Description for the suite of utilities to 
    generate cube files with GAMESS.
         Version 1.2, 23.1.07 
      FMO 3.0 or higher required
           Dmitri G. Fedorov
              AIST, Japan
-----------------------------------------


GAMESS can produce two kinds of cube files containing electron density

1. Gaussian-like
2. sparse GAMESS cube files in native format

Three basic ways to create cube files are described in:

h2o.cube.inp        Gaussian-like, total 2-body density
h2o.cube.mon.inp    Gaussian-like, selected monomer densities 
h2o.scube.inp       sparse GAMESS, total 1 and 2 body density

The way to produce "free monomer" densities (FMO0) is described in
h2o.scube0.inp and 3gly.scube0.inp. 3gly.scube.inp is also included to do
density difference plots.
 
The following utilities are provided:

scubecon.c          convert sparse -> Gaussian-like
cubediff.c          subtract two Gaussian-like cube files. Useful to
                    subtract 2 and 1-body densities.
scubemon.c          extract monomer densities from a sparse 1-body cube
                    file.
grabcube            extract cube data from a GAMESS punch file (except FMO0)
grabfmo0            extract 0-body cube data from GAMESS punch files
proccube            Automatically process cube files.

The recommended utility to plot Gaussian cube files is Molekel:
http://www.cscs.ch/molekel/

An alternative is Molden:
http://www.cmbi.kun.nl/~schaft/molden/molden.html

Sparse format is described in scube.readme. Note that sparse format is 
normally used for a grid including the total molecule or at least larger part 
of it. 

Why is the sparse format better?

1. All monomer densities are contained and can be easily extracted.
2. Much less disk space (and memory) is required (except for very small cases).
3. Computation is faster (because unneeded empty grid space is skipped
for dimers).
4. Other FMO-specific processing can be performed. 

For convenience, scripts and programs were executed for this suite as follows: 
(first you should execute all GAMESS inputs)
   grabfmo0 h2o.scube0
   grabfmo0 3gly.scube0
   grabcube h2o.cube.dat
   grabcube 3gly.scube.dat
   mv h2o.scube0.0.scube h2o.scube.0.scube
   mv 3gly.scube0.0.scube 3gly.scube.0.scube 
   scubecon < h2o.scube.0.scube > h2o.scube.0.cube
   scubecon < h2o.scube.1.scube > h2o.scube.1.cube
   scubecon < h2o.scube.2.scube > h2o.scube.2.cube
   scubecon < 3gly.scube.0.scube > 3gly.scube.0.cube
   scubecon < 3gly.scube.1.scube > 3gly.scube.1.cube
   scubecon < 3gly.scube.2.scube > 3gly.scube.2.cube
   cubediff h2o.scube.1.cube h2o.scube.0.cube > h2o.scube.1-0.cube
   cubediff 3gly.scube.1.cube 3gly.scube.0.cube > 3gly.scube.1-0.cube

You can plot any .cube file with the above described graphical utilities.
The number in the file name indicates the n-body density, or the density 
difference (e.g., 1-0 is one-body minus the free state, so that the effects
of polarisation can be seen).

version history
1.2 23.1.07  added FMO0 utilities and samples 
1.1 26.11.04 introduced scubemon.c and grabcube, slightly changed sparse cube 
             file format 
1.0 26.11.04 first release: scubecon.c, cubediff.c. 
