [cm-1]') > -1:
print l
freq.append(map(float,l.split()[2:]))
if chk and l.find('Normal Modes of low/zero frequencies') > -1:
break
l = f.readline()
if len(trs) == 0 or len(freq) == 0:
print 'cant get gradient'
sys.exit()
else:
return trs.T,np.array(freq)
if __name__ == '__main__':
mol, inp = molpro_input_parser("mlpinp0_cis.com")
wigner_distribution("mlpinp0_cis.out",mol,10,False)
import pyximport
pyximport.install()
cProfile.runctx("do()", globals(), locals(), "Profile.prof")
s = pstats.Stats("Profile.prof")
s.strip_dirs().sort_stats("time").print_stats()
sys.exit()
for i in xrange(500):
x = 1.0 + 0.1 * i
mol_mm.set_positions([[0.,0.,0.],[0.,0.,x*ang2bohr]])
pot_mm.calc()
#print x, pot_mm.get_potential_energy(), pot_mm.get_forces()[0][2]
print x, pot_mm.get_forces()
#print pot_mm.get_forces()
sys.exit()
n = 256
mol_mm = Molecule(["Ar"]*n)
SetLattice(mol_mm,1.77).set_positions()
SetMaxwellVelocities(mol_mm,30).set_velocities()
pot_mm = Potential_MM(mol_mm)
vel = VelocityVerlet(mol_mm, pot_mm, nstep=2000, dt=0.5*fs2tau)
vel.run()
sys.exit()
mol, inp = molpro_input_parser("template.com")
read_coord(mol,"coord1")
read_velocity(mol,"velocity1")
pot = Potential_TSH_CASSCF(mol, inp, now_state=1, nrange=2)
tsh = TullySurfaceHopping(mol,pot,dt=0.5*fs2tau,\
nstep=500,tsh_times=5)
tsh.run()
