hello dear users
i have attached input script.when i run the system it shows the error of ““missing bond at proc… step”…i added a command to code .i added " pair_modify mix arithmetic compute no”.and now it doesn’t show any errors.is it resonable and true?
i appreciate any help
thankyou very much
clear
units real #metal #
variable T equal 298
variable V equal vol
variable dt equal .001
variable x equal 30#23.41
variable y equal 30#23.41
variable z equal 30#23.41
variable rho equal 0.6
variable t equal 20
variable rc equal 2.5
variable p equal 200 # correlation length
variable s equal 1 # sample interval
variable d equal $p*$s # dump interval
convert from LAMMPS real units to SI
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/{A2m} #thermal conductivity
variable convert equal {atm2Pa}*{atm2Pa}{fs2s}*{A2m}{A2m}*{A2m} #*${kCal2J}
#set up problem
dimension 3
echo screen
boundary p p p
newton on
atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
#dihedral_style charmm
kspace_style pppm 1.0e-5
read_data water.data
group hydrogen type 1
group water type 1 2
group cu type 3
group oxygen type 2
lattice fcc 3.615 #Cu lattice constant
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu
set group oxygen charge -1.040 #???
set group hydrogen charge .520 #???
set group cu charge 0.000
pair_style hybrid/overlay lj/cut/coul/long 0.1521 10 eam lj/cut 10 # 10 # 5 # .583 #2.8 # 3.157 # 7.5 #@ 7
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu
for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol … cu eam cut off= 4.95 Ang
pair_modify mix arithmetic compute no #shift yes #
bond_coeff 1 11.31 .227 #1.72605 2.34
angle_coeff 1 55 104.52 #H-O-H
bond_coeff 1 450 0.9572 #O-H
#special_bonds lj 0.0 0.0 0.0
++++++++++++++++setting+++++++++++++++++++++
neighbor 2 bin #nsq#
neigh_modify delay 0 every 1 check yes #no
timestep ${dt}
thermo $d
velocity all create 298 4928459 rot yes dist gaussian # 23482341
fix 1 water shake 1e-5 200 1000 b 1 a 1 # ang 55 104.52#bond 450 0.9572
fix 12 water npt temp 298 298 100.0 iso 0.0 0.0 1000.0
unfix 1
min_style cg# quickmin# fire#
min_modify dmax 0.01
minimize 1.0e-17 1.0e-17 0 70000
run 400
reset_timestep 0
dump 1 all xyz 10000 final.xyz
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable v11 equal trap(f_SS[3]){scale}
variable v22 equal trap(f_SS[4])*{scale}
variable v33 equal trap(f_SS[5])${scale}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 # etotal enthalpy pe press ke # v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
thermo_modify flush yes
run 24000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print “average viscosity: $v [Pa.s/@ T K, {ndens} /A^3”