====== Welcome to the STIGMA Wiki! ======

**STIGMA** is an acronym for **S**canning **T**unneling **I**maging by **G**aussian **M**olecular orbital **A**nalysis. The program makes use of a Gaussian basis set and eigenvector/eigenvalue data to predict an STM image for a molecular system via the Tersoff/Hamann s-wave tip model.

Version 3.0 is written in Objective-C and lives atop the Foundation class framework that is a part of Mac OS X. The program should also function on top of the OpenStep library (precursor to Mac OS X's Foundation) available under Linux and other platforms. Version 2.x of **STIGMA** was also written in Objective-C but used string and container classes that I had created to mimic the OpenStep API. Switching to Foundation gained me lots of additional functionality without writing it myself and also ensures that I'm building on top of something likely more stable than what I created((The code that is considered by the author to be version 1.x of **STIGMA** was actually a melange of Fortran and C and (attempted) to use Gaussian's own ''util.a'' library.  It was clunky and I can't even be sure it calculated density properly since Gaussian's internal functions are undocumented and a hopeless mess of F77 spaghetti without that documentation.)).

Most of the code in this latest version has been factored out into a framework since it is useful beyond the **STIGMA** project alone. The ''QuantumCore'' framework contains all of the code to construct and evaluate Gaussian basis sets (both discrete and periodic); query a built-in periodic table for element information; construct 2D and 3D uniform, rectangular grids; and more. To point, I wrote a utility that mimics Gaussian's own ''cubegen'' utility, constructing orbital density and value grids (of course, my utility honors periodic boundary conditions while theirs doesn't (yet)) that can be viewed in GaussView.

===== Features =====

Version 3.x:

  * A C pseudo-class that provides minimal support for Gaussian basis sets:
    * Creation of basis sets from shells of arbitrary momentum and contraction degree
    * Normalization
    * Evaluation at point(s) in space
    * Does not yet implement overlap integrals or a general mechanism for calculating //n//-center integrals.
  * Molecule and wavefunction initialization from Gaussian binary and textual checkpoint files.
    * The program can handle any flavor binary checkpoint file (little or big endian, 32- or 64-bit) from revision A11 of Gaussian 98 and up.
  * Supports periodic boundary conditions (1D, 2D, and 3D) applied to a basis set.
    * Propagates atoms in molecular overlays on the STM image.
  * Molecular overlay includes both planar coordinates of atoms and a height-from-plane coordinate for perspective scaling in visualization program(s).

As far as visualization goes, version 3.x includes a native Mac OS X application called **GrayMatter** that generates images from the calculational data and adds the molecular overlay and scale/range bars.
===== Links =====

  * [[theory|Theoretical underpinnings]] of STIGMA
  * [[license|License]] for usage of the package
  * [[download|Download]] the STIGMA package for Mac OS X
  * [[screenshots|View screenshots]] of the GrayMatter visualization tool
  * [[documentation:start|General documentation]] of the STIGMA package
  * User-contributed documentation

===== About this Wiki =====

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