pymatgen.analysis.chemenv.utils.coordination_geometry_utils module

This module contains some utility functions and classes that are used in the chemenv package.

class Plane(coefficients, p1=None, p2=None, p3=None)

Bases: object

Class used to describe a plane

Initializes a plane from the 4 coefficients a, b, c and d of ax + by + cz + d = 0 :param coefficients: abcd coefficients of the plane

TEST_2D_POINTS = [array([0., 0.]), array([1., 0.]), array([0., 1.]), array([-1.,  0.]), array([ 0., -1.]), array([0., 2.]), array([2., 0.]), array([ 0., -2.]), array([-2.,  0.]), array([1., 1.]), array([2., 2.]), array([-1., -1.]), array([-2., -2.]), array([1., 2.]), array([ 1., -2.]), array([-1.,  2.]), array([-1., -2.]), array([2., 1.]), array([ 2., -1.]), array([-2.,  1.]), array([-2., -1.])]

property a

Coefficient a of the plane.

property abcd

Return a tuple with the plane coefficients.

Returns

Tuple with the plane coefficients.

property b

Coefficient b of the plane.

property c

Coefficient c of the plane.

property coefficients

Return a copy of the plane coefficients.

Returns

Plane coefficients as a numpy array.

property crosses_origin

Whether this plane crosses the origin (i.e. coefficient d is 0.0).

property d

Coefficient d of the plane.

property distance_to_origin

Distance of the plane to the origin.

distance_to_point(point)

Computes the absolute distance from the plane to the point :param point: Point for which distance is computed :return: Distance between the plane and the point

distances(points)

Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side :param points: Points for which distances are computed :return: Distances from the plane to the points (positive values on the side of the normal to the plane,

negative values on the other side)

distances_indices_groups(points, delta=None, delta_factor=0.05, sign=False)

Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed. Grouped indices are also given, for which indices of the distances that are separated by less than delta are grouped together. The delta parameter is either set explictly or taken as a fraction (using the delta_factor parameter) of the maximal point distance. :param points: Points for which distances are computed :param delta: Distance interval for which two points are considered in the same group. :param delta_factor: If delta is None, the distance interval is taken as delta_factor times the maximal

point distance.

Parameters

sign – Whether to add sign information in the indices sorting the points distances

Returns

Distances from the plane to the points (positive values on the side of the normal to the plane, negative values on the other side), as well as indices of the points from closest to furthest and grouped indices of distances separated by less than delta. For the sorting list and the grouped indices, when the sign parameter is True, items are given as tuples of (index, sign).

distances_indices_sorted(points, sign=False)

Computes the distances from the plane to each of the points. Positive distances are on the side of the normal of the plane while negative distances are on the other side. Indices sorting the points from closest to furthest is also computed. :param points: Points for which distances are computed :param sign: Whether to add sign information in the indices sorting the points distances :return: Distances from the plane to the points (positive values on the side of the normal to the plane,

negative values on the other side), as well as indices of the points from closest to furthest. For the latter, when the sign parameter is True, items of the sorting list are given as tuples of (index, sign).

fit_error(points, fit='least_square_distance')

Evaluate the error for a list of points with respect to this plane.

Parameters

• points – List of points.

• fit – Type of fit error.

Returns

Error for a list of points with respect to this plane.

fit_least_square_distance_error(points)

Evaluate the sum of squared distances error for a list of points with respect to this plane.

Parameters

points – List of points.

Returns

Sum of squared distances error for a list of points with respect to this plane.

fit_maximum_distance_error(points)

Evaluate the max distance error for a list of points with respect to this plane.

Parameters

points – List of points.

Returns

Max distance error for a list of points with respect to this plane.

classmethod from_2points_and_origin(p1, p2)

Initializes plane from two points and the origin.

Parameters

• p1 – First point.

• p2 – Second point.

Returns

Plane.

classmethod from_3points(p1, p2, p3)

Initializes plane from three points.

Parameters

• p1 – First point.

• p2 – Second point.

• p3 – Third point.

Returns

Plane.

classmethod from_coefficients(a, b, c, d)

Initialize plane from its coefficients.

Parameters

• a – a coefficient of the plane.

• b – b coefficient of the plane.

• c – c coefficient of the plane.

• d – d coefficient of the plane.

Returns

Plane.

classmethod from_npoints(points, best_fit='least_square_distance')

Initializes plane from a list of points.

If the number of points is larger than 3, will use a least square fitting or max distance fitting.

Parameters

• points – List of points.

• best_fit – Type of fitting procedure for more than 3 points.

Returns

Plane

classmethod from_npoints_least_square_distance(points)

Initializes plane from a list of points using a least square fitting procedure.

Parameters

points – List of points.

