mshqc 1.0.3__tar.gz

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  1. mshqc-1.0.3/LICENSE +190 -0
  2. mshqc-1.0.3/PKG-INFO +244 -0
  3. mshqc-1.0.3/README.md +218 -0
  4. mshqc-1.0.3/pyproject.toml +52 -0
  5. mshqc-1.0.3/python/mshqc/__init__.py +81 -0
  6. mshqc-1.0.3/python/mshqc/_mshqc.pyi +491 -0
  7. mshqc-1.0.3/python/mshqc/calculators.py +249 -0
  8. mshqc-1.0.3/python/mshqc/session.py +179 -0
  9. mshqc-1.0.3/python/mshqc/utils.py +167 -0
  10. mshqc-1.0.3/python/mshqc.egg-info/PKG-INFO +244 -0
  11. mshqc-1.0.3/python/mshqc.egg-info/SOURCES.txt +17 -0
  12. mshqc-1.0.3/python/mshqc.egg-info/dependency_links.txt +1 -0
  13. mshqc-1.0.3/python/mshqc.egg-info/not-zip-safe +1 -0
  14. mshqc-1.0.3/python/mshqc.egg-info/requires.txt +8 -0
  15. mshqc-1.0.3/python/mshqc.egg-info/top_level.txt +1 -0
  16. mshqc-1.0.3/setup.cfg +4 -0
  17. mshqc-1.0.3/setup.py +132 -0
  18. mshqc-1.0.3/tests/test_mshqc.py +131 -0
  19. mshqc-1.0.3/tests/test_mshqc2.py +93 -0
mshqc-1.0.3/LICENSE ADDED
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mshqc-1.0.3/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: mshqc
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+ Version: 1.0.3
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+ Summary: mshqc: A C++20 Quantum Chemistry Engine for Orbital-Optimized Correlation Methods
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+ Author: Muhamad Syahrul Hidayat
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+ License-Expression: Apache-2.0
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+ Project-URL: Homepage, https://github.com/syahrulhidayat/mshqc
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+ Project-URL: Bug Tracker, https://github.com/syahrulhidayat/mshqc/issues
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+ Classifier: Development Status :: 4 - Beta
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Operating System :: POSIX :: Linux
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: C++
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+ Classifier: Topic :: Scientific/Engineering :: Chemistry
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ Requires-Dist: numpy>=1.22.0
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+ Requires-Dist: scipy>=1.8.0
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+ Requires-Dist: mkl
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+ Provides-Extra: dev
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+ Requires-Dist: pytest>=7.0; extra == "dev"
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+ Requires-Dist: sphinx>=4.0; extra == "dev"
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+ Requires-Dist: matplotlib>=3.5; extra == "dev"
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+ Dynamic: license-file
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+
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+ # mshqc
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+
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+ **A C++20 quantum chemistry engine for orbital-optimized Møller–Plesset perturbation theory**
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+
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+ [![License: Apache-2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
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+ [![C++20](https://img.shields.io/badge/C++-20-blue.svg)](https://en.cppreference.com/w/cpp/20)
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+ [![Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg)](https://www.python.org/downloads/)
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+
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+ ---
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+
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+ ## Overview
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+
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+ `mshqc` is a high-performance quantum chemistry package that implements a focused set of wave-function-based electronic structure methods — Hartree–Fock (`RHF`, `UHF`, `ROHF`), canonical Møller–Plesset perturbation theory (`RMP2`, `UMP2`, `RMP3`, `UMP3`), and orbital-optimized Møller–Plesset perturbation theory (`OMP2`, `OMP3`) — in a compact C++20 core with a `nanobind` Python interface.
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+
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+ All implemented solvers share a unified integral engine supporting exact four-center Electron Repulsion Integrals (`"exact"`), pivot-based Cholesky decomposition (`"cholesky"`), and auxiliary-basis Density Fitting / Resolution of the Identity (`"df"`), coupled with [TBLIS](https://github.com/devinamatthews/tblis) tensor contractions and a matrix-free Steihaug–Toint trust-region Second-Order SCF (`TrustRegionSOSCF`) orbital optimizer.
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+
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+ ---
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+
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+ ## Statement of Need
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+
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+ Mature quantum chemistry ecosystems such as Psi4 and PySCF provide broad method coverage, but their size and deep abstraction layers create a steep barrier to entry for researchers and students prototyping new orbital-optimization algorithms, three-index tensor factorizations, or custom contraction schedules. Conversely, lightweight educational codes typically implement only canonical RHF and RMP2 in pure Python, lacking open-shell references, third-order correlation (`MP3`/`OMP3`), point-group symmetry reduction, or rank-reduced three-index integrals.
