Add examples/water

#  data

3 atoms

1 atom types

-10 10 xlo xhi

-10 10 ylo yhi

-10 10 zlo zhi

Masses

1 1.00794

Atoms

1 1 0 0 0

2 1 1.5 0 0

3 1 0 1.5 0

#LAMMPS input file

#All informations can be find on http://lammps.sandia.gov/

#choose the system of unit (real, metal, SI...)

units           real

#define the boundary conditions, periodic here

boundary        p p p

#define the atom style, bond style and angle style

atom_style      full

bond_style      harmonic

angle_style     harmonic

atom_modify	map array

#comm_modify cutoff 15

#atom_modify first water

#neigh_modify cluster yes

#choose the interaction between water molecules:

pair_style		lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0 

pair_modify		table 0

#water model is TIP4P/2005

#water molecules less than 1nm from each other interact via a cut lennard jones potential 

#water molecules interact via coulomb interactions calculated in real or conjugate space depending on the distance separating molecules

#define the long-range solver (here for long range coulombic interaction)

suffix off

newton on

kspace_style	pppm/tip4p 1.0e-5

suffix on

#neighbor 5.0 bin

#neigh_modify	every 1 check yes

#import the initial position of atoms, the coordinates of the box, etc

read_data	data.spce

replicate 2 2 2

#define the pair coeff for LJ interaction

pair_coeff      * * 0.0 0.0

pair_coeff      1 1 0.1852 3.1589

#define the coef for water molecule (distances between O-H and angle between H-O-H atoms)

bond_coeff      1 0.0 0.9572

angle_coeff     1 0.0 104.52

#define groups

group		water type 1 2

#maintain the water molecule rigid

fix             1 water shake 1.0e-4 200 0 b 1 a 1

#udate position and velocity each timesteps using constant NVE integration

fix		2 water nve

#apply Langevin thermostat on water molecules

#fix             3 water langevin 300.0 300.0 100.0 123

#choose how often you want thermodynamic info to be print during the computation

thermo          1000

thermo_modify   flush yes

thermo_style custom step etotal ke pe temp  evdwl ecoul elong press

#thermo_modify  format float "%.15g"

#give an initial random velocity to water molecule (corresponding to a temperature equal to 300K)

velocity		water create 300 123

#print the position of atoms to visualise it with VMD for example

#dump			4 all atom 1 dump.lammpstrj

#dump_modify		4 flush yes

#if $(is_active(package,gpu)) &

# then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&

# else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"

#choose the timestep, 2fs is a common choice

timestep		1

#run during 50000 timestep (0.1 ns)

run		50000