REAX/C_Change atoms in my system

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1

Dear lammps users,

I have tried to do a Reactive Molecular Dynamics Simulation using the lammps software. I installed the lammps-daily and lmp_openmpi (lammps-8Jul13) lammps packages and both of them had similar invalid results. I used a simple system in order that compare my results gaining from the lammps with those from the ReaxFF source Fortran code. Unfortunately, the lammps changes chemical composition of my system as blow:

Input simulations composition for both packages :

100 Oxygen molecules (O2)

50 1,3,5-Trinitrobenzene molecules (C6H3O6N3)

Thermodynamics conditions for both simulations been similar:

T = 300K, without any electric or magnetic field, a = 100 angstrom and NVE ensemble.

I used RDX ffield. in.RDX and param.qeq files were attached to this email.

Output from the lammps reax/c:

number of fragments chemical formula

100 H2

46 C3H6O6N3

1 C5H12O12N6

1 C

1 C6H12O12N6

Output from the ReaxFF source Fortran code:

number of fragments chemical formula

100 O2

50 C6H3O6N3

It’s clear that lammps reax/c didn’t correctly work. On the other hands, lammps reax/c has changed the atoms in the system with each other.

Can you help me what is the problem?

How I can resolve the mistake?

Thanks in advance

in.RDX (658 Bytes)

param.qeq (96 Bytes)

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The solution is pretty simple: you need to add an element keyword to the fix reax/c/species command. From the doc page:

The optional keyword element can be used to specify the chemical symbol printed for each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these symbols should be chosen to match the chemical identity of each LAMMPS atom type, as specified using the reax/c pair_coeff command and the ReaxFF force field file.

Ray