Python vasp.Poscar类代码示例

 def test_continue(self):
     # Test the continuation functionality
     with cd(os.path.join(test_dir, 'postprocess')):
         # Test default functionality
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello", auto_continue=True)
             v.setup()
             self.assertTrue(os.path.exists("continue.json"), "continue.json not created")
             v.setup()
             self.assertEqual(Poscar.from_file("CONTCAR").structure,
                              Poscar.from_file("POSCAR").structure)
             self.assertEqual(Incar.from_file('INCAR')['ISTART'], 1)
             v.postprocess()
             self.assertFalse(os.path.exists("continue.json"),
                              "continue.json not deleted after postprocessing")
         # Test explicit action functionality
         with ScratchDir('.', copy_from_current_on_enter=True) as d:
             v = VaspJob("hello", auto_continue=[{"dict": "INCAR",
                                                  "action": {"_set": {"ISTART": 1}}}])
             v.setup()
             v.setup()
             self.assertNotEqual(Poscar.from_file("CONTCAR").structure,
                                 Poscar.from_file("POSCAR").structure)
             self.assertEqual(Incar.from_file('INCAR')['ISTART'], 1)
             v.postprocess()

    def _verify_inputs(self):
        user_incar = Incar.from_file(os.path.join(os.getcwd(), "INCAR"))
        ref_incar = Incar.from_file(os.path.join(self["ref_dir"], "inputs", "INCAR"))

        # perform some BASIC tests

        # check INCAR
        params_to_check = self.get("params_to_check", [])
        defaults = {"ISPIN": 1, "ISMEAR": 1, "SIGMA": 0.2}
        for p in params_to_check:
            if user_incar.get(p, defaults.get(p)) != ref_incar.get(p, defaults.get(p)):
                raise ValueError("INCAR value of {} is inconsistent!".format(p))

        # check KPOINTS
        user_kpoints = Kpoints.from_file(os.path.join(os.getcwd(), "KPOINTS"))
        ref_kpoints = Kpoints.from_file(os.path.join(self["ref_dir"], "inputs", "KPOINTS"))
        if user_kpoints.style != ref_kpoints.style or user_kpoints.num_kpts != ref_kpoints.num_kpts:
            raise ValueError("KPOINT files are inconsistent! Paths are:\n{}\n{}".format(
                os.getcwd(), os.path.join(self["ref_dir"], "inputs")))

        # check POSCAR
        user_poscar = Poscar.from_file(os.path.join(os.getcwd(), "POSCAR"))
        ref_poscar = Poscar.from_file(os.path.join(self["ref_dir"], "inputs", "POSCAR"))
        if user_poscar.natoms != ref_poscar.natoms or user_poscar.site_symbols != ref_poscar.site_symbols:
            raise ValueError("POSCAR files are inconsistent! Paths are:\n{}\n{}".format(
                os.getcwd(), os.path.join(self["ref_dir"], "inputs")))

        # check POTCAR
        user_potcar = Potcar.from_file(os.path.join(os.getcwd(), "POTCAR"))
        ref_potcar = Potcar.from_file(os.path.join(self["ref_dir"], "inputs", "POTCAR"))
        if user_potcar.symbols != ref_potcar.symbols:
            raise ValueError("POTCAR files are inconsistent! Paths are:\n{}\n{}".format(
                os.getcwd(), os.path.join(self["ref_dir"], "inputs")))
        logger.info("RunVaspFake: verified inputs successfully")

    def _verify_inputs(self):
        """Validation of input files under user NEB directory."""
        user_incar = Incar.from_file(os.path.join(self.user_dir, "INCAR"))
        ref_incar = Incar.from_file(os.path.join(self.ref_dir_input, "INCAR"))

        # Check INCAR
        params_to_check = self.get("params_to_check", [])
        defaults = {"ICHAIN": 0, "LCLIMB": True}
        for p in params_to_check:
            if user_incar.get(p, defaults.get(p)) != ref_incar.get(p, defaults.get(p)):
                raise ValueError("INCAR value of {} is inconsistent!".format(p))

