pymatgen.analysis.ewald module¶

class
EwaldMinimizer
(matrix, m_list, num_to_return=1, algo=0)[source]¶ Bases:
object
This class determines the manipulations that will minimize an ewald matrix, given a list of possible manipulations. This class does not perform the manipulations on a structure, but will return the list of manipulations that should be done on one to produce the minimal structure. It returns the manipulations for the n lowest energy orderings. This class should be used to perform fractional species substitution or fractional species removal to produce a new structure. These manipulations create large numbers of candidate structures, and this class can be used to pick out those with the lowest ewald sum.
An alternative (possibly more intuitive) interface to this class is the order disordered structure transformation.
Author  Will Richards
 Parameters
matrix – A matrix of the ewald sum interaction energies. This is stored in the class as a diagonally symmetric array and so self._matrix will not be the same as the input matrix.
m_list – list of manipulations. each item is of the form (multiplication fraction, number_of_indices, indices, species) These are sorted such that the first manipulation contains the most permutations. this is actually evaluated last in the recursion since I’m using pop.
num_to_return – The minimizer will find the number_returned lowest energy structures. This is likely to return a number of duplicate structures so it may be necessary to overestimate and then remove the duplicates later. (duplicate checking in this process is extremely expensive)

ALGO_BEST_FIRST
= 2¶ Slowly increases the speed (with the cost of decreasing accuracy) as the minimizer runs. Attempts to limit the run time to approximately 30 minutes.
 Type
ALGO_TIME_LIMIT

ALGO_COMPLETE
= 1¶

ALGO_FAST
= 0¶

ALGO_TIME_LIMIT
= 3¶

add_m_list
(matrix_sum, m_list)[source]¶ This adds an m_list to the output_lists and updates the current minimum if the list is full.

best_case
(matrix, m_list, indices_left)[source]¶ Computes a best case given a matrix and manipulation list.
 Parameters
matrix – the current matrix (with some permutations already performed)
m_list – [(multiplication fraction, number_of_indices, indices, species)] describing the manipulation
indices – Set of indices which haven’t had a permutation performed on them.

property
best_m_list
¶

get_next_index
(matrix, manipulation, indices_left)[source]¶ Returns an index that should have the most negative effect on the matrix sum

minimize_matrix
()[source]¶ This method finds and returns the permutations that produce the lowest ewald sum calls recursive function to iterate through permutations

property
minimized_sum
¶

property
output_lists
¶

class
EwaldSummation
(structure, real_space_cut=None, recip_space_cut=None, eta=None, acc_factor=12.0, w=0.7071067811865475, compute_forces=False)[source]¶ Bases:
object
Calculates the electrostatic energy of a periodic array of charges using the Ewald technique. Ref: http://www.ee.duke.edu/~ayt/ewaldpaper/ewaldpaper.html
This matrix can be used to do fast calculations of ewald sums after species removal.
E = E_recip + E_real + E_point
Atomic units used in the code, then converted to eV.
Initializes and calculates the Ewald sum. Default convergence parameters have been specified, but you can override them if you wish.
 Parameters
structure (Structure) – Input structure that must have proper Specie on all sites, i.e. Element with oxidation state. Use Structure.add_oxidation_state… for example.
real_space_cut (float) – Real space cutoff radius dictating how many terms are used in the real space sum. Defaults to None, which means determine automagically using the formula given in gulp 3.1 documentation.
recip_space_cut (float) – Reciprocal space cutoff radius. Defaults to None, which means determine automagically using the formula given in gulp 3.1 documentation.
eta (float) – The screening parameter. Defaults to None, which means determine automatically.
acc_factor (float) – No. of significant figures each sum is converged to.
w (float) – Weight parameter, w, has been included that represents the relative computational expense of calculating a term in real and reciprocal space. Default of 0.7 reproduces result similar to GULP 4.2. This has little effect on the total energy, but may influence speed of computation in large systems. Note that this parameter is used only when the cutoffs are set to None.
compute_forces (bool) – Whether to compute forces. False by default since it is usually not needed.

CONV_FACT
= 14.399645351950547¶

compute_partial_energy
(removed_indices)[source]¶ Gives total ewald energy for certain sites being removed, i.e. zeroed out.

compute_sub_structure
(sub_structure, tol=0.001)[source]¶ Gives total ewald energy for an sub structure in the same lattice. The sub_structure must be a subset of the original structure, with possible different charges.
 Parameters
substructure (Structure) – Substructure to compute Ewald sum for.
tol (float) – Tolerance for site matching in fractional coordinates.
 Returns
Ewald sum of substructure.

property
eta
¶

property
forces
¶ The forces on each site as a Nx3 matrix. Each row corresponds to a site.

get_site_energy
(site_index)[source]¶ Compute the energy for a single site in the structure
 Parameters
site_index (int) – Index of site
 Returns
(float)  Energy of that site

property
point_energy
¶ The point energy.

property
point_energy_matrix
¶ The point space matrix. A diagonal matrix with the point terms for each site in the diagonal elements.

property
real_space_energy
¶ The real space space energy.

property
real_space_energy_matrix
¶ The real space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in real space.

property
reciprocal_space_energy
¶ The reciprocal space energy.

property
reciprocal_space_energy_matrix
¶ The reciprocal space energy matrix. Each matrix element (i, j) corresponds to the interaction energy between site i and site j in reciprocal space.

property
total_energy
¶ The total energy.

property
total_energy_matrix
¶ The total energy matrix. Each matrix element (i, j) corresponds to the total interaction energy between site i and site j.
Note that this does not include the chargedcell energy, which is only important when the simulation cell is not charge balanced.