Chimie Théorique » QMX

from math import sin, cos, pi, sqrt

import numpy as np

from ase.atoms import Atoms, Atom

from ase.units import Bohr, Ry

def read_scf(filename):

    try:

        f = open(filename + '.scf', 'r')

        pip = f.readlines()

        ene = []

        for line in pip:

            if line[0:4] == ':ENE':

                ene.append(float(line[43:59]) * Ry)

        f.close()

        return ene

    except:

        return None

def read_struct(filename, ase = True):

    f = open(filename, 'r')

    pip = f.readlines()

    lattice = pip[1][0:3]

    nat = int(pip[1][27:30])

    cell = np.zeros(6)

    for i in range(6):

        cell[i] = float(pip[3][0 + i * 10:10 + i * 10])

    cell[0:3] = cell[0:3] * Bohr

    if lattice == 'P  ':

        lattice = 'P'

    elif lattice == 'H  ':

        lattice = 'P'

        cell[3:6] = [90.0, 90.0, 120.0]

    elif lattice == 'R  ':

        lattice = 'R'

    elif lattice == 'F  ':

        lattice = 'F'

    elif lattice == 'B  ':

        lattice = 'I'

    elif lattice == 'CXY':

        lattice = 'C'

    elif lattice == 'CXZ':

        lattice = 'B'

    elif lattice == 'CYZ':

        lattice = 'A'

    else:

        print 'TEST needed'

    pos = np.array([])

    atomtype = []

    rmt = []

    neq = np.zeros(nat)

    iline = 4

    indif = 0

    for iat in range(nat):

        indifini = indif

        if len(pos) == 0:

            pos = np.array([[float(pip[iline][12:22]),

                             float(pip[iline][25:35]),

                             float(pip[iline][38:48])]])

        else:

            pos = np.append(pos, np.array([[float(pip[iline][12:22]),

                                            float(pip[iline][25:35]),

                                            float(pip[iline][38:48])]]),

                            axis = 0)

        indif += 1

        iline += 1

        neq[iat] = int(pip[iline][15:17])

        iline += 1

        for ieq in range(1, int(neq[iat])):

            pos = np.append(pos, np.array([[float(pip[iline][12:22]),

                                            float(pip[iline][25:35]),

                                            float(pip[iline][38:48])]]),

                            axis = 0)

            indif += 1

            iline += 1

        for i in range(indif - indifini):

            atomtype.append(pip[iline][0:2].replace(' ', ''))

            rmt.append(float(pip[iline][43:48]))

        iline += 4

    if ase:

        cell2 = coorsys(cell)

        atoms = Atoms(atomtype, pos, pbc = True)

        atoms.set_cell(cell2, scale_atoms = True)

        cell2 = np.dot(c2p(lattice), cell2)

        if lattice == 'R':

            atoms.set_cell(cell2, scale_atoms = True)

        else:

            atoms.set_cell(cell2)

        return atoms

    else:

        return cell, lattice, pos, atomtype, rmt

def write_struct(filename, atoms2 = None, rmt = None, lattice = 'P'):

    atoms=atoms2.copy()

    atoms.set_scaled_positions(atoms.get_scaled_positions())

    f = file(filename, 'w')

    f.write('ASE generated\n')

    nat = len(atoms)

    if rmt == None:

        rmt = [2.0] * nat

    f.write(lattice+'   LATTICE,NONEQUIV.ATOMS:%3i\nMODE OF CALC=RELA\n'%nat)

    cell = atoms.get_cell()

    metT = np.dot(cell, np.transpose(cell))

    cell2 = cellconst(metT)

    cell2[0:3] = cell2[0:3] / Bohr

    f.write(('%10.6f' * 6) % tuple(cell2) + '\n')

    #print atoms.get_positions()[0]

    for ii in range(nat):

        f.write('ATOM %3i: ' % (ii + 1))

        pos = atoms.get_scaled_positions()[ii]

        f.write('X=%10.8f Y=%10.8f Z=%10.8f\n' % tuple(pos))

        f.write('          MULT= 1          ISPLIT= 1\n')

        zz = atoms.get_atomic_numbers()[ii]

        if zz > 71:

            ro = 0.000005

        elif zz > 36:

            ro = 0.00001

        elif zz > 18:

            ro = 0.00005

        else:

            ro = 0.0001

        f.write('%-10s NPT=%5i  R0=%9.8f RMT=%10.4f   Z:%10.5f\n' %

                (atoms.get_chemical_symbols()[ii], 781, ro, rmt[ii], zz))

        f.write('LOCAL ROT MATRIX:    %9.7f %9.7f %9.7f\n' % (1.0, 0.0, 0.0))

        f.write('                     %9.7f %9.7f %9.7f\n' % (0.0, 1.0, 0.0))

        f.write('                     %9.7f %9.7f %9.7f\n' % (0.0, 0.0, 1.0))

    f.write('   0\n')

def cellconst(metT):

    aa = np.sqrt(metT[0, 0])

    bb = np.sqrt(metT[1, 1])

    cc = np.sqrt(metT[2, 2])

    gamma = np.arccos(metT[0, 1] / (aa * bb)) / np.pi * 180.0

    beta  = np.arccos(metT[0, 2] / (aa * cc)) / np.pi * 180.0

    alpha = np.arccos(metT[1, 2] / (bb * cc)) / np.pi * 180.0

    return np.array([aa, bb, cc, alpha, beta, gamma])

def coorsys(latconst):

    a = latconst[0]

    b = latconst[1]

    c = latconst[2]

    cal = np.cos(latconst[3] * np.pi / 180.0)

    cbe = np.cos(latconst[4] * np.pi / 180.0)

    cga = np.cos(latconst[5] * np.pi / 180.0)

    sal = np.sin(latconst[3] * np.pi / 180.0)

    sbe = np.sin(latconst[4] * np.pi / 180.0)

    sga = np.sin(latconst[5] * np.pi / 180.0)

    return np.array([[a, b * cga, c * cbe],

                     [0, b * sga, c * (cal - cbe * cga) / sga],

                     [0, 0, c * np.sqrt(1 - cal**2 - cbe**2 - cga**2 + 2 * cal * cbe * cga) / sga]]).transpose()

def c2p(lattice):

    # apply as eg. cell2 = np.dot(ct.c2p('F'), cell)

    if lattice == 'P':

        cell = np.eye(3)

    elif lattice == 'F':

        cell = np.array([[0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])

    elif lattice == 'I':

        cell = np.array([[-0.5, 0.5, 0.5], [0.5, -0.5, 0.5], [0.5, 0.5, -0.5]])

    elif lattice == 'C':

        cell = np.array([[0.5, 0.5, 0.0], [0.5, -0.5, 0.0], [0.0, 0.0, -1.0]])

    elif lattice == 'R':

        cell = np.array([[2.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], [-1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0], [-1.0 / 3.0, -2.0/3.0, 1.0 / 3.0]])

    else:

        print 'lattice is ' + lattice + '!'

    return cell