README

Installation

The package PyAR is available from the website: https://github.com/anooplabiitkgp/PyAR
The package should be added to PYTHONPATH variable to be able to call
it from anywhere. The package has the following dependency:

1) Python
  The program is written in python2.7. Please visit the website:
  https://www.python.org/

2) TURBOMOLE:
  The modules turbomole.py assumes that the TURBOMOLE is installed and
  all it is in the PATH. For details about TURBOMOLE, please visit the
  website: http://www.turbomole-gmbh.com/
  Please note that a modified version of the jobex script is available
  with PyAR package. This script has to call by the pathname.

3) MOPAC:
  The module mopac.py assumes that mopac is installed in the computer
  and it is is callable by 'mopac' command. Note that Python does not
  accept aliases set in the .bashrc file. So, to avoid any error, call
  the 'mopac' program with the entire path, e.g., 

  >>>with open('outputfile', 'w') as fopt:
  >>>  subprocess.Popen(['/path/to/mopac', 'outputfile'], stdout=fopt, stderr=fopt)

  Add the MOPAC path to PATH variable and create a softlink of the MOPAC2016.exe 
  or whichever version are using as 'mopac' in the installed directory. 
  For details, please visit the website: http://openmopac.net/

4) OpenBabel:
  It uses the InCHi and Smiles string functionalities from the OpenBabel
  package. It should also be callable by the command 'babel'. For 
  details, please visit the website: http://openbabel.org/wiki/Main_Page


How to Run:
1) To use the binary reaction functionality, please copy the Reactor.py 
   to the working directory. Then, the program can be run by: 
   $python2.7 Reactor.py molecule1.xyz molecule2.xyz

2) To use the aggregation functionality, please copy the nucleation_genetic.py
   file to the working directory. Then, run the program by:
   $python2.7 nucleation_genetic.py molecule1.xyz molecule2.xyz
   In this case, the program will choose molecule1.xyz as the solvent and make
   the aggregation of molecule2.xyz around molecule1.xyz.
   If the program is called by:
   $python2.7 nucleation_genetic.py molecule.xyz
   then, aggregation of only the molecule.xyz will be considered.