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Re: [lammps-users] Error: atoms lost
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Re: [lammps-users] Error: atoms lost


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 31 Jul 2017 06:28:32 -0400



On Mon, Jul 31, 2017 at 2:19 AM, Neda Rafiee via lammps-users <lammps-users@lists.sourceforge.net> wrote:
Dear users,
I am using the following commands in my input file and my data file is a box of water molecules only. I got an error indicating: " lost atoms: original 11763  current 11761 " could you please tell me where is the problem?

​SPC is a rigid water potential, but i do not see you using fix shake or fix rattle anywhere. for a flexible SPC model, however, your bond and angle force constants are not correct (when using shake/rattle, they don't matter) and your time step is too large.​

axel.

 
Thanks.
Neda

# Intialization
units          real
dimension      3
boundary       p p p
atom_style     full

# Atom Definition
read_data      data.mysys
replicate      1 1 1

#The SPC water potential
pair_style      lj/cut/coul/cut 9.8 9.8
pair_coeff      2 2 0.15535 3.166
pair_coeff      1 * 0.00000 0.0000
bond_style      harmonic
angle_style     harmonic
dihedral_style  none
improper_style  none
bond_coeff      1 100.00   1.000
angle_coeff     1 100.00 109.47
special_bonds   lj/coul 0.0 0.0 0.5


# ---------- Define neighbour list ---------------------
neighbor 3.0 bin
neigh_modify delay 10 check yes


# ---------- Dump Options ---------------------
dump        1 all xyz 1 dump.xyz

# ---------- Run Minimization ---------------------
reset_timestep 0
fix 1 all box/relax iso 0.0 vmax 0.001   #tri=triclinic pressure, vmx=max volume change
thermo 10
thermo_style custom step pe lx ly lz press
min_style cg
minimize 1e-25 1e-25 5000 10000
 
write_restart restart.relax

print "minization was already done!"

undump 1
unfix 1
#--------------- End of minimization section-------------


#----------- Equilibrium ---------------------------------

velocity all create 300 435628 dist gaussian mom yes rot yes
fix 2 all nvt temp 300 300 10 drag 1.0
reset_timestep 0
timestep 1
thermo 100
thermo_style custom step time timeremain temp press pe ke vol
dump    2 all xyz 100 dump2.xyz

run 10000
unfix 2

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.