display_gaussian - This module is designed to read the output of a
gaussian job, specifically the ascii form of the
checkpoint file. The program then uses routines
adapted from the psi88 program to compute the
molecular orbital over a grid of points. The module
provides a variety of options including the
computation of the electron density, individual
molecular orbitals, and the display of the
molecular geometry and molecular bonds.
Name
display_gaussian - This module is designed to read the output of a
gaussian job, specifically the ascii form of the
checkpoint file. The program then uses routines
adapted from the psi88 program to compute the
molecular orbital over a grid of points. The module
provides a variety of options including the
computation of the electron density, individual
molecular orbitals, and the display of the
molecular geometry and molecular bonds.
Summary
Name display_gaussian
Type Data Input
Inputs:
NONE
Outputs:
out3d_fld - field 3D 3-space scalar rectilinear float
out_geom - geom
Parameters:
Name Type Default Choices
---- ---- ------- -------
chkpt file browser "" Filename
Representation radio_buttons ball and stick ball and stick:cpk:
colored stick
Sphere Scale typein_real 1.0 0.0 5.0
MO selected typein_integer 0 0 0
Compute Choice radio_buttons None MO:Density:None
Grid Spacing typein_real 0.4 0.00 100.00
Extent typein_real 4.0 0.00 50.00
Description
The display_gaussian module is designed to be a flexible and
extensible module to allow the extraction and visualization of data output
from GAUSSIAN 92. The main features of the module are as described above. The
module reads the ascii version of an output checkpoint file from gaussian.
These can be generated using the "program" formcheck provided with g92. This
file contains the molecular composition and geometry as well as the basis type
used and the eigenvectors associated with the basis set. The display_gaussian
module supports 6-31g, 3-21g, and sto-3g type basis sets. The information
extracted from the checkpoint file is used to display the stucture and bond
information of the molecule. Furthermore, from the eigenvectors, the module
can compute the molecular orbital (MO), as selected by the user,over a grid of
points Associated with each supported basis set is a FORTRAN subroutine which
computes the MO on a grid of points for the selected MO. These FORTRAN
subroutines are basically the same ones used in the psi88 programs that were
developed by Daniel L. Severance and William L. Jorgensen, currently at Yale
University. The modular nature of the module structure allows the user easy
access to the molecular orbital so as to be able to compute any property of
interest that is related to the MO. [Note: The output is a field which can be
manipulated directly by field math and similar modules.] In addition
to the MO, the electron density can be displayed. This is computed by
summing the squares of all the MO's times their occupation number. Since this
is done over all MO's it can be quite a lengthy calculation for a large
molecule, thus it is recommended that this be done just once and the result
written to disk with the write_field module (Note, all MO's are computed on
the fly, none are stored). Finally, the compute choice of None can be
selected, this is useful if one desires to use the module just as a coordinate
and bond viewer.
The compute choice selected is output as a three dimensional,
rectilinear field. The grid for this field is calculated in the
compute_gridpoints function. The spacing between gridpoints is the same in all
three directions but the number of gridpoints in any direction will vary
depending upon the molecular shape and the settings (see PARAMETERS) of grid
spacing and extent.
Inputs
None
Parameters
chkpt file
ouput checkpoint file from gaussian (ascii version)
Representation
display type for the molecular geometry and bonds
Sphere Scale
atoms are represented by spheres, this parm scales them
MO selected
if the Compute Choice is to display a MO, this specifies
which MO is computed and displayed
Compute Choice
Specifies which quantity is to be calculated and output as the
output 3d field
Grid Spacing
Specifies the distance between grid points in Angstroms
Extent
Specifies how far (in Angstroms) beyond the outermost atoms to
extend the grid
Outputs
out3d_fld
the output field is a 3D grid which contains the scalar value
of the chosen property (specified in compute choice) at that
spatial location
out_geom
outputs the molecular geometry and bonds
Example networks
---------------------
| display_gaussian |
---------------------
| |
| |
--------------------- | | ---------------------
| generate colormap | | | | generate colormap |
--------------------- | | ---------------------
| | | |
| | | --------------------|
| | | |
| |-------+-------------<------+--------->----+-----|
| | | | | | |
--------------------- | ---------------------
| isosurface | | | isosurface |
--------------------- | ---------------------
| | |
| | |
|-------------------+---------------------|
|
|
---------------------
| geometry viewer |
---------------------
COMPILATION:
Please see the notes in the example Makefile. It is necessary to
include the correct FORTRAN libraries when building the C executable.
References
Gaussian 92, Revision A, M.J. Frisch, G.W. Trucles,
M. Head-Gordon, P.W.Gill, M.W. Wong, J.B. Foreman, B.G. Johnson,
H.B. Schlegel, M.A. Robb, E.S. Replogle, R. Gomperts, J.L. Andes,
K, Raghavachavi, G.S. Binkley, C. Gonzalez, R.L. Martin, D.J. Fox,
D.J, Duprees, J. Baker, J.J.P. Stewart and J.A. Pople, Gaussian Inc.
Pittsburgh, PA (1992)
Related modules
display_mopac
DMOL_to_field
coord2geom
See also
K.M. Flurchick and Lee Bartolotti, "Visualizing Properties of
Atomic and Molecular Systems", accepted by Journal of Molecular
Graphics.
Ken Flurchick, Lee Bartolotti and Mark Reed, "Visualizing
Atomic and Molecular Properties Using AVS", AVS'94 Proceedings.