Usage

Whenever you want to use picometer, first re-activate the virtual environment created during installation following instructions therein. Running the program with no arguments produces the help string.

Picometer inputs its settings and instructions from an input .yaml file. The file can contain a dictionary of settings, as well as a list of instructions. The list of instructions, called also a “routine”, must include only single-element maps in the - instruction: detail or - instruction: {details} format. Examples of instruction files are available in the tests directory. The easiest way to generate your file is to prepare it based on the example provided.

Instructions

The following instructions are currently supported by picometer (as of version 0.1.2):

  • Input/output instructions

    • load model from a cif file, given filename or mapping syntax: {path: filename.cif, block: cif_block}.

    • write table with all evaluations to a csv file.

  • Selection instructions

    • select atoms, groups, or shapes to be used; use raw element names or provide symmetry relation / recenter using mapping syntax, for example: {label: C(11), symm: x;-y;z+1/2, at: Fe(1)}. By default, selection is cleared after calling select with no arguments or calling an aggregating or evaluating instruction.

    • recenter selection around a new centroid; this action is applied to every selected item individually, so to recenter fixed group of atoms, group them first and recenter this group - otherwise you will recenter individual atoms instead.

  • Aggregation instructions

    • group current selection into a new object with fixed elements.

    • fit centroid to the current atom / centroid selection;

    • fit line to the current atom / centroid selection;

    • fit plane to the currect atom / centroid selection;

  • Evaluation instructions

    • measure distance between 2 selected objects; if the selection includes groups of atoms, measure closes distance to the group of atoms.

    • measure angle between 2–6 selected objects; if the selection includes (ordered) atoms, calculate direct or dihedral angle between presumed bonds.