clean up whitespace, indentation, isolate all cauchystat-related code, remove extraneous examples

units		metal

atom_style	atomic

atom_modify	map array

processors      1 1 1

# Box and atom positions:

boundary p p p

# Defining lattice and creating simulation

# box with atoms inside

lattice          fcc 4.05

region           simbox prism 0 5 0 5 0 5 0 0 0 units lattice

create_box       2 simbox

create_atoms     2 box

# Atomic mass:

mass 1 58.69

mass 2 26.98154

# Potential, Al fcc crystal

pair_style eam/alloy

pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al

thermo 100

thermo_style custom step temp pxx pyy pzz pxy pxz pyz

compute cna all cna/atom 2.8

fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none

dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna

timestep 0.002

variable px equal pxx

variable py equal pyy

variable pz equal pzz

variable sxy equal pxy

variable sxz equal pxz

variable syz equal pyz

variable t equal temp

fix avg all ave/time 1 100 100 v_t v_px v_py v_pz v_sxy v_sxz v_syz file avg.txt

variable lx equal lx

variable ly equal ly

variable lz equal ly

variable xy equal xy

variable xz equal xz

variable yz equal yz

fix box all ave/time 1 100 100 v_lx v_ly v_lz v_xy v_xz v_yz file box.txt

velocity all create 1200 4928459 rot yes dist gaussian

run 10000

unfix 1

fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 xy -10000.0 -10000.0 0.1 couple none

run 10000

unfix 1

fix 1 all npt temp 600.0 600.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1  xy -10000.0 -10000.0 0.1 couple none

run 10000

units		metal

atom_style	atomic

atom_modify	map array

processors      1 1 1

# Box and atom positions:

boundary p p p

read_data input.dat

# Atomic mass:

mass 1 58.69

mass 2 26.98154

# Potential, Al fcc crystal

pair_style eam/alloy

pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al

thermo 100

thermo_style custom step temp pxx pyy pzz lx ly lz

compute cna all cna/atom 2.8

velocity all create 2400.0 4928459 rot yes dist gaussian

fix 1 all npt temp 1200.0 1200.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 no

dump 1 all cfg 1000 test*.cfg mass type xs ys zs type c_cna

timestep 0.002

variable l equal lz

variable p equal pzz

variable t equal temp

fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt

velocity all create 2400 4928459 rot yes dist gaussian

run 10000

unfix 1

fix 1 all npt temp 1200.0 300.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z -2800.0 -2800.0 0.1 couple none cauchystat 0.001 yes

run 100000

units		metal

atom_style	atomic

atom_modify	map array

processors      1 1 1

# Box and atom positions:

boundary p p p

read_data input.dat

# Atomic mass:

mass 1 58.69

mass 2 26.98154

# Potential, Al fcc crystal

pair_style eam/alloy

pair_coeff * * ../Mishin-Ni-Al-2009.eam.alloy Ni Al

thermo 100

thermo_style custom step temp pxx pyy pzz lx ly lz

compute cna all cna/atom 2.8

velocity all create 1000.0 4928459 rot yes dist gaussian

fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 0.0 0.1 couple none cauchystat 0.001 no

dump 1 all cfg 5000 test*.cfg mass type xs ys zs type c_cna

timestep 0.002

variable l equal lz

variable p equal pzz

variable t equal temp

fix avg all ave/time 1 1000 1000 v_t v_l v_p file avg.txt

velocity all create 2400 4928459 rot yes dist gaussian

run 10000

unfix 1

fix 1 all npt temp 500.0 500.0 1.0 x 0.0 0.0 0.1 y 0.0 0.0 0.1 z 0.0 -14000.0 0.1 couple none cauchystat 0.001 yes

run 350000