CLAUDE.md

This file provides guidance for Claude Code when working with the pyquante2 codebase.

Project Overview

PyQuante2 is a Python quantum chemistry suite for developing and testing quantum chemistry methods. It includes implementations of Hartree-Fock (RHF, UHF), DFT, and MP2, with optional Cython extensions for performance-critical routines.

Status: Published on PyPI as

pyquante2

(current version: 0.2.0)

Project Structure

pyquante2/
├── src/pyquante2/       # Main source code
│   ├── basis/           # Gaussian basis sets (PGBF, CGBF)
│   ├── cints/           # Cython/C integral routines
│   ├── dft/             # Density functional theory
│   ├── geo/             # Molecular geometry (atoms, molecules)
│   ├── graphics/        # Visualization tools
│   ├── grid/            # Numerical grids for DFT
│   ├── hylleraas/       # Hylleraas variational methods
│   ├── ints/            # Integral evaluation (one/two-electron)
│   ├── pt/              # Perturbation theory (MP2)
│   ├── scf/             # SCF solvers and Hamiltonians
│   └── viewer/          # Molecular viewer
├── tests/               # Test suite
├── attic/               # Archived/deprecated code
├── docs/                # Documentation
├── CHANGELOG.md         # Release history
├── VERSION_MANAGEMENT.md # Version bump checklist
├── FUTURE_TASKS.md      # Planned improvements
├── CODE_REVIEW.md       # Code quality findings
└── TODO.md              # Original task list

Development Commands

# Install with dev dependencies
uv sync --extra dev

# Run tests (preferred)
make test

# Or directly with pytest
uv run pytest

# Run tests with doctests
uv run pytest --doctest-modules --ignore=attic

# Build package for PyPI
make clean          # Clean old builds
make build          # Build wheel + source distribution
uv run twine check dist/*  # Verify package

# Publish to PyPI (see VERSION_MANAGEMENT.md first!)
make install_test   # Upload to TestPyPI
make install        # Upload to PyPI

Testing

Tests are in
```
tests/
```
directory using pytest
Many modules include doctests in docstrings
Run
```
make test
```
to run all tests including doctests
3 DFT tests are skipped (conditional functionality)

Code Style

Python 3.11+ required
Uses numpy extensively for numerical operations
Classes use lowercase names (e.g.,
```
molecule
```
,
```
atom
```
,
```
cgbf
```
)
Doctests serve as both documentation and tests
No type annotations currently used

Key Concepts

PGBF: Primitive Gaussian Basis Function
CGBF: Contracted Gaussian Basis Function
HGP: Head-Gordon-Pople integral algorithm
RHF/UHF: Restricted/Unrestricted Hartree-Fock
DFT: Density Functional Theory (LDA, GGA functionals)

Dependencies

Core: numpy, ipykernel
Dev/Test: pytest, matplotlib, build, twine
Build: setuptools, Cython (for C extensions)

Notes

Cython extensions in
```
src/pyquante2/cints/
```
are optional but improve performance
The
```
attic/
```
directory contains archived code - ignore when searching
Uses
```
uv
```
for package management (uv.lock present)
Before version bumps: Review
```
VERSION_MANAGEMENT.md
```
checklist
For future tasks: See
```
FUTURE_TASKS.md
```
PyPI package: Available at https://pypi.org/project/pyquante2/

Project Structure

pyquante2/
├── src/pyquante2/       # Main source code
│   ├── basis/           # Gaussian basis sets (PGBF, CGBF)
│   ├── cints/           # Cython/C integral routines
│   ├── dft/             # Density functional theory
│   ├── geo/             # Molecular geometry (atoms, molecules)
│   ├── graphics/        # Visualization tools
│   ├── grid/            # Numerical grids for DFT
│   ├── hylleraas/       # Hylleraas variational methods
│   ├── ints/            # Integral evaluation (one/two-electron)
│   ├── pt/              # Perturbation theory (MP2)
│   ├── scf/             # SCF solvers and Hamiltonians
│   └── viewer/          # Molecular viewer
├── tests/               # Test suite
├── attic/               # Archived/deprecated code
├── docs/                # Documentation
├── CHANGELOG.md         # Release history
├── VERSION_MANAGEMENT.md # Version bump checklist
├── FUTURE_TASKS.md      # Planned improvements
├── CODE_REVIEW.md       # Code quality findings
└── TODO.md              # Original task list

Development Commands

# Install with dev dependencies
uv sync --extra dev

# Run tests (preferred)
make test

# Or directly with pytest
uv run pytest

# Run tests with doctests
uv run pytest --doctest-modules --ignore=attic

# Build package for PyPI
make clean          # Clean old builds
make build          # Build wheel + source distribution
uv run twine check dist/*  # Verify package

# Publish to PyPI (see VERSION_MANAGEMENT.md first!)
make install_test   # Upload to TestPyPI
make install        # Upload to PyPI

Notes

Cython extensions in

src/pyquante2/cints/

are optional but improve performance

The

attic/

directory contains archived code - ignore when searching

Uses

uv

for package management (uv.lock present)

Before version bumps: Review

VERSION_MANAGEMENT.md

checklist

For future tasks: See

FUTURE_TASKS.md

PyPI package: Available at https://pypi.org/project/pyquante2/

CLAUDE.md

CLAUDE.md

Project Overview

Project Structure

Development Commands

Testing

Code Style

Key Concepts

Dependencies

Notes

Related Skills

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CLAUDE.md

Project Overview

Project Structure

Development Commands

Testing

Code Style

Key Concepts

Dependencies

Notes