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Shell Programming and Scripting
Globbing slash Wildcarding Question
Post 302105442 by sb008 on Thursday 1st of February 2007 05:58:05 PM
02-01-2007
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LEARN ABOUT LINUX
geom
geom(1) geom(1) NAME
geom - analyzes a molecular geometry input in Cartesian coordinates. DESCRIPTION
The program geom reads a set of Cartesian coordinates and determines from them the bond distances (Bohr and angstrom), bond angles, tor- sional angles, out-of-plane angles (optional), moments of inertia, and rotational constants. FILES REQUIRED
input.dat - Input file and one of the following: geom.dat - geometry file file11.dat - PSI-format geometry/gradient file FILES GENERATED
geom.out - file containing the analysis INPUT OPTIONS
The geom program has the following options: -h Print help information (these options). -aces [filename] Read the input in an ACES output format, with each line consisting of atomic symbol, atomic number, and Cartesian coordinates (in Bohr). The optional argument is the name of the geometry input file, which defaults to geom.dat. -qchem [filename] Read the input in an QCHEM output format, with each line consisting of the atom number, the atomic symbol, and Cartesian coordinates (in Angstroms). The optional argument is the name of the geometry input file, which defaults to geom.dat. -xyz [filename] Read the input in an XYZ output format. The first line contains the number of atoms and the second line is a comment line. Subse- quent lines each contain the atomic symbol and Cartesian X Y and Z coordinates (in Angstroms). The optional argument is the name of the geometry input file, which defaults to geom.dat. -oop Print out-of-plane angles, where the angle a-b-c-d is defined as the angle formed by the vector a-d and the plane defined by atoms b, c, and d. DO_OOP = boolean Same as command-line switch -oop described above. ISOTOPES = matrix of reals/strings Used to specify masses to be used in the calculation of the center of mass and rotational constants. One array is provided for each isotopomer to be calculated. The arrays can mix floating point numbers with strings which designate isotopes. If this array is not given and file11.dat is present, then the masses will be obtained by converting the atomic numbers in file11. If masses are not given by ISOTOPES or by file11, then no mass-related quantities will be calculated. -g [filename] Read Cartesian coordinates from a file other than file11.dat. If a filename is not given, the default is geom.dat. The alternative file is assumed to be in a format similar to that of PSI's geom.dat. Since such files do not contain atomic numbers, the moments of inertia and rotational constants are not calculated if this option is used. READ_GEOM = boolean This option in input.dat tells geom to read the geometry from geom.dat in the PSI geom.dat format. -a Print parameters for all pair distances. PRINT_ALL_DIST = boolean Same as -a flag described above. -d distance Only print parameters involving pairs of atoms which are less than distance bohr apart (default value is 4.0 bohr). PRINT_DISTANCE = value Same as -d flag described above. -angstrom The input coordinates are in angstroms, not bohr. ANGSTROM = boolean If TRUE, the input coordinates are in angstroms instead of bohr. The default is FALSE. The following example is for calculating the geometrical information for water with several different isotopes. The geometry is read from geom.dat rather than from file11.dat. geom: ( read_geom = true isotopes = ( (O H H) (O D D) (O18 1.007825 1.007825) ) ) 5 June, 1998 geom(1)