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


From: Ray Shan <rshan@...1795...>
Date: Fri, 24 Nov 2017 23:42:12 +0000

Before using that particular ReaxFF description, have you characterized whether it is appropriate for describing CL20?  Have you looked at its structural properties, cold curve, and isotherms?  If not, how can you be sure it describes the shock properties of CL20?  The errors you saw are typical of a mismatch between the material and potential parameters.

Besides, from the fix msst doc page, “To perform a simulation, choose a value of q that provides volume compression on the timescale of 100 fs to 1 ps.

Ray

On 11/14/17, 6:03 PM, "张亚平" <zhangyaping1989@...223...> wrote:



        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