Solid State Adaptive Natural Density Partitioning (SSAdNDP)

This project is originally written by Alexander Boldyrev @ Utah State University. Forked from http://ion.chem.usu.edu/~boldyrev/ssadndp.php.

The source code has been updated by replacing several deprecated routine-calling scheme, and a modified Makefile for it to work with newest intel compiler and MKL version 2022.1.1

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Solid State Adaptive Natural Density Partitioning (SSAdNDP) [1] is an extension of the AdNDP method [2] to periodic systems and as such was derived from periodic implementation [3] of the Natural Bond Orbital (NBO) analysis [4]. SSAdNDP allows the interpretation of chemical bonding in systems with translational symmetry in terms of classical lone pairs and two-center bonds, as well as multi-center delocalized bonding. Similar to AdNDP, the bonding pattern is expressed as a set of n-center - 2-electron (nc-2e) bonds. See the AdNDP page and AdNDP and SSAdNDP publications [1,2] for details on this approach to interpretation of chemical bonding.

Getting Started

These instructions will get you a copy of the project up and running.

This package comes in three part:

1. DFT interface and projection executable.
2. SSAdNDP calculation executable.
3. Visualization executable.

Prerequisites

The code is written in Fortran 90, and requires the BLAS95 and LAPACK95 libraries as implemented in MKL, as well as libraries used for OpenMP parallelization.

Installing DFT interfaces

1. VASP (compatible with VASP v5.4.4)

• copy interfaces/VASP_interface/projection_output.F into directory containing VASP source code ./scr.
• apply interfaces/VASP_interface/proj_VASP_5.4.patch by putting it in VASP source code's root directory and:

patch -p0 < proj_VASP_5.4.patch

• Compile VASP as usual.

2. CRYSTAL

• No modification needed.

Installing SSAdNDP software

1. Go to SSAdNDP folder, modify Makefile by changing the corresponding MKLROOT.
2. Use the following command to generate a Makefile:

./mkmf -t Makefile.template -p ssadndp.exe

3. Type make to get ssadndp.exe

4. To compile projection.exe, go to the projection folder and modify the file Makefile by changing the corresponding MKLROOT, then type:

Make

5. To compile visual.exe, go to the visualization folder and type:

ifort visual.f90 -o visual.exe

Usage

The workflow of SSAdNDP is:

1. Calculate the system with DFT code and generate the wavefunctions (wavefunction.dat)

   1. Put LNBO=.T. into INCAR. Make sure NPAR is the default value and ISYM=0 is set.
   2. Run VASP as usual and the code will generate wavefunction.dat.

2. Projecting the wavefunctions onto atomic orbitals (basis.inp) to get the projection coefficients (NBO.out)

   1. Construct a basis.inp using basisexchange.

   NOTE: Remember to put **** at the beginning of the first species and make sure the ordering of species matches the ordering of VASP's POTCAR file.

   NOTE: A suitable basis set is very important and can have huge impact on later analysis. 2. Run projection.exe by:

   projection.exe basis.inp wavefunction.dat NBO.out
   

3. Calculate the NBOs with predefined parameters (SSAdNDP*.inp)

   1. Construct a SSAdNDP.inp (or SSAdNDP-UD.inp) file for general search (or user-directed search). A set of exemplary inputs can be found in manual folde.
   2. Run SSAdNDP to generate vis_*_bond.out by:

   ssadndp.exe SSAdNDP.inp
   

   NOTE: ulimit -s unlmited maybe needed when running ssadndp.exe.

4. (optional) Plot the NBOs:

   1. run visualization program by:

   visual.exe vis_ud_bonds.out
   

   2. use vesta to visualize, first open the lattice_vec.cube and unselect show section, then Edit -> Edit Data -> phase -> Import to import *_bond_*.cube. Select the first entry of *_bond_*.cube and change the three numbers under this layer to 0.5 0.5 0.5.

Please checkout SSAdNDP_manual.pdf.

References

The author request that anyone who downloads and utilizes the code cite:

[1] Solid state adaptive natural density partitioning: a tool for deciphering multi-center bonding in periodic systems Timur R. Galeev, Benjamin D. Dunnington, J. R. Schmidt, and Alexander I. Boldyrev Phys. Chem. Chem. Phys., 2013, 15, 5022-5029

[2] Developing paradigms of chemical bonding: adaptive natural density partitioning Dmitry Yu. Zubarev, and Alexander I. Boldyrev Phys. Chem. Chem. Phys., 2008, 10, 5207-5217

[3] Generalization of Natural Bond Orbital Analysis to Periodic Systems: Applications to Solids and Surfaces via Plane-Wave Density Functional Theory Benjamin D. Dunnington and J. R. Schmidt J. Chem. Theory Comput., 2012, 8, 1902-1911

[4] See NBO references and bibliography

License

This project is licensed under the GNU License - see the LICENSE.md for details.