• Working with DFTB+ Files

    Introduction

    DFTB+ is a program that implements a variety of density-functional tight binding methods. The DFTB wavefunction calculated by DFTB+ has an linear combination of atomic orbitals (LCAO) expression using Slater-type orbitals. For instructions on setting up the program as well as the different calculation levels and how to run a calculation, please refer to the package documentation.

    Reading and Writing Structures

    Critic2 understands molecular and crystal geometries read and written by DFTB+, in its .gen format. A gen file looks like this:

    16 F
 C O N H
1 1 0.000000000000       0.500000000000       0.326000000000
[...]
0.000000000000       0.000000000000       0.000000000000
5.565000000001       0.000000000000       0.000000000000
0.000000000000       5.565000000001       0.000000000000
0.000000000000       0.000000000000       4.684000000002

    where the system is treated as a molecule or a crystal depending on whether the final four lines (the lattice vectors) are present. A gen file can be used as input for DFTB+ and it can also be written during a geometry optimization using the OutputPrefix keyword in Driver. On the other hand, critic2 can also write arbitrary crystal structures in gen format:

    crystal library urea
write urea.gen

    as well as molecular structures:

    molecule library benzene
write benzene.gen

    This is useful for setting up new DFTB+ calculations.

    Reading DFTB+ Wavefunctions

    Three files are required to read a wavefunction calculated by DFTB+ files:

    • A detailed.xml file, which is written by activating the WriteDetailedXML keyword in the DFTB+ input.

    • The eigenvec.bin file, which is written by DFTB+ when the WriteEigenVectors keyword is used.

    • The .hsd file containing the STO coefficients corresponding to the parametrization used in the calculation. These are provided by the DFTB+ authors and can be obtained online.

    The kinetic energy density can be calculated from a DFTB+ wavefunction.

    Two different types of systems can be run in DFTB+: crystals under periodic boundary conditions, and molecules in the gas-phase. In the first case, if using k-points other than Gamma, the wavefunction is complex, and the evaluation of the density is relatively slow. Molecules use real wavefunctions and they tend to be less crowded than crystals, so using molecular DFTB fields should be considerably faster.

    Examples

    Two complete examples are given in the package below: a molecule (benzene) and a solid (graphite). To run them, execute dftb+ in the corresponding directories. Output files are already provided.

    A critic2 example input for reading the DFTB+ structure and wavefunction of a molecule is:

    # Read the benzene molecule from the gen file
molecule benzene.gen 2

# Load the DFTB+ wavefunction
# In DFTB+, only valence electrons are used. Hence, we need core-augmentation
# to account for the missing core density. Set ZPSP to the number
# of valence electrons associated with a given atom (4 for carbon,
# 5 for nitrogen, 6 for oxygen,...)
load detailed.xml eigenvec.bin ../3ob-3-1/wfc.3ob-3-1.hsd zpsp c 4

# Find the critical points
auto

# Write a vmd file with the critical points
cpreport benzene.vmd cell molcell graph

# Calculate the electron density on a plane
plane 0 -3 -3  0 3 -3  0 -3 3  101 101 contour log 41 relief 0 1

    For a crystal:

    # Read the graphite crystal from the gen file
crystal graphite.gen

# Load the DFTB+ wavefunction
# In DFTB+, only valence electrons are used. Hence, we need core-augmentation
# to account for the missing core density. Set ZPSP to the number
# of valence electrons associated with a given atom (4 for carbon,
# 5 for nitrogen, 6 for oxygen,...)
load detailed.xml eigenvec.bin ../3ob-3-1/wfc.3ob-3-1.hsd zpsp c 4

# Calculate the electron density on a plane
plane 0 0 1/4  1 0 1/4  0 1 1/4  101 101  contour log 41 file plane

    Example Files Package

    Files: example_07_01.tar.xz.

    Updated: