#AUTOPot

####A wrapping library for the POTLIB2001 standard to Mathematica

####Written By Aaron Tagliaboschi and Dr. Jeremy Maddox

####Department of Chemistry, Western Kentucky University

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##Abstract

Chemical reactions may be described theoretically using Born-Oppenheimer potential energy surfaces. For many chemical systems, these have been incorporated within an on-line repository of FORTRAN codes (POTLIB). The goal of this project is to be able to install and utilize POTLIB subroutines in higher level languages, such as Mathematica. To do this we have utilized the GNU C compiler and FORTRAN compiler to link the object files along with MathLink drivers written in C. We have found this to be an effective method and can now successfully generate MathLink executables and call the POTLIB functions from within Mathematica without a serious cost to runtime. This is helpful for analyzing reactions in Mathematica and using some of its higher- level numerical functions. Thus far, we have been able to make graphs of the potential energy surface in internal coordinates and Jacobi coordinates, as well as apply numerical methods for finding the minimum energy reaction coordinate and tracing Newtonian trajectories.

##Installation

No installation is necessary beyond simply saving the folder to the computer. To use the included scripts and to build the libraries, you will need GCC, GFORTRAN, and perl installed on your system. If you are using Linux, these are normally installed by default. Compiling on/building for Windows is possible, but you will to install Cygwin. See below for more details.

##Usage Instruction

###Configure

To use this library, you have to build the POTLIB source library against pot.c and utility.f along with generating code for MathLink using the mprep utility that comes with the MathLink libraries. To make things simpler, two scripts are included with this package to automatically generate everything needed to create a build package, including all generated code, the library file itself, and a makefile.

The first script configure is a shell script for single packages and is the backbone of the batch script as well. The call format is:

./configure POTLIBfile

The first argument POTLIBfile is the actual POTLIB FORTRAN file to be used. The script copies the library to the AUTOPot folder and seds through the templates for the makefile and mprep MathLink template files, along with finding the install directory of Mathematica and copying the FORTRAN file into the src directory.

Note: The script creates a file called mathdir that stores the absolute location to the utilities, libraries, and header files needed for MathLink. If you have these files installed in a different location, or you with to use a different version of Mathematica's MathLink (which, for this library, shouldn't matter), then create this file and change it before running configure. The location stored in this file is hard-coded into the makefile generated and the mprep stored in that location is used to generate the pot.tm.c MathLink code.

###Batch-make

The second script batch-make compiles batches of MathLink excecutables It's format is:

./batch-make POTfolder binfolder

The first argument POTfolder is the folder containing the POTLIB FORTRAN files ready for compiling. The second argument binfolder is the folder the resulting executables will go.

This script builds each .f file in POTfolder using the configure script.

##Cygwin

To compile MathLink executables on Windows, this package uses Cygwin, a Linux emulator, and MinGW, a minimalist GCC compiler for Windows. In Cygwin, you need to have the following packages installed:

• mingw-gcc
• mingw-gfortran
• make
• perl

You will also have to install the mprep executable, ML32i3 library, and mathlink.h in the correct locations. Other than that, it works exactly as in Linux. The final product is a MathLink executable.

Note: Because of licensing of cygwin1.dll, if you distribute Cygwin-built MathLink executables you much release the source code under the GPLv3 or a compatible license.

##License

This software is licensed under the GPLv3. For more information, please see COPYING