[EXTERNAL] Re: spc/e bond energy

One more comment: use of equal-and-opposite fix heat commands will not necessarily guarantee total energy conservation for your system. It is possible that you are losing energy through a different mechanism. Try turning off all of your fix heat commands and see that your system conserves energy. Then, if so, you can try again with sensible equal-and-opposite fix heat commands turned on, and it should probably conserve energy.


Yes I switch to the NVE during the run which imposes the heat flux. However on a semi-related note, could you confirm with me that all fixes from a previous run are removed when one uses a restart file? I was fairly sure this was the case however now am worried in case the NVT fix has remained on after the restart from the equilibration run.

I have also performed energy conservation tests for the system without the "fix heat" and there appears to be no significant drift.

I will attach the input script that is used for the applied heatflux section of the run in case that is of any help in determining my problem.

Many thanks, Jeff.

in.spce (941 Bytes)

Fix info is stored in the restart file, but you have to reissue the fix commands in order to get them imposed again. See: http://lammps.sandia.gov/doc/read_restart.html

"The list of fixes used for a simulation is not stored in the restart file. This means the new input script should specify all fixes it will use. Note that some fixes store an internal "state" which is written to the restart file. This allows the fix to continue on with its calculations in a restarted simulation. To re-enable such a fix, the fix command in the new input script must use the same fix-ID and group-ID as was used in the input script that wrote the restart file. If a match is found, LAMMPS prints a message indicating that the fix is being re-enabled. If no match is found before the first run or minimization is performed by the new script, the "state" information for the saved fix is discarded. See the doc pages for individual fixes for info on which ones can be restarted in this manner."

So your fixes from your previous run were indeed removed, unless you reissued the same fix command.

You might try your energy conservation test without shake. You may need to use a smaller timestep size though. It is possible that interplay between fix shake and fix heat is causing the non-conservation of energy that you are observing.


The tolerance you use for SHAKE can also affect energy conservation.
Search the mail list for comments on that.