Returns

Plane.

classmethod from_npoints_maximum_distance(points)

Initializes plane from a list of points using a max distance fitting procedure.

Parameters

points – List of points.

Returns

Plane.

indices_separate(points, dist_tolerance)

Returns three lists containing the indices of the points lying on one side of the plane, on the plane and on the other side of the plane. The dist_tolerance parameter controls the tolerance to which a point is considered to lie on the plane or not (distance to the plane) :param points: list of points :param dist_tolerance: tolerance to which a point is considered to lie on the plane

or not (distance to the plane)

Returns

The lists of indices of the points on one side of the plane, on the plane and on the other side of the plane

init_3points(nonzeros, zeros)

Initialialize three random points on this plane.

Parameters

• nonzeros – Indices of plane coefficients ([a, b, c]) that are not zero.

• zeros – Indices of plane coefficients ([a, b, c]) that are equal to zero.

Returns

None

is_in_list(plane_list)

Checks whether the plane is identical to one of the Planes in the plane_list list of Planes :param plane_list: List of Planes to be compared to :return: True if the plane is in the list, False otherwise

is_in_plane(pp, dist_tolerance)

Determines if point pp is in the plane within the tolerance dist_tolerance :param pp: point to be tested :param dist_tolerance: tolerance on the distance to the plane within which point pp is considered in the plane :return: True if pp is in the plane, False otherwise

is_same_plane_as(plane)

Checks whether the plane is identical to another Plane “plane” :param plane: Plane to be compared to :return: True if the two facets are identical, False otherwise

orthonormal_vectors()

Returns a list of three orthogonal vectors, the two first being parallel to the plane and the third one is the normal vector of the plane :return: List of orthogonal vectors :raise: ValueError if all the coefficients are zero or if there is some other strange error

orthonormal_vectors_old()

Returns a list of three orthogonal vectors, the two first being parallel to the plane and the third one is the normal vector of the plane :return: List of orthogonal vectors :raise: ValueError if all the coefficients are zero or if there is some other strange error

classmethod perpendicular_bisector(p1, p2)

Initialize a plane from the perpendicular bisector of two points.

The perpendicular bisector of two points is the plane perpendicular to the vector joining these two points and passing through the middle of the segment joining the two points.

Parameters

• p1 – First point.

• p2 – Second point.

Returns

Plane.

project_and_to2dim(pps, plane_center)

Projects the list of points pps to the plane and changes the basis from 3D to the 2D basis of the plane :param pps: List of points to be projected :return: :raise:

project_and_to2dim_ordered_indices(pps, plane_center='mean')

Projects each points in the point list pps on plane and returns the indices that would sort the list of projected points in anticlockwise order :param pps: List of points to project on plane :return: List of indices that would sort the list of projected points

projectionpoints(pps)

Projects each points in the point list pps on plane and returns the list of projected points :param pps: List of points to project on plane :return: List of projected point on plane

anticlockwise_sort(pps)

Sort a list of 2D points in anticlockwise order :param pps: List of points to be sorted :return: Sorted list of points

anticlockwise_sort_indices(pps)

Returns the indices that would sort a list of 2D points in anticlockwise order :param pps: List of points to be sorted :return: Indices of the sorted list of points

changebasis(uu, vv, nn, pps)

For a list of points given in standard coordinates (in terms of e1, e2 and e3), returns the same list expressed in the basis (uu, vv, nn), which is supposed to be orthonormal. :param uu: First vector of the basis :param vv: Second vector of the basis :param nn: Third vector of the bais :param pps: List of points in basis (e1, e2, e3) :return: List of points in basis (uu, vv, nn)

collinear(p1, p2, p3=None, tolerance=0.25)

Checks if the three points p1, p2 and p3 are collinear or not within a given tolerance. The collinearity is checked by computing the area of the triangle defined by the three points p1, p2 and p3. If the area of this triangle is less than (tolerance x largest_triangle), then the three points are considered collinear. The largest_triangle is defined as the right triangle whose legs are the two smallest distances between the three

points ie, its area is : 0.5 x (min(|p2-p1|,|p3-p1|,|p3-p2|) x secondmin(|p2-p1|,|p3-p1|,|p3-p2|))

Parameters

• p1 – First point

• p2 – Second point

• p3 – Third point (origin [0.0, 0.0, 0.0 if not given])

• tolerance – Area tolerance for the collinearity test (0.25 gives about 0.125 deviation from the line)

Returns

True if the three points are considered as collinear within the given tolerance, False otherwise

diamond_functions(xx, yy, y_x0, x_y0)

Method that creates two upper and lower functions based on points xx and yy as well as intercepts defined by y_x0 and x_y0. The resulting functions form kind of a distorted diamond-like structure aligned from point xx to point yy.