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+
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+ `mshqc` bridges this gap by exposing a compact, inspectable C++20 codebase under a clean two-tier Python API:
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+ 1. **High-Level Pipeline API (`mshqc.run`, `MSHQCSession`, `quick_calculation`):** Run complete multi-method workflows (`SCF -> MP2 -> OMP2 -> OMP3`) in a single call with automatic point-group alignment (`PointGroup`), `PetiteList` symmetry reduction, and matched `-RI` auxiliary basis resolution.
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+ 2. **Low-Level C++20 Kernel API (`Molecule`, `BasisSet`, `IntegralEngine`, `RHF`/`UHF`/`ROHF`, `RMP2`/`UMP2`/`OMP2`, `RMP3`/`UMP3`/`OMP3`):** Instantiate C++20 solvers directly to inspect or modify intermediate matrices, orbital energies, and Cholesky/DF vectors with zero-copy `Eigen` <-> `NumPy` interoperability.
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+
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+ ---
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+
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+ ## Features
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+
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+ ### Core Infrastructure & Symmetry
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+ - Molecular geometry initialization in Bohr or Angstrom — `Molecule`, `Atom`, `build_molecule` [1]
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+ - Bundled library of 538 Gaussian basis sets (`.gbs`), including Dunning `cc-pVXZ`, `aug-cc-pVXZ`, Karlsruhe `def2`, and matched `-RI` / `-JKFIT` auxiliary basis sets — `BasisSet` [2, 7]
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+ - Automated point-group detection, canonical axis alignment, and symmetry-unique shell-pair generation — `PointGroup`, `PetiteList`, `BasisSymmetrizer` [3]
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+
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+ ### Unified Integral Engine
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+ - Analytical one- and two-electron integrals via `libcint` — `IntegralEngine` [4]
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+ - Unified `eri_method` selection across all SCF and correlated solvers:
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+ - `"exact"`: Four-center ERIs with Schwarz inequality prescreening — `Screening` [8]
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+ - `"cholesky"`: Pivot-based three-index Cholesky decomposition — `CholeskyERI` [5, 6]
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+ - `"df"`: Auxiliary-basis three-index Density Fitting (RI) with optional HDF5 out-of-core storage [7, 21]
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+
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+ ### Self-Consistent Field (SCF)
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+ - Restricted (`RHF`), Unrestricted (`UHF`), and Restricted Open-Shell (`ROHF`) Hartree–Fock [9, 10, 11]
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+ - Superposition of Atomic Densities (`SAD`) initial guess and Pulay `DIIS` extrapolation [12, 13]
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+
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+ ### Møller–Plesset Perturbation Theory & Orbital Optimization
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+ - Canonical second- and third-order perturbation theory: `RMP2`, `UMP2`, `RMP3`, `UMP3` [14, 15, 17]
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+ - Orbital-optimized second- and third-order perturbation theory: `OMP2`, `OMP3` driven by matrix-free Steihaug–Toint trust-region `SOSCF` (`TrustRegionSOSCF`) and Z-vector response densities [16, 18, 19]
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+
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+ ---
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+
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+ ## Prerequisites & Dependencies
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+
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+ | Category | Packages | Scope | Reference |
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+ |---|---|---|---|
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+ | Linear algebra & tensors | `eigen`, `tblis`, `mkl`, `mkl-include`, `liblapacke` | Build + runtime | [20, 22] |
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+ | Integrals & I/O | `libcint`, `hdf5`, `jemalloc` | Build + runtime | [4, 21] |
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+ | Parallelism | `llvm-openmp` / `libgomp` | Build + runtime | [23] |
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+ | Python bindings & runtime | `nanobind`, `numpy`, `scipy` | Build + runtime | [24, 25] |
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+ | Testing | `pytest` | Dev / test | — |
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+
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+ ---
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+
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+ ## Installation
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+
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+ A `conda-forge` environment is recommended to ensure ABI-compatible builds of MKL, HDF5, OpenMP, `libcint`, and `tblis`.
