I want to know why this error occured.
I tried to change the code from “extra/bond/per/atom 3” to “extra/bond/per/atom 10” but the error occurred in the same step. Where in the code should I modify? Please help me.
This is my code.
units real
atom_style full
bond_style harmonic
angle_style harmonic
pair_style lj/cut/coul/long 10
kspace_style pppm/electrode 1e-5
kspace_modify gewald 0.3
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 angle yes #
boundary p p p #fix wall 설정하기
region box block -30 30 -30 30 0 500
create_box 6 box &
bond/types 2 &
angle/types 1 &
extra/bond/per/atom 10 &
extra/angle/per/atom 1 &
extra/special/per/atom 5
include PARM.lammps
molecule h2omol H2O-SPCFw.mol
lattice fcc 3.615
region Cu_box block -30 30 -30 30 0.4 0.7
region Cu_box_surr block -30 30 -30 30 0.7 15.0
create_atoms 5 region Cu_box
region blo_box block -30 30 -30 30 10 100
create_atoms 0 random 10000 876660 NULL mol &
h2omol 876232 overlap 1.0 maxtry 50
create_atoms 1 random 40 765915 box overlap 1.0 maxtry 50
create_atoms 4 random 80 989009 box overlap 1.0 maxtry 50
group group_type1 type 1
group group_region_out region blo_box
group group_region_surr region Cu_box_surr
group group_Cuion intersect group_type1 group_region_out
group group_type4 type 4
group group_type5 type 5
group group_Clion intersect group_type4 group_region_out
group group_Cubox region Cu_box
group group_Cufrez intersect group_type5 group_Cubox
group group_mobile subtract all group_type5
group group_Cubox_surr intersect group_type1 group_region_surr
#지역 설정
region z0 block -30 30 -30 30 30.7 31.7 units box side in
region z1 block -30 30 -30 30 31.7 32.7 units box side in
region z2 block -30 30 -30 30 32.7 33.7 units box side in
region z3 block -30 30 -30 30 33.7 34.7 units box side in
region z4 block -30 30 -30 30 34.7 35.7 units box side in
region z5 block -30 30 -30 30 35.7 36.7 units box side in
region z6 block -30 30 -30 30 36.7 37.7 units box side in
region z7 block -30 30 -30 30 37.7 38.7 units box side in
region z8 block -30 30 -30 30 38.7 39.7 units box side in
region z9 block -30 30 -30 30 39.7 40.0 units box side in
set group group_Clion charge -1.0
set group group_Cuion charge 2.0
neigh_modify every 1 delay 0 check yes one 10000
group H2O type 2 3
info coeff
minimize 1.0e-4 1.0e-6 100 100000
reset_timestep 0
fix mynvt2 group_mobile nvt temp 300 300 100
fix fxconp group_Cubox electrode/conp 0.0 1.805 couple group_mobile v_v symm on algo cg 1.0e-4
variable v equal ramp(3.0,0.0)
fix cbond all bond/create 1 5 1 3.0 1
variable my_time equal step
fix widom0 all widom 1000 30 6 124476 300 region z0
variable mu_ex0 equal f_widom0[1]
fix mu_ex0_out all print 10 “{my_time} {mu_ex0}” file mu_ex30.dat screen no
fix widom1 all widom 1000 30 6 124477 300 region z1
variable mu_ex1 equal f_widom1[1]
fix mu_ex1_out all print 10 “{my_time} {mu_ex1}” file mu_ex31.dat screen no
fix widom2 all widom 1000 30 6 124478 300 region z2
variable mu_ex2 equal f_widom2[1]
fix mu_ex2_out all print 10 “{my_time} {mu_ex2}” file mu_ex32.dat screen no
fix widom3 all widom 1000 30 6 124479 300 region z3
variable mu_ex3 equal f_widom3[1]
fix mu_ex3_out all print 10 “{my_time} {mu_ex3}” file mu_ex33.dat screen no
fix widom4 all widom 1000 30 6 124480 300 region z4
variable mu_ex4 equal f_widom4[1]
fix mu_ex4_out all print 10 “{my_time} {mu_ex4}” file mu_ex34.dat screen no
fix widom5 all widom 1000 30 6 124481 300 region z5
variable mu_ex5 equal f_widom5[1]
fix mu_ex5_out all print 10 “{my_time} {mu_ex5}” file mu_ex35.dat screen no
fix widom6 all widom 1000 30 6 124482 300 region z6
variable mu_ex6 equal f_widom6[1]
fix mu_ex6_out all print 10 “{my_time} {mu_ex6}” file mu_ex36.dat screen no
fix widom7 all widom 1000 30 6 124483 300 region z7
variable mu_ex7 equal f_widom7[1]
fix mu_ex7_out all print 10 “{my_time} {mu_ex7}” file mu_ex37.dat screen no
fix widom8 all widom 1000 30 6 124484 300 region z8
variable mu_ex8 equal f_widom8[1]
fix mu_ex8_out all print 10 “{my_time} {mu_ex8}” file mu_ex38.dat screen no
fix widom9 all widom 1000 30 6 124485 300 region z9
variable mu_ex9 equal f_widom9[1]
fix mu_ex9_out all print 10 “{my_time} {mu_ex9}” file mu_ex39.dat screen no
dump mydmp all atom 50 dump.lammpstrj
variable mytemp equal temp
variable myvol equal vol
fix myat1 all ave/time 10 10 100 v_mytemp file temperature.dat
fix myat2 all ave/time 10 10 100 v_myvol file volume.dat
variable myoxy equal count(H2O)/3
variable mydensity equal ${myoxy}/v_myvol
fix myat3 all ave/time 10 10 100 v_mydensity file density.dat
thermo 1000
compute com_Cu group_Cubox_surr count/type atom
fix myatom1 all ave/time 10 10 100 c_com_Cu file computeCuion.dat mode vector
timestep 1.0
run 100000
write_data H2O.data
-----this is error code-------
ERROR on proc 0: New bond exceeded special list size in fix bond/create (src/MC/fix_bond_create.cpp:554)
… : run 100000