Source code for httk.atomistic.structurephasediagram

#    The high-throughput toolkit (httk)
#    Copyright (C) 2012-2015 Rickard Armiento
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU Affero General Public License as
#    published by the Free Software Foundation, either version 3 of the
#    License, or (at your option) any later version.
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    GNU Affero General Public License for more details.
#    You should have received a copy of the GNU Affero General Public License
#    along with this program.  If not, see <>.
import sys
from httk.atomistic.structure import Structure
from httk.core import FracScalar, httk_typed_init
from httk.core.httkobject import HttkObject
from httk.analysis.matsci.phasediagram import PhaseDiagram

[docs]class StructurePhaseDiagramCompetingIndicies(HttkObject): @httk_typed_init({'indices': [int]}) def __init__(self, indices): """ Private constructor, as per httk coding guidelines. Use .create method instead. """ self.indices = indices
[docs] @classmethod def create(cls, indices): return cls(indices)
[docs]class StructurePhaseDiagram(HttkObject): """ Represents a phase diagram of structures """ @httk_typed_init({'structures': [Structure], 'energies': [FracScalar], 'hull_indices': [int], 'competing_indices': [StructurePhaseDiagramCompetingIndicies], 'hull_competing_indices': [StructurePhaseDiagramCompetingIndicies], 'hull_distances': [FracScalar], 'coord_system': [str], 'phase_lines': [int, int]}, index=['structures']) def __init__(self, structures, energies, hull_indices, competing_indices, hull_competing_indices, hull_distances, coord_system, phase_lines): """ Private constructor, as per httk coding guidelines. Use Cell.create instead. """ self.structures = structures self.energies = energies self.hull_indices = hull_indices self.competing_indices = competing_indices self.hull_competing_indices = hull_competing_indices self.hull_distances = hull_distances self.coord_system = coord_system self.phase_lines = phase_lines #def create(cls, basis=None, a=None, b=None, c=None, alpha=None, beta=None, gamma=None, volume=None, scale=None, niggli_matrix=None, orientation=1, lengths=None, angles=None, normalize=True):
[docs] @classmethod def create(cls, structures, energies): """ """ pd = setup_phasediagram(structures, energies) competing_indices = [StructurePhaseDiagramCompetingIndicies.create(x) for x in pd.competing_indices] hull_competing_indices = [StructurePhaseDiagramCompetingIndicies.create(x) for x in pd.hull_competing_indices] return cls(structures, energies, pd.hull_indices, competing_indices, hull_competing_indices, pd.hull_distances, pd.coord_system, pd.phase_lines)
[docs] def get_phasediagram(self): competing_indices = [x.indices for x in self.competing_indices] hull_competing_indices = [x.indices for x in self.hull_competing_indices] pd = setup_phasediagram(self.structures, self.energies) pd.set_hull_data(self.hull_indices, competing_indices, hull_competing_indices, self.hull_distances, self.coord_system, self.phase_lines) return pd
from httk.core import FracVector
[docs]def setup_phasediagram(structures, energies): pd = PhaseDiagram() for i in range(len(structures)): struct = structures[i] energy = energies[i] formula = struct.uc_formula uc_formula_symbols = struct.uc_formula_symbols uc_formula_counts = struct.uc_formula_counts pd.add_phase(uc_formula_symbols, uc_formula_counts, formula, energy) return pd
[docs]def main(): pass
if __name__ == "__main__": main()