gold simulating

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1

Hi,
I’m simulating gold nanoparticle by lammps.
My in.file is showed below.

units metal
dimension 3
atom_style atomic
boundary p p p
lattice fcc 4.07
region box sphere 0 0 0 0.708 units lattice

create_box 1 box
change_box triclinic
create_atoms 1 region box
mass 1 196.96

pair_style eam
pair_coeff * * Au_u3.eam

velocity all create 310.0 234242
fix 1 all nvt temp 300 300 1
fix 2 all temp/berendsen 300.0 300.0 1

timestep 0.000001
thermo 500
thermo_modify lost ignore norm no
dump 1 all xyz 100 dump.xyz
run 10000
neigh_modify every 1 delay 0 check yes

min_style hftn
minimize 1.0e-4 1.0e-6 1000 1000
variable natoms equal “count(all)”
print “Number of atoms = ${natoms};”

in simulations I’ve encountered with a few problems:
1 - When i consider the radius of region 0/708, 13 gold atoms are placed in it but when Iconsider it 0/707 gives the following error:
ERROR: Attempting to rescale a 0.0 temperature

2-I want to simulate the gold nanoparticles with 1-300 atoms. It is the only way to determine the number of atoms through the region command

, or is there another solution?

3-my system is in NVT ensemble, but when I use
fix 1 all nvt temp 300 300 0.1
temperture is variable during the simulation, and also when i use
fix 1 all nvt temp 300 300 0.1
fix 2 all temp/berendsen 300.0 300.0 10.0
the same result is repeated.

Thank you for your attention
Fatemeh Ramezani

2

Hi,
I'm simulating gold nanoparticle by lammps.
My in.file is showed below.

units metal
dimension 3
atom_style atomic

boundary p p p

why periodic boundary conditions?
the way you set up your calculations,
you will *not* model a nano particle,
but a bulk system.

lattice fcc 4.07
region box sphere 0 0 0 0.708 units lattice

create_box 1 box
change_box triclinic

why a triclinic box?

create_atoms 1 region box
mass 1 196.96

pair_style eam
pair_coeff * * Au_u3.eam

velocity all create 310.0 234242
fix 1 all nvt temp 300 300 1
fix 2 all temp/berendsen 300.0 300.0 1

using two thermostat algorithms at the same time
is *very* wrong and will lead to bogus results.

timestep 0.000001
thermo 500
thermo_modify lost ignore norm no
dump 1 all xyz 100 dump.xyz
run 10000
neigh_modify every 1 delay 0 check yes

min_style hftn
minimize 1.0e-4 1.0e-6 1000 1000
variable natoms equal "count(all)"
print "Number of atoms = ${natoms};"

in simulations I've encountered with a few problems:
1 - When i consider the radius of region 0/708, 13 gold atoms are placed in
it but when Iconsider it 0/707 gives the following error:
ERROR: Attempting to rescale a 0.0 temperature

because then your system has only one atom left
and for a single atom there is no temperature.

2-I want to simulate the gold nanoparticles with 1-300 atoms. It is the only
way to determine the number of atoms through the region command
, or is there another solution?

if you want to run specific size systems, write a small
program that generates the initial coordinates in the form
of a data file or create individual atoms through the
single option of the create_atoms command.

3-my system is in NVT ensemble, but when I use
fix 1 all nvt temp 300 300 0.1
temperture is variable during the simulation, and also when i use

yes. why should not not oscillate? this topic
has been discussed to death on this mailing
list. you have to improve your understanding
of statistical mechanics. LAMMPS is correct.

fix 1 all nvt temp 300 300 0.1
fix 2 all temp/berendsen 300.0 300.0 10.0
the same result is repeated.

yes. as it should and this is even worse. since
using two "competing" thermostat methods at
the same time on the same atoms is plain wrong.

however, it doesn't change the basic principles.

axel.