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This repository contains all resources for the manuscript Electronic exchange and correlation in van der Waals systems: Balancing semilocal and nonlocal energy contributions.

This is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final editedand published work see DOI acs.jctc.7b01172.

Requirements

All Python code in the repository requires Python 3.6. The required python packages can be installed with pip install -r requirements.txt.

Further, to generate figures and the manuscript:

To calculate raw data:

  • FHI-aims for DFT calculations, commit b4905993 (2017-04-05).
  • Quantum Espresso for VV10 calculations, version 6.1.
  • The D3 code for D3 calculations, version 3.2.
  • The MBD code for MBD calculations, commit 6a3cde27 (2017-03-17).

Organization

  • /pub/: Contains the LaTeX files that generate the manuscript. The manuscript can be regenerated by running make.

  • /media/: Contains figures used in the manuscript, both generated from the calculated data as well as exported from GUI programs.

  • /src/: Contains python scripts and Jupyter notebooks used to analyze the data and generate figures. To regenerate all figures and numbers used in the manuscript, evaluate the notebooks /src/2017-05-05-figures.ipynb and /src/2017-07-01-figures-si.py.

  • /data/: This empty directory holds processed data. These can be generated either by running all /src/collect_*.py scripts, or downloaded from here.

  • /calc/: This folder contains all raw calculations organized in four subfolders. Each of them is managed with Caf, which is already included individually in each subfolder. With Caf, one can in principle regenerate all inputs files from scratch (the calculations in each subfolder are defined in cscript.py), and then use it to run all the calculations to obtain the output files. But this requires nontrivial amount of computational time and is not documented here. Instead, all generated input and output files are provided as tar archives which can be downloaded from here. The tar archives are unpacked with tar -xf <archive> in each subfolder. Once unpacked, the files can be verified by running ./caf status. The complete organized directory tree of all input and output files can be checked out with ./caf checkout.

    The FHI-aims and QE executables referred to as aims.master and qe.master should point to the respective patched versions (see /patches/).

    Pseudopotentials used in Quantum Espresso, which are not part of the input files, were downloaded from here and here.

    One figure for the manuscript is generated by running calc/2017-07-10-uracil-dimer-curve/cscript.py.

  • /patches/: Contains patches of FHI-aims and Quantum Espresso used for the calculations. These would need to be applied if one wanted to recalculate the output files. They are to be applied against the commits stated on the first line of the patches with patch -p1 <PATCHFILE.