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()
def test3():
from Atom import Atom
from Molecule import Molecule
from VelocityVerlet import VelocityVerlet
from Constants import fs2tau
at1 = Atom(symbol='Ar', position=[5,0,0])
at2 = Atom(symbol='Ar', position=[0,0,0])
at3 = Atom(symbol='Ar', position=[0,5,0])
mol = Molecule([at1,at2,at3])
pot = Potential_MM(mol)
md = VelocityVerlet(mol,pot,deltat=0.5*fs2tau ,nstep=200)
md.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()
