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lightspeed's Issues

Python 3 and OpenMM Error

Hi Rob,

I'm trying to run LS with OpenMM using Python 3. However, I get the following error
File "<stdin>", line 1, in <module> File "/global/software/OpenMM/7.1-intel-2016.0.109-CUDA-8.0.44/lib/python2.7/site-packages/simtk/openmm/__init__.py", line 19, in <module> from simtk.openmm.openmm import * File "/global/software/OpenMM/7.1-intel-2016.0.109-CUDA-8.0.44/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 28, in <module> _openmm = swig_import_helper() File "/global/software/OpenMM/7.1-intel-2016.0.109-CUDA-8.0.44/lib/python2.7/site-packages/simtk/openmm/openmm.py", line 24, in swig_import_helper _mod = imp.load_module('_openmm', fp, pathname, description) File "/global/software/Anaconda3/5.2.0/lib/python3.6/imp.py", line 243, in load_module return load_dynamic(name, filename, file) File "/global/software/Anaconda3/5.2.0/lib/python3.6/imp.py", line 343, in load_dynamic return _load(spec) ImportError: dynamic module does not define module export function (PyInit__openmm)

Which is due to the conflict in the python version. The OpenMM module is loading python 2, while Lightspeed is expecting Python 3.

I've attempted to get around this by setting up my own lua module which contains a python openmm

help([[Python/C++ environment for electronic structure.]])whatis([[Python/C++ environment for electronic structure.]])

local root = "/home/caldaz/programs/1.03"

conflict("lightspeed")

load("libxc")

load("Boost/1.63.0-intel-2016.0.109-Anaconda3-5.2.0")
-- removed problematic OpenMM loads
--load("OpenMM")
--load("TeraChem/2018.07-intel-2016.0.109-MPICH2-1.4.1p1")
load("Anaconda3/5.2.0")

--- added necessary TeraChem libraries
local root2 = "/global/software/TeraChem/2018.07-intel-2016.0.109-MPICH2-1.4.1p1"
load("protobuf/3.2.0-intel-2016.0.109")
load("CUDA/8.0.44")
load("MPICH2/1.4.1p1-intel-2016.0.109")
--

prepend_path("CPATH", pathJoin(root2, "include"))
prepend_path("LD_LIBRARY_PATH", pathJoin(root2, "lib"))
prepend_path("LIBRARY_PATH", pathJoin(root2, "lib"))
prepend_path("PATH", pathJoin(root2, "bin"))
setenv("EBROOTTERACHEM", root2)
setenv("EBVERSIONTERACHEM", "2018.07")
setenv("TeraChem", root2)

prepend_path("LD_LIBRARY_PATH", pathJoin(root, "build/lib"))
prepend_path("LIBRARY_PATH", pathJoin(root, "build/lib"))
prepend_path("PATH", pathJoin(root, "build/bin"))
setenv("LIGHTSPEED_ROOT", root)

prepend_path("PYTHONPATH", pathJoin(root, "build/python"))
prepend_path("PYTHONPATH", root)
prepend_path("PYTHONPATH", pathJoin(root, "apps/aiscat"))
prepend_path("PYTHONPATH","/home/caldaz/.conda/envs/py3/lib/python3.6/site-packages/simtk")

This successfully get's past the openmm problem above, however it now complains about

Traceback (most recent call last):
  File "test.py", line 61, in <module>
    E= ref.compute_energy()
  File "/home/caldaz/programs/1.03/est/rhf.py", line 430, in compute_energy
    self.dft_functional = ls.Functional.build(self.options['dft_functional'])
RuntimeError: LibXCFunctionalImpl: No LibXC - should not construct

Any help on compiling LS with Python 3 would be appreciated!

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