pyextal.symmetryΒΆ
Symmetry Operations and Grouping.
This module provides tools for handling crystallographic symmetry operations. It includes a class for grouping symmetry-equivalent reflections and functions for applying symmetry operations to find all equivalent reflections for a given vector. The functionalities rely on the spgr common block from the Fortran Bloch wave code, which must be initialized before use.
for phaseDict, it is calculated to take account for the phase difference due to translation in symmetry operation. see Waser et al. (1955), Acta Cryst. DOI:10.1107/S0365110X55001862 For example, if we have a set of symmetry equivalent beams O, A, B O: reference beam A: beam that we input for structure factor adjustment B: another symmetry equivalent beam, which we need to adjust in Ugh matrix then the phase factor for A and B are calculated as: .. math:: phase_A = exp(2*pi*O*TRP_A) $ngle F_{(A)} = phase_A + ngle F_{(O)}$ phase_B = exp(2*pi*O*TRP_B) $ngle F_{(B)} = phase_B + ngle F_{(O)}$ given $F_{(A)}$, we can calculate $F_{(B)}$ as: $ngle F_{(B)} = phase_B - phase_A + ngle F_{(A)}$
Functions
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Calculates symmetry-equivalent reflections and their structure factors. |
Retrieves the active symmetry operations. |
Classes
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Groups symmetry-equivalent beams and manages their relationships. |