cp2k-spm-tools 1.5.0

CP2K Scanning Probe Microscopy tools.

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

Installation

The package requires an MPI implementation to be available on your system for mpi4py. One option is mpich, which you can install with:

• On Linux: through your package manager (e.g., apt install mpich or yum install mpich)
• On macOS: through Homebrew (brew install mpich)
• Or via conda, but then it's recommended to install it together with mpi4py: conda install -c conda-forge mpi4py mpich

Then install the package with pip:

pip install cp2k-spm-tools

Or, for development:

git clone https://github.com/nanotech-empa/cp2k-spm-tools.git
cd cp2k-spm-tools
pip install -e .[dev]

Command Line Tools

The package provides several command-line tools, including:

• cp2k-stm-sts-wfn: STM/STS analysis from wavefunction files
• cp2k-cube-from-wfn: Create cube files from wavefunction files
• cp2k-bader-bond-order: Bond order analysis based on Bader basins

Use --help with each command to see its options.

Example Usage

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).

Python API Example

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, can change very slightly
    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)

Here's the resulting cube file, illustrating the constrained region of evaluation:

For maintainers:

In order to make a new release of the library and publish to PYPI, run

bumpver update --major/--minor/--patch

This will

• update version numbers, make a corresponding git commit and a git tag;
• push this commit and tag to Github, which triggers the Github Action that makes a new Github Release and publishes the package to PYPI.