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QMView reads a variety of input files either through the use
of command line options or from the interactive menu with the
exception of density data files. Some of the conventions for file names
suffixes are:
By default, QMView reads a MOLPLT file: a file format written by
the program GAMESS. QMView my be invoked by typing
QMView file.mol
A MOLPLT files consist of four parts:
1. Molecule descriptions give the total number of atoms, the number of different types of atoms, the number of bonds, bond widths and a dummy character string. The character string describes the molecule type, but QMView does not use this value. The following keywords specify the information:
2. Atom specifications give the name of each atom, its color index and initial radius. The color index refers to a predefined set of colors that may be changed via the COLOR menu item, which is described on page 17. The number of atoms specified correspond to the number NKINDS.
3. Atom coordinates list the atom types followed by the respective x, y, and z coordinates. The x and y axes are parallel to the plane of the screen. The z axis is orthogonal to the plane of the screen. The center of the object is centered on the screen. The number of atoms listed must correspond to the number for NATOMS.
Optional data
4. List of bonds are given in pairs after the BONDATOMS keyword. Up to eight pairs may be listed per line. A negative number indicates that the bond will gradually increase towards the other atom.
5. Frequency and vibrational modes are specified by giving the number of modes, followed the frequency and the displacement vector for each mode. Masses may be read in as well for mass weighted coordinates.
6. Vector data corresponding to one vector on each atom may be displayed. An example would be force or velocity (in the case of dynamics) components on each atom. A set of x,y,z coordinates following the atomic coordinates on the same line of the input file defines the vector (see the example below).
The following example describes a molecule which consists of 6 atoms, 2 nitrogen and 4 oxygen atoms. There are 5 bonds between the atoms, with the bonds having an initial bondwidth of 0.060. Each nitrogen atom will be color blue (color index 3) with an initial radius of 0.30. The oxygen atoms will be displayed in Magenta (color index 5) with an initial radius of 0.50. Table 1 shows the colors associated with the default color index and their respective red, green, and blue values. There will be bonds between the third and first atoms, the fourth and second atoms, the fifth and first atoms, the sixth and second atoms and the first and second atoms. In this example, each set of cartesian coordinates are followed by x,y,z vector values that will be displayed as a vector.
QMView can read the atomic positions from a GAMESS input file as well as the GAMESS keywords and their values. The coordinates can be cartesian, or in Z matrix format. (reading of "fragments" has not yet been implemented). In addition, QMView can read the symmetry group and generate the additional atoms.
A surface data file contains density values. It is written in a free format with one restriction: the density index must vary from fastest to slowest in x, y, z order, or in z,y,x order (such as that output in a GAUSSIAN "cube" file).
The surface specification file contains information on grid edges
(only rectangular grids may be used), grid resolution, coordinates of the grid
origin, range of density values, and number of surfaces requested.
The first line specifies the number of grid points on each axis
minus 1. The second line specifies the number of requested surfaces
and what order the data is in (x,y,z) "0", or (z,y,x), "1".
The next three lines give the range for the x, y, and z values, respectively.
The last line gives the range of the density values.
The command line input is:
QMView.opengl -i file.dens file.mol < surfin
A 3D molecular orbital file is created by the 3D version of PLTORB (extension .mdm), and contains pltorb option setting information, atomic position and a 61x61x61 grid of the molecular orbital data. Instructions concerning the preparation of input and execution of 3DPLTORB can be found in the manual distributed with the 2D PLTORB code.
The command line input is:When GAMESS runs an optimization calculation with the MOVIE option a file is written on the IRC file unit containing the coordinate updates of each optimization iteration. When an IRC calculation is run, a file with a slightly different format is written to the IRC unit containing the coordinates along the reaction path.
The command line inputs are:Whenever QMView writes to an output device, two files specified by the system name and a time stamp are written to disk. One file is an ascii file containing coordinate data, colors, and display types. The other file is binary and contains data such as matrix transformations. The files contain all the data and information necessary to reproduce the image in the same orientation, display types, and colors. When QMView is started with the "-r" option the original system file name and the time stamp value, the structure is redisplayed. If "-r" is not specified, QMView looks for checkpoint files where "0" is appended rather then the time stamp and uses those files. These files may be written out at any time by pressing the W key. The user is prompted for a file prefix. These files are appended by a "0" rather then a time stamp.