pyscf

Python module for quantum chemistry

version 0.6

2014-10-17

Pyscf is a python module for quantum chemistry program. The module aims to provide a simple, light-weight and efficient platform for quantum chemistry code developing and calculation. The program is developed in the principle of

• Easy to install, to use, to extend and to be embedded;
• Minimal requirements on libraries (No Boost, MPI) and computing resources (perhaps losing efficiency to reduce I/O);
• 90/10 Python/C, only computational hot spots were written in C;
• 90/10 functional/OOP, unless performance critical, functions are pure.

Installation

• Prerequisites

  • Cmake 2.8 or higher
  • Python 2.6 or higher
  • Numpy 1.6.2 or higher (1.6.1 has bug in einsum)
  • Scipy 0.10 or higher
  • HDF5 1.8.4 or higher
  • h5py 1.3.0 or higher

• Compile core module

  cd lib mkdir build; cd build cmake .. make

• To make python be able to find pyscf, edit environment variable PYTHONPATH, e.g. if pyscf is installed in /opt/pyscf

  export PYTHONPATH=/opt:$PYTHONPATH

• Use Intel MKL as BLAS library. cmake with options -DBLA_VENDOR=Intel10_64lp

  BLA_VENDOR=Intel10_64lp cmake ..

  If cmake is still not able to find MKL, just define BLAS_LIBRARIES in CMakeLists.txt

  set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_intel_lp64.so") set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_sequential.so") set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_core.so") set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_avx.so")

Adding new features

For developrs who has interests to add new features in this program, there are few rules to follow

• New features first being placed in pyscf/future.
• Code at least should work under python-2.7, gcc-4.8.
• Not enforced, it's preferred
  • Compatibile with 2.5 - 3.3 for Python code;
  • Following C89 standard for C code;
  • Using ctypes to bridge C/python functions, (to keep minimal dependence on third-party tools)
  • Avoid using other program language if possible, to keep package light-weight
• Loose-coupling principle
  • Reinventing-wheel is encouraged if it reduces the coupling to the rest of the package.

Known problems

Bug report

Qiming Sun [email protected]

Changes log

Version 0.1 (2014-05-03):

• Setup pyscf

Version 0.2 (2014-05-08):

• Integral transformation

Version 0.3 (2014-07-03):

• Change import layout

Version 0.4 (2014-08-17):

• Module "future" for upcoming functions
• One-line command to run QC calculation with pyscf
• Fix bug of AO to MO transformation in OpenMP environment

Version 0.5 (2014-10-01):

• Change basis format
• Remove Cython dependence
• Upgrade dft to use libxc-2.0.0
• Add DFT, FCI, CASSCF, HF-gradients (NR and R), HF-NMR (NR and R)

Version 0.6 (2014-10-17):

• Fix bug in dhf
• add future/lo for localized orbital

Version 0.7 (2014-11-12):

• Fix memory leaks
• Runtime keywords checking
• Add MP2 density matrix
• Add FCI based on uhf integrals
• Add CCSD in future module
• Move FCI from future module to regular dir
• Move MCSCF from future module to regular dir