pymatgen.phasediagram.maker module¶

class
CompoundPhaseDiagram
(entries, terminal_compositions, normalize_terminal_compositions=True)[source]¶ Bases:
pymatgen.phasediagram.maker.PhaseDiagram
Generates phase diagrams from compounds as terminations instead of elements.
Initializes a CompoundPhaseDiagram.
Parameters:  entries ([PDEntry]) – Sequence of input entries. For example, if you want a Li2OP2O5 phase diagram, you might have all LiPO entries as an input.
 terminal_compositions ([Composition]) – Terminal compositions of phase space. In the Li2OP2O5 example, these will be the Li2O and P2O5 compositions.
 normalize_terminal_compositions (bool) – Whether to normalize the terminal compositions to a per atom basis. If normalized, the energy above hulls will be consistent for comparison across systems. Nonnormalized terminals are more intuitive in terms of compositional breakdowns.

amount_tol
= 1e05¶

transform_entries
(entries, terminal_compositions)[source]¶ Method to transform all entries to the composition coordinate in the terminal compositions. If the entry does not fall within the space defined by the terminal compositions, they are excluded. For example, Li3PO4 is mapped into a Li2O:1.5, P2O5:0.5 composition. The terminal compositions are represented by DummySpecies.
Parameters:  entries – Sequence of all input entries
 terminal_compositions – Terminal compositions of phase space.
Returns: Sequence of TransformedPDEntries falling within the phase space.

class
GrandPotentialPhaseDiagram
(entries, chempots, elements=None)[source]¶ Bases:
pymatgen.phasediagram.maker.PhaseDiagram
A class representing a Grand potential phase diagram. Grand potential phase diagrams are essentially phase diagrams that are open to one or more components. To construct such phase diagrams, the relevant free energy is the grand potential, which can be written as the Legendre transform of the Gibbs free energy as follows
Grand potential = G  u_X N_X
The algorithm is based on the work in the following papers:
 S. P. Ong, L. Wang, B. Kang, and G. Ceder, LiFePO2 Phase Diagram from First Principles Calculations. Chem. Mater., 2008, 20(5), 17981807. doi:10.1021/cm702327g
 S. P. Ong, A. Jain, G. Hautier, B. Kang, G. Ceder, Thermal stabilities of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first principles calculations. Electrochem. Comm., 2010, 12(3), 427430. doi:10.1016/j.elecom.2010.01.010
Standard constructor for grand potential phase diagram.
Parameters:  entries ([PDEntry]) – A list of PDEntrylike objects having an energy, energy_per_atom and composition.
 {Element (chempots) – float}: Specify the chemical potentials of the open elements.
 elements ([Element]) – Optional list of elements in the phase diagram. If set to None, the elements are determined from the the entries themselves.

class
PhaseDiagram
(entries, elements=None)[source]¶ Bases:
monty.json.MSONable
Simple phase diagram class taking in elements and entries as inputs. The algorithm is based on the work in the following papers:
 S. P. Ong, L. Wang, B. Kang, and G. Ceder, LiFePO2 Phase Diagram from First Principles Calculations. Chem. Mater., 2008, 20(5), 17981807. doi:10.1021/cm702327g
 S. P. Ong, A. Jain, G. Hautier, B. Kang, G. Ceder, Thermal stabilities of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first principles calculations. Electrochem. Comm., 2010, 12(3), 427430. doi:10.1016/j.elecom.2010.01.010
..attribute: all_entries
All entries provided for Phase Diagram construction. Note that this does not mean that all these entries are actually used in the phase diagram. For example, this includes the positive formation energy entries that are filtered out before Phase Diagram construction.Standard constructor for phase diagram.
Parameters: 
all_entries_hulldata
¶

formation_energy_tol
= 1e11¶

get_form_energy
(entry)[source]¶ Returns the formation energy for an entry (NOT normalized) from the elemental references.
Parameters: entry – A PDEntrylike object. Returns: Formation energy from the elemental references.

get_form_energy_per_atom
(entry)[source]¶ Returns the formation energy per atom for an entry from the elemental references.
Parameters: entry – An PDEntrylike object Returns: Formation energy per atom from the elemental references.

pd_coords
(comp)[source]¶ The phase diagram is generated in a reduced dimensional space (n_elements  1). This function returns the coordinates in that space. These coordinates are compatible with the stored simplex objects.

simplices
¶

stable_entries
¶ Returns the stable entries in the phase diagram.

unstable_entries
¶ Entries that are unstable in the phase diagram. Includes positive formation energy entries.

exception
PhaseDiagramError
[source]¶ Bases:
Exception
An exception class for Phase Diagram generation.

get_facets
(qhull_data, joggle=False)[source]¶ Get the simplex facets for the Convex hull.
Parameters:  qhull_data (np.ndarray) – The data from which to construct the convex hull as a Nxd array (N being number of data points and d being the dimension)
 joggle (boolean) – Whether to joggle the input to avoid precision errors.
Returns: List of simplices of the Convex Hull.