Python module for quantum chemistry
Version 1.0.1
2015-11-6
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.
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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)
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Compile core module
cd lib mkdir build; cd build cmake .. make
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To make python be able to find pyscf, edit environment variable
PYTHONPATH
, e.g. if pyscf is installed in /opt/pyscfexport PYTHONPATH=/opt:$PYTHONPATH
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Use Intel MKL as BLAS library. cmake with options
-DBLA_VENDOR=Intel10_64lp_seq
BLA_VENDOR=Intel10_64lp_seq cmake ..
If cmake is still not able to find MKL, just define BLAS_LIBRARIES in CMakeLists.txt
set(BLAS_LIBRARIES "${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")
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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.
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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.
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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
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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
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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
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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
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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 [email protected]