MOLDEN: Introducing Vibration Modes Threshold

         Valentine Ananikov
        MOLDEN: Introducing Vibration Modes Threshold

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      CONTENTS
         * Introduction
         * Applying the Patch
         * Using New Feature
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Introduction

    MOLDEN is general purpose molecular and electronic structure displaying program written by G.Schaftenaar.
The official MOLDEN site is: http://www.caos.kun.nl/~schaft/molden/molden.html

    The program can be used to plot vibration modes to postscript file as atom centered arrows. However, by default the arrows for all atoms are plotted out independently on the vector length. These may confuse in some cases, since even for zero length vector an arrow is present. In addition, preparation of high quality pictures and presentations usually makes it desirable to select the vectors with a threshold based on the vector size.
    In this document a short patch to Molden is described to introduce threshold for normal modes plotting to postscript file.

Applying the Patch

ATTENTION:
The patch has been incorporated into MOLDEN at 24/02/2000, so all you need now is to download a new version of the package (3.6 oh later): ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/
You do not have to apply any patches to get the threshold working ! Use '-y' option as described below (in the original patch the '-t' option was used, now it is changed to '-y').

Using New Feature

A new '-y' option can be used to set up the threshold. Default value is 0.0, which means - plot all vectors independently on the length (old type plot). Running the program as 'molden -y1.0' will increase the threshold and in this case only vectors larger than the arrow will be plotted out. Further threshold increasing excludes small vectors from resulted postscript picture.
The feature is exemplified on Fig.1, where the left ethane molecule shows default plot. The arrows on both carbon atoms could be confusing, since the vibration represents rotation around C-C bond and corresponding vectors for carbon atoms displacement should be nearly zero. Using '-y1.0' option eliminates both arrows from the picture (Fig.1, right).


'gaussian.freq' test file, mode No1; default plot	'gaussian.freq' test file, mode No1; threshold with '-y1.0' option

Fig.1

The threshold sets the lower vectors length limit. The example on Fig.2 illustrates selection of the vibration vectors with high amplitude. Large threshold used to generate plot file for the right molecule (Fig.2) makes the picture more easy and clear.


'mopac.freq' test file, mode No3; default plot	'mopac.freq' test file, mode No3; threshold with '-y2.0' option

Fig.2

January 20, 1999

Valentine P. Ananikov

NMR Group
N.D. Zelinsky Institute of Organic Chemistry
http://nmr.ioc.ac.ru/Staff/AnanikovVP/