pymatgen.analysis.phase_diagram module¶

class
CompoundPhaseDiagram
(entries, terminal_compositions, normalize_terminal_compositions=True)[source]¶ Bases:
pymatgen.analysis.phase_diagram.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
GrandPotPDEntry
(entry, chempots, name=None)[source]¶ Bases:
pymatgen.analysis.phase_diagram.PDEntry
A grand potential pd entry object encompassing all relevant data for phase diagrams. Chemical potentials are given as a elementchemical potential dict.
Parameters:  entry – A PDEntrylike object.
 chempots – Chemical potential specification as {Element: float}.
 name – Optional parameter to name the entry. Defaults to the reduced chemical formula of the original entry.

is_element
¶ True if the entry is an element.

class
GrandPotentialPhaseDiagram
(entries, chempots, elements=None)[source]¶ Bases:
pymatgen.analysis.phase_diagram.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
PDEntry
(composition, energy, name=None, attribute=None)[source]¶ Bases:
monty.json.MSONable
An object encompassing all relevant data for phase diagrams.

composition
¶ The composition associated with the PDEntry.

energy
¶ The energy associated with the entry.

name
¶ A name for the entry. This is the string shown in the phase diagrams. By default, this is the reduced formula for the composition, but can be set to some other string for display purposes.

attribute
¶ A arbitrary attribute.
Parameters:  composition (Composition) – Composition
 energy (float) – Energy for composition.
 name (str) – Optional parameter to name the entry. Defaults to the reduced chemical formula.
 attribute – Optional attribute of the entry. This can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, or else … Used for further analysis and plotting purposes. An attribute can be anything but must be MSONable.

energy_per_atom
¶ Returns the final energy per atom.

static
from_csv
(filename)[source]¶ Imports PDEntries from a csv.
Parameters: filename – Filename to import from. Returns: List of Elements, List of PDEntries

is_element
¶ True if the entry is an element.


class
PDPlotter
(phasediagram, show_unstable=0, **plotkwargs)[source]¶ Bases:
object
A plotter class for phase diagrams.
Parameters:  phasediagram – PhaseDiagram object.
 show_unstable (float) – Whether unstable phases will be plotted as well as red crosses. If a number > 0 is entered, all phases with ehull < show_unstable will be shown.
 **plotkwargs –
Keyword args passed to matplotlib.pyplot.plot. Can be used to customize markers etc. If not set, the default is {
”markerfacecolor”: (0.2157, 0.4941, 0.7216), “markersize”: 10, “linewidth”: 3}

get_chempot_range_map_plot
(elements, referenced=True)[source]¶ Returns a plot of the chemical potential range _map. Currently works only for 3component PDs.
Parameters:  elements – Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of all LiCoO phases wrt to uLi and uO, you will supply [Element(“Li”), Element(“O”)]
 referenced – if True, gives the results with a reference being the energy of the elemental phase. If False, gives absolute values.
Returns: A matplotlib plot object.

get_contour_pd_plot
()[source]¶ Plot a contour phase diagram plot, where phase triangles are colored according to degree of instability by interpolation. Currently only works for 3component phase diagrams.
Returns: A matplotlib plot object.

get_plot
(label_stable=True, label_unstable=True, ordering=None, energy_colormap=None, process_attributes=False, plt=None)[source]¶

pd_plot_data
¶ Plot data for phase diagram. 2comp  Full hull with energies 3/4comp  Projection into 2D or 3D Gibbs triangle.
Returns:  lines is a list of list of coordinates for lines in the PD.
 stable_entries is a {coordinate : entry} for each stable node
in the phase diagram. (Each coordinate can only have one stable phase)  unstable_entries is a {entry: coordinates} for all unstable nodes in the phase diagram.
Return type: (lines, stable_entries, unstable_entries)

plot_chempot_range_map
(elements, referenced=True)[source]¶ Plot the chemical potential range _map. Currently works only for 3component PDs.
Parameters:  elements – Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of all LiCoO phases wrt to uLi and uO, you will supply [Element(“Li”), Element(“O”)]
 referenced – if True, gives the results with a reference being the energy of the elemental phase. If False, gives absolute values.

plot_element_profile
(element, comp, show_label_index=None, xlim=5)[source]¶ Draw the element profile plot for a composition varying different chemical potential of an element. X value is the negative value of the chemical potential reference to elemental chemical potential. For example, if choose Element(“Li”), X= (µLiµLi0), which corresponds to the voltage versus metal anode. Y values represent for the number of element uptake in this composition (unit: per atom). All reactions are printed to help choosing the profile steps you want to show label in the plot.
Parameters:  element (Element) – An element of which the chemical potential is considered. It also must be in the phase diagram.
 comp (Composition) – A composition.
 show_label_index (list of integers) – The labels for reaction products you want to show in the plot. Default to None (not showing any annotation for reaction products). For the profile steps you want to show the labels, just add it to the show_label_index. The profile step counts from zero. For example, you can set show_label_index=[0, 2, 5] to label profile step 0,2,5.
 xlim (float) – The max x value. x value is from 0 to xlim. Default to 5 eV.
Returns: Plot of element profile evolution by varying the chemical potential of an element.