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+
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+ ```bash
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+ # 1. Create and activate the Conda environment
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+ conda env create -f environment.yml
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+ conda activate mshqc_314
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+
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+ # 2. Build and install mshqc in editable mode
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+ pip install -v -e . --no-build-isolation
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+ ```
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+
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+ ### Build Options
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+
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+ By default, `mshqc` compiles with `-O3 -march=native` on local machines. When building portable binaries for heterogeneous clusters, override the C++ flags via `CMAKE_ARGS`:
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+
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+ ```bash
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+ CMAKE_ARGS="-DCMAKE_CXX_FLAGS='-O3 -mavx2 -mfma -DNDEBUG'" pip install -v -e . --no-build-isolation
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+ ```
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+
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+ ---
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+
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+ ## Quickstart
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+
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+ ### 1. High-Level One-Liner API (`mshqc.run`)
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+
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+ `mshqc.run()` automatically detects molecular point-group symmetry, builds the `PetiteList`, resolves the auxiliary basis (`cc-pVTZ-RI` for `eri_method="df"`), and executes the requested method hierarchy in compiled C++20:
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+
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+ ```python
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+ import mshqc
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+
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+ h2o_xyz = """
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+ O 0.0000000000 0.0000000000 0.1173000000
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+ H 0.0000000000 0.7572000000 -0.4692000000
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+ H 0.0000000000 -0.7572000000 -0.4692000000
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+ """
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+
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+ results = mshqc.run(
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+ h2o_xyz,
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+ method=["RHF", "RMP2", "OMP2", "OMP3"],
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+ basis="cc-pVTZ",
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+ eri_method="df",
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+ units="angstrom",
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+ threshold=1e-9,
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+ )
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+
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+ for method_name, info in results.items():
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+ print(f"{method_name:<5} : {info['energy']:.10f} Ha ({info['time']:.3f} s)")
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+ ```
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+
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+ ### 2. Low-Level C++20 Kernel API
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+
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+ For method development and direct inspection of intermediate quantities, instantiate the C++20 classes directly:
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+
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+ ```python
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+ import mshqc
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+
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+ # 1. Initialize molecule (supports atomic symbols/numbers and "angstrom" or "bohr" units)
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+ mol = mshqc.Molecule(charge=0, multiplicity=1)
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+ mol.add_atom("O", 0.0000, 0.0000, 0.1173, units="angstrom")
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+ mol.add_atom("H", 0.0000, 0.7572, -0.4692, units="angstrom")
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+ mol.add_atom("H", 0.0000, -0.7572, -0.4692, units="angstrom")
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+
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+ # 2. Load basis set and analytical integral engine
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+ basis = mshqc.BasisSet("cc-pVTZ", mol)
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+ integrals = mshqc.IntegralEngine(mol, basis)
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+
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+ # 3. Run RHF with Cholesky-decomposed ERIs (threshold = 1e-9 Ha)
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+ scf_conf = mshqc.SCFConfig(eri_method="cholesky", threshold=1e-9)
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+ scf_res = mshqc.RHF(mol, basis, integrals, scf_conf).compute()
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+ print(f"RHF Total Energy : {scf_res.energy_total:.10f} Ha")
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+
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+ # 4. Run RMP2, OMP2, and OMP3 on the converged SCF reference
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+ mp2_conf = mshqc.MP2Config(eri_method="cholesky", threshold=1e-9, gradient_threshold=1e-5)
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+
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+ rmp2_res = mshqc.RMP2(mol, basis, integrals, scf_res, mp2_conf).compute()
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+ omp2_res = mshqc.OMP2(mol, basis, integrals, scf_res, mp2_conf).compute()
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+ omp3_res = mshqc.OMP3(mol, basis, integrals, scf_res, mp2_conf).compute()
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+
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+ print(f"RMP2 Total Energy : {rmp2_res.energy_total:.10f} Ha (Corr: {rmp2_res.energy_mp2_corr:.10f} Ha)")
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+ print(f"OMP2 Total Energy : {omp2_res.energy_total:.10f} Ha")
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+ print(f"OMP3 Total Energy : {omp3_res.energy_total:.10f} Ha")
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+ ```
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+
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+ See [`docs/QUICKSTART.md`](docs/QUICKSTART.md) for open-shell (`UHF`/`ROHF`/`UMP2`/`UMP3`), symmetry-adapted, and session-managed examples, and [`docs/TROUBLESHOOTING.md`](docs/TROUBLESHOOTING.md) for build and runtime diagnostics.
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+
178
+ ---
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+
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+ ## Testing
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+
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+ Run the automated validation test suite via `pytest`:
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+
184
+ ```bash
185
+ pytest tests/ -v
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+ ```
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+
188
+ ---
189
+
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+ ## Contributing
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+
192
+ Bug reports and pull requests are welcome via the [GitHub issue tracker](https://github.com/syahrulhidayat/mshqc/issues). Please include your OS, compiler version, and `conda list` output when reporting build or runtime issues.
