gausssum(1) [debian man page]

GAUSSSUM(1)						      General Commands Manual						       GAUSSSUM(1)

NAME

       gausssum - parses the output of a Gaussian, GAMESS or HyperChem job

SYNOPSIS

       gausssum [filename]

DESCRIPTION

       gausssum  parses the output file of a Gaussian, GAMESS or HyperChem computational chemistry job to extract useful information. It uses gnu-
       plot(1) to graphically display of the output. GaussSum can do the following: (Gau=Gaussian, GAM=GAMESS, Hyp=HyperChem)

       o      display all lines containing a certain phrase (any)

       o      follow the progress of the SCF convergence (Gau,GAM)

       o      follow the progress of a geometry optimisation (Gau,GAM)

       o      extract molecular orbital information, including contributions of groups of atoms to the molecular orbitals (Gau,GAM)

       o      plot the density of states spectrum (and the partial density of states, in the case of groups of atoms) (Gau,GAM)

       o      plot the crystal orbital overlap population (COOP) spectrum, which gives information on the bonding/anti-bonding nature of an  over-
	      lap between atoms/groups (Gau,GAM)

       o      extract information on the UV-Vis transitions (Gau,Hyp), including the change in the charge density of groups of atoms (Gau)

       o      plot the UV-Vis spectrum (Gau,Hyp) and the circular dichroism spectrum (Gau)

       o      automate	the creation of electron density difference maps, which visually show the change in charge density associated with a given
	      electronic transition (Gau)

       o      extract information on IR (Gau,GAM) and Raman vibrations (Gau)

       o      plot the IR and Raman spectra, which may be scaled using general or individual scaling factors (Gau)

CITATION

       If you use GaussSum to obtain results for publication, please cite it as follows:

	      N. M. O'Boyle, A. L. Tenderholt and K. M. Langner. J. Comp. Chem. 2008, 29, 839-845.

SEE ALSO

       gnuplot(1)

       /usr/share/doc/gausssum/html/ (or equivalent on your system)

AUTHOR

       This manual page was written by Jordan Mantha <mantha@ubuntu.com> for the Debian system (but may be used by others). Permission is  granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								 February 15, 2008						       GAUSSSUM(1)

VIEWMOL(1)																VIEWMOL(1)

NAME

       viewmol - a graphical front end for computational chemistry programs

SYNOPSIS

       viewmol

DESCRIPTION

       viewmol is a graphical front end for computational chemistry programs.  It is able to graphically aid in the generation of molecular struc-
       tures for computations and to visualize their results. The program's capabilities include:

       o Building and editing of molecules

       o Visualization of the geometry of a molecule

       o Tracing of a geometry optimization or a MD trajectory

       o Animation of normal vibrations or to show them as arrows

       o Drawing of IR, Raman, and inelastic neutron scattering spectra

       o Drawing of an MO energy level or density of states diagram

       o Drawing of basis functions, molecular orbitals, and electron densities

       o Display of forces acting on each atom in a certain configuration

       o Display of Miller planes in crystals

       o Calculation of thermodynamic properties for molecules andreactions

       o Drawings generated by viewmol can be saved as TIFF, HPGL, or PostScript files

       o Animations of normal modes can be converted to a video file (MPEG), e. g. for inclusion into World Wide  Web  documents  (requires  addi-
	 tional programs available on the Internet)

       o Interface to the freeware ray tracing program RAYSHADE (input file generation and use of RAYSHADE from within viewmol)

       o Input	and  output in a variety of formats, new formats can be added easily by the user viewmol includes a Python interpreter for automa-
	 tion.

       At present viewmol includes input filters for DISCOVER, DMOL, GAMESS, GAUSSIAN 9X, GULP, MOPAC, and TURBOMOLE outputs as well  as  for  PDB
       files  (viewmol	is  therefore suited as a viewer for structural data on the World Wide Web). Structures can be saved as MSI car-files, MDL
       files, and TURBOMOLE coordinate files. viewmol's file format has been added to BABEL so that BABEL can serve as an input as well as an out-
       put filter for coordinates.

       viewmol supports a space ball as input device.

       The  support programs for converting to and from the various coordinate file types may potentially be useful as stand alone utilities. They
       are split between /usr/share/viewmol (scripts) and /usr/lib/viewmol (C binaries), but individual documentation for them is not available.

SEE ALSO

       rasmol (1), gperiodic (1).

       Complete HTML documentation may be found in /usr/share/doc/viewmol.

AUTHOR

       viewmol was written by Jorg-Rudiger Hill <joehill@users.sourceforge.net>.

       This manual page was written by Drew Parsons <dparsons@debian.org> for the Debian GNU/Linux system (but may be used by others).

								   18 March 2008							VIEWMOL(1)