time step dt

hello dear
i had read the manual (time step,dt,units)but when i try time step dt=.1 or .001 (real ,metal).i got error and when i changed it to 20e10-*12 i got the resonable answer.

i tried everything even minimization.can i use delete bond …
thankyou for your attentions.
regard

errors :
bond atom missing at proc or reallocate atoms,lammps simulation is running out of memory "error

units real #metal #

variable T equal 298
variable V equal vol
variable dt equal .01

variable x equal 23.41
variable y equal 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 2 # 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

atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-4
pair_modify mix arithmetic
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 4 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 lj/cut/coul/long 0.1521 3.157 eam lj/cut 5 # 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

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2.0 bin #nsq#
neigh_modify delay 0 every 1 check yes #no

min_style fire
min_modify dmax 0.01
minimize 1.0e-4 1.0e-5 0 3000

timestep ${dt}
thermo $d

velocity all create 298 4928459 rot yes dist gaussian #23482341

fix 1 hydrogen shake 1e-6 500 0 m 1.0 a 1 #for hydrogen
fix 12 water npt temp 298 298 100.0 iso 0.0 0.0 1000.0

---------- Relaxation -----------------------------------------

minimization : avoid atoms overlapping

#min_style fire

thermo_style custom step etotal enthalpy pe press ke
thermo_modify flush yes

run 12000
reset_timestep 0

#------------------------dump--------------------------------
dump 12 all atom 10000 dump.minimize
dump_modify 1 scale no image yes

#dump 1 all custom 10000 dump.equilibrium. id type x y z vx vy vz

settings

Green-Kubo viscosity calculation

Define distinct components of symmetric traceless stress tensor

variable pxy equal pxy
variable pxz equal pxz #-press
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

v_pxy v_pxx type auto file profile.gk.3d ave running

Diagonal components of SS are larger by factor 2-2/d,

which is 4/3 for d=3, but 1 for d=2.

See Daivis and Evans, J.Chem.Phys, 100, 541-547 (1994)

#variable scale equal 1.0/$tvols*dt variable scale equal {convert}/(${kB}$T)$V*s*{dt}

variable v11 equal trap(f_SS[3]){scale} variable v22 equal trap(f_SS[4])*{scale}
variable v33 equal trap(f_SS[5])
${scale}
#**********************************#thermal conductivity
#compute myKE all ke/atom
#compute myPE all pe/atom
#compute myStress all stress/atom virial
#compute flux all heat/flux myKE myPE myStress
#variable Jx equal c_flux[1]/vol
#variable Jy equal c_flux[2]/vol
#variable Jz equal c_flux[3]/vol
#fix JJ all ave/correlate $s $p $d &

c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running

#variable scale equal {convert}/{kB}/$T/$T/$V*s*{dt}
#variable k11 equal trap(f_JJ[3]){scale} #variable k22 equal trap(f_JJ[4])*{scale}
#variable k33 equal trap(f_JJ[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 80000
#variable k equal (v_k11+v_k22+v_k33)/3.0
#variable ndens equal count(all)/vol
#print “average conductivity: $k[W/mK] @ T K, {ndens} /A^3”

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”