193
+
194
+ ---
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+
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+ ## Citing mshqc
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+
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+ If you use `mshqc` in published work, please cite:
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+
200
+ ```bibtex
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+ @software{mshqc2026,
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+ author = {Hidayat, Muhamad Syahrul},
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+ title = {mshqc: A C++20 Quantum Chemistry Engine for Orbital-Optimized M{\o}ller--Plesset Perturbation Theory},
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+ year = {2026},
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+ url = {https://github.com/syahrulhidayat/mshqc},
206
+ version = {1.0.3}
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+ }
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+ ```
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+
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+ ---
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+
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+ ## References
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+
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+ [1] Helgaker, T., Jørgensen, P., & Olsen, J. (2000). *Molecular Electronic-Structure Theory*. Wiley. https://doi.org/10.1002/9781119019572
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+ [2] Dunning, T. H., Jr. (1989). Gaussian basis sets for use in correlated molecular calculations. I. *J. Chem. Phys.*, 90(2), 1007–1023. https://doi.org/10.1063/1.456153
216
+ [3] Atkins, P. W., Child, M. S., & Phillips, C. S. G. (1970). *Tables for Group Theory*. Oxford University Press.
217
+ [4] Sun, Q. (2015). Libcint: An efficient general integral library for Gaussian basis functions. *J. Comput. Chem.*, 36(22), 1664–1671. https://doi.org/10.1002/jcc.23981
218
+ [5] Beebe, N. H. F., & Linderberg, J. (1977). Simplifications in the generation and transformation of two-electron integrals in molecular calculations. *Int. J. Quantum Chem.*, 12(4), 683–705. https://doi.org/10.1002/qua.560120408
219
+ [6] Koch, H., Sánchez de Merás, A., & Pedersen, T. B. (2003). Reduced scaling in electronic structure calculations using Cholesky decompositions. *J. Chem. Phys.*, 118(21), 9481–9484. https://doi.org/10.1063/1.1578621
220
+ [7] Weigend, F. (2002). A fully direct RI-HF algorithm: Implementation, optimised auxiliary basis sets, demonstration of accuracy and efficiency. *Phys. Chem. Chem. Phys.*, 4(18), 4285–4291. https://doi.org/10.1039/B204199P
221
+ [8] Häser, M., & Ahlrichs, R. (1989). Improvements on the direct SCF method. *J. Comput. Chem.*, 10(1), 104–111. https://doi.org/10.1002/jcc.540100111
222
+ [9] Roothaan, C. C. J. (1951). New developments in molecular orbital theory. *Rev. Mod. Phys.*, 23(2), 69–89. https://doi.org/10.1103/RevModPhys.23.69
223
+ [10] Pople, J. A., & Nesbet, R. K. (1954). Self-consistent orbitals for radicals. *J. Chem. Phys.*, 22(3), 571–572. https://doi.org/10.1063/1.1740120
224
+ [11] Roothaan, C. C. J. (1960). Self-Consistent Field Theory for Open Shells of Electronic Systems. *Rev. Mod. Phys.*, 32(2), 179–185. https://doi.org/10.1103/RevModPhys.32.179
225
+ [12] Pulay, P. (1980). Convergence acceleration of iterative sequences. The case of SCF iteration. *Chem. Phys. Lett.*, 73(2), 393–398. https://doi.org/10.1016/0009-2614(80)80396-4
226
+ [13] Pulay, P. (1982). Improved SCF convergence acceleration. *J. Comput. Chem.*, 3(4), 556–560. https://doi.org/10.1002/jcc.540030413
227
+ [14] Møller, C., & Plesset, M. S. (1934). Note on an Approximation Treatment for Many-Electron Systems. *Phys. Rev.*, 46(7), 618–622. https://doi.org/10.1103/PhysRev.46.618
228
+ [15] Head-Gordon, M., Pople, J. A., & Frisch, M. J. (1988). MP2 energy evaluation by direct methods. *Chem. Phys. Lett.*, 153(6), 503–506. https://doi.org/10.1016/0009-2614(88)85250-3
229
+ [16] Neese, F., Schwabe, T., Kossmann, S., Schirmer, B., & Grimme, S. (2009). Assessment of Orbital-Optimized, Spin-Component Scaled Second-Order Many-Body Perturbation Theory for Thermochemistry and Kinetics. *J. Chem. Theory Comput.*, 5(11), 3060–3073. https://doi.org/10.1021/ct9003299
230
+ [17] Pople, J. A., Binkley, J. S., & Seeger, R. (1976). Theoretical models incorporating electron correlation. *Int. J. Quantum Chem.*, 10(S10), 1–19. https://doi.org/10.1002/qua.560100802
231
+ [18] Bozkaya, U., Turney, J. M., Yamaguchi, Y., Schaefer, H. F., & Sherrill, C. D. (2011). Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory. *J. Chem. Phys.*, 135(10), 104103. https://doi.org/10.1063/1.3631129
232
+ [19] Bozkaya, U. (2011). Orbital-optimized third-order Møller–Plesset perturbation theory and its spin-component and spin-opposite scaled variants: Application to symmetry-breaking problems. *J. Chem. Phys.*, 135(22), 224103. https://doi.org/10.1063/1.3665134
233
+ [20] Guennebaud, G., Jacob, B., et al. (2010). *Eigen v3*. https://eigen.tuxfamily.org
234
+ [21] The HDF Group. (1997–2026). *Hierarchical Data Format, version 5*. https://www.hdfgroup.org/HDF5/
235
+ [22] Matthews, D. A. (2017). High-Performance Tensor Contraction without Transposition. *SIAM J. Sci. Comput.*, 39(6), C476–C509. https://doi.org/10.1137/16M108968X
236
+ [23] Dagum, L., & Menon, R. (1998). OpenMP: an industry standard API for shared-memory programming. *IEEE Comput. Sci. Eng.*, 5(1), 46–55. https://doi.org/10.1109/99.660313
237
+ [24] Jakob, W. (2022). *nanobind: Tiny and efficient C++/Python bindings*. https://github.com/wjakob/nanobind
238
+ [25] Harris, C. R., Millman, K. J., van der Walt, S. J., et al. (2020). Array programming with NumPy. *Nature*, 585, 357–362. https://doi.org/10.1038/s41586-020-2649-2
239
+
240
+ ---
241
+
242
+ ## License
243
+
244
+ Apache License 2.0 — see [`LICENSE`](LICENSE) for details.
