Hi All,
I am writing a LAMMPS input file for solvent evaporation. For this purpose, I am using the following command:
fix 6 water evaporate 100 30 Eve 38277 molecule yes
The output file shows the number of atoms is decreasing, but the dump file (dump 2 all xyz 100 new2.xyz) shows the system with all initial atoms. I would be grateful if you help me to dump the output file correctly to see the decreasing number of the atoms visually.
Thanks,
Atefeh
How do you visualize your results? are you sure the problem is not with your visualization tool?
when I run a small test simulation with 1500 water molecules and ask to remove 9 atoms every 10 steps and then dump the result into an xyz style dump file, I do get the expected number of atoms output in the dump file (and any format, not just xyz):
$ grep -B1 Atoms dump.xyz
4500
Atoms. Timestep: 0
Hi Axel,
I am using VMD. In the output file the number of atoms is decreasing:
Step Temp TotEng Atoms
0 309.61569 -47881.149 48531
1000 325.42888 -42665.553 39288
2000 307.36723 -38226.697 30096
3000 253.88033 -34597.176 20967
But the dump file has the information just before removing the atoms. It seems that it doesn’t save the output data when the system is deleting the molecules.
I was wondering if this command (dump 2 all xyz 100 new2.xyz) doesn’t work, because of “all”.
Which command do you use for dumping the output files?
Thanks,
Atefeh
This is a VMD issue, not a LAMMPS issue.
Which visualization software do you recommend for these kinds of simulations?
Thanks,
Atefeh
i don’t do evaporation simulations myself, so i don’t have a specific recommendation.
I do use VMD most often for visualizing LAMMPS data, there are different kinds of workarounds/hacks to bypass the “constant number of atoms” restriction in VMD, but they are not for beginners.
apart from that, you can create images/movies with LAMMPS directly or use one of the packages listed here: https://lammps.sandia.gov/prepost.html