Python vasp.Kpoints類代碼示例

    def test_setup(self):
        if "VASP_PSP_DIR" not in os.environ:
            os.environ["VASP_PSP_DIR"] = test_dir
        os.chdir(os.path.join(test_dir, 'setup_neb'))

        v = VaspNEBJob("hello", half_kpts=True)
        v.setup()

        incar = Incar.from_file("INCAR")
        count = multiprocessing.cpu_count()
        if count > 1:
            self.assertGreater(incar["NPAR"], 1)

        kpt = Kpoints.from_file("KPOINTS")
        kpt_pre = Kpoints.from_file("KPOINTS.orig")
        self.assertEqual(kpt_pre.style.name, "Monkhorst")
        self.assertEqual(kpt.style.name, "Gamma")

        shutil.copy("KPOINTS.orig", "KPOINTS")
        os.remove("INCAR.orig")
        os.remove("KPOINTS.orig")
        os.remove("POTCAR.orig")
        poscars = glob.glob("[0-9][0-9]/POSCAR.orig")
        for p in poscars:
            os.remove(p)

    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 _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 setup(self):
        """
        Performs initial setup for VaspNEBJob, including overriding any settings
        and backing up.
        """
        neb_dirs = self.neb_dirs

        if self.backup:
            # Back up KPOINTS, INCAR, POTCAR
            for f in VASP_NEB_INPUT_FILES:
                shutil.copy(f, "{}.orig".format(f))
            # Back up POSCARs
            for path in neb_dirs:
                poscar = os.path.join(path, "POSCAR")
                shutil.copy(poscar, "{}.orig".format(poscar))

        if self.half_kpts and os.path.exists("KPOINTS"):
            kpts = Kpoints.from_file("KPOINTS")
            kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1)
            kpts.kpts = kpts.kpts.astype(int).tolist()
            if tuple(kpts.kpts[0]) == (1, 1, 1):
                kpt_dic = kpts.as_dict()
                kpt_dic["generation_style"] = 'Gamma'
                kpts = Kpoints.from_dict(kpt_dic)
            kpts.write_file("KPOINTS")

        if self.auto_npar:
            try:
                incar = Incar.from_file("INCAR")
                import multiprocessing
                # Try sge environment variable first
                # (since multiprocessing counts cores on the current
                # machine only)
                ncores = os.environ.get('NSLOTS') or multiprocessing.cpu_count()
                ncores = int(ncores)
                for npar in range(int(math.sqrt(ncores)),
                                  ncores):
                    if ncores % npar == 0:
                        incar["NPAR"] = npar
                        break
                incar.write_file("INCAR")
            except:
                pass

        if self.auto_continue and \
                os.path.exists("STOPCAR") and \
                not os.access("STOPCAR", os.W_OK):
            # Remove STOPCAR
            os.chmod("STOPCAR", 0o644)
            os.remove("STOPCAR")

            # Copy CONTCAR to POSCAR
            for path in self.neb_sub:
                contcar = os.path.join(path, "CONTCAR")
                poscar = os.path.join(path, "POSCAR")
                shutil.copy(contcar, poscar)

        if self.settings_override is not None:
            VaspModder().apply_actions(self.settings_override)

def band_path(line_density):
    """
    for band calculation
    """
    poscar = Poscar.from_file('POSCAR', check_for_POTCAR=False)
    highsymmkp = MyHighSymmKpath(poscar.structure)
    kpts = highsymmkp.get_kpoints(line_density)
    args = {'comment': "Kpoints for band calc",
            'kpts': kpts[0],
            'num_kpts': len(kpts[0]),
            'labels': kpts[1],
            'style': 'Reciprocal',
            'kpts_weights': [1]*len(kpts[0])}
    kpoints = Kpoints(**args)
    kpoints.write_file('KPOINTS_band')

    def test_setup(self):
        with cd(os.path.join(test_dir, 'setup_neb')):
            with ScratchDir('.', copy_from_current_on_enter=True) as d:
                v = VaspNEBJob("hello", half_kpts=True)
                v.setup()

                incar = Incar.from_file("INCAR")
                count = multiprocessing.cpu_count()
                if count > 3:
                    self.assertGreater(incar["NPAR"], 1)

                kpt = Kpoints.from_file("KPOINTS")
                kpt_pre = Kpoints.from_file("KPOINTS.orig")
                self.assertEqual(kpt_pre.style.name, "Monkhorst")
                self.assertEqual(kpt.style.name, "Gamma")

