Added newsystem flag to be passed to latte

 LAMMPS Description

           5 atoms

           2 atom types

   0.0000000000000000        19.523000000000000      xlo xhi

   0.0000000000000000        12.757999999999999      ylo yhi

   0.0000000000000000        11.692000000000000      zlo zhi

   0.0000000000000000        0.0000000000000000        0.0000000000000000      xy xz yz

 Masses

              1   12.010000000000000     

              2   1.0078250169754028     

 Atoms

    1    1    1   0.0  -9.16600   2.05200   0.00000

    2    1    2   0.0  -8.09600   2.05200   0.00000

    3    1    2   0.0  -9.52300   2.75800  -0.72000

    4    1    2   0.0  -9.52300   2.32200   0.97200

    5    1    2   0.0  -9.52300   1.07500  -0.25200

atom_style	full

atom_modify     sort 0 0.0    # turn off sorting of the coordinates

read_data       data.graphene.boxrel

read_data       data.graphene

# replicate system if requested

# simple sucrose model with LATTE

units		metal

atom_style	full

atom_modify     sort 0 0.0    # turn off sorting of the coordinates

read_data       data.sucrose

# replicate system if requested

variable	x index 1

variable	y index 1

variable	z index 1

variable        nrep equal v_x*v_y*v_z

if              "${nrep} > 1" then "replicate $x $y $z"

# initialize system

velocity	all create 0.0 87287 loop geom

pair_style      zero 1.0

pair_coeff	* *  

neighbor	1.0 bin

neigh_modify    every 1 delay 0 check yes 

timestep        0.00025

fix		1 all nve

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal press

# dynamics

thermo          10

run		100

units           metal

atom_style      full

atom_modify     sort 0 0.0    # turn off sorting of the coordinates

read_data       data.water

# initialize system

velocity        all create 0.0 87287 loop geom

pair_style      zero 1.0

pair_coeff      * * 

neighbor        1.0 bin

neigh_modify    every 1 delay 0 check yes

timestep        0.00025

fix             1 all nve

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal press

# dynamics

thermo          10

run             10

# Clear up previus calculation

clear

# simple CH4 molecule with LATTE

units           metal

atom_style      full

atom_modify     sort 0 0.0    # turn off sorting of the coordinates

read_data       data.ch4

# initialize system

velocity        all create 0.0 87287 loop geom

pair_style      zero 1.0

pair_coeff      * * 

neighbor        1.0 bin

neigh_modify    every 1 delay 0 check yes

timestep        0.00025

fix             1 all nve

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal press

# dynamics

thermo          10

run             10