pyscf

Python module for quantum chemistry

version 0.10

2015-2-4

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, 2.7, 3.2, 3.3, 3.4
  • Numpy 1.6.2 or higher (1.6.1 has bug in einsum)
  • Scipy 0.10 or higher
  • h5py 1.3.0 or higher (requires HDF5 1.8.4 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")
  

• Using DMRG as the FCI solver for CASSCF. There are two DMRG solver interfaces avaialbe in pyscf. Block (https://github.com/sanshar/Block) CheMPS2 (https://github.com/SebWouters/CheMPS2) After installing the DMRG solver, create a file future/dmrgscf/settings.py to store the path where the DMRG solver was installed.

• Using FCIQMC as the FCI solver for CASSCF. NECI (https://github.com/ghb24/NECI_STABLE) After installing the NECI, create a file future/fciqmc/settings.py to store the path where the NECI was installed.

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 Python 2.6, 2.7, 3.2, 3.3, 3.4;
  • 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, to keep package light-weight
• Loose-coupling principle
  • Reinventing-wheel is encouraged if it reduces the coupling to the rest of the package.

Documentation

There is an online documentation http://sunqm.net/pyscf. And you can also download the PDF version from http://sunqm.net/pyscf/PySCF-0.10.pdf

Known problems

• Error message "Library not loaded: libcint.2.5.0.dylib" On OS X libcint.dylib is installed in pyscf/lib/deps/lib by default. Add "/path/to/pyscf/lib/deps/lib" to DYLD_LIBRARY_PATH

• On debian-6, the system default BLAS library (libf77blas.so.3gf) might have bug in dsyrk function. It occasionally results in NaN in mcscf solver. To fix this, change to other BLAS vendors e.g. to MKL

    BLA_VENDOR=Intel10_64lp cmake ..
  

• AttributeError: ..../libri.so: undefined symbol: RInr_fill2c2e_sph It is caused by old version of libcint. Remove the directory "pyscf/lib/deps" and rebuild pyscf to fix this problem.

• tests fail

  mcscf/test/test_addons.py test_spin_square

• Program exits with

Exception AttributeError: "'NoneType' object has no attribute 'byref'" in
<bound method VHFOpt.__del__ of <pyscf.scf._vhf.VHFOpt object at 0x2b52390>> ignored

It was observed when pyscf is used with other inspectors like profiler, pdb etc.

Bug report

Qiming Sun [email protected]