External-Python-User-Interface-for-MCCCS-Towhee

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External-Python-User-Interface-for-MCCCS-Towhee

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External Python User Interface for MCCCS Towhee

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README.md
towhee_collect.py
towhee_initialize.py
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#External Python User Interface for MCCCS Towhee

###Notes
The two Python scripts in source have been written in Python3.5 and are intended as a User Interface (UI) for 
isobaric-isothermal, canonical, and Gibbs ensemble Monte Carlo simulations with Monte Carlo for Complex 
Chemical Systems (MCCCS) Towhee version 7.1.0.

The software has been compiled with Python3.5 using the PyCharm Community Edition version 4.5.4, and with Python3.4 using
the Ubuntu command line. No warnings or weak warnings exist in the current version of the code.

###Details
The UI has been designed as an organizational, time saving, and data analysis tool for performing molecular 
simulations with Towhee on both personal computers, and clusters. The UI is composed of two scripts - towhee_initialize.py and towhee_collect.py - and has the following optional features:

1) towhee_initialize.py
  - create pressure (P), temperature (T), and set specific directories.
  - automatically copy 'towhee_input' files at specified T and P to 
    each final directory with different random number seeds
  - automatically start simulations for equilibration and production
    stages
  - automatically copy initial system configuration and molecule template
    files to directories
  - specify numerous input specifications from http://towhee.sourceforge.net/input/towhee_input_v7_0_x.html 
     within the script itself 
  - use a generic 'towhee_input' file or specify all input in the 'towhee_input' file 
  - automatically generate necessary 'towhee_parallel' and MPI executable 
    files within T directories for simulations on a cluster
    
2) towhee_collect.py
  - automatically collect various thermodynamic property results for up to two 
    simulation boxes from a single T and P for any number of sets, compute averages, 
    standard deviations, and percent standard deviations, and print all data 
    to an output file

To use the UI, the 'towhee_initialize.py', 'towhee_collect.py', and 'towhee_input' source files must be place in the same directory. A symbolic link to the Towhee executable 'towhee' must be added for personal computers. Note this is simply a matter of taste over './towhee' when running test simulations manually. This can be easily implemented from the '/home/user/' directory with the 'vi .bashrc' command, and the addition of 'alias towhee=/home/user/path_to_executable'. The only additional step is to place all force field files in a directory '/home/user/ForceFields/'. This is required because the code concatenates strings to the force fields files based on this directory stack format.

'towhee_initialize.py' is currently set to auto create directories, auto copy input files, and auto start four methane simulations as a 100 molecule equilibration in the isobaric-isothermal ensemble.  Once the simulation is finished, 'towhee_collect.py' can be executed to print an output file 'towhee_methane' with thermodynamic property averages and statistics.

*Additional detailed comments are given within the source code

###Contributors
Robert Kelly

External-Python-User-Interface-for-MCCCS-Towhee

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