Hi all,
I am trying to run a NVT simulation for a system with graphene oxide and water using the drude oscillator model. I have defined all the carbons, oxygens on the system as drude cores. However when I try to run the simulation I end up with “ERROR on proc 0: Out of range atoms - cannot compute PPPM (…/pppm.cpp:1936)”. I have checked the geometry and the data file and I could not find any mistake in those.
I believe this may be related to the command “extra/special/per/atom 9”. Can you please let me know how to determine this number 9. (Which I feel too many) Please be kind enough to let me know if I have done some mistake in the data file or in the input file which can cause this? It would be a great help.
The input file data file is as follows.
Thanks you.
Regards,
Visal
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
pair_style hybrid/overlay lj/cut/coul/long 7.5 7.5 thole 2.6 7.5
kspace_style pppm 1.0e-4
read_data go_pol.data extra/special/per/atom 9
group wATOMS type 1 2 3
group gATOMS type 4 5 6 7 8 9
group CORES type 1 4 6 7 8
group DRUDES type 10 11 12 13 14
pair_coeff 1 1 lj/cut/coul/long 0.210939 3.183950
pair_coeff 1 2 lj/cut/coul/long 0.000000 0.000000
pair_coeff 1 3 lj/cut/coul/long 0.000000 0.000000
pair_coeff 1 4 lj/cut/coul/long 0.117991 3.338237
pair_coeff 1 5 lj/cut/coul/long 0.079550 2.821325
pair_coeff 1 6 lj/cut/coul/long 0.126615 3.361997
pair_coeff 1 7 lj/cut/coul/long 0.121514 3.361997
pair_coeff 1 8 lj/cut/coul/long 0.189366 3.126456
pair_coeff 1 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 2 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 3 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 6 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 7 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 8 lj/cut/coul/long 0.000000 0.000000
pair_coeff 2 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 3 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 6 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 7 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 8 lj/cut/coul/long 0.000000 0.000000
pair_coeff 3 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 4 4 lj/cut/coul/long 0.066000 3.500000
pair_coeff 4 5 lj/cut/coul/long 0.044497 2.958040
pair_coeff 4 6 lj/cut/coul/long 0.070824 3.524911
pair_coeff 4 7 lj/cut/coul/long 0.067971 3.524911
pair_coeff 4 8 lj/cut/coul/long 0.105925 3.277957
pair_coeff 4 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 5 5 lj/cut/coul/long 0.030000 2.500000
pair_coeff 5 6 lj/cut/coul/long 0.047749 2.979094
pair_coeff 5 7 lj/cut/coul/long 0.045826 2.979094
pair_coeff 5 8 lj/cut/coul/long 0.071414 2.770379
pair_coeff 5 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 6 6 lj/cut/coul/long 0.076000 3.550000
pair_coeff 6 7 lj/cut/coul/long 0.072938 3.550000
pair_coeff 6 8 lj/cut/coul/long 0.113666 3.301288
pair_coeff 6 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 7 7 lj/cut/coul/long 0.070000 3.550000
pair_coeff 7 8 lj/cut/coul/long 0.109087 3.301288
pair_coeff 7 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 8 8 lj/cut/coul/long 0.170000 3.070000
pair_coeff 8 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff 9 9 lj/cut/coul/long 0.000000 0.000000
pair_coeff * 10*14 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes
pair_coeff 1 1 thole 0.978
pair_coeff 1 4 thole 1.416
pair_coeff 1 6 thole 1.259
pair_coeff 1 7 thole 0.989
pair_coeff 1 8 thole 1.003
pair_coeff 1 10 thole 0.978
pair_coeff 1 11 thole 1.416
pair_coeff 1 12 thole 1.259
pair_coeff 1 13 thole 0.989
pair_coeff 1 14 thole 1.003
pair_coeff 4 4 thole 2.051
pair_coeff 4 6 thole 1.823
pair_coeff 4 7 thole 1.432
pair_coeff 4 8 thole 1.452
pair_coeff 4 10 thole 1.416
pair_coeff 4 11 thole 2.051
pair_coeff 4 12 thole 1.823
pair_coeff 4 13 thole 1.432
pair_coeff 4 14 thole 1.452
pair_coeff 6 6 thole 1.620
pair_coeff 6 7 thole 1.273
pair_coeff 6 8 thole 1.290
pair_coeff 6 10 thole 1.259
pair_coeff 6 11 thole 1.823
pair_coeff 6 12 thole 1.620
pair_coeff 6 13 thole 1.273
pair_coeff 6 14 thole 1.290
pair_coeff 7 7 thole 1.000
pair_coeff 7 8 thole 1.014
pair_coeff 7 10 thole 0.989
pair_coeff 7 11 thole 1.432
pair_coeff 7 12 thole 1.273
pair_coeff 7 13 thole 1.000
pair_coeff 7 14 thole 1.014
pair_coeff 8 8 thole 1.028
pair_coeff 8 10 thole 1.003
pair_coeff 8 11 thole 1.452
pair_coeff 8 12 thole 1.290
pair_coeff 8 13 thole 1.014
pair_coeff 8 14 thole 1.028
pair_coeff 10 10 thole 0.978
pair_coeff 10 11 thole 1.416
pair_coeff 10 12 thole 1.259
pair_coeff 10 13 thole 0.989
pair_coeff 10 14 thole 1.003
pair_coeff 11 11 thole 2.051
pair_coeff 11 12 thole 1.823
pair_coeff 11 13 thole 1.432
pair_coeff 11 14 thole 1.452
pair_coeff 12 12 thole 1.620
pair_coeff 12 13 thole 1.273
pair_coeff 12 14 thole 1.290
pair_coeff 13 13 thole 1.000
pair_coeff 13 14 thole 1.014
pair_coeff 14 14 thole 1.028
variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
fix DRUDE all drude C N N C N C C C N D D D D D
velocity wATOMS create {TK} 12345
velocity gATOMS create {TK} 12345
velocity DRUDES create ${TDK} 12345
delete_bonds wATOMS multi
delete_bonds gATOMS multi
comm_modify vel yes
compute TATOM1 wATOMS temp/com
compute TATOM2 gATOMS temp/com
compute TEMP all temp/drude
fix DTDIR all drude/transform/direct
fix RIGID wATOMS rigid/nvt/small molecule temp {TK} {TK} 100
fix NVT1 gATOMS nvt temp {TK} {TK} 100
fix NVT2 DRUDES nvt temp {TDK} {TDK} 20
fix DTINV all drude/transform/inverse
dump 1 all custom 2000 dump_go_pol_nvt1.lammpstrj id type x y z vx vy vz
dump_modify 1 sort 1
thermo_style custom step cpu etotal ke pe evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] density
thermo 1000
restart 2000 restart1_go_pol_npt1 restart2_go_pol_npt1
run 1000000
write_data data_go_pol_npt1.data
write_restart restart_go_pol_npt1.restart