Chimie Théorique » QMX

""" This is a QM:MM embedded system for ASE

torsten.kerber@ens-lyon.fr

"""

import ase

import ase.atoms

import numpy as np

from general import Calculator

from ase.embed import Embed

import sys, os

class Qmx(Calculator):

    def __init__(self, calculator_low, calculator_high):

        self.string_params = {}

        self.forces=np.zeros((2,2))

        self._constraints=None

        self.calculator_low = calculator_low

        self.calculator_high = calculator_high

    def get_energy_subsystem(self, path, calculator, atoms, force_consistent):

        os.chdir(path)

        calculator.set_atoms(atoms)

        energy = calculator.get_potential_energy(atoms)

        os.chdir("..")

        return energy

    def get_forces_subsystem(self, path, calculator, atoms):

        os.chdir(path)

        calculator.set_atoms(atoms)

        forces = calculator.get_forces(atoms)

        os.chdir("..")

        return forces

    def get_potential_energy(self, embed, force_consistent=False):

        # perform energy calculations 

        e_sys_lo = self.get_energy_subsystem("system.low-level", self.calculator_low, embed.get_system(), force_consistent)

        e_cl_lo  = self.get_energy_subsystem("cluster.low-level", self.calculator_low, embed.get_cluster(), force_consistent)

        e_cl_hi  = self.get_energy_subsystem("cluster.high-level", self.calculator_high, embed.get_cluster(), force_consistent)

        # calculate energies

        energy = e_sys_lo - e_cl_lo + e_cl_hi

        print "%20s=%15s - %15s + %15s" %("E(C:S)", "E(S-MM)", "E(C-MM)", "E(C-QM)")

        print "%20f=%15f - %15f + %15f" %(energy, e_sys_lo, e_cl_lo, e_cl_hi)

        if force_consistent:

            self.energy_free = energy

            return self.energy_free

        else:

            self.energy_zero = energy

            return self.energy_zero

    def get_forces(self, embed):

        atom_map_sys_cl = embed.atom_map_sys_cl

        # get forces for the three systems

        f_sys_lo = self.get_forces_subsystem("system.low-level", self.calculator_low, embed.get_system())

        f_cl_lo  = self.get_forces_subsystem("cluster.low-level", self.calculator_low, embed.get_cluster())

        f_cl_hi  = self.get_forces_subsystem("cluster.high-level", self.calculator_high, embed.get_cluster())

        # forces correction for the atoms

        f_cl = f_cl_hi - f_cl_lo

        #number of atoms

        nat_sys = len(embed)

        # lo-sys + (hi-lo)

        for iat_sys in xrange(nat_sys):

            iat_cl = atom_map_sys_cl[iat_sys]

            if iat_cl > -1:

                f_sys_lo[iat_sys] += f_cl[iat_cl]

        # correct gradients

        # Reference: Eichler, Koelmel, Sauer, J. of Comput. Chem., 18(4). 1997, 463-477.

        for cell_L, iat_cl, iat_sys, r, iat_link in embed.linkatoms:

            # calculate the bond distance (r_bond) at the border

            xyz = embed[iat_sys].get_position() - embed.get_cluster()[iat_cl].get_position() + cell_L

            # calculate the bond lenght and the factor f

            rbond = np.sqrt(np.dot(xyz, xyz))

            f = r / rbond

            #normalize xyz

            xyz /= rbond

            # receive the gradients for the link atom

            fH = f_cl[iat_link]

            # Skalarprodukt fH, xyz

            fs = np.dot(xyz, fH)

            for idir in xrange(3):

                # correct the atom in the system

                f_sys_lo[iat_sys][idir] += f*fH[idir] - f*fs*xyz[idir]

                # correct the atom in the cluster

                f_sys_lo[iat_cl][idir] += (1-f)*fH[idir] + f*fs*xyz[idir]

        return f_sys_lo

    def set_atoms(self, atoms):

        return