[lammps-users] Water Moldeling

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1

Dear all,

I have a difficulty on establishing water only modeling by using lammps. Note that I just started to use lammps.

I started to write up the codes as you can see below, but error message showed up while I am trying to run this. Could you check this out how I improve my code?
Thank you in advance.

tip3 water simulation

dimension 3
units real
boundary p p p

atom_style full

neighbor 10 bin
neigh_modify delay 5

read in atom coord, bonds, angles --also box size,masses

read_data multi.data

lattice sc 4
region box block 0 12 0 12 0 12
create_box 2 box
create_atoms 1 box

mass 1 1.008
mass 2 15.9994

pair_style lj/cut/coul/cut 20

for H-H bond

pair_coeff 1 1 0.0460 0.400014

for O-O bond

pair_coeff 2 2 0.1521 3.188

for O-H bond

pair_coeff 1 2 0.0836 1.7753

angle_style harmonic
#for H-O-H bond in harmonic style: K theta
angle_coeff 1 55 104.52

bond_style harmonic
#for O-H bond: K r0
bond_coeff 1 450 0.9572

fix 1 all nve
fix 2 all shake 0.0001 20 0 b 1 a 1
velocity all create 300 01234567 dist gaussian

thermo 100
dump 1 all atom 100 exp.xyz
dump_modify 1 header xyz
timestep 1
run 1000

2

You can't create molecules with create_atoms, since there is
no way to specify the bond topology. You'll need to create
a data file that has the molecules in it and use read_data.

Steve

3

Dear all,
    I am new user of Lammps. I recently installed upgraded version. The
strange thing is that I couldn't run code with minimization. If I comment
the minimization line in the input file, it works fine, but with
minimization, I got core dupmed error. But the version of July20 works fine.
Anyone could help to figure out what might be the problem?

The input file, data file and force field are attached in this email.

Thanks,

Limei

in.test (3.02 KB)

data (160 KB)

mW.sw (1.51 KB)

4

This was a bug with using the SW potential in hybrid mode. When
we changed the way pair hybrid is done in the latest release, all the
pair potential files changed slightly, and the SW one did not get
changed correctly.

I'll post a patch.

Thanks,
Steve

5

Dear Steve,

thanks for the patch for the hybrid sw. It works fine if we compile serial, but still crashes for the parallel version.
The version of July 20th works well both.

The problem seems to be general for hybrid in the new release. It crashes with hybrid sw morse and
hybrid lj/cut morse too.

Do you know what the problem may be?

thanks for your help,
vale

6

I can run the script you posted originally (in.test, data, etc)
fine in parallel with the current (fully patched) version. Can you be more
specific about what script is crashing and how?

Steve