I don’t know why #qnan appear instead of numbers…
So I need a help. How should I do?
I don’t know why this errors repeat… help me please…
I attach my input file…
Thank you very much !
inputforsimulation_3.in (3.76 KB)
output2.txt (1.89 MB)
I don't know why #qnan appear instead of numbers...
because of some invalid math.
So I need a help. How should I do?
I don't know why this errors repeat... help me please..
since this happens in the first step already,
this is usually an indication of atoms that are too close.
in other words, your data file is not correct.
axel.
since this kind of thing crops up repeatedly, here isa simple recipe to find out which atoms are problematic:
define a custom dump that outputs coordinates and forces in every step.
e.g.:
dump 1 all custom 1 output.lammpstrj id type x y z fx fy fz
forces will be “nan” for “bad contacts”, but coordinates will not,
at least not in the first step.
run the input for one step so you compute the forces once and
write out one frame of the dump.
replace all “nan” with a large number: e.g.
sed -i -e ‘s,nan,9999.0,g’ output.lammpstrj
load this configuration for visualization into VMD,
but map the forces to the velocity field.
env LAMMPSREMAPFIELDS=vx=fx,vy=fy,vz=fz vmd output.lammpstrj
visualize the structure any which way you like
and then either use color by velocity or use a
selection like “vx == 9999.0” to identify the
problematic atoms.
please note that this will highlight always multiple atoms
(you need at least two to have an “invalid” force and both
will have it.) not just the one set causing it, but at least
you know where to look.
HTH,
axel.