show
(*args, **kwargs)[source]¶ Draws the phase diagram using Matplotlib and show it.
Parameters:  *args – Passed to get_plot.
 **kwargs – Passed to get_plot.

write_image
(stream, image_format=u'svg', **kwargs)[source]¶ Writes the phase diagram to an image in a stream.
Parameters:  stream – stream to write to. Can be a file stream or a StringIO stream.
 image_format – format for image. Can be any of matplotlib supported formats. Defaults to svg for best results for vector graphics.
 **kwargs – Pass through to get_plot functino.

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_chempot_range_map
(elements, referenced=True, joggle=True)[source]¶ Returns a chemical potential range map for each stable entry.
Parameters:  elements – Sequence of elements to be considered as independent variables. E.g., if you want to show the stability ranges of all LiCoO phases wrt to uLi and uO, you will supply [Element(“Li”), Element(“O”)]
 referenced – If True, gives the results with a reference being the energy of the elemental phase. If False, gives absolute values.
 joggle (boolean) – Whether to joggle the input to avoid precision errors.
Returns: [simplices]}. The list of simplices are the sides of the N1 dim polytope bounding the allowable chemical potential range of each entry.
Return type: Returns a dict of the form {entry

get_chempot_range_stability_phase
(target_comp, open_elt)[source]¶ returns a set of chemical potentials corresponding to the max and min chemical potential of the open element for a given composition. It is quite common to have for instance a ternary oxide (e.g., ABO3) for which you want to know what are the A and B chemical potential leading to the highest and lowest oxygen chemical potential (reducing and oxidizing conditions). This is useful for defect computations.
Parameters:  target_comp – A Composition object
 open_elt – Element that you want to constrain to be max or min
Returns: (mu_min,mu_max)}: Chemical potentials are given in “absolute” values (i.e., not referenced to 0)
Return type: {Element

get_critical_compositions
(comp1, comp2)[source]¶ Get the critical compositions along the tieline between two compositions. I.e. where the decomposition products change. The endpoints are also returned. :param comp1, comp2: compositions that define the tieline :type comp1, comp2: Composition
Returns:  list of critical compositions. All are of
 the form x * comp1 + (1x) * comp2
Return type: [(Composition)]

get_decomp_and_e_above_hull
(entry, allow_negative=False)[source]¶ Provides the decomposition and energy above convex hull for an entry. Due to caching, can be much faster if entries with the same composition are processed together.
Parameters:  entry – A PDEntry like object
 allow_negative – Whether to allow negative e_above_hulls. Used to calculate equilibrium reaction energies. Defaults to False.
Returns: (decomp, energy above convex hull) Stable entries should have energy above hull of 0. The decomposition is provided as a dict of {Entry: amount}.

get_decomposition
(comp)[source]¶ Provides the decomposition at a particular composition.
Parameters: comp – A composition Returns: amount} Return type: Decomposition as a dict of {Entry

get_e_above_hull
(entry)[source]¶ Provides the energy above convex hull for an entry
Parameters: entry – A PDEntry like object Returns: Energy above convex hull of entry. Stable entries should have energy above hull of 0.

get_element_profile
(element, comp, comp_tol=1e05)[source]¶ Provides the element evolution data for a composition. For example, can be used to analyze Li conversion voltages by varying uLi and looking at the phases formed. Also can be used to analyze O2 evolution by varying uO2.
Parameters:  element – An element. Must be in the phase diagram.
 comp – A Composition
 comp_tol – The tolerance to use when calculating decompositions. Phases with amounts less than this tolerance are excluded. Defaults to 1e5.
Returns: [ {‘chempot’: 10.487582010000001, ‘evolution’: 2.0, ‘reaction’: Reaction Object], …]
Return type: Evolution data as a list of dictionaries of the following format

get_equilibrium_reaction_energy
(entry)[source]¶ Provides the reaction energy of a stable entry from the neighboring equilibrium stable entries (also known as the inverse distance to hull).
Parameters: entry – A PDEntry like object Returns: Equilibrium reaction energy of entry. Stable entries should have equilibrium reaction energy <= 0.

