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[lammps-users] Problem with fix rigid
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[lammps-users] Problem with fix rigid


From: Ali Mirmohammadi <saam85@...24...>
Date: Sun, 8 Oct 2017 15:30:53 +1100

Dear All,

I am trying to relax a system including silver particle immersed in a water box. I have two problems when I use fix rigid command for nanoparticle. Firstly, the particle moves diagonally until it exits the simulation box and enters from the other edge during the simulation. Secondly, although the temperature of the whole systems is maintained at target temperature, temperature of the particle is fluctuating significantly. In case that I uncomment the rigid command, two mentioned problems are gone but the shape of the particle changes strangely and it is not sphere anymore after relaxation period. That is why I think I have to use rigid command anyway. I have tried this with different fix rigid commands such as rigid/nve, rigid/nvt and so on but no improvement observed.

Any advice and suggestions will be greatly appreciated.  

The input script is as below and I am using the Jan 2016 version of LAMMPS.

variable T equal 300
variable dt equal 0.001

# setup problem
dimension 3
boundary p p p
atom_style full
read_data       spce5nm.data
velocity all create $T 1016891 mom yes rot yes dist gaussian

region          sph1 sphere 25 25 25 7.2 units box
delete_atoms    region sph1 bond yes mol yes

# Create Empty Sphere #
region          sph11 sphere 25 25 25 6.68 units box
lattice         fcc 4.09
create_atoms    3 region sph11 units lattice
pair_style      hybrid/overlay lj/cut/coul/long 9.8 9.8 eam lj/class2 9.8 
kspace_style    pppm 0.0001

# 1:Oxygen, 2:Hydrogen, 3:Silver #

pair_coeff    1 1 lj/cut/coul/long 0.0067366153 3.166
pair_coeff    * 2 lj/cut/coul/long 0.0000 0.0000
pair_coeff    2 3 lj/class2 0.0000 0.0000

pair_coeff    2 3 lj/class2 0.005617 2.52# Ag-H interaction (Piotr Zarzycki)
pair_coeff         1 3 lj/class2 0.033 3.0855# Ag-O interaction (Heinz for 9-6 LJ)#
pair_coeff         3 3 eam agu6  


bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none

bond_coeff 1 1000 1.0
angle_coeff 1 100.0 109.47

special_bonds   lj/coul 0.0 0.0 0.5
neighbor        2.0 bin
neigh_modify delay 0 every 1 check yes
#################################################
# Group difinition #

group           hydrogen type 2
group           oxygen type 1
group           water  type 1 2
group           particle1 region sph11

compute         watertemp water temp
compute         Agtemp1  particle1  temp

#########################################################
# equilibration and thermalization

fix 1 water shake 0.0001 200 0 b 1 a 1

fix 0 particle1 rigid molecule

#fix 0 particle1 rigid/npt molecule temp $T $T 0.1 iso 1.013 1.013 0.1

run 0                             # temperature may not be 300K
velocity all scale $T          # now it should be
fix 2 water nvt temp $T $T 0.1 drag 0.2
timestep ${dt}
thermo_style   custom step temp c_watertemp c_Agtemp1 etotal press vol
thermo 100
dump 1 all xyz 500 nvtnew1.xyz 
run 500000