Python-based Simulations of Chemistry Framework

2018-12-31

• Stable release 1.6.0
• 1.7 alpha
• Changelog
• Documentation
• Installation
• Features

Installation

• Prerequisites

  • Cmake 2.8 or higher
  • Python 2.6, 2.7, 3.4 or higher
  • Numpy 1.8.0 or higher
  • Scipy 0.10 or higher (0.12.0 or higher for python 3.4 - 3.6)
  • h5py 2.3.0 or higher (requires HDF5 1.8.4 or higher)

• Compile core module

    cd pyscf/lib
    mkdir build; cd build
    cmake ..
    make
  

  Note during the compilation, external libraries (libcint, libxc, xcfun) will be downloaded and installed. If you want to disable the automatic downloading, this document shows how to manually build these packages and PySCF C libraries.

• To export PySCF to Python, you need to set environment variable PYTHONPATH. E.g. if PySCF is installed in /opt, your PYTHONPATH should be

    export PYTHONPATH=/opt/pyscf:$PYTHONPATH
  

• Using Intel MKL as BLAS library. Enabling the cmake options -DBLA_VENDOR=Intel10_64lp_seq when executing cmake

    cmake -DBLA_VENDOR=Intel10_64lp_seq ..
  

  If cmake does not find MKL, you can 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 (http://chemists.princeton.edu/chan/software/block-code-for-dmrg) 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 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
      ...
  

• Using pyberny (https://github.com/azag0/pyberny) as geometry optimizer. After downloading pyberny

  git clone https://github.com/azag0/pyberny /path/to/pyberny
  

  edit the environment variable to make pyberny a python module

  export PYTHONPATH=/path/to/pyberny:$PYTHONPATH
  

Tutorials

• A user-guide written in Ipython notebook can be found in https://github.com/nmardirossian/PySCF_Tutorial. This repository documents the basic structure of PySCF input script and the use of regular methods which were routinely executed in most quantum chemistry packages. It also provides an implementation to drive PySCF program in a simple manner.
• Developer's tutorial can be found in the online documentation http://sunqm.github.io/pyscf/tutorial.html#tutorial and the repository above https://github.com/nmardirossian/PySCF_Tutorial/blob/master/dev_guide.ipynb

Known problems

• mkl-2018.0.0-intel_3 from intelpython gives segfault update to mkl-2018.0.1-intel_4 or superior relaease

    conda update mkl
  

• Error message "Library not loaded: libcint.3.0.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

• runtime error message

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

or

  MKL FATAL ERROR: Cannot load libmkl_avx.so or libmkl_def.so.

This is a MKL 11.* bug when MKL is used with "dlopen" function. Preloading MKL libraries can solve this problem on most systems:

  export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_def.so:$MKLROOT/lib/intel64/libmkl_sequential.so:$MKLROOT/lib/intel64/libmkl_core.so

or

  export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_avx.so:$MKLROOT/lib/intel64/libmkl_core.so

• h5py installation.

  If you got problems to install the latest h5py package, you can try the old releases: https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/ https://github.com/h5py/h5py/archive/2.3.1.tar.gz

• If you are using Intel compiler (version 16, 17), compilation may be stuck at

[ 95%] Building C object CMakeFiles/cint.dir/src/stg_roots.c.o

This code is used by F12 integrals only. If you do not need F12 methods, the relevant compilation can be disabled, by searching DWITH_F12 in file lib/CMakeLists.txt and setting it to -DWITH_F12=0.

Citing PySCF

The following paper should be cited in publications utilizing the PySCF program package:

PySCF: the Python-based Simulations of Chemistry Framework, Q. Sun, T. C. Berkelbach, N. S. Blunt, G. H. Booth, S. Guo, Z. Li, J. Liu, J. McClain, E. R. Sayfutyarova, S. Sharma, S. Wouters, G. K.-L. Chan (2018), PySCF: the Python‐based simulations of chemistry framework. WIREs Comput. Mol. Sci., 8: e1340. doi:10.1002/wcms.1340

Bug report

Qiming Sun [email protected]