Molecules don‘t move

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1

Hi everyone，
I am simulating the hydrocarbon nucleation，and i want to see the movement of molecules. But during my simulation，the molecules just split hydrogen atom and the molecules don‘t move anymore. I don‘t know what is the reason for the phenomenon.

ReaxFF potential for TATB system

this run is equivalent to reax/in.reax.tatb,

units real
boundary p p p

atom_style full
read_data 300.data

pair_style reax/c NULL safezone 10 mincap 2000
pair_coeff * * ffield.reax C H

compute reax all pair reax/c

variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]

neighbor 2.0 bin
neigh_modify delay 0 every 10 check no

fix 1 all nvt temp 300 800 10
fix 2 all qeq/reax 1 0.0 5.0 1.0e-6 reax/c
fix 3 all reax/c/species 1 1 200 species.tatb
fix 4 all reax/c/bonds 200 bonds.reaxc

thermo 500
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq

timestep 0.1

dump 1 all custom 5000 paho2.lammpstrj id type q xu yu zu ix iy iz element
dump 2 all xyz 5000 paho2.xyz
dump 3 all custom 5000 paho2.lammps id type q xu yu zu ix iy iz
dump_modify 1 element C H
#dump 2 all image 5 image.*.jpg type type &

axes yes 0.8 0.02 view 60 -30

#dump_modify 2 pad 3

#dump 3 all movie 5 movie.mpg type type &

axes yes 0.8 0.02 view 60 -30

#dump_modify 3 pad 3

restart 500 coro-oh.restart

run 2500000

2

Hi everyone，
I am simulating the hydrocarbon nucleation，and i want to see the
movement of molecules. But during my simulation，the molecules just
split hydrogen atom and the molecules don‘t move anymore. I don‘t
know what is the reason for the phenomenon.

bad input, bad geometry, bad topology, or bad parameters.

axel.

3

On August 29 I replied to your exact same question and I am still awaiting for your reply and clarifications, “How did you visualize the splitting and the movement of the atoms? Did you look at the fix reax/c/bonds and reax/c/species output files?”.

Ray

4

Sorry for that，Splitting i mean is that the molecule break into small pieces, eg C10H8 break into C2，C3 .or the H atoms break away from the hydrocarbon. I want to see the move of molecules,in other words the molecules move from one place to another place and the molecules don’t break down. I have look at the reax/c/bonds and reax/c/species output files,i can see the “splitting” in species output files. But i don’t know how to get information from the reax/c/bonds files. I am wondering maybe there is somethings wrong with my potential function, but i am not sure. Thanks for your reply.

sheng wu

5

If the molecules were splitting then the molecules and atoms were definitely moving. I guess you wanted to observe movement without molecules breaking apart? I suggest you to look at your thermodynamic variables such as T, P and stresses. If they are abnormal, then what Axel’s sad were definitely true – you have bad input, structure, force field for the system or the combination of the above.

I noticed you changed the fix qeq cutoffs, why? That could be a reason for your bad dynamics.

Use the $LAMMPS_DIR/tools/reax/mol_fra.c to analyze the fix reax/c/bonds output files.

Ray