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| # coding: utf-8 | ||
| # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department | ||
| # Distributed under the terms of "New BSD License", see the LICENSE file. | ||
|
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||
| import numpy as np | ||
| import scipy | ||
| from scipy.io.netcdf import netcdf_file | ||
| import os | ||
| from pyiron.base.settings.generic import Settings | ||
| from pyiron.atomistics.volumetric.generic import VolumetricData | ||
|
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| __author__ = "Sudarsan Surendralal" | ||
| __copyright__ = ( | ||
| "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - " | ||
| "Computational Materials Design (CM) Department" | ||
| ) | ||
| __version__ = "1.0" | ||
| __maintainer__ = "Sudarsan Surendralal" | ||
| __email__ = "surendralal@mpie.de" | ||
| __status__ = "production" | ||
| __date__ = "Sep 1, 2017" | ||
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| BOHR_TO_ANGSTROM = ( | ||
| scipy.constants.physical_constants["Bohr radius"][0] / | ||
| scipy.constants.angstrom | ||
| ) | ||
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| class SphinxVolumetricData(VolumetricData): | ||
| """ | ||
| General class for parsing and manipulating volumetric static within Sphinx. | ||
| The basic idea of the Base class is adapted from the pymatgen vasp | ||
| VolumetricData class: | ||
| http://pymatgen.org/_modules/pymatgen/io/vasp/outputs.html#VolumetricData | ||
| """ | ||
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| def __init__(self): | ||
| super(SphinxVolumetricData, self).__init__() | ||
| self.atoms = None | ||
| self._diff_data = None | ||
| self._total_data = None | ||
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| def from_file(self, filename, normalize=True): | ||
| """ | ||
| Parses volumetric data from a sphinx binary (.sxb) file. | ||
| Args: | ||
| filename (str): Path of file to parse | ||
| normalize (boolean): Flag to normalize by the volume of the cell | ||
| """ | ||
| try: | ||
| vol_data_list = self._read_vol_data( | ||
| filename=filename, | ||
| normalize=normalize | ||
| ) | ||
| except (ValueError, IndexError, TypeError): | ||
| raise ValueError("Unable to parse file: {}".format(filename)) | ||
| self._total_data = vol_data_list[0] | ||
| if len(vol_data_list) == 2: | ||
| self._total_data = vol_data_list[0] + vol_data_list[1] | ||
| self._diff_data = vol_data_list[0] - vol_data_list[1] | ||
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| @staticmethod | ||
| def _read_vol_data(filename, normalize=True): | ||
| """ | ||
| Parses the Sphinx volumetric data files (rho.sxb and vElStat-eV.sxb). | ||
| Args: | ||
| filename (str): File to be parsed | ||
| normalize (bool): Normalize the data with respect to the volume | ||
| (probably sensible for rho) | ||
| Returns: | ||
| list: A list of the volumetric data (length >1 for density | ||
| files with spin) | ||
| """ | ||
| if not os.path.getsize(filename) > 0: | ||
| s = Settings() | ||
| s.logger.warning("File:" + filename + "seems to be empty! ") | ||
| return None, None | ||
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| with netcdf_file(filename, mmap=False) as f: | ||
| dim = [int(d) for d in f.variables["dim"]] | ||
| volume = 1.0 | ||
| if normalize: | ||
| cell = f.variables["cell"].data * BOHR_TO_ANGSTROM | ||
| volume = np.abs(np.linalg.det(cell)) | ||
| if "mesh" in f.variables: | ||
| # non-spin polarized | ||
| total_data_list = [ | ||
| np.array(f.variables["mesh"][:]).reshape(dim) / volume | ||
| ] | ||
| elif "mesh-0" in f.variables and "mesh-1" in f.variables: | ||
| # spin-polarized | ||
| total_data_list = [ | ||
| np.array(f.variables["mesh-0"][:]).reshape(dim) / volume, | ||
| np.array(f.variables["mesh-1"][:]).reshape(dim) / volume | ||
| ] | ||
| else: | ||
| raise ValueError( | ||
| "Unexpected keys in the netcdf file's variables: neither " | ||
| f"'mesh' nor 'mesh-0' and 'mesh-1' found in {f.variables}." | ||
| ) | ||
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| if len(total_data_list) == 0: | ||
| s = Settings() | ||
| s.logger.warning( | ||
| "File:" | ||
| + filename | ||
| + "seems to be corrupted/empty even after parsing!" | ||
| ) | ||
| return None | ||
|
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| return total_data_list | ||
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| @property | ||
| def total_data(self): | ||
| """ | ||
| numpy.ndarray: Total volumtric data (3D) | ||
| """ | ||
| return self._total_data | ||
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| @total_data.setter | ||
| def total_data(self, val): | ||
| self._total_data = val | ||
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| @property | ||
| def diff_data(self): | ||
| """ | ||
| numpy.ndarray: Volumtric difference data (3D) | ||
| """ | ||
| return self._diff_data | ||
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| @diff_data.setter | ||
| def diff_data(self, val): | ||
| self._diff_data = val | ||
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| def to_hdf(self, hdf5, group_name="volumetric_data"): | ||
| """ | ||
| Writes the data as a group to a HDF5 file | ||
| Args: | ||
| hdf5 (pyiron.base.generic.hdfio.ProjectHDFio): The | ||
| HDF file/path to write the data | ||
| group_name (str): The name of the group under which | ||
| the data must be stored | ||
| """ | ||
| with hdf5.open(group_name) as hdf_vd: | ||
| hdf_vd["TYPE"] = str(type(self)) | ||
| hdf_vd["total"] = self.total_data | ||
| if self.diff_data is not None: | ||
| hdf_vd["diff"] = self.diff_data | ||
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| def from_hdf(self, hdf5, group_name="volumetric_data"): | ||
| """ | ||
| Extract a VolumetricData instance from an HDF5 file. | ||
| Args: | ||
| hdf5 (pyiron.base.generic.hdfio.ProjectHDFio): The HDF | ||
| file/path to read the data | ||
| group_name (str): The name of the group under which | ||
| the data have been stored | ||
| Returns: | ||
| pyiron.atomistics.volumetric.generic.VolumetricData: The | ||
| VolumetricData instance | ||
| """ | ||
| with hdf5.open(group_name) as hdf_vd: | ||
| self._total_data = hdf_vd["total"] | ||
| if len(self._total_data) == 2: | ||
| self.is_spin_polarized = True | ||
| if "diff" in hdf_vd.list_nodes(): | ||
| self._diff_data = hdf_vd["diff"] |
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9 changes: 9 additions & 0 deletions
9
tests/static/sphinx/sphinx_test_2_5_hdf5/sphinx_test_2_5/relaxedStr.sx
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| cell = [[5.351704387296569, 0.0, 0.0], [3.2769738239427953e-16, 5.351704387296569, 0.0], [3.2769738239427953e-16, 3.2769738239427953e-16, 5.351704387296569]]; | ||
| species { | ||
| element = "Fe"; | ||
| atom { label = "spin_2"; coords = [0.03779452250915656, 0.0, 0.0]; } | ||
| } | ||
| species { | ||
| element = "Ni"; | ||
| atom { label = "spin_2"; coords = [2.6758521936482844, 2.6758521936482844, 2.6758521936482844]; } | ||
| } |
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tests/static/sphinx/sphinx_test_2_5_hdf5/sphinx_test_2_5/vElStat-eV.sxb
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