Setting up calculationΒΆ

How to set up a calculation?

Basic input file for the NRLMOL is called “CLUSTER”. It requires minimal input from the user and most parameters required from the calculations are obtained using default values. If you are using a recent versions (after 2012) then you can specify some parameters that control the calculations in the file called “NRLMOL_INPUT.DAT”. This file is optional, in that, if it doesn’t exist it will be created automatically with default choices. We will discuss the details of the parameters in the NRLMOL_INPUT.DAT later.

For now let’s work on setting up of the CLUSTER file. It is the minimal input needed to run the NRLMOL code. The structure of the “CLUSTER” file is as below.

You can set up CLUSTER file in number of different ways.

  1. You can cut and paste it from these pages and adapt it by hand using the editor of your choice.

  2. You can use a script called xmol-dat_2_CLUSTER.pl to create it from the XMOL.DAT. The XMOL.DAT is a file in the xyz format and has atomic numbers in the place of the atomic labels (symbols). To convert standard xmol2xyz.pl. This way of creating CLUSTER will not make use of point group symmetry. If the molecules or your system has symmetry it is advisable to make use of point group symmetry as it results in significant computational savings. To use symmetry, use the following approach. Also, ensure that your spin (moment) is correctly specified. The script will set it to 1 for odd electron systems and to 0 for an even electron system. You may want to adapt charge and spin to your needs.

  3. Let’s suppose your systems of interest is in “XMOL.DAT”, then execute the following command echo “@XMOL.DAT” > CLUSTER

    This will insert a line “@XMOL.DAT” in the CLUSTER file. Now execute the NRLMOL on the command line. NRLMOL will try to identify the available symmetry. It will find the symmetry operations and write them in the file called GRPMAT and it will create the CLUSTER. The CLUSTER file created will have fewer atoms (only inequivalent atoms are listed). The entire structure can be generated using the symmetry operations and the positions of the ineqivalent atoms. Note that often for the systems containing high symmetry (e.g, icosahedral ), NRLMOL will usually find lower point group symmetry. To overcome this you can use you can combine step 1 and step 3. It advisable to ensure that the resultant XMOL.xyz or XMOL.DAT generated during the calculations is the system of your interest.

  4. Use the NRLMOL GUI. NRLMOL GUI allows setting up of CLUSTER file and visualization of results produced by the NRLMOL. For the visulalizatin of results like DOS, it also requires the gnuplot software to be installed.