Usage - command line#

MAICoS can be used directly from the command line (cli). Using cli instead of a Jupyter notebook can sometimes be more comfortable, particularly for lengthy analysis. The cli in particular is handy because it allows for updating the analysis results during the run. You can specify the number of frames after the output is updated with the -concfreq flag. See below for details.

Note that in this documentation, we almost exclusively describe the use of MAICoS from the python interpreter, but all operations can be equivalently performed from the cli.

# -*- Mode: bash; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# Copyright (c) 2022 Authors and contributors
# (see the file AUTHORS for the full list of names)
# Released under the GNU Public Licence, v2 or any higher version
# SPDX-License-Identifier: GPL-2.0-or-later

maicos densityplanar -s slit_flow.tpr \
                     -f slit_flow.trr \
                     -atomgroup 'type OW HW'

# The density profile has been written in a file named ``density.dat`` 
# in the current directory. The written file starts with the following 
# lines

head -n 20 density.dat 

# For lengthy analysis, use the ``concfreq`` option to update the
# result during the run

maicos densityplanar -s slit_flow.tpr \
                    -f slit_flow.trr \
                    -atomgroup 'type OW HW' \
                    -concfreq '10'

# The general help of MAICoS can be accessed using

maicos -h

# Package-specific page can also be accessed from the cli

maicos densityplanar -h