pyquiver-kie 1.1.0

Calculate kinetic and equilibrium isotope effects from Hessian matrices using the Bigeleisen-Mayer equation.

PyQuiver

A user-friendly program for calculating isotope effects.

PyQuiver is an open-source Python program for calculating kinetic isotope effects (KIEs) and equilibrium isotope effects (EIEs) using harmonic frequencies and the Bigeleisen-Mayer equation. PyQuiver requires Cartesian Hessian matrices, which can be calculated using any electronic structure program.

Features

• automatically read frequencies from Gaussian (g09/g16) and ORCA output files
• excellent performance for larger systems, with optional multi-threading
• custom isotopic substitutions and arbitrary temperature
• tunnelling corrections: Wigner, Bell infinite parabola, and Skodje-Truhlar
• command line or a clean Python API with structured (pandas-ready) results

Installation

PyQuiver requires Python 3.9+ and numpy. pandas is optional (only for to_dataframe()).

Install from PyPI:

pip install pyquiver-kie            # core (numpy only)
pip install "pyquiver-kie[pandas]"  # adds DataFrame output

The distribution is named pyquiver-kie on PyPI, but you still import it as pyquiver.

Or install from a checkout:

git clone https://github.com/ekwan/PyQuiver.git
cd PyQuiver
pip install -e .

PyQuiver has been tested on PC, Mac, and Linux platforms.

Command line (deprecated)

The pyquiver command still works but is deprecated in favour of the Python API below:

pyquiver demo.config gs.out ts.out            # gaussian by default; prints a deprecation notice

Add -v/-vv for logging, -s for the style (gaussian/g16/g09, orca, pyquiver), -j for threads.

Python API

Build the configuration in Python with Config.from_dict (or load a .config file with Config(path)), then run it on a ground- and transition-state file:

from pyquiver import Config, KIE_Calculation

config = Config.from_dict(
    isotopologues={"C1": [(1, 1, "13C")], "H/D": [(7, 7, "2D"), (8, 8, "2D")]},
    temperature=393, scaling=0.9614, imag_threshold=50,
)
calc = KIE_Calculation(config, "gs.out", "ts.out", style="gaussian")

print(calc)                       # human-readable table
calc.to_dict()                    # {name: {uncorrected, wigner, infinite_parabola}}
calc.to_csv("kies.csv")           # CSV text / file
calc.to_dataframe()               # pandas DataFrame (needs the pandas extra)
calc.results["C1"].wigner         # named access to each result

System objects hold a parsed geometry and Hessian, so you can read each file once and reuse it, which is handy for a parameter scan:

from pyquiver import System

gs = System("gs.out", style="gaussian")   # parse once
ts = System("ts.out", style="gaussian")
for T in (298, 350, 393):
    cfg = Config.from_dict(isotopologues={"C1": [(1, 1, "13C")]},
                           temperature=T, scaling=0.9614, imag_threshold=50)
    print(T, KIE_Calculation(cfg, gs, ts).results["C1"].uncorrected)

KIE_Calculation(..., n_jobs=N) parallelizes the per-isotopologue work across N threads (the heavy eigvalsh step releases the GIL). The default is serial; it pays off for large systems and many isotopologues.

The uncorrected, Wigner, and Bell corrections are reported automatically. For the Skodje-Truhlar correction, supply the reactant/product/TS single-point energies (it needs the barrier height):

# energies in hartree by default (or unit="J")
calc.skodje_truhlar(reactant_energy=E_sm, product_energy=E_pr, ts_energy=E_ts)
# -> {isotopologue: corrected_KIE}

To run one configuration over many structures, use batch with a {label: (gs, ts)} dictionary and get back one table:

from pyquiver import batch

results = batch("demo.config", {
    "b3lyp": ("b3lyp_gs.out", "b3lyp_ts.out"),
    "m06":   ("m06_gs.out",   "m06_ts.out"),
})
results.to_dataframe()        # label, name, uncorrected, wigner, infinite_parabola
results["b3lyp"]              # the KIE_Calculation for that pair

You normally build that dictionary from the files on disk, e.g. {f.removesuffix("_gs.out"): (f, f.replace("_gs", "_ts")) for f in glob.glob("*_gs.out")}. Pass energies={label: (reactant, ts, product)} to add a Skodje-Truhlar column.

PyQuiver logs through the standard logging module (logger name pyquiver) and raises exceptions on bad input; it never prints on import or calls sys.exit, so it is safe to use inside scripts and notebooks.

Tutorial

To learn how to use PyQuiver, please look at the tutorial.

Further Reading

• Technical Details (compatibility with QUIVER, how to invoke PyQuiver, .config files, input files, the PyQuiver Standard format, miscellaneous notes)
• Batch processing (how to run PyQuiver on many related files)
• Snipping Utility (how to "snip" out only the relevant parts of a Gaussian output file for publication or archiving purposes)

Authors

PyQuiver was written by Thayer Anderson and Eugene Kwan. Please email [e-mail] with any questions. We will gladly try to help you.

We thank Gregor Giesen for writing the code to read ORCA output. We thank Gino Occhialini for the Skodje-Truhlar tunnelling correction. We thank Corin Wagen for miscellaneous optimization. We also thank Christoph Riplinger and Giovanni Bistoni for valuable discussions.

How to Cite

Anderson, T.L.; Kwan, E.E. PyQuiver, www.github.com/ekwan/PyQuiver (pip install pyquiver-kie)

License

This project is licensed under the Apache License, Version 2.0. See LICENSE.txt for full terms and conditions.

Copyright 2020 by Thayer L. Anderson and Eugene E. Kwan