Python vasp.VaspInput类代码示例

    def test_brmix(self):
        h = VaspErrorHandler("vasp.brmix")
        self.assertEqual(h.check(), True)

        # The first (no good OUTCAR) correction, check IMIX
        d = h.correct()
        self.assertEqual(d["errors"], ['brmix'])
        vi = VaspInput.from_directory(".")
        self.assertEqual(vi["INCAR"]["IMIX"], 1)
        self.assertTrue(os.path.exists("CHGCAR"))

        # The next correction check Gamma and evenize
        h.correct()
        vi = VaspInput.from_directory(".")
        self.assertFalse("IMIX" in vi["INCAR"])
        self.assertTrue(os.path.exists("CHGCAR"))
        if vi["KPOINTS"].style == Kpoints.supported_modes.Gamma and vi["KPOINTS"].num_kpts < 1:
            all_kpts_even = all([
                bool(n % 2 == 0) for n in vi["KPOINTS"].kpts[0]
            ])
            self.assertFalse(all_kpts_even)

        # The next correction check ISYM and no CHGCAR
        h.correct()
        vi = VaspInput.from_directory(".")
        self.assertEqual(vi["INCAR"]["ISYM"], 0)
        self.assertFalse(os.path.exists("CHGCAR"))

        shutil.copy("INCAR.nelect", "INCAR")
        h = VaspErrorHandler("vasp.brmix")
        self.assertEqual(h.check(), False)
        d = h.correct()
        self.assertEqual(d["errors"], [])

    def check(self):
        msg = "Reciprocal lattice and k-lattice belong to different class of" \
              " lattices."

        vi = VaspInput.from_directory('.')
        # According to VASP admins, you can disregard this error
        # if symmetry is off
        # Also disregard if automatic KPOINT generation is used
        if (not vi["INCAR"].get('ISYM', True)) or \
                        vi[
                            "KPOINTS"].style == Kpoints.supported_modes.Automatic:
            return False

        try:
            v = Vasprun(self.output_vasprun)
            if v.converged:
                return False
        except:
            pass
        with open(self.output_filename, "r") as f:
            for line in f:
                l = line.strip()
                if l.find(msg) != -1:
                    return True
        return False

    def correct(self):
        # if change_algo is True, change ALGO = Fast to Normal if ALGO is
        # Fast. If still not converging, following Kresse's
        # recommendation, we will try two iterations of different mixing
        # parameters. If this error is caught again, then kil the job
        vi = VaspInput.from_directory(".")
        algo = vi["INCAR"].get("ALGO", "Normal")
        amix = vi["INCAR"].get("AMIX", 0.4)
        bmix = vi["INCAR"].get("BMIX", 1.0)
        amin = vi["INCAR"].get("AMIN", 0.1)
        actions = []
        if self.change_algo:
            if algo == "Fast":
                backup(VASP_BACKUP_FILES)
                actions.append({"dict": "INCAR", "action": {"_set": {"ALGO": "Normal"}}})

            elif amix > 0.1 and bmix > 0.01:
                # try linear mixing
                backup(VASP_BACKUP_FILES)
                actions.append({"dict": "INCAR", "action": {"_set": {"AMIX": 0.1, "BMIX": 0.01, "ICHARG": 2}}})

            elif bmix < 3.0 and amin > 0.01:
                # Try increasing bmix
                backup(VASP_BACKUP_FILES)
                actions.append({"dict": "INCAR", "action": {"_set": {"AMIN": 0.01, "BMIX": 3.0, "ICHARG": 2}}})

        if actions:
            VaspModder(vi=vi).apply_actions(actions)
            return {"errors": ["Non-converging job"], "actions": actions}

        # Unfixable error. Just return None for actions.
        else:
            return {"errors": ["Non-converging job"], "actions": None}

 def test_lrf_comm(self):
     h = LrfCommutatorHandler("std_err.txt")
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d["errors"], ['lrf_comm'])
     vi = VaspInput.from_directory(".")
     self.assertEqual(vi["INCAR"]["LPEAD"], True)

def get_runs(vasp_command, target=1e-3, max_steps=10, mode="linear"):
    energy = 0
    vinput = VaspInput.from_directory(".")
    kpoints = vinput["KPOINTS"].kpts[0]
    for i in range(max_steps):
        if mode == "linear":
            m = [k * (i + 1) for k in kpoints]
        else:
            m = [k + 1 for k in kpoints]
        if i == 0:
            settings = None
            backup = True
        else:
            backup = False
            v = Vasprun("vasprun.xml")
            e_per_atom = v.final_energy / len(v.final_structure)
            ediff = abs(e_per_atom - energy)
            if ediff < target:
                logging.info("Converged to {} eV/atom!".format(ediff))
                break
            else:
                energy = e_per_atom
                settings = [
                    {"dict": "INCAR",
                     "action": {"_set": {"ISTART": 1}}},
                    {'dict': 'KPOINTS',
                     'action': {'_set': {'kpoints': [m]}}},
                    {"filename": "CONTCAR",
                     "action": {"_file_copy": {"dest": "POSCAR"}}}]
        yield VaspJob(vasp_command, final=False, backup=backup,
                      suffix=".kpoints.{}".format("x".join(map(str, m))),
                      settings_override=settings)