Schematically :

xx is symbolized by x, yy is symbolized by y, y_x0 is equal to the distance from x to a, x_y0 is equal to the distance from x to b, the lines a-p and b-q are parallel to the line x-y such that points p and q are obtained automatically. In case of an increasing diamond the lower function is x-b-q and the upper function is a-p-y while in case of a decreasing diamond, the lower function is a-p-y and the upper function is x-b-q.

Increasing diamond | Decreasing diamond

p–y x—-b

/ /| |

/ / | | q

/ / | a |

a / | | | / q | |/ / | x—-b p–y

Parameters

• xx – First point

• yy – Second point

Returns

A dictionary with the lower and upper diamond functions.

function_comparison(f1, f2, x1, x2, numpoints_check=500)

Method that compares two functions

Parameters

• f1 – First function to compare

• f2 – Second function to compare

• x1 – Lower bound of the interval to compare

• x2 – Upper bound of the interval to compare

• numpoints_check – Number of points used to compare the functions

Returns

Whether the function are equal (“=”), f1 is always lower than f2 (“<”), f1 is always larger than f2 (“>”),

f1 is always lower than or equal to f2 (“<”), f1 is always larger than or equal to f2 (“>”) on the interval [x1, x2]. If the two functions cross, a RuntimeError is thrown (i.e. we expect to compare functions that do not cross…)

get_lower_and_upper_f(surface_calculation_options)

Get the lower and upper functions defining a surface in the distance-angle space of neighbors.

Parameters

surface_calculation_options – Options for the surface.

Returns

Dictionary containing the “lower” and “upper” functions for the surface.

is_anion_cation_bond(valences, ii, jj)

Checks if two given sites are an anion and a cation. :param valences: list of site valences :param ii: index of a site :param jj: index of another site :return: True if one site is an anion and the other is a cation (from the valences)

matrixTimesVector(MM, aa)

Parameters

• MM – A matrix of size 3x3

• aa – A vector of size 3

Returns

A vector of size 3 which is the product of the matrix by the vector

my_solid_angle(center, coords)

Helper method to calculate the solid angle of a set of coords from the center.

Parameters

• center – Center to measure solid angle from.

• coords – List of coords to determine solid angle.

Returns

The solid angle.

quarter_ellipsis_functions(xx, yy)

Method that creates two quarter-ellipse functions based on points xx and yy. The ellipsis is supposed to be aligned with the axes. The two ellipsis pass through the two points xx and yy.

Parameters

• xx – First point

• yy – Second point

Returns

A dictionary with the lower and upper quarter ellipsis functions.

rectangle_surface_intersection(rectangle, f_lower, f_upper, bounds_lower=None, bounds_upper=None, check=True, numpoints_check=500)

Method to calculate the surface of the intersection of a rectangle (aligned with axes) and another surface defined by two functions f_lower and f_upper.

Parameters

• rectangle – Rectangle defined as : ((x1, x2), (y1, y2)).

• f_lower – Function defining the lower bound of the surface.

• f_upper – Function defining the upper bound of the surface.

• bounds_lower – Interval in which the f_lower function is defined.

• bounds_upper – Interval in which the f_upper function is defined.

• check – Whether to check if f_lower is always lower than f_upper.

• numpoints_check – Number of points used to check whether f_lower is always lower than f_upper

Returns

The surface of the intersection of the rectangle and the surface defined by f_lower and f_upper.

rotateCoords(coords, R)

Rotate the list of points using rotation matrix R :param coords: List of points to be rotated :param R: Rotation matrix :return: List of rotated points

rotateCoordsOpt(coords, R)

Rotate the list of points using rotation matrix R :param coords: List of points to be rotated :param R: Rotation matrix :return: List of rotated points

separation_in_list(separation_indices, separation_indices_list)

Checks if the separation indices of a plane are already in the list :param separation_indices: list of separation indices (three arrays of integers) :param separation_indices_list: list of the list of separation indices to be compared to :return: True if the separation indices are already in the list, False otherwise

sort_separation(separation)

Sort a separation.

Parameters

separation – Initial separation.

Returns

Sorted list of separation.

sort_separation_tuple(separation)

Sort a separation

Parameters

separation – Initial separation

Returns

Sorted tuple of separation

spline_functions(lower_points, upper_points, degree=3)

Method that creates two (upper and lower) spline functions based on points lower_points and upper_points.

Parameters

• lower_points – Points defining the lower function.

• upper_points – Points defining the upper function.

• degree – Degree for the spline function

Returns

A dictionary with the lower and upper spline functions.

vectorsToMatrix(aa, bb)

Performs the vector multiplication of the elements of two vectors, constructing the 3x3 matrix. :param aa: One vector of size 3 :param bb: Another vector of size 3 :return: A 3x3 matrix M composed of the products of the elements of aa and bb :

M_ij = aa_i * bb_j