    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 _verify_files(self):
     self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar)
     self.assertEqual(str(Poscar.from_file(os.path.join(module_dir, "POSCAR"))),
                      str(self.ref_poscar))
     self.assertEqual(Potcar.from_file(os.path.join(module_dir, "POTCAR")).symbols,
                      self.ref_potcar.symbols)
     self.assertEqual(str(Kpoints.from_file(os.path.join(module_dir, "KPOINTS"))),
                      str(self.ref_kpoints))

 def _verify_files(self, skip_kpoints=False, preserve_incar=False):
     if not preserve_incar:
         self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar)
         self.assertEqual(str(Poscar.from_file(os.path.join(module_dir, "POSCAR"))), str(self.ref_poscar))
         self.assertEqual((Potcar.from_file(os.path.join(module_dir, "POTCAR"))).symbols, self.ref_potcar.symbols)
         if not skip_kpoints:
             self.assertEqual(str(Kpoints.from_file(os.path.join(module_dir, "KPOINTS"))), str(self.ref_kpoints))
     else:
         self.assertEqual(Incar.from_file(os.path.join(module_dir, "INCAR")), self.ref_incar_preserve)

    def double_relaxation_run(cls, vasp_cmd, auto_npar=True, ediffg=-0.05,
                              half_kpts_first_relax=False, auto_continue=False):
        """
        Returns a list of two jobs corresponding to an AFLOW style double
        relaxation run.

        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.
            ediffg (float): Force convergence criteria for subsequent runs (
                ignored for the initial run.)
            half_kpts_first_relax (bool): Whether to halve the kpoint grid
                for the first relaxation. Speeds up difficult convergence
                considerably. Defaults to False.

        Returns:
            List of two jobs corresponding to an AFLOW style run.
        """
        incar_update = {"ISTART": 1}
        if ediffg:
            incar_update["EDIFFG"] = ediffg
        settings_overide_1 = None
        settings_overide_2 = [
            {"dict": "INCAR",
             "action": {"_set": incar_update}},
            {"file": "CONTCAR",
             "action": {"_file_copy": {"dest": "POSCAR"}}}]
        if half_kpts_first_relax and os.path.exists("KPOINTS") and \
                os.path.exists("POSCAR"):
            kpts = Kpoints.from_file("KPOINTS")
            orig_kpts_dict = kpts.as_dict()
            # lattice vectors with length < 8 will get >1 KPOINT
            kpts.kpts = np.round(np.maximum(np.array(kpts.kpts) / 2,
                                            1)).astype(int).tolist()
            low_kpts_dict = kpts.as_dict()
            settings_overide_1 = [
                {"dict": "KPOINTS",
                 "action": {"_set": low_kpts_dict}}
            ]
            settings_overide_2.append(
                {"dict": "KPOINTS",
                 "action": {"_set": orig_kpts_dict}}
            )

        return [VaspJob(vasp_cmd, final=False, suffix=".relax1",
                        auto_npar=auto_npar, auto_continue=auto_continue,
                        settings_override=settings_overide_1),
                VaspJob(vasp_cmd, final=True, backup=False, suffix=".relax2",
                        auto_npar=auto_npar, auto_continue=auto_continue,
                        settings_override=settings_overide_2)]

 def test_run(self):
     with ScratchDir(".") as d:
         for f in ["INCAR", "POSCAR", "POTCAR", "KPOINTS"]:
             shutil.copy(os.path.join('..', test_dir, f), f)
         oldincar = Incar.from_file("INCAR")
         v = GenerateVaspInputJob("pymatgen.io.vasp.sets.MPNonSCFSet",
                                  contcar_only=False)
         v.run()
         incar = Incar.from_file("INCAR")
         self.assertEqual(incar["ICHARG"], 11)
         self.assertEqual(oldincar["ICHARG"], 1)
         kpoints = Kpoints.from_file("KPOINTS")
         self.assertEqual(str(kpoints.style), "Reciprocal")

    def setUpClass(cls):
        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
        lattice = Lattice([[3.8401979337, 0.00, 0.00],
                           [1.9200989668, 3.3257101909, 0.00],
                           [0.00, -2.2171384943, 3.1355090603]])
        cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)

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

    def setUpClass(cls):
        if not SETTINGS.get("VASP_PSP_DIR"):
            SETTINGS["VASP_PSP_DIR"] = os.path.join(module_dir, "reference_files")
            print(
                "This system is not set up to run VASP jobs. "
                "Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file."
            )

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

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

    def setUpClass(cls):
        if not SETTINGS.get("VASP_PSP_DIR"):
            raise unittest.SkipTest(
                "This system is not set up to run VASP jobs. "
                "Please set VASP_PSP_DIR variable in your ~/.pmgrc.yaml file."
            )

        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
        lattice = Lattice(
            [[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
        )
        cls.struct_si = IStructure(lattice, ["Si"] * 2, coords)

        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"))