Chimie Théorique » QMX

"""

This module is the EMBED module for ASE

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 os, sys, string

from ase.units import Hartree, Bohr

from ase.io.turbomole import write_turbomole

from ase.calculators.general import Calculator

import numpy as np

class Turbomole(Calculator):

    def __init__(self, label='turbomole', calculate_energy="dscf", calculate_forces="grad", post_HF = False):

        self.label = label

        self.converged = False

        # set calculators for energy and forces

        self.calculate_energy = calculate_energy

        self.calculate_forces = calculate_forces

        # turbomole has no stress

        self.stress = np.empty((3, 3))

        # storage for energy and forces

        self.e_total = None

        self.forces = None

        self.updated = False

        # atoms must be set

        self.atoms = None

        # POST-HF method

        self.post_HF  = post_HF

    def initialize(self, atoms):

        self.numbers = atoms.get_atomic_numbers().copy()

        self.species = []

        for a, Z in enumerate(self.numbers):

            self.species.append(Z)

        self.converged = False

    def execute(self, command):

        from subprocess import Popen, PIPE

        try:

            # the sub process gets started here

            proc = Popen([command], shell=True, stderr=PIPE)

            error = proc.communicate()[1]

            # check the control file for "actual step" keyword

            file = open("control")

            data = file.read()

            if "$actual step" in data:

                raise OSError(error)

            # print "TM command: ", command, "successfully executed"

        except OSError, e:

            print >>sys.stderr, "Execution failed: ", e

            sys.exit(1)

    def get_potential_energy(self, atoms):

        # update atoms

        self.set_atoms(atoms)

        # if update of energy is neccessary

        if self.update_energy:

            # calculate energy

            self.execute(self.calculate_energy + " > ASE.TM.energy.out")

            # check for convergence of dscf cycle

            if os.path.isfile('dscf_problem'):

                print 'Turbomole scf energy calculation did not converge'

                raise RuntimeError, \

                    'Please run Turbomole define and come thereafter back'

            # read energy

            self.read_energy()

        else :

            print "taking old values (E)"

        self.update_energy = False

        return self.e_total

    def get_forces(self, atoms):

        # update atoms

        self.set_atoms(atoms)

        # complete energy calculations

        if self.update_energy:

            self.get_potential_energy(atoms)

        # if update of forces is neccessary

        if self.update_forces:

            # calculate forces

            if self.calculate_forces is not None:

                self.execute(self.calculate_forces + " > ASE.TM.forces.out")

            # read forces

            self.read_forces()

        else :

            print "taking old values (F)"

        self.update_forces = False

        return self.forces.copy()

    def get_stress(self, atoms):

        return self.stress

    def set_atoms(self, atoms):

        if self.atoms == atoms:

            return

        # performs an update of the atoms

        super(Turbomole, self).set_atoms(atoms)

        write_turbomole('coord', atoms)

        # energy and forces must be re-calculated

        self.update_energy = True

        self.update_forces = True

    def read_energy(self):

        """Read Energy from Turbomole energy file."""

        text = open('energy', 'r').read().lower()

        lines = iter(text.split('\n'))

        # Energy:

        for line in lines:

            if line.startswith('$end'):

                break

            elif line.startswith('$'):

                pass

            else:

                # print 'LINE',line

                energy_tmp = float(line.split()[1])

                if self.post_HF:

                    energy_tmp += float(line.split()[4])

        # update energy units

        self.e_total = energy_tmp * Hartree

    def read_forces(self):

        """Read Forces from Turbomole gradient file."""

        file = open('gradient','r')

        lines=file.readlines()

        file.close()

        forces = np.array([[0, 0, 0]])

        nline = len(lines)

        iline = -1

        for i in xrange(nline):

            if 'cycle' in lines[i]:

                iline = i

        if iline < 0:

            print 'Gradients not found'

            raise RuntimeError("Please check TURBOMOLE gradients")

        # next line

        iline += len(self.atoms) + 1

        # $end line

        nline -= 1

        # read gradients

        for i in xrange(iline, nline):

            line = string.replace(lines[i],'D','E')

            #tmp=np.append(forces_tmp,np.array\

            #      ([[float(f) for f in line.split()[0:3]]]))

            tmp=np.array([[float(f) for f in line.split()[0:3]]])

            forces=np.concatenate((forces,tmp))

        #note the '-' sign for turbomole, to get forces

        self.forces = (-np.delete(forces, np.s_[0:1], axis=0))*Hartree/Bohr