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Supporting programs

This is only a brief summary. For command line parameters and examples on usage, run for each program program -?.

analyze-vci

Takes list of VCI solutions with most important contributions from fundamental modes as determined by csf_harm_vci (by default saved in harm_vci_funds) 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 are found.

clone-gvib

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 the ignore_modes option, rename the Gaussian output files to match the new normal mode numbering and update the jobrc config file accordingly.

compare-geometries

Verify sameness of two molecular geometries.

compare-smatrices

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: On output, it prints two columns of indexes: the first one are the indexes bi and in the second are corresponding indexes ai.
The program is used by sort-gvib-nmodes.

compare-values

Takes two files and compares their values. It can print out differences, ratios, etc.

create-inputs

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.

find-tmatrix

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 program.

get-gauss-field

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.

gmm

GNU Molecule Maker.

gsort

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.

merge-value

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.

mode-numbering

Indexes of normal modes as printed from Gvib programs are dependent on the ignore_modes 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.

nondone-list

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.

nondone-qsub

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.

peaks-to-prn

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-constant

Print a requested constant from a given Gvib or Gaussian file.

print_matrix_el

Read Harm+VCI Hamiltonian matrix generated by csf_harm_vci and prints the requested element.

print_vci_state

Read Harm+VCI solutions generated by csf_harm_vci and prints coefficients of the requested solution. (The options vci_basis_set and vci_solutions must be set in the config file when running csf_harm_vci.)

readfile-mm

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. <

reorder

Tries to reorder atoms of the SRC geometry to match the order of atoms in the DST geometry. A name="sort-gvib-nmodes">

sort-gvib-nmodes

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_".

spectraview

Plot calculated spectra.

transfer-all-props

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.

xplot

A simple user friendly front-end to gnuplot. The purpose is to quickly review results, not to create complicated plots.