Пример #1
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 def test_cluster_from_file(self):
     self.atoms.write_file("ATOMS_test")
     mol_1 = Atoms.cluster_from_file("ATOMS_test")
     mol_2 = Atoms.cluster_from_file(os.path.join(test_dir, "ATOMS"))
     self.assertEqual(mol_1.formula, mol_2.formula)
     self.assertEqual(len(mol_1), len(mol_2))
     os.remove("ATOMS_test")
Пример #2
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 def test_get_string(self):
     header = Header.from_string(header_string)
     struc = header.struct
     central_atom = 'O'
     a = Atoms(struc, central_atom)
     atoms = a.get_string()
     self.assertEqual(atoms.splitlines()[3].split()[4], central_atom,
                      "failed to create ATOMS string")
Пример #3
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 def test_as_dict_and_from_dict(self):
     file_name = os.path.join(test_dir, 'HEADER')
     header = Header.from_file(file_name)
     struct = header.struct
     atoms = Atoms(struct, 'O', radius=10.)
     d = atoms.as_dict()
     atoms2 = Atoms.from_dict(d)
     self.assertEqual(str(atoms), str(atoms2),
                      "Atoms failed to and from dict test")
Пример #4
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    def from_directory(input_dir):
        """
        Read in a set of FEFF input files from a directory, which is
        useful when existing FEFF input needs some adjustment.
        """
        sub_d = {}
        for fname, ftype in [("HEADER", Header), ("PARAMETERS", Tags)]:
            fullzpath = zpath(os.path.join(input_dir, fname))
            sub_d[fname.lower()] = ftype.from_file(fullzpath)

        # Generation of FEFFDict set requires absorbing atom, need to search
        # the index of absorption atom in the structure according to the
        # distance matrix and shell species information contained in feff.inp

        absorber_index = []
        radius = None
        feffinp = zpath(os.path.join(input_dir, 'feff.inp'))

        if "RECIPROCAL" not in sub_d["parameters"]:
            input_atoms = Atoms.cluster_from_file(feffinp)
            shell_species = np.array([x.species_string for x in input_atoms])

            # First row of distance matrix represents the distance from the absorber to
            # the rest atoms
            distance_matrix = input_atoms.distance_matrix[0, :]

            # Get radius value
            from math import ceil
            radius = int(ceil(input_atoms.get_distance(input_atoms.index(input_atoms[0]),
                                                       input_atoms.index(input_atoms[-1]))))

            for site_index, site in enumerate(sub_d['header'].struct):

                if site.specie == input_atoms[0].specie:
                    site_atoms = Atoms(sub_d['header'].struct, absorbing_atom=site_index,
                                       radius=radius)
                    site_distance = np.array(site_atoms.get_lines())[:, 5].astype(np.float64)
                    site_shell_species = np.array(site_atoms.get_lines())[:, 4]
                    shell_overlap = min(shell_species.shape[0], site_shell_species.shape[0])

                    if np.allclose(distance_matrix[:shell_overlap], site_distance[:shell_overlap]) and \
                            np.all(site_shell_species[:shell_overlap] == shell_species[:shell_overlap]):
                        absorber_index.append(site_index)

        if "RECIPROCAL" in sub_d["parameters"]:
            absorber_index = sub_d["parameters"]["TARGET"]
            absorber_index[0] = int(absorber_index[0]) - 1