mshqc-1.0.3/README.md ADDED
@@ -0,0 +1,218 @@
1
+ # mshqc
2
+
3
+ **A C++20 quantum chemistry engine for orbital-optimized Møller–Plesset perturbation theory**
4
+
5
+ [![License: Apache-2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
6
+ [![C++20](https://img.shields.io/badge/C++-20-blue.svg)](https://en.cppreference.com/w/cpp/20)
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+ [![Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg)](https://www.python.org/downloads/)
8
+
9
+ ---
10
+
11
+ ## Overview
12
+
13
+ `mshqc` is a high-performance quantum chemistry package that implements a focused set of wave-function-based electronic structure methods — Hartree–Fock (`RHF`, `UHF`, `ROHF`), canonical Møller–Plesset perturbation theory (`RMP2`, `UMP2`, `RMP3`, `UMP3`), and orbital-optimized Møller–Plesset perturbation theory (`OMP2`, `OMP3`) — in a compact C++20 core with a `nanobind` Python interface.
14
+
15
+ All implemented solvers share a unified integral engine supporting exact four-center Electron Repulsion Integrals (`"exact"`), pivot-based Cholesky decomposition (`"cholesky"`), and auxiliary-basis Density Fitting / Resolution of the Identity (`"df"`), coupled with [TBLIS](https://github.com/devinamatthews/tblis) tensor contractions and a matrix-free Steihaug–Toint trust-region Second-Order SCF (`TrustRegionSOSCF`) orbital optimizer.
16
+
17
+ ---
18
+
19
+ ## Statement of Need
20
+
21
+ Mature quantum chemistry ecosystems such as Psi4 and PySCF provide broad method coverage, but their size and deep abstraction layers create a steep barrier to entry for researchers and students prototyping new orbital-optimization algorithms, three-index tensor factorizations, or custom contraction schedules. Conversely, lightweight educational codes typically implement only canonical RHF and RMP2 in pure Python, lacking open-shell references, third-order correlation (`MP3`/`OMP3`), point-group symmetry reduction, or rank-reduced three-index integrals.
22
+
23
+ `mshqc` bridges this gap by exposing a compact, inspectable C++20 codebase under a clean two-tier Python API:
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+ 1. **High-Level Pipeline API (`mshqc.run`, `MSHQCSession`, `quick_calculation`):** Run complete multi-method workflows (`SCF -> MP2 -> OMP2 -> OMP3`) in a single call with automatic point-group alignment (`PointGroup`), `PetiteList` symmetry reduction, and matched `-RI` auxiliary basis resolution.
25
+ 2. **Low-Level C++20 Kernel API (`Molecule`, `BasisSet`, `IntegralEngine`, `RHF`/`UHF`/`ROHF`, `RMP2`/`UMP2`/`OMP2`, `RMP3`/`UMP3`/`OMP3`):** Instantiate C++20 solvers directly to inspect or modify intermediate matrices, orbital energies, and Cholesky/DF vectors with zero-copy `Eigen` <-> `NumPy` interoperability.
