I am trying to create 256 atoms of atom_style sphere with a diameter 10(using lj units) in a simulation box of size 70.5. I am using a pair_style colloid with a cutoff of 10.6.
The two ways that I tried to do this were
- randomly create some no of atoms , gives large/large overlap error so I do a delete_atom overlap with 10(center-to-center distance) as the cutoff distance. Which leaves about 100-110 particles way below my original requirement.
- create_atom 1 box command but this again gives the large/large overlap upon using delete I am left with only 1 atom.
What I want to do is create a box with 256 particles of dia 10 such that the volume fraction is 0.5. How can I do this.
Thanks for your help
Regards
Anurag
I am trying to create 256 atoms of atom_style sphere with a diameter
10(using lj units) in a simulation box of size 70.5. I am using a pair_style
colloid with a cutoff of 10.6.
The two ways that I tried to do this were
randomly create some no of atoms , gives large/large overlap error so I do a
delete_atom overlap with 10(center-to-center distance) as the cutoff
distance. Which leaves about 100-110 particles way below my original
requirement.
create_atom 1 box command but this again gives the large/large overlap upon
using delete I am left with only 1 atom.
What I want to do is create a box with 256 particles of dia 10 such that the
volume fraction is 0.5. How can I do this.
you can just create the desired number of particles randomly, but
don't start with the colloid pair style, but rather use pair style
soft with suitable parameters and use fix adapt to "grow" the
potentials, to unoverlap the particles sufficiently and then switch to
colloid afterwards.
please see the micelle example for an example case of this nature.
axel.
Here is the script I am using I run the soft potential push run for some number of timesteps but at the end of that I still get a large large overlap. What is the correct no of steps to run it for. Also If I run this thing then how do I ensure atoms dont move from one overlap position to another. My cutoff for colloid is d + (30)^(-1/6) and I am keeping the cut off for the soft 11. And using fix adapt soft pair for varying the A prefactor in the pair_style soft.
Regards
Anurag
mean-squared displacement via compute msd
settings
variable x equal 35
variable rho equal 0.4
variable t equal 1.0
variable rc equal 10.6
problem setup
units lj
dimension 3
atom_style sphere
create system
lattice fcc ${rho}
region simbox block 0 $x 0 $x 0 $x
create_box 1 simbox
create_atoms 1 random 256 2349852 NULL units box
velocity all create $t 2349852
multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0 every 1 check yes page 500000 one 50000
comm_modify vel yes
timestep 0.0005
Soft Potential Push Off
variable prefactor equal ramp(0.0,40.0)
pair_style soft 11.0
pair_coeff * * 0.0
fix 1 all adapt 1 pair soft a * * v_prefactor
fix 2 all nve
thermo_style custom step temp etotal epair atoms vol pe ke
dump 1 all atom 500 lan_nve.dump
thermo 500
run 2000000
unfix 1
unfix 2
Main Run
pair_style colloid {rc}
pair_coeff 1 1 17.26 1.0 10.0 10.0 {rc}
fix 1 all nve
fix 2 all langevin $t $t 0.0025 498094
reset_timestep 0
factor of 4 in 2 variables is for 2d
compute msd all msd com yes
compute volP all property/atom radius
variable twopoint equal c_msd[4]/4/(stepdt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10dt)
thermo_style custom step temp etotal epair atoms vol c_msd[4]
dump 2 all atom 500 lan_nve_main_run.dump
thermo 1000
run 1000000
Here is the script I am using I run the soft potential push run for some
number of timesteps but at the end of that I still get a large large
overlap. What is the correct no of steps to run it for. Also If I run this
thing then how do I ensure atoms dont move from one overlap position to
think about how this works some more and then you'll see that this
doesn't matter.
another. My cutoff for colloid is d + (30)^(-1/6) and I am keeping the cut
off for the soft 11. And using fix adapt soft pair for varying the A
prefactor in the pair_style soft.
you cannot keep the parameters for pair style soft tuned for a
different system. you have to change them, so that they make your soft
particles large enough to represent your colloidal particles.
axel.