        # Generate the input set
        if 'XANES' in sub_d["parameters"]:
            CONFIG = loadfn(os.path.join(MODULE_DIR, "MPXANESSet.yaml"))
            if radius is None:
                radius = 10
            return FEFFDictSet(absorber_index[0], sub_d['header'].struct, radius=radius,
                               config_dict=CONFIG, edge=sub_d["parameters"]["EDGE"],
                               nkpts=1000, user_tag_settings=sub_d["parameters"])
Пример #5
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 def test_cluster_from_file(self):
     r = CifParser(os.path.join(test_dir, "CoO19128.cif"))
     structure = r.get_structures()[0]
     atoms = Atoms(structure, "O", 10.0)
     atoms.write_file("ATOMS_test")
     mol_1 = Atoms.cluster_from_file("ATOMS_test")
     mol_2 = Atoms.cluster_from_file(os.path.join(test_dir, "ATOMS"))
     self.assertEqual(mol_1.formula, mol_2.formula)
     self.assertEqual(len(mol_1), len(mol_2))
     os.remove("ATOMS_test")
Пример #6
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    def test_setup(self):
        with cd(test_dir):
            with ScratchDir('.', copy_from_current_on_enter=True):
                f = FeffJob("hello", backup=True)
                f.setup()

                parameter = Tags.from_file('feff.inp')
                parameter_orig = Tags.from_file('feff.inp.orig')
                self.assertEqual(parameter, parameter_orig)

                atom = Atoms.cluster_from_file('feff.inp')
                atom_origin = Atoms.cluster_from_file('feff.inp.orig')
                self.assertEqual(atom, atom_origin)
Пример #7
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 def test_distances(self):
     atoms_1 = self.atoms.get_lines()
     distances_1 = [float(a[5]) for a in atoms_1]
     atoms_2 = Atoms.atoms_string_from_file(os.path.join(test_dir, "ATOMS"))
     atoms_2 = atoms_2.splitlines()[3:]
     distances_2 = [float(a.split()[5]) for a in atoms_2]
     np.testing.assert_allclose(distances_1, distances_2)
Пример #8
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    def test_postfeffset(self):
        self.mp_xanes.write_input(os.path.join('.', 'xanes_3'))
        feff_dict_input = FEFFDictSet.from_directory(os.path.join('.', 'xanes_3'))
        self.assertTrue(feff_dict_input.tags == Tags.from_file(os.path.join('.', 'xanes_3/feff.inp')))
        self.assertTrue(str(feff_dict_input.header()) == str(Header.from_file(os.path.join('.', 'xanes_3/HEADER'))))
        feff_dict_input.write_input('xanes_3_regen')
        origin_tags = Tags.from_file(os.path.join('.', 'xanes_3/PARAMETERS'))
        output_tags = Tags.from_file(os.path.join('.', 'xanes_3_regen/PARAMETERS'))
        origin_mole = Atoms.cluster_from_file(os.path.join('.', 'xanes_3/feff.inp'))
        output_mole = Atoms.cluster_from_file(os.path.join('.', 'xanes_3_regen/feff.inp'))
        original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
        output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
        original_mole_shell = [x.species_string for x in origin_mole]
        output_mole_shell = [x.species_string for x in output_mole]

        self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
        self.assertTrue(origin_tags == output_tags)
        self.assertTrue(original_mole_shell == output_mole_shell)

        shutil.rmtree(os.path.join('.', 'xanes_3'))
        shutil.rmtree(os.path.join('.', 'xanes_3_regen'))

        reci_mp_xanes = MPXANESSet(self.absorbing_atom, self.structure,
                                   user_tag_settings={"RECIPROCAL": ""})
        reci_mp_xanes.write_input('xanes_reci')
        feff_reci_input = FEFFDictSet.from_directory(os.path.join('.', 'xanes_reci'))
        self.assertTrue("RECIPROCAL" in feff_reci_input.tags)

        feff_reci_input.write_input('Dup_reci')
        self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'HEADER')))
        self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'feff.inp')))
        self.assertTrue(os.path.exists(os.path.join('.', 'Dup_reci', 'PARAMETERS')))
        self.assertFalse(os.path.exists(os.path.join('.', 'Dup_reci', 'ATOMS')))
        self.assertFalse(os.path.exists(os.path.join('.', 'Dup_reci', 'POTENTIALS')))

