Tutorial 1 Understanding atomic structure using NRLMOL

Very simple tutorial to get aquainted with advanced electronic structure calculation package NRLMOL. This tutorial will explain how to run the NRLMOL for atomic calculations. For simplicity, we will assume that the open shell atoms are spherically symmetric.

February 6, 2008

The CLUSTER file is the main input file of NRLMOL. It contains the minimal information to set up the calculation. See below the CLUSTER file for the Nitrogen atom:

GGA-PBE*GGA-PBE            # Exchange-correlation parametrization
GRP                        # Point group of system 
1                          # No. of atoms 
0.0 0.0  0.0    7  ALL    # x,y,z coordinates, Atomic number, ALL means all electron
0.0 3.000                 # Charge and Moment

 Spherical atomic calculation. Input auto generated by Perl script, 
                Rajendra Zope, EL Paso, TX 79912. Wed Feb  6 15:17:59 CST 2008

We will now describe the input structure of this file.

The first line is GGA-PBE*GGA-PBE. It means that the exchange-correlation interactions in the systems are modeled within the generalized gradient approximation (GGA) using the Perdew-Burke-Ernzerhof (PBE) parametrization. This is the default functional used in NRLMOL. A few other functionals are also available.

The second line is GRP . It refers to point group symmetry. The GRP means the symmetry point group operations will be read from the GRPMAT file. For spherical atoms the GRPMAT will contain a unit matrix. You need not generate GRPMAT file. It will be created automatically.

The third line contains 1. It specifies the number of atoms in calculations. We’re running atomic calculations. So number of atoms is 1. For molecules this number will change. See tutorial on molecular calculations for more details.

The line following third line contains the cartesian position in atomic units of the atom, its atomic number, and string ALL. In this example, we are dealing with only one atom, which can be conveniently put at the origin (0, 0, 0). Followed by the xyz coordinates is the atomic charge. The example listed is for Nitrogen whose atomic number is 7. The string ALL means include all (that is 7 in this case) electrons into calculations.

The fifth line in example has two fields. The first field is 0.0 which means perform calculation for the neutral atom. If it is 1 then the calculations will be performed for singly charged cation of N atoms. The next field which is 3 in this example corresponds to number of unpaired electron in the system. The nitrogen has three unpaired electrons in the 2p orbitals. Lines after Charge and Moment line are ignored.

Now, copy the example input in the file called CLUSTER and run the calculation for nitrogen atom using the following sequences of commands at the prompt. It is recommeded that you run each NRLMOL calculation in a separate directory.

$ rm -f GEOCNVRG SYMBOL

$ ./cluster > print.SCF

Open the GEOCNVRG file and write down the energy. If you have done everything correctly then it should be -54.535482 Hartree.

Now, browse through the file print.SCF and look at the energies printed at each iteration. The difference between total energy in two successive iterations should diminish as the self consistent process progresses. When this difference is smaller than the threshold value set in SCFDAT the SCF process will stop. Also, look at the EVALUES file in which Kohn-Sham eigenvalues and occupation numbers are printed. Try to understand the SCF process, occupation numbers, degeneracy of orbitals.