[ase-users] Error with tkinter & matplotlib

[Clayton Spencer]

I'm new to ASE (and also to Python and CentOS 7). Please forgive my
ignorance.

I successfully ran the ethaneNEB.py file.  I wanted to view the energy
profile along the converged NEB approximation to the MEP.  I modified the
ethaneNEB.py file according to the "Diffusion of Au on Al(100) surface
(NEB)" (https://wiki.fysik.dtu.dk/ase/tutorials/neb/diffusion.html).

Running that file (shown below) with:
$ python ethaneNEB.py > ethaneNEB.out 2>&1 &

produced the follow errors in the .out file:

Traceback (most recent call last):
  File "ethaneNEB.py", line 5, in <module>
    import matplotlib.pyplot as plt
  File
"/home/cfspence/.local/lib/python2.7/site-packages/matplotlib/pyplot.py",
line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show =
pylab_setup()
  File
"/home/cfspence/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
line 62, in pylab_setup
    [backend_name], 0)
  File
"/home/cfspence/.local/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py",
line 4, in <module>
    from . import tkagg  # Paint image to Tk photo blitter extension.
  File
"/home/cfspence/.local/lib/python2.7/site-packages/matplotlib/backends/tkagg.py",
line 5, in <module>
    from six.moves import tkinter as Tk
  File "/home/cfspence/.local/lib/python2.7/site-packages/six.py", line
203, in load_module
    mod = mod._resolve()
  File "/home/cfspence/.local/lib/python2.7/site-packages/six.py", line
115, in _resolve
    return _import_module(self.mod)
  File "/home/cfspence/.local/lib/python2.7/site-packages/six.py", line 82,
in _import_module
    __import__(name)
ImportError: No module named Tkinter

I get a similar "No module named Tkinter" when running ase gui from the
command line.  For reference I'm running on CentOS 7 which uses Python
2.7.5.

Please advise on how to fix the matplotlib and tkinter issues.  Thanks, in
advance, for your help!

--Clayton

The modified ethaneNEB.py file is shown below:
+++++++++++++++++++++++++++++++++++++++++++++++++++

from ase.build import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE as QuasiNewton
import matplotlib.pyplot as plt
from ase.neb import NEBTools
from ase.io import read

# Optimise molecule
initial = molecule('C2H6')
initial.set_calculator(EMT())
relax = QuasiNewton(initial)
relax.run(fmax=0.05)

# Create final state
final = initial.copy()
final.positions[2:5] = initial.positions[[3, 4, 2]]

# Generate blank images
images = [initial]

for i in range(9):
    images.append(initial.copy())

for image in images:
    image.set_calculator(EMT())

images.append(final)

# Run IDPP interpolation
neb = NEB(images)
neb.interpolate()

# Run NEB calculation
qn = QuasiNewton(neb, trajectory='ethane_linear.traj',
                 logfile='ethane_linear.log')
qn.run(fmax=0.05)

#Read in the images
images = read('ethane_linear.traj at -11')

nebtools = NEBTools(images)

#Get the calculated barrier and the energy change from inital to final
configuration
Ef, dE = nebtools.get_barrier()
print(Ef, dE)

#Get the barrier without any interpolation between highest images.
Ef, dE = nebtools.get_barrier(fit=FALSE)
print(Ef, dE)

#Create a figure like that coming from ASE-GUI.
fig = nebtools.plot_band()
fig.savefig('ethane-rotationBarrier.png')
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