Dear lammps users,
I simulate the cnt connected to reservoirs of water, then delete the reservoirs. but after that i want to change the size of the simulation box using change_box command. but it give an error of cannot compute pppm and in the log file I see:
Step CPU Tliq Tpar TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz
150000 0 605.91011 608.1286 17175.576 -nan -nan -nan -nan -nan -nan -nan
I do not know why this problem appear.I use these commands:
region R1 block -51.65 51.65 -51.12 51.12 -115.0 2.5
delete_atoms region R1 compress yes bond yes mol yes
change_box all x final -21.0 21.0 y final -21.0 21.0 z final 0.0 102.0 set remap units box
any idea is appreciated.
Many thanks in advance.
Aisan
Dear lammps users,
I simulate the cnt connected to reservoirs of water, then delete the
reservoirs. but after that i want to change the size of the simulation box
using change_box command. but it give an error of cannot compute pppm and in
the log file I see:
Step CPU Tliq Tpar TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz
150000 0 605.91011 608.1286 17175.576 -nan
-nan -nan -nan -nan -nan -nan
I do not know why this problem appear.I use these commands:
region R1 block -51.65 51.65 -51.12 51.12 -115.0 2.5
delete_atoms region R1 compress yes bond yes mol yes
change_box all x final -21.0 21.0 y final -21.0 21.0 z final 0.0 102.0 set
remap units box
any idea is appreciated.
you are making a very drastic change to your system, it is quite
optimistic to assume that you can just continue your simulation as if
nothing had happened. have you checked whether your system is
meaningful after the change? has no close contacts (including through
PBC)? or whether it may need to relieve high potential energy through
relaxation where you cut things away.
axel.
thanks Dear Alex,
yes after deleting the atoms I visualize my system in vmd and i think it does not have any problem, but when i add the change_box command, the problem will be appear.do i need any other command after change_box or not?
Best regards
Aisan
thanks Dear Alex,
yes after deleting the atoms I visualize my system in vmd and i think it
does not have any problem, but when i add the change_box command, the
problem will be appear.do i need any other command after change_box or not?
that is a dumb question to ask based on the (lack of) information you
provided. how should i know? i don't have a crystal ball, and i cannot
read minds.
like i said, what you are doing is a drastic change and thus you have
to respect that by treating the system as if you are starting a new
simulation.
how can i know whether you are doing this properly? the fact that you
get invalid forces/pressure suggests that you don't.
axel.