How to use the gc3pie.gc3apps.gamess.grundb.GamessDb function in gc3pie

return default


if "__main__" == __name__:
    if len(args) < 1:
        logger.critical("%s: Need at least the ACTION argument."
                        " Type '%s --help' to get usage help."
                        % (PROG, PROG))
        sys.exit(1)

    #try:
    if 'new' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        session = get_optional_argument(args, 2, "SESSION")
        if subset == 'ALL':
            subsets = GamessDb().list().keys()
        else:
            subsets = subset.split(',')
        for subset in subsets:
            new(subset, session, options.template)

    elif 'progress' == args[0]:
        session = get_required_argument(args, 1, "SESSION")
        progress(session)

    elif 'abort' == args[0]:
        session = get_optional_argument(args, 1, "SESSION")
        abort(session)

    elif 'refdata' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        for r,d in GamessDb().get_reference_data(subset):

else:
            subsets = subset.split(',')
        for subset in subsets:
            new(subset, session, options.template)

    elif 'progress' == args[0]:
        session = get_required_argument(args, 1, "SESSION")
        progress(session)

    elif 'abort' == args[0]:
        session = get_optional_argument(args, 1, "SESSION")
        abort(session)

    elif 'refdata' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        for r,d in GamessDb().get_reference_data(subset):
            print ("%s = %.3f"
                   % (str.join(' + ',
                               [ ("%d*%s" % (qty, sy)) for sy,qty in r.items() ]),
                      d))

    elif 'download' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        GamessDb().get_geometries(subset)

    elif 'list' == args[0]:
        print ("Available subsets of GMTKN24:")
        ls = GamessDb().list()
        for name, url in ls.items():
            print ("  %s --> %s" % (name, url))

    elif 'doctest' == args[0]:

elif 'abort' == args[0]:
        session = get_optional_argument(args, 1, "SESSION")
        abort(session)

    elif 'refdata' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        for r,d in GamessDb().get_reference_data(subset):
            print ("%s = %.3f"
                   % (str.join(' + ',
                               [ ("%d*%s" % (qty, sy)) for sy,qty in r.items() ]),
                      d))

    elif 'download' == args[0]:
        subset = get_required_argument(args, 1, "SUBSET")
        GamessDb().get_geometries(subset)

    elif 'list' == args[0]:
        print ("Available subsets of GMTKN24:")
        ls = GamessDb().list()
        for name, url in ls.items():
            print ("  %s --> %s" % (name, url))

    elif 'doctest' == args[0]:
        import doctest
        doctest.testmod(name="gmtkn24",
                        optionflags=doctest.NORMALIZE_WHITESPACE)

    else:
        logger.critical("Unknown ACTION word '%s'."
                        " Type '%s --help' to get usage help."
                        % (args[0], PROG))

subsets.add(job.subset)
        # map each molecule to its computed energy
        energy = dict([ (job.molecule, job.energy)
                        for job in jobs.values() ])
        print ("")
        print ("STOICHIOMETRY DATA")
        print ("")
        print ("%-40s  %-12s  (%-s; %-s)"
               % ("Reaction", "Comp. energy", "Ref. data", "deviation"))
        print (78 * "=")
        for subset in sorted(subsets):
            # print subset name, centered
            print ((78 - len(subset)) / 2) * ' ' + subset
            print (78 * "-")
            # print reaction data
            for reaction,refdata in GamessDb().get_reference_data(subset):
                # compute corresponding energy
                computed_energy = sum([ (627.509*qty*energy[sy]) for sy,qty in reaction.items() ])
                deviation = computed_energy - refdata
                print ("%-40s  %+.2f  (%+.2f; %+.2f)"
                       % (
                        # symbolic reaction
                        str.join(' + ',
                             [ ("%d*%s" % (qty, sy)) for sy,qty in reaction.items() ]),
                        # numerical data
                        computed_energy, refdata, deviation)
                       )

Download geometry files for the specified GAMESS.UZH subset,
        and save them into a `output_dir` subdirectory of the current
        working directory.

