kbkit 1.0.4

KBKit: Kirkwood-Buff Analysis Toolkit

KBKit: Kirkwood-Buff Analysis Toolkit

KBKit is a Python package for automated Kirkwood-Buff (KB) analysis of molecular simulation data. It provides tools to parse simulation outputs, compute Kirkwood-Buff integrals, and extract thermodynamic properties for binary and multicomponent systems. KBKit supports flexible workflows, including:

• Parsing and processing of simulation data (e.g., RDFs, densities)
• Calculation of KB integrals and related thermodynamic quantities
• Integration of activity coefficient derivatives (numerical or polynomial)
• Automated pipelines for batch analysis
• Calculation of static structure factor and X-ray intensities in the limit of q → 0
• Visualization tools for KB integrals, thermodynamic properties, and static structure factors

KBKit is designed for researchers in computational chemistry, soft matter, and statistical mechanics who need robust, reproducible KB analysis from simulation data. The package is modular, extensible, and integrates easily with Jupyter notebooks and Python scripts.

Installation

Quick install via PyPI

pip install kbkit

Developer install (recommended for contributors or conda users)

Clone the GitHub repository and use the provided Makefile to set up your development environment:

git clone https://github.com/aperoutka/kbkit.git
cd kbkit
make setup-dev

This one-liner creates the kbkit-dev conda environment, installs kbkit in editable mode, and runs the test suite.

To install without running tests:

make dev-install

To build and install the package into a clean user environment:

make setup-user

For a full list of available commands:

make help

File Organization

For running kbkit.core.KBPipeline or its dependencies, the following file structure is required: a structured directory layout that separates mixed systems from pure components. This organization enables automated parsing, reproducible KB integrals, and scalable analysis across chemical systems.

• NOTE: KBKit currently only supports parsing for GROMACS files.

An example of file structure:

kbi_dir/
├── project/
│   └── system/
│       ├── rdf_dir/
│       │   ├── mol1_mol1.xvg
│       │   ├── mol1_mol2.xvg
│       │   └── mol1_mol2.xvg
│       ├── system_npt.edr
│       ├── system_npt.gro
│       └── system.top
└── pure_components/
    └── molecule1/
        ├── molecule1_npt.edr
        └── molecule1.top

Requirements:

• Each system to be analyzed must include:
  • rdf_dir/ containing .xvg RDF files for all pairwise interactions
  • either .top topology file or .gro structure file (.gro is recommended)
  • .edr energy file
• Each pure component must include:
  • either .top topology file or .gro structure file (.gro is recommended)
  • .edr energy file
  • all other files (optional)

Examples

Below are several examples on various ways to implement KBKit.

Calculating Kirkwood-Buff integrals on a single RDF

from kbkit.analysis import KBIntegrator

# create integrator object from single RDF file
integrator = KBIntegrator(rdf_file)

# calculate running-KBI
rkbi = integrator.rkbi()

# calculate KBI in thermodynamic limit
kbi = integrator.integrate()

# visualize KBI integration and extrapolation
integrator.plot()

Run an automated pipeline for batch analysis

from kbkit.core import KBPipeline

# Set up and run the pipeline
pipe = KBPipeline(
    base_path="/path/to/systems",                # directory with system data
    pure_path="/path/to/pure_components",        # directory with pure component data
    pure_systems=["acetone_300", "water_300"],   # list of pure systems
    ensemble="npt",                              # ensemble type: npt or nvt
    gamma_integration_type="numerical",          # integration method
    verbose=False                                # logging verbosity
)

# run kbkit pipeline
results = pipe.run()

# Access the results properties
# stored in dataclass (ThermoProperty); attributes: name, value, units
# example for excess energy
ge_obj = results.ge
ge_array = ge_obj.value
ge_units = ge_obj.units
print("GE summary: ", ge_array.shape, ge_units)

# Convert units from kJ/mol -> kcal/mol
# default units will be those from GROMACS
pipe.convert_units("ge", "kcal/mol")

Create plots for thermodynamic properties from pipeline

from kbkit.viz import Plotter

# Map molecule IDs (as present in .top files) to names for figures
molecule_map = {
    "ACETO": "Acetone",
    "TIP4P": "Water",
}
x_mol = "ACETO"  # molecule for x-axis labels

plotter = Plotter(pipeline=pipe, x_mol=x_mol, molecule_map=molecule_map)

# Plot Kirkwood-Buff integrals
plotter.plot("kbi")

# Plot log of activity coefficients
plotter.plot("lngammas")

# Generate all figures (saved to /path/to/systems/kb_analysis)
plotter.make_figures()

Parse GROMACS files

from kbkit.parsers import TopFileParser, EdrFileParser, GroFileParser

# determines molecules present in simulation and their counts
top_parser = TopFileParser(top_file.top)
print("molecule dict: ", top_parser.molecule_counts)
print("molecule names: ", top_parser.molecules)
print("total molecule number: ", top_parser.total_molecules)

# determines electron count for each molecule type
gro_parser = GroFileParser(gro_file.gro)
print("electron dict: ", gro_parser.electron_count)
print("box volume: ", gro_parser.compute_box_volume())

# computes energy properties by calling gmx energy
edr_parser = EdrFileParser(edr_file.edr)
print("List of available properties: ", edr_parser.available_properties())
print("Density array over simulation time: ", edr_parser.extract_timeseries("density"))
print("Average density with std deviation: ", edr_parser.average_property("density", return_std=True))

Calculate static structure factors and x-ray intensities as q → 0

from kbkit.calculators import StaticStructureCalculator

"""
Requires:
    - mol fraction matrix: shape(num compositions, num components)
    - molar_volume: shape(num components), units cm^3/mol
    - n_electrons: shape(num components)
"""
calculator = StaticStructureCalculator(mol_fr, molar_volume, n_electrons)

# update conditions
# if conditions are not updated all calculations will use previous values
calculator.update_conditions(T, Hessian, isothermal_compressibility)

# calculate x-ray intensity
calculator.i0()

Credits

This package was created with Cookiecutter and the jevandezande/pixi-cookiecutter project template.