    def test_check_correct(self):
        h = VaspErrorHandler("vasp.teterror")
        h.check()
        d = h.correct()
        self.assertEqual(d["errors"], ['tet'])
        self.assertEqual(d["actions"],
                         [{'action': {'_set': {'ISMEAR': 0}},
                           'dict': 'INCAR'}])

        h = VaspErrorHandler("vasp.teterror", errors_subset_to_catch=["eddrmm"])
        self.assertFalse(h.check())

        h = VaspErrorHandler("vasp.sgrcon")
        h.check()
        d = h.correct()
        self.assertEqual(d["errors"], ['rot_matrix'])
        self.assertEqual(set([a["dict"] for a in d["actions"]]),
                         {"KPOINTS"})

        h = VaspErrorHandler("vasp.real_optlay")
        h.check()
        d = h.correct()
        self.assertEqual(d["errors"], ['real_optlay'])
        self.assertEqual(d["actions"],
                         [{'action': {'_set': {'LREAL': False}},
                           'dict': 'INCAR'}])

        subdir = os.path.join(test_dir, "large_cell_real_optlay")
        os.chdir(subdir)
        shutil.copy("INCAR", "INCAR.orig")
        h = VaspErrorHandler()
        h.check()
        d = h.correct()
        self.assertEqual(d["errors"], ['real_optlay'])
        vi = VaspInput.from_directory(".")
        self.assertEqual(vi["INCAR"]["LREAL"], True)
        h.check()
        d = h.correct()
        self.assertEqual(d["errors"], ['real_optlay'])
        vi = VaspInput.from_directory(".")
        self.assertEqual(vi["INCAR"]["LREAL"], False)
        shutil.copy("INCAR.orig", "INCAR")
        os.remove("INCAR.orig")
        os.remove("error.1.tar.gz")
        os.remove("error.2.tar.gz")
        os.chdir(test_dir)

    def test_oom(self):
        vi = VaspInput.from_directory(".")
        from custodian.vasp.interpreter import VaspModder
        VaspModder(vi=vi).apply_actions([{"dict": "INCAR",
                                          "action": {"_set": {"KPAR": 4}}}])
        h = StdErrHandler("std_err.txt.oom", correct_out_of_memory=True)
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['out_of_memory'])
        self.assertEqual(d["actions"],
                         [{'dict': 'INCAR',
                           'action': {'_set': {'KPAR': 2}}}])

        h = StdErrHandler("std_err.txt.oom2", correct_out_of_memory=True)
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['out_of_memory'])
        self.assertEqual(d["actions"],
                         [{'dict': 'INCAR',
                           'action': {'_set': {'KPAR': 1}}}])

        vi = VaspInput.from_directory(".")
        from custodian.vasp.interpreter import VaspModder
        VaspModder(vi=vi).apply_actions([{"dict": "INCAR",
                                          "action": {"_set": {"KPAR": 4}}}])
        h = StdErrHandler("std_err.txt.emlsp", correct_out_of_memory=True)
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['out_of_memory'])
        self.assertEqual(d["actions"],
                         [{'dict': 'INCAR',
                           'action': {'_set': {'KPAR': 2}}}])

        vi = VaspInput.from_directory(".")
        from custodian.vasp.interpreter import VaspModder
        VaspModder(vi=vi).apply_actions([{"dict": "INCAR",
                                          "action": {"_set": {"KPAR": 4}}}])
        h = StdErrHandler("std_err.txt.insufficient_mem", correct_out_of_memory=True)
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['out_of_memory'])
        self.assertEqual(d["actions"],
                         [{'dict': 'INCAR',
                           'action': {'_set': {'KPAR': 2}}}])

 def check(self):
     vi = VaspInput.from_directory(".")
     nelm = vi["INCAR"].get("NELM", 60)
     try:
         oszicar = Oszicar(self.output_filename)
         esteps = oszicar.electronic_steps
         if len(esteps) > self.nionic_steps:
             return all([len(e) == nelm for e in esteps[-(self.nionic_steps + 1) : -1]])
     except:
         pass
     return False

    def test_lrf_comm(self):
        h = StdErrHandler("std_err.txt")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['lrf_comm'])
        vi = VaspInput.from_directory(".")
        self.assertEqual(vi["INCAR"]["ISTART"], 1)

        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['lrf_comm'])
        self.assertEqual(d["actions"], [])  # don't correct twice

    def correct(self):
        backup(VASP_BACKUP_FILES | {self.output_filename})
        actions = []
        vi = VaspInput.from_directory(".")

