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lammpslib.py - failing in test cases #6

@alvarovm

Description

@alvarovm

The test case in https://svn.fysik.dtu.dk/projects/ase-extra/trunk/ase/test/testlammpslib.py
fails with lammps & ase trunk versions
the test.log has:
----------------------------------- test.log start -----------------------------------------------------------
LAMMPS (26 Jan 2017)
units metal
atom_style atomic
atom_modify map array sort 0 0
boundary p p s
region cell prism 0 5.72756492761 0 4.96021672914 0 0.0 0.0 0.0 0.0 units box
ERROR: Illegal region prism command (../region_prism.cpp:88)
Last command: region cell prism 0 5.72756492761 0 4.96021672914 0 0.0 0.0 0.0 0.0 units box
Total wall time: 0:00:00
----------------------------------- test.log end -----------------------------------------------------------

Similarly this case fails:

---------------------------------------- lammpslib-example.py Start---------------------------------------------------
from ase import Atom, Atoms
from lammpslib import LAMMPSlib
cmds = ["pair_style eam/alloy",
"pair_coeff * * NiAlH_jea.eam.alloy Al H"]
a = 4.05
al = Atoms([Atom('Al')], cell=(a, a, a), pbc=True)
h = Atom([Atom('H')])
alh = al + h
lammps = LAMMPSlib(lmpcmds = cmds, logfile='test.log')
alh.set_calculator(lammps)
print "Energy ", alh.get_potential_energy()
---------------------------------lammpslib-example.py End -----------------------------------------------------------

I get in the stdout this:
Traceback (most recent call last):
File "pymatnest-example.py", line 10, in
alh = al + h
File "/home/vama/install/local/anaconda2/lib/python2.7/site-packages/ase/atoms.py", line 866, in add
atoms += other
File "/home/vama/install/local/anaconda2/lib/python2.7/site-packages/ase/atoms.py", line 872, in extend
other = self.class([other])
File "/home/vama/install/local/anaconda2/lib/python2.7/site-packages/ase/atoms.py", line 150, in init
atoms = self.class(None, *data)
File "/home/vama/install/local/anaconda2/lib/python2.7/site-packages/ase/atoms.py", line 195, in init
self.new_array('numbers', numbers, int)
File "/home/vama/install/local/anaconda2/lib/python2.7/site-packages/ase/atoms.py", line 391, in new_array
a = np.array(a, dtype)
TypeError: long() argument must be a string or a number, not 'Atom'

Thanks,

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