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Tutorial for aims-chembond (v0.0.1)

About

aims-chembond is a post-processing tool to perform crystal orbital overlap population (COOP) analysis using FHI-aims.

The following projections are available:

  • atom-projected DOS (Partial DOS)
  • atom pair COOP
  • orbital pair COOP
  • atom-orbital pair COOP

Compiling FHI-aims

Add set(USE_COOP ON CACHE STRING "") to initial_cache.cmake, and compile following the same procedure as in the original FHI-aims. This should create the aims.chembond.0.0.1.x executable file of aims-chembond.

Using aims-chembond

Using this functionality requires a two-step process. First, perform electronic structure calculations with FHI-aims, then use the results as input for aims-chembond to perform the chemical bonding analysis.

Warning

When using aims-chembond for COOP calculations in periodic systems, care should be taken when interpreting COOP from primitive cell calculations. It is generally safer to perform calculations using a supercell. This is because when calculating COOP, the unit cell is expanded to a supercell, and the influence of equivalent atoms in adjacent unit cells is included in the results.

Running FHI-aims

In the control.in file, please add the following output specification:

output coop_set
This write command activates the generation of two output files:

  • eigenvec.out - Contains eigenvector information
  • coop_set.out - Contains the remaining information necessary for COOP analysis

These files will serve as inputs for the subsequent chemical bonding analysis step with aims-chembond.

Running aims-chembond

After performing the FHI-aims calculation, you will perform chemical bonding analysis using the aims.chembond.0.0.1.x. To use aims-chembond, you need three input files: eigenvec.out, coop_set.out, and control_chembond.in.

aims-chembond provides functionality to calculate both PDOS (Partial Density of States) and COOP (Crystal Orbital Overlap Population). To calculate PDOS, include the following content in your control_chembond.in file:

output pdos -20 20 401 0.3
atom 1
atom 2
Here, output pdos -20 20 401 0.3 defines the energy window parameters for the PDOS spectra: the lower bound, the upper bound, the number of points, and the Gaussian broadening factor. The atom tag specifies the atom index for which to calculate the PDOS.

Similarly, to calculate COOP, include or append the following content to the control_chembond.in file: 

output coop -20 20 401 0.3
atom_pair 1 2
orbital_pair 3 18
atom_orb_pair 1 3s 2 3p
In the example above, atom_pair 1 2 calculates the COOP between atom 1 and atom 2. orbital_pair 3 18 calculates the COOP between the 3rd orbital and the 18th orbital. atom_orb_pair 1 3s 2 3p calculates the COOP between the 3s orbital component of atom 1 and the 3p orbital component of atom 2.

aims-chembond is parallelized across k-points. You can execute the calculation using MPI with a command like: mpiexec -n 6 aims.chembond.0.0.1.x.

Information

PDOS and COOP analyses are highly dependent on the choice of basis functions. While the "light" basis set offers a good starting point, you should carefully validate your results to ensure their accuracy and reliable interpretation.

Citing

If you find aims-chembond helpful, please consider citing:

Izumi Takahara, Kiyou Shibata, and Teruyasu Mizoguchi
"Crystal orbital overlap population based on all-electron ab initio simulation with numeric atom-centered orbitals and its application to chemical-bonding analysis in Li-intercalated layered materials"
Modelling Simul. Mater. Sci. Eng. 32 055028 (2024).
https://doi.org/10.1088/1361-651X/ad4c82