I’ve been trying my hand at rewriting some examples using PyLammps, and I have the following difficulty with my rewrite of USER/DIFFUSE/in.msd.2d 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 “msd2d.py”, line 51, in
L.run(10000)
File “/opt/lammps/python/lammps.py”, line 689, in run
self.runs += get_thermo_data(output)
File “/opt/lammps/python/lammps.py”, 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/collections.py”, 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]’
-gideon