def do():
n = 50
mol_mm = SetLattice("Ar",n,1.77).set_molecule()
SetMaxwell(mol_mm,30).set_velocities()
pot_mm = Potential_MM(mol_mm)
vel = VelocityVerlet(mol_mm, pot_mm, nstep=200, dt=0.5*fs2tau)
vel.run()
from MakeInitial import SetLattice
from Potential import Potential_MM
from MonteCarlo import MonteCarlo_Ex
# Set the initial coordinate
# lattice structure of 500 Ar atoms
n = 50
lattice = SetLattice("Ar", n, 1.77)
vlength = lattice.get_lattice_length()
# define the potential
pot = Potential_MM(mol, check_pbc=True, vlength=vlength)
# make the instance
delta = [0.2] * (len(mol))
mc = MonteCarlo_Ex(mol, pot, delta, 100000, 30.0, restart=False)
# adjust the frequency of the output reloading
mc.access_writeoutput().set_freq_xyz(10000)
mc.access_writeoutput().set_freq_trajectory(10000)
mc.access_writeoutput().set_freq_energy(10000)
# run montecarlo
mc.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()
from MakeInitial import SetLattice
from Potential import Potential_MM
from MonteCarlo import MonteCarlo_Ex
# Set the initial coordinate
# lattice structure of 500 Ar atoms
n = 50
lattice = SetLattice("Ar",n,1.77)
vlength = lattice.get_lattice_length()
# define the potential
pot = Potential_MM(mol, check_pbc=True, vlength=vlength)
# make the instance
delta = [0.2] * (len(mol))
mc = MonteCarlo_Ex(mol, pot, delta, 100000, 30.0, restart=False)
# adjust the frequency of the output reloading
mc.access_writeoutput().set_freq_xyz(10000)
mc.access_writeoutput().set_freq_trajectory(10000)
mc.access_writeoutput().set_freq_energy(10000)
# run montecarlo
mc.run()
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()
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()