Fast C-routines to calculate distance arrays from coordinate arrays.
Calculate all distances d_ij between the coordinates ref[i] and conf[j] in the numpy arrays ref and conf. If an orthorhombic box is supplied then a minimum image convention is used before calculating distances.
If a 2D numpy array of dtype numpy.float64 with the shape (len(ref), len(conf)) is provided in result then this preallocated array is filled. This can speed up calculations.
Calculate all distances d_ij between atoms i and j in the reference coordinates ref for all N coordinates. Other options as in distance_array().
If a 1D numpy array of dtype numpy.float64 with N*(N-1)/2 elements is provided in result then this preallocated array is filled. This can speed up calculations.
Calculate all distances between a pair of atoms. atom1 and atom2 are both arrays of coordinates, where atom1[i] and atom2[i] represent a bond. The optional argument box applies minimum image convention if supplied.
box can be either orthogonal or triclinic
If a 1D numpy array of dtype numpy.float64 with len(atom1) elements is provided in result then this preallocated array is filled. This can speed up calculations.
Calculates the angle formed between three atoms, over a list of coordinates. All atom inputs are lists of coordinates of equal length, with atom2 representing the apex of the angle. Returns the angle in radians.
If a 1D numpy array of dtype numpy.float64 with len(atom1) elements is provided in result then this preallocated array is filled. This can speed up calculations.
Calculate the torsional angle formed by four atoms, over a list of coordinates. Returns the angle in radians.
If a 1D numpy array of dtype numpy.float64 with len(atom1) elements is provided in result then this preallocated array is filled. This can speed up calculations.
Shift a set of coordinates to lie within the primary unit cell
Works with both orthogonal and triclinic boxes