AVS Modules display_mopac 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.