Documentation - fmauger1/QMol-grid GitHub Wiki

Documentation

The QMol-grid package provides facilities for run-time documentation, including handling of bibliographic references that can be displayed at the end of the documentation output.

By default and unless otherwise specified, all parameters in the QMol-grid package are specified in atomic units.

Run-time documentation

Most classes in the QMol-grid package provide run-time documentation features providing information about their function as well as the specific values of their parameters (class properties). The specific prototype for accessing each class' run-time documentation can vary and we refer to their specific documentation for details. Most often, objects need to have been initialized before the run-time documentation can be queried.

Component list

Display the list of components in the QMol-grid package

QMol_doc.showComponents;

References

The documentation part of the QMol-grid package enables dynamic compilation of the list of cited references when running the code. These references are defined in the QMol_doc (for kernel-level components) and QMol_info (for implementation components) classes. The two combined, the current list of citable references are

  • [Anderson 1965] D.G. Anderson, "Iterative procedures for nonlinear integral equations," Journal of the ACM 12, 547 (1965).
  • [Baker 2015] T.E. Baker, E.M. Stoudenmire, L.O. Wagner, K. Burke, and S.R. White, "One-dimensional mimicking of electronic structure: The case for exponentials," Physical Review B 91, 235141 (2015).
  • [Blanes 2002] S. Blanes and P.C. Moan, "Practical symplectic partitioned Runge-Kutta and Runge-Kutta-Nystrom methods," Journal of Computational and Applied Mathematics 142, 313 (2002).
  • [Casa 2006] F. Casas and A. Iserles, "Explicit Magnus expansions for nonlinear equations," Journal of Physics A: Mathematical and General 39, 5445 (2006).
  • [Forest 1990] E. Forest and R.D. Ruth, "Fourth-order symplectic integration," Physica D: Nonlinear Phenomena 43, 105 (1990).
  • [Helbig 2011] N. Helbig, J.I. Fuks, M. Casula, M.J. Verstraete, M.A.L. Marques, I.V. Tokatly, and A. Rubio, "Density functional theory beyond the linear regime: Validating an adiabatic local density approximation," Physical Review A 83, 032503 (2011).
  • [Javanainen 1988] J. Javanainen, J.H. Eberly, and Q. Su, "Numerical simulations of multiphoton ionization and above-threshold electron spectra," Physical Review A 38, 3430 (1988).
  • [Johnson 1988] D. D. Johnson, "Modified Broyden''s method for accelerating convergence in self-consistent calculations," Physical Review B 38, 12807 (1988).
  • [Kohn 1965] W. Kohn and L.J. Sham, "Self-Consistent Equations Including Exchange and Correlation Effects," Physical Review 140, A1133 (1965).
  • [Legrand 2002] C. Legrand, E. Suraud, and P.-G. Reinhard, "Comparison of self-interaction-corrections for metal clusters," Journal of Physics B: Atomic, Molecular and Optical Physics 35, 1115 (2002).
  • [Mauger 2024] F. Mauger, C. Chandre, M.B. Gaarde, K. Lopata, and K.J. Schafer, "Hamiltonian formulation and symplectic split-operator schemes for time-dependent density-functional-theory equations of electron dynamics in molecules," Communications in Nonlinear Science and Numerical Simulation 129, 107685 (2024).
  • [Mauger 2024b] F. Mauger and C. Chandre, "QMol-grid: A MATLAB package for quantum-mechanical simulations in atomic and molecular systems," arXiv:2406.17938 (2024).
  • [REF] Missing reference.

References in the QMol_doc and QMol_info classes are handled in a similar fashion. Future versions of the QMol-grid package might move some of the reference from QMol_info to QMol_doc without warning.

Contributors

Code development

  • Francois Mauger

Algorithms and release

  • Cristel Chandre
  • Francois Mauger

Tutorials

  • William DeNooyer
  • Francois Mauger

For developers

The QMol-grid package does not provide automatic listing of its components. These must be specified in

  • QMol_doc (showComponents method) for kernel components
  • QMol_info (showComponents method) for implementation-specific components
  • QMol_testInfo (testList method) for test-suite components