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.

get_hull_energy
(comp)[source]¶ Parameters: comp (Composition) – Input composition Returns: Energy of lowest energy equilibrium at desired composition. Not normalized by atoms, i.e. E(Li4O2) = 2 * E(Li2O)

get_transition_chempots
(element)[source]¶ Get the critical chemical potentials for an element in the Phase Diagram.
Parameters: element – An element. Has to be in the PD in the first place. Returns: A sorted sequence of critical chemical potentials, from less negative to more negative.

getmu_vertices_stability_phase
(target_comp, dep_elt, tol_en=0.01)[source]¶ returns a set of chemical potentials corresponding to the vertices of the simplex in the chemical potential phase diagram. The simplex is built using all elements in the target_composition except dep_elt. The chemical potential of dep_elt is computed from the target composition energy. This method is useful to get the limiting conditions for defects computations for instance.
Parameters:  target_comp – A Composition object
 dep_elt – the element for which the chemical potential is computed from the energy of
 stable phase at the target composition (the) –
 tol_en – a tolerance on the energy to set
Returns: mu}]: An array of conditions on simplex vertices for which each element has a chemical potential set to a given value. “absolute” values (i.e., not referenced to element energies)
Return type: [{Element

numerical_tol
= 1e08¶

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.

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:
exceptions.Exception
An exception class for Phase Diagram generation.

class
ReactionDiagram
(entry1, entry2, all_entries, tol=0.0001, float_fmt=u'%.4f')[source]¶ Bases:
object
Analyzes the possible reactions between a pair of compounds, e.g., an electrolyte and an electrode.
Parameters:  entry1 (ComputedEntry) – Entry for 1st component. Note that corrections, if any, must already be preapplied. This is to give flexibility for different kinds of corrections, e.g., if a particular entry is fitted to an experimental data (such as EC molecule).
 entry2 (ComputedEntry) – Entry for 2nd component. Note that corrections must already be preapplied. This is to give flexibility for different kinds of corrections, e.g., if a particular entry is fitted to an experimental data (such as EC molecule).
 all_entries ([ComputedEntry]) – All other entries to be considered in the analysis. Note that corrections, if any, must already be preapplied.
 tol (float) – Tolerance to be used to determine validity of reaction.
 float_fmt (str) – Formatting string to be applied to all floats. Determines number of decimal places in reaction string.

class
TransformedPDEntry
(comp, original_entry)[source]¶ Bases:
pymatgen.analysis.phase_diagram.PDEntry
This class repesents a TransformedPDEntry, which allows for a PDEntry to be transformed to a different composition coordinate space. It is used in the construction of phase diagrams that do not have elements as the terminal compositions.
Parameters:  comp (Composition) – Transformed composition as a Composition.
 original_entry (PDEntry) – Original entry that this entry arose from.

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.

order_phase_diagram
(lines, stable_entries, unstable_entries, ordering)[source]¶ Orders the entries (their coordinates) in a phase diagram plot according to the user specified ordering. Ordering should be given as [‘Up’, ‘Left’, ‘Right’], where Up, Left and Right are the names of the entries in the upper, left and right corners of the triangle respectively.
Parameters:  lines – list of list of coordinates for lines in the PD.
 stable_entries – {coordinate : entry} for each stable node in the phase diagram. (Each coordinate can only have one stable phase)
 unstable_entries – {entry: coordinates} for all unstable nodes in the phase diagram.
 ordering – Ordering of the phase diagram, given as a list [‘Up’, ‘Left’,’Right’]
Returns:  newlines is a list of list of coordinates for lines in the PD.
 newstable_entries is a {coordinate : entry} for each stable node
in the phase diagram. (Each coordinate can only have one stable phase)  newunstable_entries is a {entry: coordinates} for all unstable nodes in the phase diagram.
Return type: (newlines, newstable_entries, newunstable_entries)

tet_coord
(coord)[source]¶ Convert a 3D coordinate into a tetrahedron based coordinate system for a prettier phase diagram.
Parameters: coordinate – coordinate used in the convex hull computation. Returns: coordinates in a tetrahedronbased coordinate system.

triangular_coord
(coord)[source]¶ Convert a 2D coordinate into a trianglebased coordinate system for a prettier phase diagram.
Parameters: coordinate – coordinate used in the convex hull computation. Returns: coordinates in a triangularbased coordinate system.

uniquelines
(q)[source]¶ Given all the facets, convert it into a set of unique lines. Specifically used for converting convex hull facets into line pairs of coordinates.
Parameters: q – A 2dim sequence, where each row represents a facet. E.g., [[1,2,3],[3,6,7],…] Returns: A set of tuple of lines. E.g., ((1,2), (1,3), (2,3), ….) Return type: setoflines