        # Check KPOINTS
        user_kpoints = Kpoints.from_file(os.path.join(self.user_dir, "KPOINTS"))
        ref_kpoints = Kpoints.from_file(os.path.join(self.ref_dir_input, "KPOINTS"))
        if user_kpoints.style != ref_kpoints.style or user_kpoints.num_kpts != ref_kpoints.num_kpts:
            raise ValueError("KPOINT files are inconsistent! "
                             "Paths are:\n{}\n{} with kpts = {} {}".format(
                self.user_dir, self.ref_dir_input, user_kpoints, ref_kpoints))

        # Check POTCAR
        user_potcar = Potcar.from_file(os.path.join(self.user_dir, "POTCAR"))
        ref_potcar = Potcar.from_file(os.path.join(self.ref_dir_input, "POTCAR"))
        if user_potcar.symbols != ref_potcar.symbols:
            raise ValueError("POTCAR files are inconsistent! "
                             "Paths are:\n{}\n{}".format(self.user_dir, self.ref_dir_input))

        # Check POSCARs
        for u, r in zip(self.user_sdir, self.ref_sdir_input):
            user_poscar = Poscar.from_file(os.path.join(u, "POSCAR"))
            ref_poscar = Poscar.from_file(os.path.join(r, "POSCAR"))
            if user_poscar.natoms != ref_poscar.natoms or \
                            user_poscar.site_symbols != ref_poscar.site_symbols:
                raise ValueError("POSCAR files are inconsistent! Paths are:\n{}\n{}".format(u, r))

def mp_id(mpid):
    """
    materials project の ID から POSCAR を作成
    """
    mpr = MPRester("WTxsDhRV7g2Mcbqw")
    strctr = mpr.get_structure_by_material_id(mpid)
    poscar = Poscar(strctr)
    poscar.write_file('POSCAR_{0}'.format(mpid))

def refined(src):
    """
    refined poscar を 作成する
    """
    srcpos = Poscar.from_file(src)
    finder = SpacegroupAnalyzer(srcpos.structure, symprec=5e-1, angle_tolerance=8)
    scr_std = finder.get_refined_structure()
    dstpos = Poscar(scr_std)
    dst = "POSCAR_refined"
    Cabinet.reserve_file(dst)
    dstpos.write_file(dst)

def prim(src):
    """
    primitive cell に変換
    """
    srcpos = Poscar.from_file(src)
    finder = SpacegroupAnalyzer(srcpos.structure)
    prim_str = finder.get_primitive_standard_structure()
    dstpos = Poscar(prim_str)
    dst = 'POSCAR_prim'
    Cabinet.reserve_file(dst)
    dstpos.write_file(dst)

def std(src='POSCAR'):
    """
    conventional standard cell に変換
    """
    srcpos = Poscar.from_file(src)
    finder = SpacegroupAnalyzer(srcpos.structure)
    std_str = finder.get_conventional_standard_structure()
    dstpos = Poscar(std_str)
    dst = 'POSCAR_std'
    Cabinet.reserve_file(dst)
    dstpos.write_file(dst)

def refined(src='POSCAR'):
    """
    refined cell を 作成する
    """
    srcpos = Poscar.from_file(src)
    finder = SpacegroupAnalyzer(srcpos.structure,
                                symprec=5e-1, angle_tolerance=8)
    std_str = finder.get_refined_structure()
    dstpos = Poscar(std_str)
    dst = 'POSCAR_refined'
    Cabinet.reserve_file(dst)
    dstpos.write_file(dst)

    def run_task(self, fw_spec):

        transformations = []
        transformation_params = self.get("transformation_params",
                                         [{} for i in range(len(self["transformations"]))])
        for t in self["transformations"]:
            found = False
            for m in ["advanced_transformations", "defect_transformations",
                      "site_transformations", "standard_transformations"]:
                mod = import_module("pymatgen.transformations.{}".format(m))
                try:
                    t_cls = getattr(mod, t)
                except AttributeError:
                    continue
                t_obj = t_cls(**transformation_params.pop(0))
                transformations.append(t_obj)
                found = True
            if not found:
                raise ValueError("Could not find transformation: {}".format(t))

