Python QCInput.write_file方法代碼示例

# 需要導入模塊: from pymatgen.io.qchem.inputs import QCInput [as 別名]
# 或者: from pymatgen.io.qchem.inputs.QCInput import write_file [as 別名]
    def opt_with_frequency_flattener(cls,
                                     qchem_command,
                                     multimode="openmp",
                                     input_file="mol.qin",
                                     output_file="mol.qout",
                                     qclog_file="mol.qclog",
                                     max_iterations=10,
                                     max_molecule_perturb_scale=0.3,
                                     check_connectivity=True,
                                     **QCJob_kwargs):
        """
        Optimize a structure and calculate vibrational frequencies to check if the
        structure is in a true minima. If a frequency is negative, iteratively
        perturbe the geometry, optimize, and recalculate frequencies until all are
        positive, aka a true minima has been found.

        Args:
            qchem_command (str): Command to run QChem.
            multimode (str): Parallelization scheme, either openmp or mpi.
            input_file (str): Name of the QChem input file.
            output_file (str): Name of the QChem output file.
            max_iterations (int): Number of perturbation -> optimization -> frequency
                iterations to perform. Defaults to 10.
            max_molecule_perturb_scale (float): The maximum scaled perturbation that
                can be applied to the molecule. Defaults to 0.3.
            check_connectivity (bool): Whether to check differences in connectivity
                introduced by structural perturbation. Defaults to True.
            **QCJob_kwargs: Passthrough kwargs to QCJob. See
                :class:`custodian.qchem.jobs.QCJob`.
        """

        min_molecule_perturb_scale = 0.1
        scale_grid = 10
        perturb_scale_grid = (
            max_molecule_perturb_scale - min_molecule_perturb_scale
        ) / scale_grid

        if not os.path.exists(input_file):
            raise AssertionError('Input file must be present!')
        orig_opt_input = QCInput.from_file(input_file)
        orig_opt_rem = copy.deepcopy(orig_opt_input.rem)
        orig_freq_rem = copy.deepcopy(orig_opt_input.rem)
        orig_freq_rem["job_type"] = "freq"
        first = True
        reversed_direction = False
        num_neg_freqs = []

        for ii in range(max_iterations):
            yield (QCJob(
                qchem_command=qchem_command,
                multimode=multimode,
                input_file=input_file,
                output_file=output_file,
                qclog_file=qclog_file,
                suffix=".opt_" + str(ii),
                backup=first,
                **QCJob_kwargs))
            first = False
            opt_outdata = QCOutput(output_file + ".opt_" + str(ii)).data
            if opt_outdata["structure_change"] == "unconnected_fragments" and not opt_outdata["completion"]:
                print("Unstable molecule broke into unconnected fragments which failed to optimize! Exiting...")
                break
            else:
                freq_QCInput = QCInput(
                    molecule=opt_outdata.get("molecule_from_optimized_geometry"),
                    rem=orig_freq_rem,
                    opt=orig_opt_input.opt,
                    pcm=orig_opt_input.pcm,
                    solvent=orig_opt_input.solvent)
                freq_QCInput.write_file(input_file)
                yield (QCJob(
                    qchem_command=qchem_command,
                    multimode=multimode,
                    input_file=input_file,
                    output_file=output_file,
                    qclog_file=qclog_file,
                    suffix=".freq_" + str(ii),
                    backup=first,
                    **QCJob_kwargs))
                outdata = QCOutput(output_file + ".freq_" + str(ii)).data
                errors = outdata.get("errors")
                if len(errors) != 0:
                    raise AssertionError('No errors should be encountered while flattening frequencies!')
                if outdata.get('frequencies')[0] > 0.0:
                    print("All frequencies positive!")
                    break
                else:
                    num_neg_freqs += [sum(1 for freq in outdata.get('frequencies') if freq < 0)]
                    if len(num_neg_freqs) > 1:
                        if num_neg_freqs[-1] == num_neg_freqs[-2] and not reversed_direction:
                            reversed_direction = True
                        elif num_neg_freqs[-1] == num_neg_freqs[-2] and reversed_direction:
                            if len(num_neg_freqs) < 3:
                                raise AssertionError("ERROR: This should only be possible after at least three frequency flattening iterations! Exiting...")
                            else:
                                raise Exception("ERROR: Reversing the perturbation direction still could not flatten any frequencies. Exiting...")
                        elif num_neg_freqs[-1] != num_neg_freqs[-2] and reversed_direction:
                            reversed_direction = False

                    negative_freq_vecs = outdata.get("frequency_mode_vectors")[0]
#.........這裏部分代碼省略.........