ERROR: Fix gcmc cannot exchange individual atoms belonging to a molecule (src/MC/fix_gcmc.cpp:507)

LAMMPS LAMMPS General Discussion
1

Dear LAMMPS experts,

I am trying to insert Li atoms inside my simulation box which contains oxygen molecule and zeolite templated carbon structure. However, I am getting below error,

“ERROR: Fix gcmc cannot exchange individual atoms belonging to a molecule (src/MC/fix_gcmc.cpp:507)”

Could you please guide me how to fix this error? I have attached input script below;

-------------------- Init Section -----------------------

units real
boundary p p p
atom_style full
#bond_style harmonic
#angle_style harmonic
#dihedral_style harmonic
pair_style lj/cut/coul/long 12.8
kspace_style ewald 1e-05
kspace_modify gewald 1e5

-------------------- Atom Definition Section ------------

region cathode block 0.545001 35.961001 -4.785577 25.885579 -7.220522 21.696521
read_data FAU_o21.data
#replicate 2 2 2

group ztc molecule 1
group carbon type 1
group O2 molecule 2 3
group o1 type 2
group o2 type 3

molecule lithium Li.xyz #offset 1 0 0 0 0

group Li type 4

set group carbon charge 0
#set group O2 charge -1

pair_coeff * * 0.0000 0.0000 # no LJ interaction between structure and adsorbed atoms
#pair_coeff 1 1 0.1871 3.000 # C-C(C) LJ
pair_coeff 1 2 0.087148348 3.3755 # C1(MOF)-O(O2) LJ ; ARITHMETIC AVERAGE FOR SIGMA AND GEOMETRIC AVERAGE FOR EPSILON, ACCORDING TO THE LORENTZ-BERTHELOT MIXING RULES (SIGMA_MIX=(SIGMA1+SIGMA2)/2) (EPSILON_MIX=SQRT(EPS1*EPS2))
pair_coeff 1 3 0.087148348 3.3755 # C1(MOF)-X(O2) LJ
pair_coeff 2 3 0.072331662 3.3200 # O(O2)-O(O2) LJ
pair_coeff 1 4 0.871 2.000 # C-Li(Li) LJ
pair_coeff 4 4 0.871 1.900 # Li-Li(Li) LJ
pair_coeff 2 4 0.871 1.900 # Li-o2(o2) LJ
pair_coeff 3 4 0.871 1.900 # Li-o2(o2) LJ

-------------------- Settings Section -------------------

compute_modify thermo_temp dynamic yes
neighbor 2 bin
neigh_modify every 1 delay 0 check no one 100000 page 5000000
neigh_modify exclude group carbon carbon
variable Liad equal (atoms-1526)
#variable o2ad equal (atoms-1488-v_Liad)

-------------------- Run Section ------------------------

fix 1 all rigid single force 1 off off off torque 1 off off off
#fix 2 o2 rigid single force 1 off off off torque 1 off off off
#fix 3 o2 rigid single force 1 off off off torque 1 off off off
#fix 1 Li rigid single force 1 off off off torque 1 off off off
#fix 2 Li deposit 38 1 10 12456 mol lithium region cathode

fix fxgc Li gcmc 1 1 1 1 124356789 100.0 -0.5 0.5 group Li pressure 100 full_energy
#fix fxgc o2 gcmc 10 100 100 2 124356789 77.0 -0.5 0.5 pressure 100000 full_energy

thermo 10
thermo_style custom step epair etotal temp press atoms v_Liad #v_o2ad evdwl ecoul emol density

dump 2 all custom 5 FAU_186C_Li*.lammpstrj id type x y z

run 500

write_data FAU_LiO21.end

2

As indicated by the error message, LAMMPS will refuse to exchange individual atoms with a molecule ID != 0, as that is usually an indication that this atom is part of a molecule with bonded interactions and the gcmc code has no provisions for breaking bonds and updating topology data accordingly.

This is a heuristic check, so manually setting the molecule ID for such atoms to 0 will bypass the check.
However, the restrictions from above still apply and when trying to add/remove atoms that have bonds you will create an inconsistent topology which will lead to errors about lost bond atoms at the next neighbor list update.

3

Thank You. It’s working now.

Regards

4

can you tell me how it is done?

5

How what is done?

6

actually I want to study the adsorption of H2S and NH3 using gcmc simulation in lammps with a Cof structure and I am not able to add the H2S molecule in the input file for lammps? Can you help.

7

Not based on such a vague description. What have you tried exactly? and what are the specific issues?

In addition, please start a new discussion topic with a new subject line since your request has nothing to do with this discussion thread.

It is considered very bad style to “hijack” an existing discussion for a completely different topic.

8