update fix latte examples and virial

fix to add the potential energy computed by LATTE to the system's

potential energy as part of "thermodynamic output"_thermo_style.html.

The "fix_modify"_fix_modify.html {virial} option is supported by this

fix to add the LATTE DFTB contribution to the system's virial as part

of "thermodynamic output"_thermo_style.html.  The default is {virial

yes}

This fix computes a global scalar which can be accessed by various

"output commands"_Section_howto.html#howto_15.  The scalar is the

potential energy discussed above.  The scalar value calculated by this

You must use metal units, as set by the "units"_units command to use

this fix.

LATTE does not currently compute per-atom energy or per-atom virial

contributions.  So they will not show up as part of the calculations

performed by the "compute pe/atom"_compute_pe_atom.html or "compute

stress/atom"_compute_stress_atom.html commands.

Currently, LAMMPS must be run in serial or as a single MPI task, to

use this fix.  This is typically not a bottleneck, since LATTE will be

doing 99% or more of the work to compute quantum-accurate forces.

atom_style	full

atom_modify     sort 0 0.0    # turn off sorting of the coordinates

read_data       data.sucrose.lmp

read_data       data.sucrose

# replicate system if requested

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal

thermo_style    custom step temp pe etotal press

# dynamics

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal

thermo_style    custom step temp pe etotal press

# dynamics

fix             2 all latte NULL

fix_modify      2 energy yes

thermo_style    custom step temp pe etotal

thermo_style    custom step temp pe etotal press

# minimization

thermo          1

thermo          10

min_style fire

minimize        1.0e-9 1.0e-9 1000 1000

minimize        1.0e-9 1.0e-9 500 500