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DOI

CP2K Scanning Probe Microscopy tools

Library and scripts to perform scanning probe microscopy simulations based on a CP2K calculation.

Features include:

  • Processing the various output files of CP2K, including the .wfn file
  • Scanning Tunnelling Microscopy and Spectroscopy (STM/STS) analysis
  • Fourier-Transformed STS analysis for finite cutouts of periodic systems
  • Orbital hybridization analysis for adsorbed systems
  • High-resolution STM (HRSTM) simulations

Requirements:

  • numerical and scientific python libraries numpy, scipy
  • Atomistic simulation environment ase
  • mpi4py provides MPI parallelization

Installation:

  • mpi4py requires an external MPI implementation (e.g. mpich) available. One can install it together with mpi4py with 
    conda install -c conda-forge mpi4py mpich
  • the rest of the dependencies can be installed with pip 
    git clone [email protected]:nanotech-empa/cp2k-spm-tools.git
cd cp2k-spm-tools
pip install .

When everything is set up correctly, the bash scripts in examples/ folder can be executed without any further input and illustrate the usage of the various scripts. For example example/benzene_stm/run_stm_sts_from_wfn.sh evaluates the STM/STS signatures of isolated benzene at each orbital energy (out/orb/) as well as in an arbitrary energy range (out/stm/). The corresponding CP2K calculation is included in the repository.

NB: In all cases, the underlying DFT calculation has to be performed with the diagonalization algorithm rather than orbital transformation (OT).

Evaluating molecular orbitals on an arbitrary grid

Most of the functionality of this library is built on top of the possibility to evaluate the Kohn-Sham orbitals encoded in the .wfn file on an arbitrarily defined grid. This is illustrated by the following script applied for a nanographene adsorbed on a Au(111) slab (total of 1252 atoms and 10512 electrons):

from cp2k_spm_tools.cp2k_grid_orbitals import Cp2kGridOrbitals

### Create the gridding object and load the cp2k data ###
cgo = Cp2kGridOrbitals()
cgo.read_cp2k_input("./cp2k.inp")
cgo.read_xyz("./geom.xyz")
cgo.read_basis_functions("./BASIS_MOLOPT")
cgo.load_restart_wfn_file("./PROJ-RESTART.wfn", n_occ=2, n_virt=2)

### Evaluate the orbitals in the specific region ###
cgo.calc_morbs_in_region(
    dr_guess = 0.15,                          # grid spacing
    x_eval_region = None,                     # take whole cell in x
    y_eval_region = [0.0, cgo.cell_ang[1]/2], # half cell in y
    z_eval_region = [19.0, 24.0],             # around the molecule in z
)

cgo.write_cube("./homo.cube", orbital_nr=0)

The evaluated HOMO orbital in the defined region: