`positions` not found

[cortner]

using JuLIP, JuLIP.ASE, TightBinding
TB = TightBinding;
NRLTB = TightBinding.NRLTB;

β = 30.0
at = bulk("C", pbc = true, cubic = true)
bzq = TB.MPGrid(at, (4,4,4))
nrltb = TB.NRLTB.NRLTBModel(:C, TB.FermiDiracSmearing(β), bzquad = bzq, cutoff = :original);

TB.spectrum(nrltb,at)

this creates an exception on @ettersi 's linux laptop. (both in release and master of JuLIP)

[cortner]

I can't reproduce it on Kaiju.

[cortner]

@ettersi : Could you please do the following:

• pull the latest master of TightBinding
• Pkg.rm("JuLIP"); Pkg.add("JuLIP")
• JULIPVISUALISE = false then run this script again and report back here the error message?

[ettersi]

I deleted both JuLIP and TightBinding (TightBinding depends on JuLIP, so Pkg.rm("JuLIP") does not actually remove JuLIP) and reinstalled, using Pkg.clone("git@github.com:cortner/TightBinding.jl.git") for TightBinding. The first time I forgot typing JULIPVISUALISE = false and got the same error message as before:

ERROR: KeyError: key "positions" not found
 in getindex(::PyCall.PyObject, ::String) at /home/simon/.julia/v0.5/PyCall/src/PyCall.jl:268
 in length at /home/simon/.julia/v0.5/JuLIP/src/ASE.jl:113 [inlined]
 in ndofs at /home/simon/.julia/v0.5/TightBinding/src/types.jl:68 [inlined]
 in band_structure(::TightBinding.TBModel{TightBinding.NRLTB.NRLHamiltonian{4,Function},TightBinding.FermiDiracSmearing}, ::JuLIP.ASE.ASEAtoms) at /home/simon/.julia/v0.5/TightBinding/src/calculators.jl:216
 in spectrum(::TightBinding.TBModel{TightBinding.NRLTB.NRLHamiltonian{4,Function},TightBinding.FermiDiracSmearing}, ::JuLIP.ASE.ASEAtoms) at /home/simon/.julia/v0.5/TightBinding/src/calculators.jl:229

Then I removed and added again, made sure I added the JULIPVISUALISE line and ran again, and now it crashes with

Intel MKL FATAL ERROR: Cannot load /home/simon/anaconda3/lib/python3.5/site-packages/numpy/core/../../../../libmkl_core.so.

[ettersi]

I suspect something is wrong with my Python/ASE installation, but I have no idea how to check that.

[cortner]

this is a bigger request: is there a way to switch to Python 2.7?

[ettersi]

Is that what you are using?

[cortner]

yes

[cortner]

Sunrise:~ ortner$ ipython
Python 2.7.12 |Anaconda custom (x86_64)| (default, Jul  2 2016, 17:43:17)
Type "copyright", "credits" or "license" for more information.

[ettersi]

Ok, I'll look into it

[ettersi]

It works! Hard to tell what really caused the issue, though, because changing the Python version also required me to reinstall ASE and matscipy. In any case, it seems to work so no point digging deeper for now.

[cortner]

I'm relieved. And to be on the safe side I just pushed an update to JuLIP that gives a warning if the Python version is > 2.7.x.