Lammps MD simulation help

Dear all,

I am a new user to lammps with chemistry background, and I am particularly interested in the gas-phase reaction chemistry of hydrogen. In the past, I was using ADF and ReaxFF to perform MD-computations of H2/O2 systems, and we decided to also explore LAMMPS for this application. In this regard, I am contacting you to ask for your advice on using LAMMPS for MD-calculations of gas-phase systems.

  1. We are currently looking at a stoichiometric H2/O2 systems, and were using the ReaxFF force field from Dr. van Duin. Initial conditions are 4000K and 100 bar. We previously performed NVE/NVT-computations using the serial ReaxFF and ADF and obtained reasonable results for temperature/species evolutions. We performed initial LAMMPS computations for the same system, and we’re observing a very rapid reaction onset that we didn’t see with the other codes. For your information, I am attaching the input file that I used to this email as well as a figure that shows the difference between lammps and ADF. The purple line represents the results from ADF, which indicates the reaction ignites at 0.16ns, while the lammps results indicate that the reaction starts right away after I remove the temperature constrain. I wanted to ask, whether you could give me some advice on how to correctly set up NVE/NVT gas-phase computations in LAMMPS.

lammps-input.tar.gz (198 KB)

PastedGraphic-1.pdf (68.8 KB)

lammps-nve.tar.gz (198 KB)

Hi Qing,

Comments and replies below, thanks.

Ray

Dear all,

I am a new user to lammps with chemistry background, and I am particularly
interested in the gas-phase reaction chemistry of hydrogen. In the past, I
was using ADF and ReaxFF to perform MD-computations of H2/O2 systems, and we
decided to also explore LAMMPS for this application. In this regard, I am
contacting you to ask for your advice on using LAMMPS for MD-calculations of
gas-phase systems.

1) We are currently looking at a stoichiometric H2/O2 systems, and were
using the ReaxFF force field from Dr. van Duin. Initial conditions are 4000K
and 100 bar. We previously performed NVE/NVT-computations using the serial
ReaxFF and ADF and obtained reasonable results for temperature/species
evolutions. We performed initial LAMMPS computations for the same system,
and we're observing a very rapid reaction onset that we didn't see with the
other codes. For your information, I am attaching the input file that I used
to this email as well as a figure that shows the difference between lammps
and ADF. The purple line represents the results from ADF, which indicates
the reaction ignites at 0.16ns, while the lammps results indicate that the
reaction starts right away after I remove the temperature constrain. I
wanted to ask, whether you could give me some advice on how to correctly set
up NVE/NVT gas-phase computations in LAMMPS.

I would try again without the control file "lmp_control". The default
settings in the control file are the same as the stand-alone code, so
you don't need to change any control parameters. Make sure you use
the most recent distribution.

2) The second question is related to the evaluation of the species
compostion. In particular, we are interested in determining the species
composition during the MD-computations. I wanted to ask whether LAMMPS has
capabilities that would allow me to directly evaluate the species
composition during the LAMMPS runs. If not, I was planning to develop
subroutines for this, and wanted to know how they could best be integrated
into LAMMPS.

Check out "fix reax/c/bonds" which outputs bonding information during
the run, but you need to post-process the file to acquire species
information. Check out /tools/reax for post-processing codes.

If you want to develop something along this line which outputs
chemical species on-the-fly, you can start with fix_reaxc_bonds.cpp.
Actually this is also I am currently working on.