display_mopac - This module is designed to read the output of a MOPAC
6.0 run, specifically the gpt file. The program then
uses routines adapted from the psi88[see REFERENCES]
program to compute the molecular orbitals over a grid
of points. The module provides a variety of options
including the computation of the electron density,
individual molecular orbitals, the electrostatic
potential by two different methods (one faster the
other more accurate), and the display of the molecular
geometry and molecular bonds.
Name
display_mopac - This module is designed to read the output of a MOPAC
6.0 run, specifically the gpt file. The program then
uses routines adapted from the psi88[see REFERENCES]
program to compute the molecular orbitals over a grid
of points. The module provides a variety of options
including the computation of the electron density,
individual molecular orbitals, the electrostatic
potential by two different methods (one faster the
other more accurate), and the display of the molecular
geometry and molecular bonds.
Summary
Name display_mopac
Type Data Input
Inputs:
NONE
Outputs:
out3d_fld - field 3D 3-space scalar rectilinear float
out_geom - geom
Parameters:
Name Type Default Choices
---- ---- ------- -------
gpt 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:
Pt Q Esp:Esp:None
Grid Spacing typein_real 0.4 0.00 100.00
Extent typein_real 4.0 0.00 50.00
Description
The display_mopac module is designed to be a flexible and extensible
module to allow the extraction and visualization of data output from MOPAC 6.0
[see REFERENCES]. The module reads an output checkpoint file from MOPAC
(typically, filename.gpt). This file contains the molecular composition,
geometry and the eigenvectors from the semi-empirical calculation. This
information is used to display the electronic stucture information of the
molecule. Furthermore, from the eigenvectors, the module can compute the,
molecular orbital (MO), user selectable, over a grid of points. This is done
in a function called compute_wavefnct, which was adapted from a psi88
subroutine that was developed by Daniel L. Severance and William L. Jorgensen.
The modular nature of this function 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 the density can be
selected as the output field 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). In addition to MO's and density, the user has the option of computing
the electrostatic potential via two different means. The first method
calculate the esp from a point-charge model. The second method calculates the
esp directly from the electron density. The code for the latter method was
taken from MOPAC 6.0 by James J.P. Stewart. 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
gpt file
ouput checkpoint file from MOPAC
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_mopac |
---------------------
| |
| |
--------------------- | | ---------------------
| 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
MOPAC, J. Stewart, J. Computer-Aided Mol. Design, Vol. 4 (1990)
Quantum Chemsitry Program Exchange #455
Related modules
display_gaussian
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.