        # TODO: @matk86 - should prev_calc_dir use CONTCAR instead of POSCAR? Note that if
        # current dir, maybe it is POSCAR indeed best ... -computron
        structure = self['structure'] if not self.get('prev_calc_dir', None) else \
            Poscar.from_file(os.path.join(self['prev_calc_dir'], 'POSCAR')).structure
        ts = TransformedStructure(structure)
        transmuter = StandardTransmuter([ts], transformations)
        final_structure = transmuter.transformed_structures[-1].final_structure.copy()
        vis_orig = self["vasp_input_set"]
        vis_dict = vis_orig.as_dict()
        vis_dict["structure"] = final_structure.as_dict()
        vis_dict.update(self.get("override_default_vasp_params", {}) or {})
        vis = vis_orig.__class__.from_dict(vis_dict)
        vis.write_input(".")

        dumpfn(transmuter.transformed_structures[-1], "transformations.json")

    def run_task(self, fw_spec):

        transformations = []
        transformation_params = self.get("transformation_params", [{} for i in range(len(self["transformations"]))])
        for t in self["transformations"]:
            for m in [
                "advanced_transformations",
                "defect_transformations",
                "site_transformations",
                "standard_transformations",
            ]:
                mod = import_module("pymatgen.transformations.{}".format(m))
                try:
                    t_cls = getattr(mod, t)
                except AttributeError:
                    continue
                t_obj = t_cls(**transformation_params.pop(0))
                transformations.append(t_obj)

        structure = (
            self["structure"]
            if "prev_calc_dir" not in self
            else Poscar.from_file(os.path.join(self["prev_calc_dir"], "POSCAR")).structure
        )
        ts = TransformedStructure(structure)
        transmuter = StandardTransmuter([ts], transformations)
        final_structure = transmuter.transformed_structures[-1].final_structure.copy()

        vis_orig = self["vasp_input_set"]
        vis_dict = vis_orig.as_dict()
        vis_dict["structure"] = final_structure.as_dict()
        vis_dict.update(self.get("override_default_vasp_params", {}) or {})
        vis = vis_orig.__class__.from_dict(vis_dict)
        vis.write_input(".")

 def test_run_subfolders(self):
     #raise SkipTest
     ingdir="%s/writedir/single_label1" % testdir
     recipedir="%s/writedir" % testdir
     topmetad = MASTFile("files/top_metadata_single")
     topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
     topmetad.to_file("writedir/metadata.txt")
     metad = MASTFile("files/metadata_single")
     metad.to_file("%s/metadata.txt" % ingdir)
     kdict=dict()
     kdict['mast_program'] = 'vasp'
     kdict['mast_kpoints'] = [2,2,2,"M"]
     kdict['mast_xc'] = 'pw91'
     my_structure = Poscar.from_file("files/perfect_structure").structure
     for subfolder in ['sub1','sub2','sub3','sub4']:
         subname = "%s/%s" % (ingdir, subfolder)
         os.mkdir(subname)
         shutil.copy("files/metadata_single","%s/metadata.txt" % subname)
         mywr = ChopIngredient(name=subname, program_keys = kdict, structure=my_structure)
         mywr.write_singlerun()
     myri = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
     myri.run_subfolders()
     self.assertFalse(myri.checker.is_ready_to_run())
     for subfolder in ['sub1','sub2','sub3','sub4']:
         subname = "%s/%s" % (ingdir, subfolder)
         myri.checker.keywords['name'] = subname
         self.assertTrue(myri.checker.is_ready_to_run())
     mysubmit = MASTFile("%s/submitlist" % self.test_control)
     self.assertEquals(mysubmit.data[0], "%s/sub1\n" % ingdir)
     self.assertEquals(mysubmit.data[1], "%s/sub2\n" % ingdir)
     self.assertEquals(mysubmit.data[2], "%s/sub3\n" % ingdir)
     self.assertEquals(mysubmit.data[3], "%s/sub4\n" % ingdir)

