occupytenter.py 文件源码

def run(self):
        # Create directory contain POSCARs
        import random
        import string
        import tempfile

        rd_suffix = ''.join(random.choices(string.ascii_uppercase
                                           + string.digits, k=5))
        working_path = os.getcwd()
        poscars_dir = os.path.join(working_path,
                                   'STRUCTURES_{0:}_{1:}'.format(self.comment,
                                                              rd_suffix))
        if not os.path.exists(poscars_dir):
            os.makedirs(poscars_dir)
        else:
            shutil.rmtree(poscars_dir)
            os.makedirs(poscars_dir)

        ogg = OccupyGenerator(self.cell)
        g = ogg.gen_nodup_trinary_alloy(Specie(self.s1), self.n1,
                                        Specie(self.s2), self.n2)

        if self.tr is not None:
            tr = (Specie(self.tr[0]), self.tr[1])
            applied_restriction = MinDistanceRestriction(tr)

        # For diff outmode
        if self.outmode == 'vasp':
            Output = VaspPOSCAR
            prefix = 'POSCAR_A{:}B{:}C{:}_'
            suffix = '.vasp'
        else:
            Output = YamlOutput
            prefix = 'STRUCTURE_A{:}B{:}C{:}_'
            suffix = '.yaml'

        for n_count, c in enumerate(g):
            if self.mpr:
                if self.tr is not None:
                    condition = c.is_primitive() and applied_restriction.is_satisfied(c)
                else:
                    condition = c.is_primitive()
            else:
                if self.tr is not None:
                    condition = applied_restriction.is_satisfied(c)
                else:
                    condition = True

            if condition:
                if self.refined:
                    c = c.get_refined_pcell()
                poscar = Output(c, 1)
                tf = tempfile.NamedTemporaryFile(mode='w+b', dir=poscars_dir,
                                                 prefix=prefix.format(self.n0, self.n1, self.n2),
                                                 suffix=suffix, delete=False)
                poscar.write(tf.name)