chemistrykit#

chemistrykit is a unified numerical toolkit for computational chemistry, spanning 14 domains – from reaction kinetics to crystallography – sharing common ODE integrators and chemical constants under one NumPy-based API. It’s built for chemistry students working through a textbook problem, curious learners exploring a topic on their own, and educators building a demonstration. All 14 domains from chemistrykit-spec.md (in the repository root) are implemented, listed below.

Every subpackage is grounded in the chemistry it implements, not just coded against it: public functions carry runnable, CI-checked examples, and each subpackage’s history page traces the breakthroughs behind it – from Wilhelmy’s 1850 first rate law to the Brunauer-Emmett-Teller isotherm, whose co-discoverer Paul Emmett went on to develop uranium-separation barrier materials for the Manhattan Project – each one linked to the code that reproduces it.

  • chemistrykit.analytical – analytical chemistry: redox and complexometric (EDTA) titration-curve simulation with equivalence-point detection, alongside chemistrykit.solutions’s acid-base titrations; chromatographic plate theory and the van Deemter equation; linear-regression calibration curves with IUPAC-convention limits of detection/quantitation; and propagation-of-uncertainty formulas plus Dixon’s Q-test for outlier rejection.

  • chemistrykit.crystal – crystallography and solid-state chemistry: the 7 crystal systems and general unit-cell volume; hard-sphere packing (packing fraction, coordination number) for SC/BCC/FCC/HCP lattices; ionic-crystal lattice energy via the Born-Lande and Kapustinskii equations, backed by a genuinely converging (Evjen-method) numerical Madelung constant; Bragg’s law and powder-XRD peak positions with structure factors and systematic absences; and Schottky/Frenkel point-defect equilibrium.

  • chemistrykit.electrochem – electrochemistry: the Nernst equation for standard and concentration cells with Debye-Huckel activity corrections; a curated standard-reduction-potential table with redox-couple balancing; Butler-Volmer electrode kinetics and Tafel-plot linearization; galvanic vs. electrolytic cells and Faraday’s laws of electrolysis; and a simplified constant-current battery discharge model with Peukert’s-law rate dependence.

  • chemistrykit.kinetics – reaction kinetics: integrated rate laws, the Arrhenius equation, Michaelis-Menten enzyme kinetics, a general stoichiometric reaction-network engine, and the Brusselator oscillator.

  • chemistrykit.md – molecular dynamics and force fields: the Lennard-Jones fluid in reduced units (periodic boundary conditions, a Verlet neighbor list, pressure, g(r)), Morse/Buckingham/harmonic bonded potentials, and velocity-rescaling/Nose-Hoover thermostats.

  • chemistrykit.photochem – photochemistry: Jablonski-diagram excited-state kinetics built on chemistrykit.kinetics’s reaction-network engine; fluorescence/phosphorescence quantum yields and the photochemical quantum yield via Beer-Lambert; Stern-Volmer quenching with a static-vs-dynamic diagnostic; and photostationary- state kinetics for a two-state photoswitch.

  • chemistrykit.polymer – polymer chemistry: ideal random-walk chain statistics and the Flory exponent for real chains under theta/good/poor solvent conditions; molecular-weight-distribution statistics and the closed-form Flory-Schulz distribution; step-growth kinetics via the Carothers equation; and chain-growth/ free-radical polymerization kinetics built on chemistrykit.kinetics’s reaction-network engine.

  • chemistrykit.quantum – quantum chemistry: particle-in-a-box models (with the free-electron model of conjugated-dye color); the quantum harmonic oscillator vs. the exact Morse potential; the rigid rotor; hydrogen-like orbitals; Huckel molecular-orbital theory and its 4n+2 aromaticity rule; a minimal variational treatment of H2+; and Rayleigh-Schrodinger perturbation theory for the anharmonic oscillator.

  • chemistrykit.solutions – solution chemistry: pH/pOH and weak acid/base equilibria with Henderson-Hasselbalch buffers, titration curves, Ksp solubility equilibria, and Debye-Huckel activity coefficients.

  • chemistrykit.spectro – spectroscopy: the Beer-Lambert absorbance law and its stray-light deviation from linearity; rigid-rotor rotational spectra with isotope shifts; harmonic vs. Morse vibrational band positions plus a Wilson GF-matrix triatomic normal-mode calculation; Franck-Condon vibronic progressions; and a first-order NMR multiplet simulator.

  • chemistrykit.statmech – statistical mechanics of molecules: translational/rotational/vibrational partition functions and their thermodynamic functions, the Maxwell-Boltzmann speed distribution, and a canonical-ensemble lattice-gas adsorption model.

  • chemistrykit.structure – molecular structure and bonding: a lightweight Molecule container; VSEPR geometry prediction with real 3D coordinate generation; point-group determination from 3D coordinates and character tables; bond order from the Pauling length correlation and Huckel-theory MO coefficients; and formal-charge/ oxidation-state assignment from a Lewis structure.

  • chemistrykit.surface – surface chemistry and catalysis: Langmuir, Freundlich, and BET adsorption isotherms with their standard linearizations for fitting parameters from data; Langmuir-Hinshelwood single- and dual-site surface-reaction kinetics; and a turnover-frequency/rate-enhancement catalysis model built on chemistrykit.kinetics’s Arrhenius equation.

  • chemistrykit.thermo – chemical thermodynamics: equations of state (ideal gas, van der Waals, Redlich-Kwong), Clausius-Clapeyron phase boundaries, reaction equilibrium (Kp/Kc, van’t Hoff, and a Gibbs-energy-minimization equilibrium-composition solver), and Raoult’s/Henry’s law mixtures with colligative properties.

Conventionally imported as ck:

import chemistrykit as ck

network = ck.kinetics.StoichiometricNetwork.consecutive(k1=1.0, k2=0.3)
result = network.integrate((0.0, 10.0), dt=1e-3, method="rk4")

acid = ck.solutions.WeakAcid(Ca=0.1, Ka=1.8e-5)
print(acid.pH())

fluid = ck.md.LJFluid.from_lattice(n_per_side=6, density=0.7, temperature=1.0)
result = fluid.run(dt=0.002, n_steps=2000)