I have three different types of atoms and three different types of bond types, which are used for each atom type. But the number of bonds attached is way less than the number of bonds that are broken, so by the end of the simulation I am left with only particles.
Could you help me with this?
The code:
units lj
dimension 2
boundary p p p
Specify atoms and bond attributes
atom_style bond
special_bonds lj 1 1 1 coul 1 1 1
newton on off
#Defining a lattice of atoms
lattice sq2 1.0
region rbound sphere 0 0 0 25 units box side in
region sbound sphere 0 0 0 20 units box side in
region boxsim block -30 30 -30 30 -0.1 0.1 units box
create_box 3 boxsim bond/types 3 extra/bond/per/atom 1000 extra/special/per/atom 1000
variable x equal 30
variable y equal 30
variable xx internal 0.0
variable yy internal 0.0
variable v equal “(v_xx)^2 + (v_yy)^2 < 400.0”
variable v2 equal “(v_xx)^2 + (v_yy)^2 > 431.0 && (v_xx)^2 + (v_yy)^2 < 610.0”
variable v1 equal “(v_xx)^2 + (v_yy)^2 > 625.0”
create_atoms 1 box var v set x xx set y yy
create_atoms 2 box var v1 set x xx set y yy
create_atoms 3 box var v2 set x xx set y yy
mass * 1.0
group 1 type 1
group 2 type 2
group 3 type 3
fix 3 3 rigid single reinit yes
pair_style yukawa 1.0 2.5
pair_coeff 1 1 0.3
pair_coeff 2 2 0.3
pair_coeff 3 3 0.3
pair_coeff 2 3 0.8
pair_coeff 1 3 0.5
bond_style harmonic
bond_coeff 1 2.0 1.0
bond_coeff 2 2.0 1.0
bond_coeff 3 2.0 1.0
neighbor 3.0 bin
compute nbond all nbond/atom
compute tbond all reduce sum c_nbond
compute 1 all property/local btype batom1 batom2
compute 2 all bond/local dist engpot
dump dump32 all custom 1000 rand.dump type id x y z
dump bondsdump all local 1000 rc.dump index c_1[] c_2[]
thermo_style custom step ke pe c_tbond
thermo 1000
run 10000
fix 1 all brownian 1.0 12908410 gamma_t 1.0 rng none
fix createbonds 1 bond/create 1 1 1 2.0 1 iparam 6 1 jparam 6 1 prob 1.0 1234
fix createbonds2 2 bond/create 1 2 2 2.0 2 iparam 6 1 jparam 6 1 prob 1.0 1234 #change the bond type to 2 when trying for bond types
fix createbonds3 3 bond/create 1 3 3 2.0 3 iparam 6 1 jparam 6 1 prob 1.0 1234
run 10000
pair_coeff * * 0.01
unfix createbonds
unfix createbonds2
unfix createbonds3
fix createbonds 1 bond/create 1000 1 1 2.0 1 iparam 6 1 jparam 6 1 prob 0.1 1234
fix breakbonds 1 bond/break 1000 1 0.0 prob 0.1 1234
fix createbonds1 all bond/create 1000 2 2 0.0 2 iparam 6 1 jparam 6 1 prob 0.1 1234
fix breakbonds1 all bond/break 1000 2 0.0 prob 0.1 12345
fix createbonds6 all bond/create 1000 3 3 0.0 3 iparam 6 1 jparam 6 1 prob 0.1 1234
fix breakbonds6 all bond/break 1000 3 0.0 prob 0.1 1234
run 250000