Source code for pyretis.analysis.order_analysis

# -*- coding: utf-8 -*-
# Copyright (c) 2021, PyRETIS Development Team.
# Distributed under the LGPLv2.1+ License. See LICENSE for more info.
"""Module defining functions for analysis of order parameters.

Important methods defined here

analyse_orderp (:py:func:`.analyse_orderp`)
    Run a simple order parameter analysis.
from pyretis.analysis.analysis import analyse_data, mean_square_displacement

__all__ = ['analyse_orderp']

[docs]def analyse_orderp(orderdata, settings): """Run the analysis on several order parameters. The results are collected into a structure which is convenient for plotting. Parameters ---------- orderdata : numpy.arrays The data read from the order parameter file. settings : dict This dictionary contains settings for the analysis. Returns ------- results : numpy.array For each order parameter `key`, `results[key]` contains the result of the analysis. See Also -------- `analyse_data` in `` Note ---- We here (and in the plotting routines) make certain assumptions about the structure, i.e. the positions are assumed to have a specific meaning: column zero is the time, column one the order parameter and so on. """ results = [] _, col = orderdata.shape for i in range(col): if i == 0: # first column is just the time, skip it pass else: result = analyse_data(orderdata[:, i], settings) if i == 1: # assume that we want the MSD analysis here: ndt = settings['analysis']['maxordermsd'] result['msd'] = mean_square_displacement( orderdata[:, i], ndt=ndt ) results.append(result) return results