    def strout2poscar(src='str.out'):
        """
        str.outをposcarの記述に変換し, Poscar objをreturn
        """
        with open(src, 'r') as rfile:
            lines = rfile.readlines()
        latt_tmp = [[float(x) for x in y.split()] for y in lines[0:3]]
        trans = [[float(x) for x in y.split()] for y in lines[3:6]]
        sites_tmp = [[float(x) for x in y.split()[0:3]] for y in lines[6:]]
        elements = [x.split()[3].split('+')[0].split('-')[0] for x in lines[6:]]
        num_atoms = [elements.count(e)
                     for e in sorted(set(elements), key=elements.index)]
        latt = np.dot(np.array(trans), np.array(latt_tmp))
        sites = np.dot(np.array(sites_tmp), np.array(latt_tmp))

        posc_str = "posc_orig\n"
        posc_str += "1.00\n"
        posc_str += "\n".join(["  ".join([str(f) for f in l]) for l in latt])
        posc_str += "\n"
        posc_str += "  ".join(sorted(set(elements), key=elements.index)) + "\n"
        posc_str += "  ".join([str(d) for d in num_atoms]) + "\n"
        posc_str += "Cartesian\n"
        posc_str += "\n".join(["  ".join([str(f) for f in s]) for s in sites])

        return Poscar.from_string(posc_str)

    def setUpClass(cls):
        if not os.environ.get("VASP_PSP_DIR"):
            os.environ["VASP_PSP_DIR"] = os.path.join(module_dir,
                                                      "reference_files")
            print(
                'Note: This system is not set up to run VASP jobs. '
                'Please set your VASP_PSP_DIR environment variable.')

        cls.struct_si = PymatgenTest.get_structure("Si")

        cls.ref_incar = Incar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test", "INCAR"))
        cls.ref_poscar = Poscar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "POSCAR"))
        cls.ref_potcar = Potcar.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "POTCAR"))
        cls.ref_kpoints = Kpoints.from_file(
            os.path.join(module_dir, "reference_files", "setup_test",
                         "KPOINTS"))
        cls.ref_incar_preserve = Incar.from_file(os.path.join(module_dir,
                                                              "reference_files",
                                                              "preserve_incar",
                                                              "INCAR"))

    def full_opt_run(cls, vasp_cmd, auto_npar=True, vol_change_tol=0.05,
                     max_steps=10):
        """
        Returns a generator of jobs for a full optimization run. Basically,
        this runs an infinite series of geometry optimization jobs until the
        % vol change in a particular optimization is less than vol_change_tol.

        Args:
            vasp_cmd (str): Command to run vasp as a list of args. For example,
                if you are using mpirun, it can be something like
                ["mpirun", "pvasp.5.2.11"]
            auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
                number of cores) as recommended by VASP for DFT calculations.
                Generally, this results in significant speedups. Defaults to
                True. Set to False for HF, GW and RPA calculations.
            vol_change_tol (float): The tolerance at which to stop a run.
                Defaults to 0.05, i.e., 5%.
            max_steps (int): The maximum number of runs. Defaults to 10 (
                highly unlikely that this limit is ever reached).

        Returns:
            Generator of jobs.
        """
        for i in xrange(max_steps):
            if i == 0:
                settings = None
                backup = True
            else:
                backup = False
                initial = Poscar.from_file("POSCAR").structure
                final = Poscar.from_file("CONTCAR").structure
                vol_change = (final.volume - initial.volume) / initial.volume

                logging.info("Vol change = %.1f %%!" % (vol_change * 100))
                if abs(vol_change) < vol_change_tol:
                    logging.info("Stopping optimization!")
                    break
                else:
                    settings = [
                        {"dict": "INCAR",
                         "action": {"_set": {"ISTART": 1}}},
                        {"file": "CONTCAR",
                         "action": {"_file_copy": {"dest": "POSCAR"}}}]
            logging.info("Generating job = %d!" % (i+1))
            yield VaspJob(vasp_cmd, final=False, backup=backup,
                          suffix=".relax%d" % (i+1), auto_npar=auto_npar,
                          settings_override=settings)

def five(src):
    """
    VASP ver.5 のフォーマットに変換
    元素名を 5 行目に追加
    """
    srcpos = Poscar.from_file(src)
    dst = "POSCAR_five"
    srcpos.write_file(dst)