Commit 7f448a02 authored by Vsevak's avatar Vsevak
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Add examples/water

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#  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
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#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