I’m trying to generate an amorphous silica structure with melting and quenching approach. When I run my input file by lammps, no numbers are generated in log or output file and the program doesn’t give me any error. Any one can help me find the problem?
I’m using following commend for running lammps:
/usr/bin/lammps-daily < in.a-si > out.a-si
Please see the attachment for my input and output files.
Your periodic conditions are wrong. The problem goes away if you switch to
shrink-wrapped boundaries.
boundary conditions are usually a choice made based on the system that
one wants to simulate. however, the fact that problems go away when
turning off periodicity is a hint that most likely the initial
coordinates are bad for the given choice of boundary conditions and
that there are overlaps or close contacts.
Your periodic conditions are wrong. The problem goes away if you switch to
shrink-wrapped boundaries.
boundary conditions are usually a choice made based on the system that
one wants to simulate. however, the fact that problems go away when
turning off periodicity is a hint that most likely the initial
coordinates are bad for the given choice of boundary conditions and
that there are overlaps or close contacts.
yup. visualization of the data file confirms that in z-directions atoms overlap.
but x- and y-directions aren't right either, they have holes.
If the files you sent are not test examples you should be revising as well your chosen procedure for amorphization. Typically, the idea is to generate non-crystalline samples that correspond to low enthalpy (almost energy in your case due to low pressure) configurations in the landscape. You heating/cooling phases seem to me very short lived despite the relatively small system size you have. Amorphous sample != mess
Thanks for your technical comments. You are right I’m getting very unreasonable structures. In my input file I have three annealing, one heating and one cooling processes. Which ones do I need to make longer? Any comment would be highly appreciated.
Hypothetically they all matter but typically the cooling part is the key step. You want to cool the system slowly. As with previous posts of mine I got in with more guts and hunches than with factual info as I have never worked on generating amorphous samples of your particular system. Check the lit and play with your parameters. Find some physical property(ies) to reproduce and leave space for “reasonable doubt” when it comes to suggestions from the mailing list. We try to help but don’t know it all.
You could also look for quenching rate values in the literature. Eg papers from McGaughey et al (PhysRevB.89.144303 perhaps). You could try to reproduce the full process, but authors often don’t include all the details and the parameters in their papers. Mind the potential used also.
If you want to evaluate the quality of your amorphous silica phase, look for density, g(r), angle/bond length distribution, and ring statistics - perhaps also vibrational features.