        tags_original = Tags.from_file(os.path.join('.', 'xanes_reci/feff.inp'))
        tags_output = Tags.from_file(os.path.join('.', 'Dup_reci/feff.inp'))
        self.assertTrue(tags_original == tags_output)

        stru_orig = Structure.from_file(os.path.join('.', 'xanes_reci/Co2O2.cif'))
        stru_reci = Structure.from_file(os.path.join('.', 'Dup_reci/Co2O2.cif'))
        self.assertTrue(stru_orig.__eq__(stru_reci))

        shutil.rmtree(os.path.join('.', 'Dup_reci'))
        shutil.rmtree(os.path.join('.', 'xanes_reci'))
Пример #9
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    def test_post_distdiff(self):
        feff_dict_input = FEFFDictSet.from_directory(os.path.join(test_dir, 'feff_dist_test'))
        self.assertTrue(feff_dict_input.tags == Tags.from_file(os.path.join(test_dir, 'feff_dist_test/feff.inp')))
        self.assertTrue(
            str(feff_dict_input.header()) == str(Header.from_file(os.path.join(test_dir, 'feff_dist_test/HEADER'))))
        feff_dict_input.write_input('feff_dist_regen')
        origin_tags = Tags.from_file(os.path.join(test_dir, 'feff_dist_test/PARAMETERS'))
        output_tags = Tags.from_file(os.path.join('.', 'feff_dist_regen/PARAMETERS'))
        origin_mole = Atoms.cluster_from_file(os.path.join(test_dir, 'feff_dist_test/feff.inp'))
        output_mole = Atoms.cluster_from_file(os.path.join('.', 'feff_dist_regen/feff.inp'))
        original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
        output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
        original_mole_shell = [x.species_string for x in origin_mole]
        output_mole_shell = [x.species_string for x in output_mole]

        self.assertTrue(np.allclose(original_mole_dist, output_mole_dist))
        self.assertTrue(origin_tags == output_tags)
        self.assertTrue(original_mole_shell == output_mole_shell)

        shutil.rmtree(os.path.join('.', 'feff_dist_regen'))
Пример #10
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    def run_task(self, fw_spec):
        calc_dir = os.getcwd()
        if "calc_dir" in self:
            calc_dir = self["calc_dir"]
        elif self.get("calc_loc"):
            calc_dir = get_calc_loc(self["calc_loc"], fw_spec["calc_locs"])["path"]

        logger.info("PARSING DIRECTORY: {}".format(calc_dir))

        db_file = env_chk(self.get('db_file'), fw_spec)

        cluster_dict = None
        tags = Tags.from_file(filename="feff.inp")
        if "RECIPROCAL" not in tags:
            cluster_dict = Atoms.cluster_from_file("feff.inp").as_dict()
        doc = {"input_parameters": tags.as_dict(),
               "cluster": cluster_dict,
               "structure": self["structure"].as_dict(),
               "absorbing_atom": self["absorbing_atom"],
               "spectrum_type": self["spectrum_type"],
               "spectrum": np.loadtxt(os.path.join(calc_dir, self["output_file"])).tolist(),
               "edge": self.get("edge", None),
               "metadata": self.get("metadata", None),
               "dir_name": os.path.abspath(os.getcwd()),
               "last_updated": datetime.today()}

        if not db_file:
            with open("feff_task.json", "w") as f:
                f.write(json.dumps(doc, default=DATETIME_HANDLER))
        # db insertion
        else:
            db = MMFeffDb.from_db_file(db_file, admin=True)
            db.insert(doc)

        logger.info("Finished parsing the spectrum")

        return FWAction(stored_data={"task_id": doc.get("task_id", None)})
Пример #11
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 def test_atoms_from_file(self):
     filepath = os.path.join(test_dir, 'ATOMS')
     atoms = Atoms.atoms_string_from_file(filepath)
     self.assertEqual(atoms.splitlines()[3].split()[4], 'O',
                      "failed to read ATOMS file")