26
+
27
+ ---
28
+
29
+ ## Features
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+
31
+ ### Core Infrastructure & Symmetry
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+ - Molecular geometry initialization in Bohr or Angstrom — `Molecule`, `Atom`, `build_molecule` [1]
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+ - Bundled library of 538 Gaussian basis sets (`.gbs`), including Dunning `cc-pVXZ`, `aug-cc-pVXZ`, Karlsruhe `def2`, and matched `-RI` / `-JKFIT` auxiliary basis sets — `BasisSet` [2, 7]
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+ - Automated point-group detection, canonical axis alignment, and symmetry-unique shell-pair generation — `PointGroup`, `PetiteList`, `BasisSymmetrizer` [3]
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+
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+ ### Unified Integral Engine
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+ - Analytical one- and two-electron integrals via `libcint` — `IntegralEngine` [4]
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+ - Unified `eri_method` selection across all SCF and correlated solvers:
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+ - `"exact"`: Four-center ERIs with Schwarz inequality prescreening — `Screening` [8]
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+ - `"cholesky"`: Pivot-based three-index Cholesky decomposition — `CholeskyERI` [5, 6]
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+ - `"df"`: Auxiliary-basis three-index Density Fitting (RI) with optional HDF5 out-of-core storage [7, 21]
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+
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+ ### Self-Consistent Field (SCF)
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+ - Restricted (`RHF`), Unrestricted (`UHF`), and Restricted Open-Shell (`ROHF`) Hartree–Fock [9, 10, 11]
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+ - Superposition of Atomic Densities (`SAD`) initial guess and Pulay `DIIS` extrapolation [12, 13]
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+
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+ ### Møller–Plesset Perturbation Theory & Orbital Optimization
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+ - Canonical second- and third-order perturbation theory: `RMP2`, `UMP2`, `RMP3`, `UMP3` [14, 15, 17]
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+ - Orbital-optimized second- and third-order perturbation theory: `OMP2`, `OMP3` driven by matrix-free Steihaug–Toint trust-region `SOSCF` (`TrustRegionSOSCF`) and Z-vector response densities [16, 18, 19]
50
+
51
+ ---
52
+
53
+ ## Prerequisites & Dependencies
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+
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+ | Category | Packages | Scope | Reference |
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+ |---|---|---|---|
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+ | Linear algebra & tensors | `eigen`, `tblis`, `mkl`, `mkl-include`, `liblapacke` | Build + runtime | [20, 22] |
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+ | Integrals & I/O | `libcint`, `hdf5`, `jemalloc` | Build + runtime | [4, 21] |
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+ | Parallelism | `llvm-openmp` / `libgomp` | Build + runtime | [23] |
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+ | Python bindings & runtime | `nanobind`, `numpy`, `scipy` | Build + runtime | [24, 25] |
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+ | Testing | `pytest` | Dev / test | — |
62
+
63
+ ---
64
+
65
+ ## Installation
66
+
67
+ A `conda-forge` environment is recommended to ensure ABI-compatible builds of MKL, HDF5, OpenMP, `libcint`, and `tblis`.
68
+
69
+ ```bash
70
+ # 1. Create and activate the Conda environment
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+ conda env create -f environment.yml
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+ conda activate mshqc_314
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+
74
+ # 2. Build and install mshqc in editable mode
75
+ pip install -v -e . --no-build-isolation
76
+ ```
77
+
78
+ ### Build Options
79
+
80
+ By default, `mshqc` compiles with `-O3 -march=native` on local machines. When building portable binaries for heterogeneous clusters, override the C++ flags via `CMAKE_ARGS`:
81
+
82
+ ```bash
83
