Python module for quantum chemistry

Version 1.0

2015-10-8

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.

• 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 (0.12.0 or higher for python 3.3, 3.4)
  • 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_seq

    BLA_VENDOR=Intel10_64lp_seq 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.

• Using optimized integral library on X86 platform. Qcint (https://github.com/sunqm/qcint.git) is a branch of libcint library. It is heavily optimized against X86_64 platforms. To replace the default libcint library with qcint library, edit the URL of the integral library in lib/CMakeLists.txt file

    ExternalProject_Add(libcint
      GIT_REPOSITORY https://github.com/sunqm/qcint.git
      ...
  

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

• Code at least should work under python-2.7, gcc-4.8.
• Not enforced
  • 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

There is an online documentation http://www.pyscf.org. And you can also download the PDF version from http://www.pyscf.org/PySCF-1.0.pdf

• Error message "Library not loaded: libcint.2.5.1.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

• Fails at runtime with error message

  OSError: ... mkl/lib/intel64/libmkl_avx.so: undefined symbol: ownLastTriangle_64fc

This problem relates to MKL v11.1 on intel64 architecture. Currently, there is no solution for the combination of Python + MKL 11.1 + AVX. You need either change to other MKL version (10.*, 11.0, 11.2) or disable mkl_avx:

    BLA_VENDOR=Intel10_64lp_seq cmake .. -DDISABLE_AVX=1

• tests fail

    mcscf/test/test_bz_df.py     test_mc2step_9o8e
    mcscf/test/test_addons.py    test_ucasscf_spin_square
    cc/test/test_h2o.py          test_h2o_without_scf
  

• Program exits with

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.

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 inspectors like profiler, pdb etc.

Qiming Sun osirpt.sun@gmail.com