Resources

• DFTB+ PLUMED interface : I. Mitchell, B. Aradi, and A.J. Page, J. Comput. Chem. 39(29), 2452-2458 (2018).
  • Methods: metadynamics, umbrella sampling and steered molecular dynamics
  • Example 1: intramolecular proton transfer in malonaldehyde
  • Example 2: bowl inversion in corannulene
  • Example 3: oxygen diffusion on graphene
• Replica exchange molecular dynamics (REMD) with DFTB+ (via i-PI)

Installation

module load gcc/11.2.0
module load openmpi/4.0.3
module load scalapack/2.2.0
module load cmake/3.24.3
export LD_LIBRARY_PATH=/home/tang/opt/plumed/plumed-2.9.0-MPI-gcc-11.2.0/lib:$LD_LIBRARY_PATH
export CMAKE_PREFIX_PATH=$LD_LIBRARY_PATH
FC=gfortran CC=gcc cmake -DCMAKE_INSTALL_PREFIX=/home/tang/opt/dftbplus/dftbplus-23.1-install -DWITH_SOCKETS=YES -DWITH_TBLITE=YES -DWITH_MPI=YES -DTOOLCHAIN=gnu -DSCALAPACK_LIBRARY=libscalapack.so -DBLAS_LIBRARY=libblas.so -DWITH_PLUMED=YES -DPLUMED_LIBRARY="libplumed.so;libplumedKernel.so" -B _build .
cmake --build _build -- -j12
cmake --install _build

Parameter

Most DFTB parameters are fitted on PBE data.

Gold

• Au-Au: auorg-1-1-cc
• Au-Au_chi: J. Phys. Chem. A 2016, 120, 42, 846-8483
  • Modified auorg-1-1-cc parameter, changing p orbital energy from -2.785941987392E-02 Ha to -1.000000000000E-05 Ha
  • The modification leads better descriptions on 2D–3D structural transitions of gold clusters than the original parameter set (also called Au-Au_alpha in this paper).

Pt clusters on TiO2

• Van-Quan Vuong et al, J. Chem. Theory Comput. 2023, 19, 18, 6471–6483: Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support

Input

The filename of DFTB+ input has to be dftb_in.hsd. After DFTB+ processes the input file, a parsed input file dftb_pin.hsd will be created. It explicitly defines all default settings and can be used for a repeated calculation with a newer version of code. In the manual, different letters represent different option types

• l: logical
• i: integer
• r: real
• s: string
• p: property list
• m: method type

Mandatory settings are

• Geometry
• Hamiltonian

Optional settings are

• Driver
• Options
• Analysis
• ExcitedState
• ElectronDynamics
• REKS
• InputVersion
• ParserOptions
• Parallel

Geometry

Genformat

1. The first line contains the number of atoms n and type of geometry
   • C: cluster (non-periodic)
   • S: 3D supercell in Cartesian coordinates
   • F: 3D supercell in fractions of the lattice vectors
   • H: 1D periodic helical cells
2. The second line contains chemical symbols

An example of geo_end.gen for Au12 cluster

12  C    
Au   
#Index Type     Coordinates
1      1     -1.058470083999518     -2.574803797709034      1.335212287719941
2      1      1.261061377273184     -2.353875865354785      0.138288550717673
3      1     -1.189631822037944     -1.677562213239463     -1.132537261086825
4      1      1.112790971561282     -0.774909543704287     -1.993495375179098
5      1      0.240018936282667      1.700242659041175      0.851484342922601
6      1     -2.116323537871406      2.503572137769062      0.128532492576260
7      1     -0.800940744858599      0.923599091604642     -1.466860818634363
8      1     -3.366320339156098     -2.080473409654889      0.272006361950864
9      1      2.264178582611124      0.187326763686970      0.199011042001595
10     1      3.399770679168582     -1.689730826991322     -1.188190202263868
11     1     -1.899692756503666      0.001406193265081      0.825523380173758
12     1      0.520163039456403     -0.623082382719713      1.998652107821417