This is only a brief summary. For command line parameters and
examples on usage, run for each program program -?
Takes list of VCI solutions with most important contributions from fundamental modes
as determined by csf_harm_vci
(by default saved in
) and prints list of
fundamental modes (and possibly intensities). Note that assignment of VCI states to fundamentals
is artificial and can be ambiguous. The script will exit with an error when conflicting states
Create a new gvib project directory by cloning
existing anharmonic data. The data will be only symlinked to save disk space. When cloning
a project with Gaussian jobs displaced along normal modes, clone-gvib will on request change
option, rename the Gaussian
output files to match the new normal mode numbering and update the jobrc config file accordingly.
Verify sameness of two molecular geometries.
Having transformation T which maps geometry a to b, i.e. T(a) = b,
the program compares order of normal modes in smatrices corresponding to a and b.
It does so by comparing every column of the transformed smatrix T(smatrix_a) with every column
of the smatrix_b.
On input, the program takes the following arguments:
- tmatrix - transformation matrix such that T(geom1) = geom2.
- nq - number of normal modes, the smatrices have dimension (3*natoms,nq)
- dir1, dir2 - directories containing the mass-weighted smatrices
and masses used to mass-weight the smatrices. Columns
of smatrices correspond to a constant normal mode index,
the rows to a constant cartesian coordinate.
On output, it prints two columns of indexes: the first
one are the indexes bi and in the second are corresponding
The program is used by sort-gvib-nmodes
Takes two files and compares their values. It can print out
differences, ratios, etc.
Create Gaussian input files for calculation of force-field constants
at (possibly optimized) geometry and displaced geometries. The geometries are by default
displaced along cartesian coordinates, but also geometries displaced along normal modes
can be generated. If neither _along_nm nor _along_cc is given, only the files for the original
geometry will be prepared.
Given geometries a,b the program will find transformation matrix T such that T a = b.
The matrix is declared as tmatrix(4,3), the fourth column being translation.
The program returns nonzero status on error.
Note: So far, only 5 first atoms are used for finding the matrix, which is defined as parameter
in the find_tmatrix subroutine. The program is used by the sort-gvib-nmodes
This script will extract a field from G03 output file or ascii checkpoint file.
(The latter may be obtained by the formchk utility.) If told so, the script can
also parse the fields of the section with normal mode analysis, results of
potential energy scan (PES), or molecular geometries.
GNU Molecule Maker.
Sort lines of a file according to a specified column. The script can also split
lines and sort all values. Sorting can be done in either ascending or descending
order. Sorting of absolute values is also supported.
Takes the given files and on output prints their
content in separate columns. It can extract a given column from
the files (see the -c and -s options), or it can read the content
sequentially (see the -S option). The values in the input files are
assumed to be whitespace separated.
Indexes of normal modes as printed from Gvib programs are dependent on
option. This utility will
print 'absolute' indexes of the given modes, as if none mode was freezed.
For example, if the modes 1-6 are freezed, than the index 1 on input will
produce 7 on output. Also the reverse direction from absolute to relative
indexes is recognised.
Walk through a directory set up by gvib and report
all unfinished gaussian jobs. The standard directory structure and file names
of gvib project is assumed.
Run PBS jobs from a project directory set up by gvib.
All scripts from the subdirectory "todo" will be run using the "qsub" command
and moved to the directory "running". The scripts should then move themselves
to the directory "done" and run this script to put more jobs in the queue.
Convert a list of peaks to the .prn format.
On the input are expected couples of numbers in the order (frequency intensity).
On the output is returned a curve with lorentz peaks, centered around the given points.
Print a requested constant from a given Gvib or Gaussian file.
Read Harm+VCI Hamiltonian matrix generated by csf_harm_vci
and prints the requested element.
Read Harm+VCI solutions generated by csf_harm_vci
and prints coefficients of the requested solution. (The options vci_basis_set
must be set in the config file when running
Reads a given file containing some molecular geometry,
tries to read it and outputs in a format suitable for reading by the
gmm (GNU Molecule Maker). It can parse many text formats - just try it out!
If it fails, extend it and send me a patch.
Tries to reorder atoms of the SRC geometry to match the order of atoms in the DST geometry.
Harmonic frequencies calculated for a given molecular geometry at different level of electronic theory will
be in general different and even the order of the normal modes can differ. To be able to compare between
two Gvib projects GVIB_A and GVIB_B, the program will try to identify normal modes and create sorted variants
of all cminv_* and ir_*, iraman_* and iroa_* files, so that the resulting files in GVIB_B will be ordered
as the corresponding modes in GVIB_A. The new files will be prefixed by the string "sorted_".
Plot calculated spectra.
Reads Gaussian output and transfers all recognised tensors
to the molecular geometry given as a command line parameter. Alternatively,
the script will transfer all files from a given gvib project.
See also [ref
] and cctn
A simple user friendly front-end to gnuplot. The purpose is to quickly
review results, not to create complicated plots.