        Return list of extracted molecules/filenames.
        """
        if not os.path.exists(output_dir):
            os.mkdir(output_dir)
        # download all links pointing to ".inp" files
        subset_url = self._subsets[subset]
        html = BeautifulSoup(self._browser.open(subset_url))
        links = html.findAll(name="a", attrs={'class':"mapitem"})
        molecules = [ ]
        for a in links:
            if a.string is not None:
                name = GamessDb._illegal_chars_re.sub('_', a.string)
                # ignore links that don't look like `.inp` files ...
                if not GamessDb._inp_filename_re.search(name):
                    continue
                # mechanize.retrieve always uses temp files
                (filename, headers) = self._browser.retrieve(urlparse.urljoin(subset_url, a['href']))
                shutil.copy(filename, os.path.join(output_dir, name))
                molecules.append(os.path.splitext(name)[0])
        logger.info("%s geometries downloaded into file '%s'", subset, output_dir)
        return molecules

grid = Grid()
    session_file_name = add_extension(session, 'csv')
    logger.info("Will save jobs status to file '%s'", session_file_name)
    session_inp_dir = add_extension(session, '.inp.d')
    if not os.path.exists(session_inp_dir):
        os.mkdir(session_inp_dir)
    session_out_dir = add_extension(session, '.out.d')
    if not os.path.exists(session_out_dir):
        os.mkdir(session_out_dir)
    template = read_file_contents(template_file_name)
    # download geometries
    subset_inp_dir = os.path.join(session_inp_dir, subset)
    if not os.path.exists(subset_inp_dir):
        os.mkdir(subset_inp_dir)
    logger.info("Downloading %s geometries into '%s' ...", subset, subset_inp_dir)
    molecules = GamessDb().get_geometries(subset, subset_inp_dir)
    # prefix them with the GAMESS file snippet
    for name in molecules:
        dest_file_name = os.path.join(subset_inp_dir, name + '.inp')
        geometry = read_file_contents(dest_file_name)
        inp = open(dest_file_name, 'w')
        inp.write(template)
        inp.write(geometry)
        inp.close()
    # open session file
    logger.info("Loading session file '%s' ...", session_file_name)
    jobs = _load_jobs(session_file_name)
    logger.info("Loaded %d jobs from session file.", len(jobs))
    # append new jobs
    for name in molecules:
        inp_file_name = os.path.join(subset_inp_dir, name + '.inp')
        # XXX: order of the following statements *is* important!

def _list_subsets(self):
        """Return dictionary mapping GAMESS.UZH subset names to download URLs."""
        html = BeautifulSoup(self._browser.open(GamessDb.BASE_URL))
        links = html.findAll(name="a", attrs={'class':"mapitem"})
        result = { }
        for a in links:
            if a.string is not None:
                name = a.string
                result[name] = urlparse.urljoin(GamessDb.BASE_URL, a['href'])
        return result

working directory.

        Return list of extracted molecules/filenames.
        """
        if not os.path.exists(output_dir):
            os.mkdir(output_dir)
        # download all links pointing to ".inp" files
        subset_url = self._subsets[subset]
        html = BeautifulSoup(self._browser.open(subset_url))
        links = html.findAll(name="a", attrs={'class':"mapitem"})
        molecules = [ ]
        for a in links:
            if a.string is not None:
                name = GamessDb._illegal_chars_re.sub('_', a.string)
                # ignore links that don't look like `.inp` files ...
                if not GamessDb._inp_filename_re.search(name):
                    continue
                # mechanize.retrieve always uses temp files
                (filename, headers) = self._browser.retrieve(urlparse.urljoin(subset_url, a['href']))
                shutil.copy(filename, os.path.join(output_dir, name))
                molecules.append(os.path.splitext(name)[0])
        logger.info("%s geometries downloaded into file '%s'", subset, output_dir)
        return molecules