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Coulombo

P. T. Różański & M. Zieliński: Efficient computation of Coulomb and exchange integrals for multi-million atom nanostructures, Computer Physics Communications 238 (2019), pp. 254–261, DOI: 10.1016/j.cpc.2018.12.011

What is it?

Coulombo is a ready-to-use implementation for calculating Coulomb matrix elements for a given set of input wavefunctions. This implementation is based on the approach introduced in [1], using fast Fourier transform to compute convolution. In this work we further significantly improved the method by eliminating the need to extend the computational domain with padding, thus reducing the memory consumption by a factor of 8. The optimal computational plan for each run is prepared by calculating a minimal vertex cover on a graph representing a subset of requested Coulomb matrix elements.

The implementation is fully parallelized in distributed-memory model, using MPI and parallel routines from FFTW [2]. Minimal vertex cover is computed by a greedy approximation algorithm, which we found to perform significantly better than the standard text-book heuristic.

[1] P. T. Różański & M. Zieliński,
“Linear scaling approach for atomistic calculation of excitonic properties of 10-million-atom nanostructures”, Phys. Rev. B 94 (2016) 045440

[2] M. Frigo & Steven G. Johnson,
“The Design and Implementation of FFTW3”, Proceedings of the IEEE 93 (2), 216–231 (2005), Invited paper, Special Issue on Program Generation, Optimization, and Platform Adaptation

Package directory structure

  • example — includes an example input/output specification with a shell script
  • src — includes all auxiliary C++ source files (the header files as well)
  • coulombo.cpp — main C++ source file (the one with main() function)
  • LICENCE — licence for the program distribution
  • Makefile — makefile script for program compilation and testing
  • README.md — description of the package (this file)
  • run-tests.cpp — additional source file consisting of all unit tests

How to use it?

Compilation

Run “make”. This will produce a single executable file called “coulombo”. To make it available system-wide, run “sudo make install”, which will copy it to /usr/local/bin/.

Tests

To run the unit tests, execute “make test”. This will compile the test executable and run it, resulting (hopefully) in displaying the “OK” message.

Requirements

To compile the software, one needs an C++ compiler with support for 2011 standard and a MPI wrapper (mpic++). OpenMP support is also enabled by default.

Coulombo has two external library dependencies:

  • Fast Fourier Transform implementation FFTW (version 3),
  • armadillo C++ linear algebra library.

Both of the above can be installed in a standard way (e.g. apt) in the most of the major Linux distributions.

Running Coulombo

Coulombo should be run with a set of command line parameters. Results of the computation (values of the Coulomb matrix elements) will be written to the standard output, whereas all diagnostic and error message will be written to the standard error stream.

Most important part of command line parameters are the paths to the wavefunction data in form of binary files in armadillo machine-dependent format (one file per wavefunction, unless --spin flag is given, see below). At least one input file path should be specified.

List of all possible parameters can be displayed by running coulombo with no additional arguments. They are, in alphabetical order:

  • --dielectric=VALUE specifies the relative dielectric constant for the calculation of Coulomb potential. If this option is not given, the dielectric constant of 1 (as for vacuum) is assumed.

Example: coulombo ... --dielectric=10.89
for high-frequency dielectric constant of GaAs

  • --integrals=LIST specifies the comma-separated list of integrals to be computed. If this option is not given, all possible integrals (M⁴ where M is the number of wavefunctions) will be computed.

Example: coulombo ... --integrals=1212 f1.bin f2.bin
computes only the single integral 1212
(defined as ∫ f₁*(r⃗) f₂*(r⃗') G(r⃗-r⃗') f₁(r⃗') f₂(r⃗) dr³ dr'³)

Example: coulombo ... --integrals=ijji f1.bin f2.bin
computes integrals 1111, 1221, 2112, 2222

Example: coulombo ... --integrals=1*1* f1.bin f2.bin
computes integrals 1111, 1112, 1211, 1212

  • --spin specifies that the calculations should include spin. Each wavefunction should be specified with two consecutive file paths, representing spin-up and spin-down parts of the wavefunction. Order of up/down parts is not relevant, as long as it is consistent across all wavefunctions.

Example: coulombo ... --spin f1-U.bin f1-D.bin f2-U.bin f2-D.bin
assumes that the calculation should be performed for two wavefunctions: first given by files f1-U.bin and f1-D.bin and the second given by files f2-U.bin and f2-D.bin.

  • --step=VALUE specifies the size of the grid step (in ångströms) of the provided wavefunction files. This option is mandatory.

Example: coulombo --step=0.8 ...
assumes that the wavefunction files have the grid step of 0.8 Å (0.08 nm)

  • --threads-per-node=N specifies the requested number of OpenMP threads per each MPI node. If this option is not given, one thread per node is assumed and no OpenMP parallelization is used.

Example: coulombo --threads-per-node=4 ...
runs four OpenMP threads per each MPI node

  • --tf-lattice=VALUE specifies the lattice constant for the Thomas-Fermi-Resta dielectric screening model. If the option is not given, only the simple screening model (defined by dielectric parameter) is used.

Example: coulombo --tf-lattice=5.65325 ...
uses the Thomas-Fermi-Resta model for the lattice constant of GaAs

Example

Subdirectory “example” contains a small example consisting of two wavefunctions. The wavefunctions represent the first electron state (LUMO) and the second hole state (a Kramers-degenerate counterpart to the HOMO state) of a InAs/InP quantum dot. The example is run as

coulombo --dielectric=12.4 --spin --step=10 \
         --integrals=1111,1122,1221,2222 \
         e1-D.arma e1-U.arma h2-D.arma h2-U.arma

by requesting four integrals:

  • 1111 equivalent to Jee electron-electron Coulomb integral,
  • 1122 equivalent to exchange integral ⟨e₁h₁e₂h₂⟩ due to Kramers degeneracy,
  • 1221 equivalent to Jeh electron-hole Coulomb integral,
  • 2222 equivalent to Jhh hole-hole Coulomb integral.

The results are as follows:

 1  1  1  1   0.017643339  0.000000000
 1  1  2  2  -0.000026347  0.000040578
 1  2  2  1   0.017413492  0.000000000
 2  2  2  2   0.017726404  0.000000000

which, by taking absolute values of the integrals, translate to

  • Jee = 17.64 meV
  • ⟨e₁h₁e₂h₂⟩ = 48.4 µeV
  • Jeh = 17.41 meV
  • Jhh = 17.72 meV

Licence

This software is provided under a Creative Commons Attribution 4.0 International Public License, which should be provided as the LICENCE file.

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Parallelized implementation for calculating Coulomb matrix elements

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