References

The entries below are the primary sources for the estimators PQAnalysis implements. Each analysis page cites the entries that define the quantity it reports, so a documented estimator can be checked against its original definition rather than against this implementation alone.

Molecular simulation and liquid-state theory

[Allen2017]

Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids, 2nd ed.; Oxford University Press: Oxford, 2017. ISBN 978-0-19-880319-5. doi:10.1093/oso/9780198803195.001.0001

[Frenkel2002]

Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed.; Academic Press: San Diego, 2002. ISBN 978-0-12-267351-1. doi:10.1016/B978-0-12-267351-1.X5000-7

[Hansen2013]

Hansen, J.-P.; McDonald, I. R. Theory of Simple Liquids: with Applications to Soft Matter, 4th ed.; Academic Press: Oxford, 2013. ISBN 978-0-12-387032-2. doi:10.1016/C2010-0-66723-X

Transport coefficients and time correlation functions

[Einstein1905]

Einstein, A. Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen. Annalen der Physik 1905, 322 (8), 549-560. doi:10.1002/andp.19053220806

[Green1954]

Green, M. S. Markoff Random Processes and the Statistical Mechanics of Time-Dependent Phenomena. II. Irreversible Processes in Fluids. The Journal of Chemical Physics 1954, 22 (3), 398-413. doi:10.1063/1.1740082

[Kubo1957]

Kubo, R. Statistical-Mechanical Theory of Irreversible Processes. I. General Theory and Simple Applications to Magnetic and Conduction Problems. Journal of the Physical Society of Japan 1957, 12 (6), 570-586. doi:10.1143/JPSJ.12.570

[Rahman1964]

Rahman, A. Correlations in the Motion of Atoms in Liquid Argon. Physical Review 1964, 136 (2A), A405-A411. doi:10.1103/PhysRev.136.A405

Spectra from time correlation functions

[Wiener1930]

Wiener, N. Generalized harmonic analysis. Acta Mathematica 1930, 55, 117-258. doi:10.1007/BF02546511

[Khintchine1934]

Khintchine, A. Korrelationstheorie der stationären stochastischen Prozesse. Mathematische Annalen 1934, 109 (1), 604-615. doi:10.1007/BF01449156

[Dickey1969]

Dickey, J. M.; Paskin, A. Computer Simulation of the Lattice Dynamics of Solids. Physical Review 1969, 188 (3), 1407-1418. doi:10.1103/PhysRev.188.1407

[Thomas2013]

Thomas, M.; Brehm, M.; Fligg, R.; Vöhringer, P.; Kirchner, B. Computing vibrational spectra from ab initio molecular dynamics. Physical Chemistry Chemical Physics 2013, 15 (18), 6608-6622. doi:10.1039/C3CP44302G

[Harris1978]

Harris, F. J. On the use of windows for harmonic analysis with the discrete Fourier transform. Proceedings of the IEEE 1978, 66 (1), 51-83. doi:10.1109/PROC.1978.10837

Normal modes and infrared intensities

[Wilson1955]

Wilson, E. B., Jr.; Decius, J. C.; Cross, P. C. Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra; McGraw-Hill: New York, 1955. Reprinted by Dover: New York, 1980. ISBN 978-0-486-63941-3.

[Person1974]

Person, W. B.; Newton, J. H. Dipole moment derivatives and infrared intensities. I. Polar tensors. The Journal of Chemical Physics 1974, 61 (3), 1040-1049. doi:10.1063/1.1681972

Software provenance

Several PQAnalysis kernels reproduce the arithmetic of older programs bit for bit so that historical results remain reproducible. That provenance is recorded here as software attribution, not as literature.

[thhTools]

The thh_tools collection of legacy analysis programs: the RDF C code, the Diffcalc mean-square-displacement code, the FreqCalc and Fluxfreqcalc correlation codes, the ftvac (ft.f) Fourier transformation code and thh_momentum/equipartition.jl. The collection is not publicly distributed and has no release version or DOI. PQAnalysis reproduces its operation order only on the compatibility paths described on the individual analysis pages, and pins that behavior with the parity fixtures described in Scientific Validation.

Citing PQAnalysis

PQAnalysis has no journal article, no CITATION.cff file and no minted DOI. Do not cite a DOI for it, because none exists.

Cite the software by repository and by the exact release you ran:

PQAnalysis (version <release>), MolarVerse.
https://github.com/MolarVerse/PQAnalysis

Report the version string from pqanalysis --version or from PQAnalysis.__version__. Reported analyses should also name the simulation engine that produced the input data, normally PQ, and the method-specific settings that change the reported numbers, such as bin width, correlation window, apodization function or Hessian unit.

If a DOI is minted for a future release, cite that DOI instead of this section.