Exemplo n.º 1
0
def build_db(update='.', prefix='datas'):
    user = os.getenv('USER')
    print('Reading.....')
    dbfile = '%s.db' % prefix
    with connect(dbfile) as db:
        calc = Espresso()
        cwd = os.getcwd()
        for dire, j, y in os.walk(update):
            prefix = is_espresso(dire)
            if prefix:
                calc.prefix = prefix
            else:
                continue
            print(dire)
            label = dire
            inputfile = dire + '/%s.pwi' % calc.prefix
            calc.directory = os.path.join(cwd, dire)
            calc.prefix = prefix
            print(inputfile)
            atoms, input_data, pseudopotentials, kpts = read_espresso_input(
                inputfile)
            newcalc = Espresso(label=dire,
                               prefix=prefix,
                               pseudopotentials=pseudopotentials,
                               input_data=input_data,
                               kpts=kpts)
            converged, fromfile, meg0 = calc.read_convergence()
            calc.results = {}
            try:
                calc.read_results()
                atoms = calc.results['atoms']
            except Exception as e:
                print('=' * 30, '\n', dire, e)
            # atoms.calc = newcalc
            print('dire: ', dire, converged)
            nid = 0
            for row in db.select(label=label):
                dbid = row.id
                nid += 1
            if nid > 0:
                db.write(atoms, id=dbid, label=label, converged=meg0)
            else:
                db.write(atoms, label=label)
    print('Finished')
Exemplo n.º 2
0
def summary(updates=[], prefix='datas'):
    import pandas as pd
    columns = [
        'label', 'atoms', 'cell', 'positions', 'energy', 'forces', 'stress'
    ]
    file = '%s.pickle' % prefix
    db = '%s.db' % prefix
    if os.path.exists(file):
        with open(file, 'rb') as f:
            datas, df = pickle.load(f)
    else:
        datas = {}
        df = pd.DataFrame(columns=columns)
    calc = Espresso()
    print('Reading.....')
    for update in updates:
        cwd = os.getcwd()
        for i, j, y in os.walk(update):
            output = is_espresso(i)
            if output:
                os.chdir(i)
                print('dire:', i)
                calc.directory = cwd + '/' + i
                calc.prefix = output[0:-4]
                try:
                    calc.results = {}
                    calc.read_results()
                    # gap, p1, p2 = bandgap(calc)
                    # calc.results['gap'] = gap
                    # t = calc.get_time()
                    # calc.results['time'] = t
                    datas[i] = calc.results
                    atoms = calc.results['atoms']
                    atoms.write(
                        os.path.join(calc.directory, '%s.cif' % calc.prefix))
                    # results = ana(i, calc)
                    # df.loc[len(df)] = results
                except Exception as e:
                    print('=' * 30, '\n', i, e)
            os.chdir(cwd)
    with open(file, 'wb') as f:
        pickle.dump([datas, df], f)
    print('Finished')