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[lammps-users] Some errors with lammps
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[lammps-users] Some errors with lammps


From: 张亚平 <zhangyaping1989@...223...>
Date: Wed, 15 Nov 2017 10:03:38 +0800 (CST)



        Dear all
                  I was trying to do shock simulation study of CL20 with ReaxFF-lg by applying MSST method in the lammps-11Aug17. Here is the details of the in.data:

# REAX potential for CL20 system
# .....

#initiation

units          real
dimension       3 
boundary        p p p
atom_style      charge

# ##
read_restart       restart.50000

neighbor        2 nsq
pair_style      reax/c lmp_control
pair_style      reax/c NULL lgvdw yes
pair_coeff * * ffield.reax.lg O N C H
neigh_modify    every 10 delay 0 check yes

###
compute reax all pair reax/c
variable eb      equal c_reax[1]
variable ea      equal c_reax[2]
variable elp     equal c_reax[3]
variable emol    equal c_reax[4]
variable ev      equal c_reax[5]
variable epen    equal c_reax[6]
variable ecoa    equal c_reax[7]
variable ehb     equal c_reax[8]
variable et      equal c_reax[9]
variable eco     equal c_reax[10]
variable ew      equal c_reax[11]
variable ep      equal c_reax[12]
variable efi     equal c_reax[13]
variable eqeq    equal c_reax[14]

####
#fix             1 all qeq/reax 1 0.0 10.0 1e-6 param.qeq

##############
#velocity        all create 300.0 500000 dist uniform
#min_style       sd
#minimize        1.0e-4 1.0e-6 100 1000

###############
#fix 2 all npt temp 300.0 300.0 1.0 iso 0.0 0.0 1000.0

fix             5 all reax/c/species 10 100 1000 species.out element O N C H cutoff 1 1 0.55 cutoff 1 2 0.4 cutoff 1 3 0.55 cutoff 1 4 0.4 cutoff 2 2 0.55 cutoff 2 3 0.3 cutoff 2 4 0.65 cutoff 3 3 0.55 cutoff 3 4 0.4 cutoff 4 4 0.65

timestep 0.1

#restart 10000 restart 
#thermo    100
#thermo_style    custom step temp density press pe ke etotal enthalpy evdwl ecoul epair lx ly lz xlat ylat zlat cella cellb cellc cellalpha cellbeta cellgamma vol
#thermo_modify   line one
#run  50000
#############

#unfix 2


thermo    10

# MSST fix
fix msst all msst x 0.09 q 10 tscale 0.001 

# this is needed to make etotal equal the MSST conserved quantity  
fix_modify msst energy yes

variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]

thermo_style custom step temp density press pe ke etotal enthalpy evdwl ecoul epair lx ly lz vol v_dhug v_dray v_lgr_vel v_lgr_pos f_msst 

fix             41 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix             42 all reax/c/bonds 100 bonds.t

compute         peatom all pe/atom
compute         keatom all ke/atom

dump            43 all custom 100 cl20.lammpstrj id type x y z c_peatom c_keatom

dump xyz all xyz 100 X10.xyz
dump_modify xyz element O N C H



run        1000000


Q1. And the ε-CL20 system is 4*2*2 supercell. During MSST, I used a long sets of parameters like "q" from 0.1 to 2000. When the  parameters q was under 1, error reporting in 52000 step with: too many ghost atoms, the job step aborted. When the  parameters q was 1~10, error reporting in same 52000 step with: failed to allocate 767693472 bytes for array list. The shock velocity was from 6~15 km/s in the X or Y or Z direction. Here is the question, can anybody suggest me some initial value of parameters q? 

Q2. I was doing the initial decomposition with the ε-CL20 4*2*2 supercell system. Here is the in.data:

# REAX potential for CL20 system
# .....

#initiation

units           real
dimension       3 
boundary        p p p
atom_style      charge

# ##
read_data       data.CL20

# ##
neighbor        2 nsq
pair_style      reax/c lmp_control lgvdw yes
pair_coeff	* * ffield.reax.lg O N C H
neigh_modify    every 10 delay 0 check no

###

####
fix             1 all qeq/reax 1 0.0 10.0 1e-6 param.qeq

##############
velocity        all create 300.0 500000 dist uniform
min_style       sd
minimize        1.0e-4 1.0e-6 100 1000

###############
fix		2 all npt temp 300.0 300.0 1.0 iso 0.0 0.0 1000.0


#############
fix             4 all reax/c/bonds 10000 bonds.t
fix             5 all reax/c/species 10 100 1000 species.out element O N C H position 10000 CL20.pos

###########3
timestep	0.1

##########
thermo          100
thermo_style    custom step temp density press pe ke etotal enthalpy evdwl ecoul epair 
thermo_modify   line one

dump		1 all atom 1000 dump.reax.CL20
dump            2 all xyz 10000 CL20
dump_modify     2 element O N C H

##############
run		50000

unfix           2

fix             7 all nvt temp 3000 3000 10
run 1000000

When the temp was set to 3000K or higher, error reported with: hbondchk failed: H=33 end(H)=2511 str(H+1)=2505. But when the temp was set from 1500K-2500K, there was no error. Can someone tell me why this error happened?

Thanks a lot!

Zhang