# [lammps-users] Water and gold hybrid simulation

Dear all,

I am very grateful for the responses I have been receiving and really
appreciate this. I am new to LAMMPS and it has been very helpful. I am
still having problems running this system. The error this time is "Out
of range atoms--cannot compute PPPM".

1) Is it possible for FFTW to go wrong and cause this problem?
2) Is the problem solved by reducing the number of atoms in the
system? (There are currently 8336 atoms and 4624 bonds for the entire
system)
3) Is the problem solved by adjusting some of the commands in LAMMPS?
4) If it is an equilibration issue? How do I resolve this?

The input script is shown below:

# Nanofluid simulation input script

dimension 3
units metal
boundary p p p

neighbor 0.3 bin
neigh_modify delay 5

atom_style full
kspace_style pppm/tip4p 1.0e-4

#Pair_style hybrid definition

pair_style hybrid lj/cut/coul/long/tip4p 2 1 1 1 0.1250 2.5 eam lj/cut 2.5

#Definition of pair coefficients

#Water

pair_coeff 1*2 1*2 lj/cut/coul/long/tip4p 0.0 0.0 2.5 #pair
coefficients for tip4p between OH (LJ parameters set to zero)
pair_coeff 1 1 lj/cut/coul/long/tip4p 0.0 0.0 2.5 #pair
coefficients for tip4p between HH (LJ parameters set to zero)
pair_coeff 2 2 lj/cut/coul/long/tip4p 0.16275 3.16435 2.5 #pair
coefficients for tip4p between OO

bond_style harmonic
bond_coeff 1 450.000000 1.000000 #still not sure about these. How
did you work out that K is 450.000000!

angle_style harmonic
angle_coeff 1 55.000000 104.52 #still not sure about these. How did
you work out that K is 55.000000!

#Gold

pair_coeff 3 3 eam Au_u3.eam #pair coefficients for gold - where did
this come from???

#Water and gold together

pair_coeff 1*2 3 lj/cut 0.0 0.0 2.5 #pair coefficients for
interaction between water and gold is this correctly defined???

group hydrogen type 1
group oxygen type 2
group gold type 3

group all union hydrogen oxygen gold

fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d

thermo 50
run 1000

Once again thanks for your help.

Kind regards,

Folayo Osekita
MEng Student, Queen Mary, University of London

Hi,

I am kind of new to lammps and basically shifting from Dlpoly to Lammps.

I have tried to input bond coeffs in 2 different ways and for both cases I
am expecting same result but I am getting different results.

Please let me know what I am doing wrong in the case where I am inputting it
in DATA file rather than input file as for the case when I am giving
bond_coeffs in input file I am getting the expected results.

1. In the DATA_FILE, I am mentioning bond_coeffs like:
Bond Coeffs

1 327.8159977500 1.5330000000
2 327.8159977500 1.5310000000

2. In the input file, I am mentioning bond_coeffs like
bond_style harmonic

bond_coeff 1 327.8159977500 1.5330000000
bond_coeff 2 327.8159977500 1.5310000000

How many processors are you running on?
Do you get the problem on 1 proc or a small
number of procs (2,4, etc)?

Again, it is usually bad dynamics that causes
this problem. Have you done viz on your dump
files. Are the atoms moving too far in single
timesteps?

Steve

They should be exactly the same. If you
set them twice (e.g. both ways) then the
latter settings will take precedence.

Steve