def write_vel_xyz(self,self_md):
if self.count_vel_xyz == self.freq_vel_xyz:
self.count_vel_xyz = 0
mol_tot = bind_molecule(self_md.mol,self_md.mol_mm)
mess = "No.{} Time: {} fs [bohr/tau]".format(self_md.count, self_md.elaptime * tau2fs)
with open(self.file_vel_xyz,'a') as f:
f.write(mol_tot.get_velocities_formated(unit="bohr/tau",label=False,message=mess))
else: self.count_vel_xyz += 1
def write_xyz(self,self_tsh):
if self.count_xyz == self.freq_xyz:
self.count_xyz = 0
mol_tot = bind_molecule(self_tsh.mol,self_tsh.mol_mm)
mess = "No.{} Time: {} fs [ang]".format(self_tsh.count, self_tsh.elaptime * tau2fs)
with open(self.file_xyz,'a') as f:
f.write(mol_tot.get_positions_formated(unit="ang",label=False,message=mess))
else: self.count_xyz += 1
def write_xyz(self,self_mc):
if self.count_xyz == self.freq_xyz:
self.count_xyz = 0
mol_tot = bind_molecule(self_mc.mol_qm,self_mc.mol)
mess = "No.{}".format(self_mc.count)
with open(self.file_xyz,'a') as f:
f.write(mol_tot.get_positions_formated(unit="ang",label=False,message=mess))
else: self.count_xyz += 1
def write_xyz(self, self_mc):
if self.count_xyz == self.freq_xyz:
self.count_xyz = 0
mol_tot = bind_molecule(self_mc.mol_qm, self_mc.mol)
mess = "No.{}".format(self_mc.count)
with open(self.file_xyz, 'a') as f:
f.write(
mol_tot.get_positions_formated(unit="ang",
label=False,
message=mess))
else:
self.count_xyz += 1
def write_xyz(self, self_tsh):
if self.count_xyz == self.freq_xyz:
self.count_xyz = 0
mol_tot = bind_molecule(self_tsh.mol, self_tsh.mol_mm)
mess = "No.{} Time: {} fs [ang]".format(self_tsh.count,
self_tsh.elaptime * tau2fs)
with open(self.file_xyz, 'a') as f:
f.write(
mol_tot.get_positions_formated(unit="ang",
label=False,
message=mess))
else:
self.count_xyz += 1
def write_vel_xyz(self, self_md):
if self.count_vel_xyz == self.freq_vel_xyz:
self.count_vel_xyz = 0
mol_tot = bind_molecule(self_md.mol, self_md.mol_mm)
mess = "No.{} Time: {} fs [bohr/tau]".format(
self_md.count, self_md.elaptime * tau2fs)
with open(self.file_vel_xyz, 'a') as f:
f.write(
mol_tot.get_velocities_formated(unit="bohr/tau",
label=False,
message=mess))
else:
self.count_vel_xyz += 1
from IO_MOLPRO import molpro_input_parser
from MakeInitial import SetLattice, SetMaxwell, superpositioned_atoms_delete
from Potential import Potential_MM
from MonteCarlo import MonteCarlo, MonteCarlo_Ex
import numpy as np
import sys
mol_qm, inp = molpro_input_parser("template.com")
mol_qm.read_coord_from_file("coord1")
n = 500
lattice = SetLattice("Ar",n,1.77)
vlength = lattice.get_lattice_length()
mol_mm = lattice.get_molecule()
mol_mm = superpositioned_atoms_delete(mol_mm, mol_qm)
mol_tot = bind_molecule(mol_qm,mol_mm)
pot_tot = Potential_MM(mol_tot, check_pbc=True, vlength=vlength)
#print mol_tot.get_positions_formated()
#print mol_tot.get_atomnames()
#sys.exit()
print len(mol_tot)
delta = [0.2] * (len(mol_tot))
#mc = MonteCarlo(mol_tot, pot_tot, delta, 1000000, 30.0, restart=False, frozen_atom_number = [0,1,2,3,4])
mc = MonteCarlo_Ex(mol_tot, pot_tot, delta, 1000000, 30.0, restart=False, treated_as_molecule = [0,1,2,3,4], delta_mol = [0.02,0.02])
#mc = MonteCarlo_Ex(mol_tot, pot_tot, delta, 100000, 30.0, restart=False,frozen_atom_number = [0,1,2,3,4])
mc.access_writeoutput().set_freq_xyz(1000)
mc.access_writeoutput().set_freq_trajectory(1000)
mc.access_writeoutput().set_freq_energy(1000)
mc.run()
from IO_MOLPRO import molpro_input_parser
from MakeInitial import SetLattice, SetMaxwell, superpositioned_atoms_delete
from Potential import Potential_MM
from MonteCarlo import MonteCarlo, MonteCarlo_Ex
import numpy as np
import sys
mol_qm, inp = molpro_input_parser("template.com")
mol_qm.read_coord_from_file("coord1")
n = 500
lattice = SetLattice("Ar", n, 1.77)
vlength = lattice.get_lattice_length()
mol_mm = lattice.get_molecule()
mol_mm = superpositioned_atoms_delete(mol_mm, mol_qm)
mol_tot = bind_molecule(mol_qm, mol_mm)
pot_tot = Potential_MM(mol_tot, check_pbc=True, vlength=vlength)
#print mol_tot.get_positions_formated()
#print mol_tot.get_atomnames()
#sys.exit()
print len(mol_tot)
delta = [0.2] * (len(mol_tot))
#mc = MonteCarlo(mol_tot, pot_tot, delta, 1000000, 30.0, restart=False, frozen_atom_number = [0,1,2,3,4])
mc = MonteCarlo_Ex(mol_tot,
pot_tot,
delta,
1000000,
30.0,
restart=False,
treated_as_molecule=[0, 1, 2, 3, 4],