        if "lrf_comm" in self.errors:
            if Outcar(zpath(os.path.join(
                    os.getcwd(), "OUTCAR"))).is_stopped is False:
                if not vi["INCAR"].get("LPEAD"):
                    actions.append({"dict": "INCAR",
                                    "action": {"_set": {"LPEAD": True}}})

        VaspModder(vi=vi).apply_actions(actions)
        return {"errors": list(self.errors), "actions": actions}

 def test_seg_fault(self):
     vi = VaspInput.from_directory(".")
     from custodian.vasp.interpreter import VaspModder
     VaspModder(vi=vi).apply_actions([{"dict": "INCAR",
                                       "action": {"_set": {"KPAR": 4}}}])
     h = StdErrHandler("std_err.txt.seg_fault", correct_seg_fault=True)
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d["errors"], ['seg_fault'])
     self.assertEqual(d["actions"],
                      [{'dict': 'INCAR',
                        'action': {'_set': {'ISMEAR': '0'}}}])
     self.assertEqual(h.check(), True)
     d = h.correct()
     self.assertEqual(d["errors"], ['seg_fault'])
     # no fix if still seg fault
     self.assertEqual(d["actions"], [])

    def __init__(self, actions=None, strict=True, vi=None):
        """
        Initializes a Modder for VaspInput sets

        Args:
            actions ([Action]): A sequence of supported actions. See
                :mod:`custodian.ansible.actions`. Default is None,
                which means DictActions and FileActions are supported.
            strict (bool): Indicating whether to use strict mode. In non-strict
                mode, unsupported actions are simply ignored without any
                errors raised. In strict mode, if an unsupported action is
                supplied, a ValueError is raised. Defaults to True.
            vi (VaspInput): A VaspInput object from the current directory.
                Initialized automatically if not passed (but passing it will
                avoid having to reparse the directory).
        """
        self.vi = vi or VaspInput.from_directory('.')
        actions = actions or [FileActions, DictActions]
        super(VaspModder, self).__init__(actions, strict)

    def run(self):
        """
        Perform the actual VASP run.

        Returns:
            (subprocess.Popen) Used for monitoring.
        """
        cmd = list(self.vasp_cmd)
        if self.auto_gamma:
            vi = VaspInput.from_directory(".")
            kpts = vi["KPOINTS"]
            if kpts.style == "Gamma" and tuple(kpts.kpts[0]) == (1, 1, 1):
                if self.gamma_vasp_cmd is not None and which(
                        self.gamma_vasp_cmd[-1]):
                    cmd = self.gamma_vasp_cmd
                elif which(cmd[-1] + ".gamma"):
                    cmd[-1] += ".gamma"
        logging.info("Running {}".format(" ".join(cmd)))
        with open(self.output_file, 'w') as f:
            p = subprocess.Popen(cmd, stdout=f)
        return p

    def test_brmix(self):
        h = VaspErrorHandler("vasp.brmix")
        self.assertEqual(h.check(), True)
        d = h.correct()
        self.assertEqual(d["errors"], ['brmix'])

        vi = VaspInput.from_directory(".")
        chgcar_exists = os.path.exists("CHGCAR")
        if h.error_count['brmix'] > 1:
            self.assertFalse(chgcar_exists)
        else:
            self.assertTrue(chgcar_exists)
            if vi["KPOINTS"].style == Kpoints.supported_modes.Gamma and vi["KPOINTS"].num_kpts < 1:
                all_kpts_even = all([
                    bool(n % 2 == 0) for n in vi["KPOINTS"].kpts[0]
                ])
                self.assertFalse(all_kpts_even)

        shutil.copy("INCAR.nelect", "INCAR")
        h = VaspErrorHandler("vasp.brmix")
        self.assertEqual(h.check(), False)
        d = h.correct()
        self.assertEqual(d["errors"], [])

    def run(self):
        """
        Perform the actual VASP run.

        Returns:
            (subprocess.Popen) Used for monitoring.
        """
        cmd = list(self.vasp_cmd)
        if self.auto_gamma:
            vi = VaspInput.from_directory(".")
            kpts = vi["KPOINTS"]
            if kpts.style == Kpoints.supported_modes.Gamma \
                    and tuple(kpts.kpts[0]) == (1, 1, 1):
                if self.gamma_vasp_cmd is not None and which(
                        self.gamma_vasp_cmd[-1]):
                    cmd = self.gamma_vasp_cmd
                elif which(cmd[-1] + ".gamma"):
                    cmd[-1] += ".gamma"
        logger.info("Running {}".format(" ".join(cmd)))
        with open(self.output_file, 'w') as f_std, \
                open(self.stderr_file, "w", buffering=1) as f_err:
            # use line buffering for stderr
            p = subprocess.Popen(cmd, stdout=f_std, stderr=f_err)
        return p