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],