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[lammps-users] pylammps thermo_style issue
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[lammps-users] pylammps thermo_style issue

From: Gideon Simpson <gideon.simpson@...24...>
Date: Mon, 16 Oct 2017 21:56:57 -0700

I’ve been trying my hand at rewriting some examples using PyLammps, and I have the following difficulty with my rewrite of USER/DIFFUSE/ which makes an estimate of the mean square displacement.  The following is giving me trouble

If I use the lines

L.compute("msd", "all", "msd", "com", "yes")
L.variable("msd", "equal", "c_msd[4]")
L.thermo_style("custom","step", "v_msd")

It works as expected, but

L.compute("msd", "all", "msd", "com", "yes")
L.thermo_style("custom","step", “c_msd[4]")

generates the error

Traceback (most recent call last):
  File "", line 51, in <module>
  File "/opt/lammps/python/", line 689, in run
    self.runs += get_thermo_data(output)
  File "/opt/lammps/python/", line 633, in get_thermo_data
    thermo_data = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/", line 351, in namedtuple
    'alphanumeric characters and underscores: %r' % name)
ValueError: Type names and field names can only contain alphanumeric characters and underscores: 'c_msd[4]'