+ CMAKE_ARGS="-DCMAKE_CXX_FLAGS='-O3 -mavx2 -mfma -DNDEBUG'" pip install -v -e . --no-build-isolation
84
+ ```
85
+
86
+ ---
87
+
88
+ ## Quickstart
89
+
90
+ ### 1. High-Level One-Liner API (`mshqc.run`)
91
+
92
+ `mshqc.run()` automatically detects molecular point-group symmetry, builds the `PetiteList`, resolves the auxiliary basis (`cc-pVTZ-RI` for `eri_method="df"`), and executes the requested method hierarchy in compiled C++20:
93
+
94
+ ```python
95
+ import mshqc
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+
97
+ h2o_xyz = """
98
+ O 0.0000000000 0.0000000000 0.1173000000
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+ H 0.0000000000 0.7572000000 -0.4692000000
100
+ H 0.0000000000 -0.7572000000 -0.4692000000
101
+ """
102
+
103
+ results = mshqc.run(
104
+ h2o_xyz,
105
+ method=["RHF", "RMP2", "OMP2", "OMP3"],
106
+ basis="cc-pVTZ",
107
+ eri_method="df",
108
+ units="angstrom",
109
+ threshold=1e-9,
110
+ )
111
+
112
+ for method_name, info in results.items():
113
+ print(f"{method_name:<5} : {info['energy']:.10f} Ha ({info['time']:.3f} s)")
114
+ ```
115
+
116
+ ### 2. Low-Level C++20 Kernel API
117
+
118
+ For method development and direct inspection of intermediate quantities, instantiate the C++20 classes directly:
119
+
120
+ ```python
121
+ import mshqc
122
+
123
+ # 1. Initialize molecule (supports atomic symbols/numbers and "angstrom" or "bohr" units)
124
+ mol = mshqc.Molecule(charge=0, multiplicity=1)
125
+ mol.add_atom("O", 0.0000, 0.0000, 0.1173, units="angstrom")
126
+ mol.add_atom("H", 0.0000, 0.7572, -0.4692, units="angstrom")
127
+ mol.add_atom("H", 0.0000, -0.7572, -0.4692, units="angstrom")
128
+
129
+ # 2. Load basis set and analytical integral engine
130
+ basis = mshqc.BasisSet("cc-pVTZ", mol)
131
+ integrals = mshqc.IntegralEngine(mol, basis)
132
+
133
+ # 3. Run RHF with Cholesky-decomposed ERIs (threshold = 1e-9 Ha)
134
+ scf_conf = mshqc.SCFConfig(eri_method="cholesky", threshold=1e-9)
135
+ scf_res = mshqc.RHF(mol, basis, integrals, scf_conf).compute()
136
+ print(f"RHF Total Energy : {scf_res.energy_total:.10f} Ha")
137
+
138
+ # 4. Run RMP2, OMP2, and OMP3 on the converged SCF reference
139
+ mp2_conf = mshqc.MP2Config(eri_method="cholesky", threshold=1e-9, gradient_threshold=1e-5)
140
+
141
+ rmp2_res = mshqc.RMP2(mol, basis, integrals, scf_res, mp2_conf).compute()
142
+ omp2_res = mshqc.OMP2(mol, basis, integrals, scf_res, mp2_conf).compute()
143
+ omp3_res = mshqc.OMP3(mol, basis, integrals, scf_res, mp2_conf).compute()
144
+
145
+ print(f"RMP2 Total Energy : {rmp2_res.energy_total:.10f} Ha (Corr: {rmp2_res.energy_mp2_corr:.10f} Ha)")
146
+ print(f"OMP2 Total Energy : {omp2_res.energy_total:.10f} Ha")
147
+ print(f"OMP3 Total Energy : {omp3_res.energy_total:.10f} Ha")
148
+ ```
149
+
150
+ See [`docs/QUICKSTART.md`](docs/QUICKSTART.md) for open-shell (`UHF`/`ROHF`/`UMP2`/`UMP3`), symmetry-adapted, and session-managed examples, and [`docs/TROUBLESHOOTING.md`](docs/TROUBLESHOOTING.md) for build and runtime diagnostics.
151
+
152
+ ---
153
+
154
+ ## Testing
155
+
156
+ Run the automated validation test suite via `pytest`:
157
+
158
+ ```bash
159
+ pytest tests/ -v
160
+ ```
161
+
162
+ ---
163
+
164
+ ## Contributing
165
+
166
+ Bug reports and pull requests are welcome via the [GitHub issue tracker](https://github.com/syahrulhidayat/mshqc/issues). Please include your OS, compiler version, and `conda list` output when reporting build or runtime issues.
167
+
168
+ ---
169
+
170
+ ## Citing mshqc
171
+
172
+ If you use `mshqc` in published work, please cite:
173
+
174
+ ```bibtex
175
+ @software{mshqc2026,
176
+ author = {Hidayat, Muhamad Syahrul},
177
+ title = {mshqc: A C++20 Quantum Chemistry Engine for Orbital-Optimized M{\o}ller--Plesset Perturbation Theory},
178
+ year = {2026},
179
+ url = {https://github.com/syahrulhidayat/mshqc},
180
+ version = {1.0.3}
181
+ }
182
+ ```
183
+
184
+ ---
185
+
186
+ ## References
187
+
188
+ [1] Helgaker, T., Jørgensen, P., & Olsen, J. (2000). *Molecular Electronic-Structure Theory*. Wiley. https://doi.org/10.1002/9781119019572
189
+ [2] Dunning, T. H., Jr. (1989). Gaussian basis sets for use in correlated molecular calculations. I. *J. Chem. Phys.*, 90(2), 1007–1023. https://doi.org/10.1063/1.456153
190
+ [3] Atkins, P. W., Child, M. S., & Phillips, C. S. G. (1970). *Tables for Group Theory*. Oxford University Press.
