octp-pp 0.1.3

Post-processing toolkit for OCTP LAMMPS molecular-dynamics output

octp-pp

Post-processing toolkit for OCTP (Order-n Transport Properties) output files from LAMMPS molecular dynamics simulations.

The computationally intensive work — file parsing, MSD fitting, and all physical-property models — is compiled to native code via a PyO3/maturin Rust extension. Interactive visualisations use Plotly.

Features

• Rust core — parsing, diffusivity fitting, Laliberte density/viscosity, Dewane and Gilliam conductivity models, and concentration conversions all run natively; the Brent–Dekker molarity→molality inversion is ~570× faster than an equivalent scipy.fsolve loop
• Automatic run averaging — pass a list of parallel-run folders; means and standard deviations are computed automatically
• Biased Random Walk (BRW) correction — built-in correction for proton-hopping contributions (OH⁻ / H₃O⁺) matched against experimental conductivity
• Configurable constants — ion charges, molecular weights, hop distance, etc. live in a JSONL file and can be overridden at runtime without touching code

Installation

pip install octp-pp

From source

git clone https://github.com/JelleLagerweij/octp-pp
cd octp-pp
pip install maturin
maturin develop            # debug build  (fast compile, slower runtime)
maturin develop --release  # release build (slow compile, fast runtime)

maturin build (and pip install .) always use the release profile. maturin develop defaults to debug — ideal during active development.

Quick start

import octp_pp as octp
import octp_pp.helpers as hf

# Five parallel NVT runs stored under data/run_1 … data/run_5
mixture = octp.PP_OCTP(
    "data",
    [f"run_{i}" for i in range(1, 6)],
    groups=["wat", "Na", "OH", "SCN"],
    dt=2,           # timestep in fs
    plotting=True,  # interactive Plotly figures
)

# Configure non-default file names (if needed)
mixture.filenames(Diff_Onsag="diffonsag.dat", Diff_self="diffself.dat")
mixture.changefit(Minc=7, Mmax=45, er_max=0.05)

# State properties
mixture.density()
mixture.molality("OH",  "wat", hf.MOLECULAR_WEIGHTS["WAT"])
mixture.molality("SCN", "wat", hf.MOLECULAR_WEIGHTS["WAT"])

# Transport properties
mixture.viscosity()
mixture.self_diffusivity(YH_correction=True)
mixture.onsager_coeff()

# Conductivity
octp.cond_NE(mixture,  ion_names=["Na", "OH", "SCN"], ion_charges=[1, -1, -1])
octp.cond_Ons(mixture, ion_names=["Na", "OH", "SCN"], ion_charges=[1, -1, -1])

# BRW correction (requires experimental Excel file)
octp.biassed_random_walk(mixture, "Experiments_total.xlsx")

mixture.store()   # writes postprocessed.csv next to the data folder

Physical-property helpers (octp_pp.helpers)

All functions are vectorised and delegate to the Rust core.

Function	Model	Output
statepoint_Laliberte(T, m, salt, fits)	Laliberte (2004)	density (kg/m³), molarity (mol/L)
viscosity_Laliberte(T, m, salt, fits)	Laliberte (2007)	dynamic viscosity (Pa·s)
dewane_conductivity(T, m, salt, ...)	Dewane and Hammer	conductivity (S/m)
KOH_conductivity_Gilliam_combined(T, m, salt, fits)	Gilliam	conductivity (S/m)
molarity_to_molality(c, T, salt, fits)	Brent–Dekker root finder	molality (mol/kg)
molality_to_mass_fraction(m, salt)	exact	mass fraction
mass_fraction_to_molality(w, salt)	exact	molality (mol/kg)
molality_to_mol_fraction(m, solvent)	exact	mole fraction
mol_fraction_to_molality(x, solvent)	exact	molality (mol/kg)
tau_calculator(sig_exp, sig_MD, T, L, N, δ)	Lagerweij	lifetime τ (s)
diffusion_adjustment(tau)	Lagerweij	D_hop (m²/s)

Fit parameters are stored in a user-provided JSON file (see test/fits_laliberte.json for the expected structure).

Global constants

Loaded from octp_pp/constants.jsonl at import time. Override at runtime without editing any file:

# Add a custom salt for this session
hf.load_constants(updates={"MOLECULAR_WEIGHTS": {"MYMAT": 123.45}})

# Inspect what is loaded
print(hf.MOLECULAR_WEIGHTS)
print(hf.DELTA_HOP)

API reference

PP_OCTP class

Method	Description
filenames(**kwargs)	Set LAMMPS output file names
changefit(margin, Minc, Mmax, er_max)	Tune MSD log-log fitting
check_succesfull(T_min)	Drop runs shorter than T_min ns
mandatory_properties()	Volume, box size, temperature, particle counts
pressure(plotting, mov_ave)	Pressure (Pa)
density()	Density (kg/m³) from NPT run
molarity(group)	Molarity (mol/L)
molality(group, solvent, MW_solvent)	Molality (mol/kg)
viscosity(plotting)	Shear + bulk viscosity (Pa·s)
thermal_conductivity(plotting)	Thermal conductivity (W/m/K)
self_diffusivity(YH_correction, ...)	Self-diffusion coefficients (m²/s)
onsager_coeff(box_size_check, ...)	Onsager cross-coefficients (m²/s)
coord_number(solvent, ...)	Coordination number from RDF
bond_angles(start, stop, ...)	Bond-angle distribution
store(location, name, for_excel)	Save results DataFrame to CSV / Excel

All optional methods call mandatory_properties() automatically if it has not yet been run.

Module-level functions

Function	Description
cond_NE(mixture, ion_names, ion_charges)	Nernst–Einstein conductivity (S/m)
cond_Ons(mixture, ion_names, ion_charges)	Onsager conductivity (S/m)
biassed_random_walk(mixture, exp_file)	BRW correction; writes back to mixture.results
read(datafile, export)	Read OCTP MSD file → DataFrame
local_maximum_finder(data, start, n)	First local maximum in g(r)

License

MIT