README.md

SMFA

SMFA is a general program package for performing quantum chemistry calculations on large molecules, using an energy-based fragmentation approach. The program can calculate electronic energies, energy gradients and second derivatives; perform geometry optimization; find first order saddle points (transition states); perform energy optimized scans along a user-defined path; and evaluate various molecular properties. The program can use any of the following quantum chemistry packages: GAMESS(US), GAUSSIAN, NWChem and Q-Chem. In addition, SMFA provides a number of utility programs that, inter alia, calculate vibrational frequencies and infrared spectra with isotopic substitutions, the electrostatic potential on the solvent-accessible-surface, and isodesmic and higher order near-iso-energetic reaction schemes. Calculations of the electronic energy and related properties can be carried out using a scheme that provides a computation time that is linearly dependent on the size of the molecule or, if the user has enough processing units available, in a computation time that is independent of the size of the molecule.

Table of contents:

• Requirements
• Installation
• SMFA Publications
• Examples
• Licensing

Requirements

• Fortran compiler (gfortran, intel-fc)
• cmake
• perl
• DALTON
• At least one of the following Quantum Chemistry programs:
  • GAMESS
  • Gaussian
  • NWChem
  • QChem
• System running the PBS scheduling software

The SMFA_Users_Guide.pdf (Section 2.7) in SMFAPAC/doc contains information about how to get SMFA to "load" each (at least one) of these quantum chemistry packages.

Several Perl modules are also required, and these can be installed with the following commands (administrator privileges required):

> sudo cpan App::cpanminus
> sudo cpanm Shell
> sudo apt-get install libncurses5-dev 
> sudo cpanm Curses

One of the optional utility programs in SMFA requires the openbabel program (see Section 5.2 in SMFA_Users_Guide.pdf), so you will need to install openbabel if you want to use this feature. You can install openbabel at any time (the build below does not require it).

Installation

> git clone https://github.com/mickcollins/SMFAPAC
> mkdir build
> cd build
> cmake ../
> make install

make install compiles the binaries and also moves them to the SMFAPAC/exe directory. If you need to rebuild, simply remove all files in the build directory and make install again.

The SMFAPAC/bin directory must be on the user's path, which can be achieved by adding the following to the appropriate rc file:

For ~/.cshrc:

> set path = ( $path /path/to/SMFAPAC/bin)

For ~/.bashrc:

> export PATH=$PATH:/path/to/SMFAPAC/bin

Ensure /path/to is replaced with the actual path to the directory.

SMFA Publications

1. The user guide can be found in doc/SMFA_Users_Guide.pdf and contains detailed instructions on how to use the package.

2. Collins, M. A. Physical Chemistry Chemical Physics 2012, 14, 7744–7751.

Licensing

Version

1.0rc1