Chimie Théorique » QMX

#!/usr/bin/env python

# Copyright 2008, 2009

# CAMd (see accompanying license files for details).

from optparse import OptionParser, SUPPRESS_HELP

import ase.gui.gtkexcepthook

#ase.gui.gtkexcepthook.feedback = "schiotz@fysik.dtu.dk"

#ase.gui.gtkexcepthook.smtphost = "mail.fysik.dtu.dk"

def build_parser():

    parser = OptionParser(usage='%prog [options] [file[, file2, ...]]',

                          version='%prog 0.1',

                          description='See the online manual ' +

                          '(https://wiki.fysik.dtu.dk/ase/ase/gui.html) ' +

                          'for more information.')

    parser.add_option('-n', '--image-number',

                      default=':', metavar='NUMBER',

                      help='Pick image(s) from trajectory.  NUMBER can be a '

                      'single number (use a negative number to count from '

                      'the back) or a range: start:stop:step, where the '

                      '":step" part can be left out - default values are '

                      '0:nimages:1.')

    parser.add_option('-u', '--show-unit-cell', type='int',

                      default=1, metavar='I',

                      help="0: Don't show unit cell.  1: Show unit cell.  "

                      '2: Show all of unit cell.')

    parser.add_option('-r', '--repeat',

                      default='1',

                      help='Repeat unit cell.  Use "-r 2" or "-r 2,3,1".')

    parser.add_option('-R', '--rotations', default='',

                      help='Examples: "-R -90x", "-R 90z,-30x".')

    parser.add_option('-o', '--output', metavar='FILE',

                      help='Write configurations to FILE.')

    parser.add_option('-g', '--graph',

                      metavar='EXPR',

                      help='Plot x,y1,y2,... graph from configurations or '

                      'write data to sdtout in terminal mode.  Use the '

                      'symbols: i, s, d, fmax, e, ekin, A, R, E and F.  See '

                      'https://wiki.fysik.dtu.dk/ase/ase/gui.html#plotting-data '

                      'for more details.')

    parser.add_option('-t', '--terminal',

                      action='store_true',

                      default=False,

                      help='Run in terminal window - no GUI.')

    parser.add_option('--aneb',

                      action='store_true',

                      default=False,

                      help='Read ANEB data.')

    parser.add_option('--interpolate',

                      type='int', metavar='N',

                      help='Interpolate N images between 2 given images.')

    parser.add_option('-b', '--bonds',

                      action='store_true',

                      default=False,

                      help='Draw bonds between atoms.')

    #parser.add_option('--read-pickled-data-from-file',

    #                  type='string', help=SUPPRESS_HELP)

    return parser

def main():

    parser = build_parser()

    opt, args = parser.parse_args()

    try:

        import ase

    except ImportError:

        import sys

        from os.path import dirname, join, pardir

        sys.path.append(join(dirname(__file__), pardir))

    from ase.gui.images import Images

    from ase.atoms import Atoms

    def run(opt, args):

        images = Images()

        if opt.aneb:

            opt.image_number = '-1'

        if len(args) > 0:

            from ase.io import string2index

            images.read(args, string2index(opt.image_number))

        else:

            images.initialize([Atoms()])

        if opt.interpolate:

            images.interpolate(opt.interpolate)

        if opt.aneb:

            images.aneb()

        if opt.repeat != '1':

            r = opt.repeat.split(',')

            if len(r) == 1:

                r = 3 * r

            images.repeat_images([int(c) for c in r])

        if opt.output is not None:

            images.write(opt.output, rotations=opt.rotations,

                        show_unit_cell=opt.show_unit_cell)

            opt.terminal = True

        if opt.terminal:

            if opt.graph is not None:

                data = images.graph(opt.graph)

                for line in data.T:

                    for x in line:

                        print x,

                    print

        else:

            from ase.gui.gui import GUI

            gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)

            gui.run(opt.graph)

    import traceback

    try:

        run(opt, args)

    except KeyboardInterrupt:

        pass

    except Exception:

        traceback.print_exc()

        print """

An exception occurred!  Please report the issue to

ase-developers@listserv.fysik.dtu.dk - thanks!  Please also report this if

it was a user error, so that a better error message can be provided

next time."""