added rerun example dir

python:   use of PYTHON package to invoke Python code from input script

qeq:      use of QEQ package for charge equilibration

reax:     RDX and TATB and several other models using ReaxFF

rerun:    use of rerun and read_dump commands

rigid:    rigid bodies modeled as independent or coupled

shear:    sideways shear applied to 2d solid, with and without a void

snap:     examples for using several bundled SNAP potentials

# 3d Lennard-Jones melt

variable	x index 1

variable	y index 1

variable	z index 1

variable	xx equal 20*$x

variable	yy equal 20*$y

variable	zz equal 20*$z

units		lj

atom_style	atomic

lattice		fcc 0.8442

region		box block 0 ${xx} 0 ${yy} 0 ${zz}

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 1.44 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	delay 0 every 20 check no

fix		1 all nve

dump            1 all custom 100 lj.dump id type x y z vx vy vz

thermo          100

run		1000

# 3d Lennard-Jones melt

variable	x index 1

variable	y index 1

variable	z index 1

variable	xx equal 20*$x

variable	yy equal 20*$y

variable	zz equal 20*$z

units		lj

atom_style	atomic

lattice		fcc 0.8442

region		box block 0 ${xx} 0 ${yy} 0 ${zz}

create_box	1 box

create_atoms	1 box

mass		1 1.0

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

thermo          100

read_dump       lj.dump 200 x y z vx vy vz

run             0 post no

read_dump       lj.dump 800 x y z vx vy vz

run             0 post no

read_dump       lj.dump 600 x y z vx vy vz

run             0 post no

read_dump       lj.dump 400 x y z vx vy vz

run             0 post no

# 3d Lennard-Jones melt

variable	x index 1

variable	y index 1

variable	z index 1

variable	xx equal 20*$x

variable	yy equal 20*$y

variable	zz equal 20*$z

units		lj

atom_style	atomic

lattice		fcc 0.8442

region		box block 0 ${xx} 0 ${yy} 0 ${zz}

create_box	1 box

create_atoms	1 box

mass		1 1.0

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

thermo          100

rerun           lj.dump first 200 last 800 every 200 &

                dump x y z vx vy vz

LAMMPS (09 Jan 2020)

# 3d Lennard-Jones melt

variable	x index 1

variable	y index 1

variable	z index 1

variable	xx equal 20*$x

variable	xx equal 20*1

variable	yy equal 20*$y

variable	yy equal 20*1

variable	zz equal 20*$z

variable	zz equal 20*1

units		lj

atom_style	atomic

lattice		fcc 0.8442

Lattice spacing in x,y,z = 1.6796 1.6796 1.6796

region		box block 0 ${xx} 0 ${yy} 0 ${zz}

region		box block 0 20 0 ${yy} 0 ${zz}

region		box block 0 20 0 20 0 ${zz}

region		box block 0 20 0 20 0 20

create_box	1 box

Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)

  1 by 2 by 2 MPI processor grid

create_atoms	1 box

Created 32000 atoms

  create_atoms CPU = 0.00173283 secs

mass		1 1.0

velocity	all create 1.44 87287 loop geom

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	delay 0 every 20 check no

fix		1 all nve

dump            1 all custom 100 lj.dump id type x y z vx vy vz

thermo          100

run		1000

Neighbor list info ...

  update every 20 steps, delay 0 steps, check no

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4, bins = 24 24 24

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 

     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 

     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 

     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 

     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 

     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 

     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 

     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 

     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 

     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 

    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 

Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms

Performance: 68193.673 tau/day, 157.856 timesteps/s

99.8% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 4.3538     | 4.6712     | 5.0021     |  12.8 | 73.74

Neigh   | 0.59378    | 0.65229    | 0.75202    |   8.0 | 10.30

Comm    | 0.28101    | 0.69839    | 1.0586     |  38.5 | 11.02

Output  | 0.21601    | 0.21682    | 0.21718    |   0.1 |  3.42

Modify  | 0.074002   | 0.074803   | 0.075779   |   0.2 |  1.18

Other   |            | 0.0214     |            |       |  0.34

Nlocal:    8000 ave 8049 max 7942 min

Histogram: 1 0 0 1 0 0 0 1 0 1

Nghost:    8632.5 ave 8685 max 8591 min

Histogram: 1 0 0 1 1 0 0 0 0 1

Neighs:    299934 ave 303105 max 295137 min

Histogram: 1 0 0 0 0 0 1 1 0 1

Total # of neighbors = 1199738

Ave neighs/atom = 37.4918

Neighbor list builds = 50

Dangerous builds not checked

Total wall time: 0:00:06