Lammps Tutorial Stuff

lj.lammps

units lj #Lennard Jones - derived units
atom_style atomic #This says, we're using particles with interatomic forces

#THESE ARE MAGIC!
neighbor 1 bin
atom_modify map array sort 10 6


#-------------------------------------------------
#----------THESE COMMANDS SET-UP SIM BOX----------
#-------------------------------------------------

boundary p p p # periodic in xyz
#command name - options
region bbox block 0 10 0 10 0 10
#command 1 - number of atom types
create_box 1 bbox

#-------------------------------------------------
#----------THESE COMMANDS PUT ATOMS IN BOX--------
#-------------------------------------------------

#make a lattice (fcc) with Lennard-Jones density of 0.25
lattice fcc 0.25
#create atoms in the box, and units are in box units
create_atoms 1 box
mass 1 1.0

dump dcheck all xyz 1 initial.xyz

run 0

undump dcheck

#-------------------------------------------------
#----------SET-UP FORCE FIELD---------------------
#-------------------------------------------------


pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0

#create velocity for all at temperature 1.0, with random number seed
# 549.... "rot yes" mean remove rotation and "dist gaussian" means
# gaussian distribution
velocity all create 1.0 5493108 rot yes dist gaussian

timestep 0.001

#-------------------------------------------------
#----------NVE ENSEMBLE---------------------------
#-------------------------------------------------


dump dnve all xyz 1 nve.xyz

fix nve_int all nve
thermo 10

run 1000

undump dnve
unfix nve_int

#-------------------------------------------------
#----------NVT (Nose-Hoover) ENSEMBLE-------------
#-------------------------------------------------



dump dnvt all xyz 1 nvt.xyz

fix nvt_nh all nvt temp 1.0 1.0 0.5
fix com_remove all momentum 100 linear 1 1 1

run 10000

spcsingle.data

LAMMPS data for SPC Water 

       3 atoms
       2 bonds
       1 angles

       2 atom types
       1 bond types
       1 angle types

    0.0 3.1      xlo xhi
    0.0 3.1      ylo yhi
    0.0 3.1      zlo zhi

Masses

     1 1
     2 16

Atoms

      1    1  2 -0.82    1.55000    1.55000    1.50000
      2    1  1  0.41    1.55000    2.36649    2.07736
      3    1  1  0.41    1.55000    0.73351    2.07736

Bonds

      1   1      1      2
      2   1      1      3

Angles

      1   1      2      1      3

water.lammps

# OXYGEN = 2
# HYDROGEN = 1

units real # Angstrom, kcal, fs
atom_style full # allows charge, angle, bond, etc

bond_style harmonic
angle_style harmonic
pair_style lj/cut/coul/long 10.0
kspace_style pppm 1.0e-5
pair_modify tail yes

read_data spcsingle.data

pair_coeff 1 1 0.0 0.0
pair_coeff 1 2 0.0 0.0
pair_coeff 2 2 0.1553 3.166

bond_coeff 1 0.0 1.0
angle_coeff 1 0.0 109.47

replicate 4 4 4

velocity all create 0.1 43892390 rot yes mom yes dist gaussian

fix wshake all shake 0.0001 20 0 b 1 a 1
fix com_remove all momentum 1 linear 1 1 1

#neighbor 2.0 bin
#neigh_modify every 1 delay 0 check yes

timestep 2.0

write_data water_replicated.data
dump dcheck all xyz 1 check.xyz

run 0

undump dcheck

fix nvt_int all nvt temp 300.0 300.0 10.0

thermo 100

run 10000


unfix nvt_int

dump dnvt all xyz 10 nvt.xyz
fix nve_int all nve

compute oordf all rdf 100 2 2
fix oordf_avg all ave/time 250 1 250 c_oordf  file oo.rdf mode vector ave running overwrite

run 15000