SIMS_File_Readers
Christina Lam
August 22, 1993

Summary: Description of file readers developed at SIMS

Extensions to SciAn Developed at SIMS
=====================================

New SciAn file readers were developed at SIMS, to allow SciAn
to visualize input data from additional file formats for use in chemistry.
The SIMS readers allow SciAn to interpret data in XMol's XYZ format, 
standard N-M1G basis sets from Gaussian92, a transition-type basis set 
format for molecular orbital information from other programs, and 3D PLOT
grid data from BioSym's DMol software.  These readers were written
under communication with John Tse from the Molecular Dynamics Group and
Rene Fournier and Fabrizia Negri in Theoretical Chemistry.

File Reader Descriptions
========================
The XYZ file reader will visualize molecules in ball-stick or wireframe 
form.  Multi-frame XYZ files may be read for animation of molecules.  
The bonds may be guessed based on either the covalent radii of atoms or
an arbitrary minimum interatomic distance.  This file reader uses the
XYZ format specified by Minnesota SuperComputer's program, XMol.  The XYZ
format is often convenient because it requires minimal information, namely,
the number of atoms, atomic type, and cartesian coordinates of the nuclei.

The GSN file reader will extract the coefficients and exponents
of gaussian primitives from a G92 output file, and approximate 
the molecular orbitals by a linear combination of the primitives. 
The GSN file reader can read standard N-M1G basis sets, with
or without additional polarization or diffuse functions.
The reader will recognize S,P,D shell types, but not F orbitals.
In addition, it will take the atomic coordinate information in
the G92 output file to generate a ".atoms" dataset for visualizing
the molecule in ball-and-or-stick form.  The combined visualization
of the molecular orbitals and the ball/stick molecule can be
quite informative.  

The GSN1/2 file readers are scaled-down versions of the GSN reader.
These file readers are intended for basis set information from programs
other than Gaussian.  The information required are the grid boundaries
and resolution, and the shell coefficients, types, exponents, and 
atomic centre coordinates for each primitive.

The GRD file reader is intended for DMol users only.  It will take
data generated by DMol's PLOT command as discussed on pages B31-35
of the DMol User's Manual.

Technical Notes on Modifications
================================
The new file readers were developed on top of SciAn Beta release version
0.82.  The following files were changed:

	ScianSIMSFiles.c
	ScianSIMSFiles.h
	ScianPeriodicTable.h

and #define SIMSFILES was added to machine.h.

The main sources of information tapped during the development of the file 
readers were Chapter 7 of the SciAn reference manual, code for other
file readers, and personal communication with the authors of SciAn,
especially Eric Pepke.  

The ideas, file specifications, and data files for testing came from
John Tse (Molecular Dynamics), Rene Fournier and Fabrizia Negri 
(Theoretical Chemistry).

The modified code has been released to SciAn, to be distributed freely
to anyone who would like it.

The GSN file reader can read standard N-M1G basis sets, with
or without additional polarization or diffuse functions.
The reader will recognize S,P,D shell types, but not F orbitals.
  
====================
Christina Lam
August 1993
Summer Student
email: lamchri@ecf.utoronto.ca
(until May 1994)