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pyGSM

=> Please see LICENCE for licensing and copyright information <=
==========> Zimmerman Group, University of Michigan <==========

Overview

pyGSM (Python + GSM) combines the powerful tools of python with the Growing String Method to allow for rapid prototyping and improved readability.

Download instructions

git clone git@github.com:ZimmermanGroup/pyGSM.git
(need to have github ssh key activated)

Install instructions

install the code from source, run "python setup.py install". \ To install the latest release from anaconda, run ? (to be done)

Requirements

anaconda 2.5.1 or greater
python 2.7
numpy
matplotlib
six
networkx

Running as Executable

setup.py installs all the required packages, and creates an executable.
To execute the gsm, run "gsm". Use "-h" to see the list of command line options. Generally, you will need a .xyz file for the coordinates and one of the supported quantum chemistry software packages installed on your system.

Running as API

within a python script run import pygsm (assuming you've run setup.py).
You can also install the necessary packages within conda environment.\

  1. create a conda environment if necessary
    1. conda create -n gsm_env python=2.7
    2. source activate gsm_env
    3. conda install -c networkx
    4. conda install numpy
  2. source conda environmet
    1. source activate gsm_env

LICENCE Notifications

This project contains source material from the geomeTRIC package.
Copyright 2016-2019 Regents of the University of California and the Authors
Authors: Lee-Ping Wang, Chenchen Song\ https://github.com/leeping/geomeTRIC/blob/master/LICENSE

Contributors:

Cody Aldaz (lead author)
Khoi Dang
Prof. Paul Zimmerman
Josh Kammeraad
Prof. Todd Martinez Group