The Sherrill Group: Resources: Utility Programs

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Some Utility Programs for Electronic Structure

b2a: A simple script to convert the coordinates in an XYZ file from bohr to angstroms or vice versa. To convert bohr to angstroms: b2a molecule.xyz, output is written as molecule.a.xyz. To convert angstroms to bohr: b2a -r molecule.xyz, output is written as molecule.b.xyz. (Written by Tony Tauer)
babel: A program designed to convert many file formats used in molecular modeling (xyz, spartan, gaussian, etc.).

dvi2pdf: Shell script which embeds fonts in PDF files to make them look correct when generated from dvi files. (Written by David Sherrill)

geom: A program to read geometries and print out bond lengths, bond angles, torsional angles, out-of-plane angles, rotational constants, and perform isotopic analysis. This utility is part of the PSI3 package. It reads geometries from PSI (file11.dat or geom.dat), Q-Chem outputs, ACES II outputs, and XYZ files. For Q-Chem and ACES II, the geometry must be pasted into a separate file containing only the geometry. Useful for careful analysis of small molecules. For larger molecules, results can be obtained from jmol, described below. (Written by David Sherrill)

gimp: The GNU Image Manipulation Program. This is a graphics program which works like Adobe Photoshop.

gnuplot: The GNU plotting program. This is useful for quickly plotting data.

jmol: Jmol is a free, open source molecule viewer. It displays molecules; allows one to measure distances, angles, etc; animates vibrational modes (see qvibs below); exports images. Warning: jmol seems to measure torsional angles incorrectly! They can be off by several degrees! Use geom instead.

jsub: This is a java program which facilitates submission to the loadleveler queue on the IBM SP or the PBS queue on the group workstations. It can generate batch queue submission files (.cmd) and then submit the jobs to the queue. The status of jobs may be conveniently monitored via xloadl on cgate or xpbs on the workstations. (Written by Alfred Park)

Molden: Molden is a pre- and post processing program of molecular and electronic structure. It can serve as a molecular builder and minimizer via its 'Zmatrix Editor'. More importantly it has powerful visualization features for electron densities, orbital plots, electrostatic surfaces, ... etc.
Molden can interface with Tinker such that Tinker force fields can be used in the initial minimization of structures generated by Molden. To use this feature, one would have to add a line setting a Tinker path in their command file - add 'setenv TNK_ROOT /usr/local/tinker ' into ~/.tcshrc or whatever shell command file one runs

mp2xyz: A program to parse a Molpro output file, grab the Cartesian geometry, convert it from bohr to angstoms, and put it into XYZ format. Usage: mp2xyz file1.out [file2.out ...] (Written by Tony Tauer)

povmol: A program to create input files for the PovRay ray-tracer from Q-Chem or XYZ data.
Download the source code here: Povmol
(Program by Ryan Cohen and Alfred Park)
A compatible version of MegaPovPlus is available here: MegaPovPlus

pyjob: A Python script that extracts the n-th job from a multiple job Q-Chem output file. To see the usage, just enter pyjob. (Written by Fuchang Yin)

pyxyz: A Python script that extracts Cartesian coordinates from a Q-Chem output file. It can either extract Cartesian coordinates after every cycle or for a specific set of cycle(s). To see the usage, just enter pyxyz. (Written by Fuchang Yin)

qc2xyz: A program to parse a Q-Chem output file and grab the final geometry and put it into XYZ format. Usage: qc2xyz file.out file.xyz. (Written by Alfred Park)

thermo: A Perl script that can:
(1) read a vibrational frequencies output file from a Q-Chem or ACES II file and create an XYZ file containing 20 cartesian displacements of a chosen virational mode about equilibrium. xmakemol or jmol can read the XYZ file and animate the chosen vibrational mode. Usage: thermo output.file vibration-number for analytic second derivatives, otherwise thermo opt_geom_file freq_file vibration-number for finite difference frequencies (since the frequency output will not contain the optimized geometry in Q-Chem).
(2) read vibrational frequencies from Q-Chem, ACES or MOLPRO and compute finite temperature corrections to enthalpies [H(T=298)-H(0)]. Usage: thermo -p output.file. It can also read a set of frequencies from a text file formatted as ($i \t $freq[$i]\n) and compute finite temperature corrections. Usage: thermo -t output.file (Written by Berhane Temelso)

Making movies of vibrational modes: NOTE - One must have vibs (described above), Molekel, makempeg. How would one make a movie of a vibrational mode, lets say from a frequency calculation done with Q.Chem 2.0 or ACES II? (Tutorial written by Berhane Temelso)

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