191
+ [4] Sun, Q. (2015). Libcint: An efficient general integral library for Gaussian basis functions. *J. Comput. Chem.*, 36(22), 1664–1671. https://doi.org/10.1002/jcc.23981
192
+ [5] Beebe, N. H. F., & Linderberg, J. (1977). Simplifications in the generation and transformation of two-electron integrals in molecular calculations. *Int. J. Quantum Chem.*, 12(4), 683–705. https://doi.org/10.1002/qua.560120408
193
+ [6] Koch, H., Sánchez de Merás, A., & Pedersen, T. B. (2003). Reduced scaling in electronic structure calculations using Cholesky decompositions. *J. Chem. Phys.*, 118(21), 9481–9484. https://doi.org/10.1063/1.1578621
194
+ [7] Weigend, F. (2002). A fully direct RI-HF algorithm: Implementation, optimised auxiliary basis sets, demonstration of accuracy and efficiency. *Phys. Chem. Chem. Phys.*, 4(18), 4285–4291. https://doi.org/10.1039/B204199P
195
+ [8] Häser, M., & Ahlrichs, R. (1989). Improvements on the direct SCF method. *J. Comput. Chem.*, 10(1), 104–111. https://doi.org/10.1002/jcc.540100111
196
+ [9] Roothaan, C. C. J. (1951). New developments in molecular orbital theory. *Rev. Mod. Phys.*, 23(2), 69–89. https://doi.org/10.1103/RevModPhys.23.69
197
+ [10] Pople, J. A., & Nesbet, R. K. (1954). Self-consistent orbitals for radicals. *J. Chem. Phys.*, 22(3), 571–572. https://doi.org/10.1063/1.1740120
198
+ [11] Roothaan, C. C. J. (1960). Self-Consistent Field Theory for Open Shells of Electronic Systems. *Rev. Mod. Phys.*, 32(2), 179–185. https://doi.org/10.1103/RevModPhys.32.179
199
+ [12] Pulay, P. (1980). Convergence acceleration of iterative sequences. The case of SCF iteration. *Chem. Phys. Lett.*, 73(2), 393–398. https://doi.org/10.1016/0009-2614(80)80396-4
200
+ [13] Pulay, P. (1982). Improved SCF convergence acceleration. *J. Comput. Chem.*, 3(4), 556–560. https://doi.org/10.1002/jcc.540030413
201
+ [14] Møller, C., & Plesset, M. S. (1934). Note on an Approximation Treatment for Many-Electron Systems. *Phys. Rev.*, 46(7), 618–622. https://doi.org/10.1103/PhysRev.46.618
202
+ [15] Head-Gordon, M., Pople, J. A., & Frisch, M. J. (1988). MP2 energy evaluation by direct methods. *Chem. Phys. Lett.*, 153(6), 503–506. https://doi.org/10.1016/0009-2614(88)85250-3
203
+ [16] Neese, F., Schwabe, T., Kossmann, S., Schirmer, B., & Grimme, S. (2009). Assessment of Orbital-Optimized, Spin-Component Scaled Second-Order Many-Body Perturbation Theory for Thermochemistry and Kinetics. *J. Chem. Theory Comput.*, 5(11), 3060–3073. https://doi.org/10.1021/ct9003299
204
+ [17] Pople, J. A., Binkley, J. S., & Seeger, R. (1976). Theoretical models incorporating electron correlation. *Int. J. Quantum Chem.*, 10(S10), 1–19. https://doi.org/10.1002/qua.560100802
205
+ [18] Bozkaya, U., Turney, J. M., Yamaguchi, Y., Schaefer, H. F., & Sherrill, C. D. (2011). Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory. *J. Chem. Phys.*, 135(10), 104103. https://doi.org/10.1063/1.3631129
206
+ [19] Bozkaya, U. (2011). Orbital-optimized third-order Møller–Plesset perturbation theory and its spin-component and spin-opposite scaled variants: Application to symmetry-breaking problems. *J. Chem. Phys.*, 135(22), 224103. https://doi.org/10.1063/1.3665134
207
+ [20] Guennebaud, G., Jacob, B., et al. (2010). *Eigen v3*. https://eigen.tuxfamily.org
208
+ [21] The HDF Group. (1997–2026). *Hierarchical Data Format, version 5*. https://www.hdfgroup.org/HDF5/
209
+ [22] Matthews, D. A. (2017). High-Performance Tensor Contraction without Transposition. *SIAM J. Sci. Comput.*, 39(6), C476–C509. https://doi.org/10.1137/16M108968X
210
+ [23] Dagum, L., & Menon, R. (1998). OpenMP: an industry standard API for shared-memory programming. *IEEE Comput. Sci. Eng.*, 5(1), 46–55. https://doi.org/10.1109/99.660313
211
+ [24] Jakob, W. (2022). *nanobind: Tiny and efficient C++/Python bindings*. https://github.com/wjakob/nanobind
212
+ [25] Harris, C. R., Millman, K. J., van der Walt, S. J., et al. (2020). Array programming with NumPy. *Nature*, 585, 357–362. https://doi.org/10.1038/s41586-020-2649-2
213
+
214
+ ---
215
+
216
+ ## License
217
+
218
+ Apache License 2.0 — see [`LICENSE`](LICENSE) for details.