JANPA program

This is the 'central' program of the package and its task is to perform
conversion from basis set functions (AOs) into Natural Atomic Orbitals (NAOs).
When these orbitals are prepared, density matrix is converted into their basis
and its diagonal elements are used for Natural Population Analysis (NPA), while
off-diagonal elements are used for Wiberg-Mayer bond indexes calculation.

MOLDEN files

Janpa uses MOLDEM-compatible files in the 'extended' format (used to represent
all possible results of Cartesian-to-pure conversion of basis functions).
To be used as an input files for JANPA, MOLDEN files should have three essential components:

• Geometry description ([Atoms] section)
• Basis set description ([GTO] section)
• Molecular orbital (MO) or natural orbital (NO) information ([MO] section(s))

Some basic information about MOLDEN format can be found on the web-page of
MOLDEN program.

How to run the program

You must have Java Runtime Environment installed on your system.
Then, simply type in the command line

java -jar janpa.jar INPUTFILE.molden

or

java -jar janpa.jar -i INPUTFILE.molden [options]

where INPUTFILE.molden is a suitable MOLDEN file, and [options] can contain multiple
options.
Run

java -jar janpa.jar

to get an information about the possible options.

Understanding the output

Janpa prints lots of information... Here we'd like to give some comments on the most
essential output.

It begins with a copyright note

     * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
     * Janpa: A cross-platform open-source implementation of NPA with Java * 
     *   A part of JANPA package, http://sourceforge.net/projects/janpa    * 
     *                    Version:  1.0 (09-06-2014)                        * 
     * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *

     (c) Tymofii Nikolaienko, 2014

     If any results obtained with this program are published,
     or for any other reasons, please, cite this work as: 
      T.Yu.Nikolaienko, L.A.Bulavin, D.M.Hovorun; J.Comput.Chem.(2014) submitted.

followed by the list of the values of all available program options.

Then a 'statistical' information about input MOLDEN file is printed:

    Loading MOLDEN from socl2_avtz.molden
    Basis functions are spherical: true
    Total number of basis functions: 196
    Total number of different contractions (radial parts): 62
    Highest angular momentum: f (Lmax = 3)
    Total number of MO: 196

    Data loaded successfully
     Number of basis functions: 196; number of molecular orbitals: 196

After this, the program computes the overlap and the density matrices based
ob the data from input MOLDEN file.

    Building overlap matrix S...
    Checking whether the basis functions are unity-normalized...
     Maximum deviation of the basis function norm2 from unity: BFN 0 (0-based num.), max|norm2-1| = 2.545E-10 
    Checking for the eigenvalues (linear (in)dependency) of the basis function overlap matrix...
    The smallest eigenvalue of the basis function overlap matrix: 2.343E-04 
    Checking whether the orbitals are unity-normalized...
    Checking MO overlap matrix...
     Maximum of MO |norm2-1|: 1.348E-08 (MO  177)
     Maximum absolute value of off-diagonal MO overlap element: 4.163E-08 (< MO   19 | MO  119 >)
    First-order reduced density matrix is OK.

The last message is very important since different programs can produce a variety of
MOLDEN-semi-compatible files (which differ by basis functions normalization, MO/NO sing
convention etc.). Therefore, the user should check whether:

• the basis functions are unity-normalized (max|norm2-1| should be small)
• the orbitals are unity-normalized (|norm2-1| should be small)
• the orbitals are orthogonal (Maximum absolute value of off-diagonal MO overlap element should be small)

It is also desirable that all basis functions were strongly linearly independent (The smallest eigenvalue of the basis function overlap matrix should not be very small).
If and only if all these criteria are met (within some internal thresholds), the program says that First-order reduced density matrix is OK.

In order to finally assure that everything is OK with input data, the program integrates
electron density, computes the total number of electrons and uses it to compute total
charge (with the sum of nuclei charges included):

    Building density matrix D... done.
    Building D.S... done.
    Total number of electrons: 58.000000
    Sum of electrons charges and the nuclei charges: -0.00000

The last value is typically known a priori and hence can be used as the final test.