Chimie Théorique » QMX

"""

This module is the MOPAC module for ASE, based on the PyMD MOPAC Module by R. Bulo, 

implemented by T. Kerber

Torsten Kerber, ENS LYON: 2011, 07, 11

This work is supported by Award No. UK-C0017, made by King Abdullah

University of Science and Technology (KAUST)

"""

import commands

import numpy as np

from ase.atoms import Atoms

from ase.units import kcal, mol

from ase.calculators.general import Calculator

kcal_mol = kcal / mol

class Mopac(Calculator):

    def __init__(self, files=None, restart=0, geomopt=False, functional="PM6"):

        self.restart = restart

        self.geomopt = geomopt

        self.functional = functional

        self.spin = 0

        self.occupations = None

        self.stress = None

        self.energy_zero = None

        self.energy_free = None

        self.forces = None

        self.atoms_old = None

    def write_moldata(self):

        """

        Writes the files that have to be written each timestep

        """

        # Change labels variable if necessary

        # FIXME: what does norderats stands for????

        norderats = 0

        for el in self.atoms.get_chemical_symbols():

            norderats += 1

        if norderats != self.atoms.get_number_of_atoms():

            self.labels = self.get_labels()

        input = self.get_input_block()

        pyfile = open('pymopac.in','w')

        pyfile.write(input)

        pyfile.close()

    def run(self):

        self.write_moldata()

        print '<MOPAC calculation started>'

        out = commands.getoutput('mopac pymopac.in')

        outputfile = open('pymopac.in.out')

        outfile = open('mopac%02i.out'%(self.restart),'w')

        for line in outputfile:

            outfile.write(line)

        outfile.close()

        outputfile.close()

        energy = self.read_energy()

        if energy == None:

            energy = self.rerun()

        self.forces = self.read_forces()

        print '<MOPAC calculation finished>'

        self.energy_zero = energy

        self.energy_free = energy

        self.first = False

    def read_energy(self, charges=True):

        outfile = open('pymopac.in.out')

        lines = outfile.readlines()

        outfile.close()

        chargelines = 0

        if charges:

            nats = len(self.atoms)

            block = ''

        for line in lines:

            if line.find('HEAT OF FORMATION') != -1:

                words = line.split()

                energy = float(words[5])

            if line.find('H.o.F. per unit cell') != -1:

                words = line.split()

                energy = float(words[5])

            if line.find('"""""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE') != -1:

                energy = None

            if charges:

                if line.find('NET ATOMIC CHARGES') != -1:

                    chargelines += 1

            if chargelines > 0 and chargelines <= nats+3:

                chargelines += 1

                block += line

        if charges:

            chargefile = open('charge%02i.out'%(self.restart),'a')

            chargefile.write(block)

            chargefile.close()

        return energy

    def read_forces(self):

        outfile = open('pymopac.in.aux')

        lines = outfile.readlines()

        outfile.close()

        outputforces = None

        nats = len(self.atoms)

        forces = np.zeros((nats, 3), float)

        for i,line in enumerate(lines):

            if line.find('GRADIENTS:') != -1:

                l = 0

                for j in range(nats * 3):

                    if j%10 == 0:

                        l += 1

                        gline = lines[i+l]

                    k = j -((l-1)*10)

                    try:

                        f = -float(gline[k*18:(k*18)+18])

                    except ValueError:

                        if outputforces == None:

                            outputforces = self.read_output_forces()

                        f = outputforces[j]

                    forces[j/3, j%3] = f

                break

        forces *= kcal_mol

        return forces

    def read_output_forces(self):

        outfile = open('pymopac.in.out')

        lines = outfile.readlines()

        outfile.close()

        nats = len(self.atoms)

        forces = np.zeros((nats, 3), float)

        for i,line in enumerate(lines):

            if line.find('GRADIENT\n') != -1:

                for j in range(nats * 3):

                    gline = lines[i+j+1]

                    forces[j/3, j%3] = -float(gline[49:62])

                break

        return forces

    def get_input_block(self):

        # For restarting I can use 'DENOUT' and 'OLDENS' at some point 

        block = ''

        block += '%s '%(self.functional)

        #if self.functional == 'PM6-DH2':

        block += 'NOANCI '

        block += '1SCF GRADIENTS '

        block += 'AUX(0,PRECISION=9) '

        block += 'RELSCF = 0.0001 '

        charge = 0

        if charge != 0:

            block += 'CHARGE=%i '%(charge)

        if self.spin == 1.:

            block += 'DOUBLET '

        elif self.spin == 2.:

            block += 'TRIPLET '

        block += '\n'

        block += 'Title: ASE job\n\n'

        constraints = self.atoms._get_constraints()

        nconstraints = len(constraints)

        for iat in xrange(len(self.atoms)):

            f = [1, 1, 1]

            if iat < nconstraints:

                if constraints[iat] is not None:

                    f = [0, 0, 0]

            atom = self.atoms[iat]

            xyz = atom.position

            block += ' %2s'%atom.symbol

            block += '    %16.5f %i    %16.5f %i    %16.5f %i \n'%(xyz[0],f[0],xyz[1],f[1],xyz[2],f[2])

        if self.atoms.pbc.any():

            for v in self.atoms.get_cell(): 

                block += 'Tv %8.3f %8.3f %8.3f\n'%(v[0],v[1],v[2])

        return block

    def update(self, atoms):

        if self.atoms_old != atoms:

            self.atoms = atoms.copy()

            self.atoms_old = atoms.copy()

            self.run()