Add examples for the USER-YAFF package

mof5:

    NPT simulation of MOF5 using a QuickFF force field

mil53al:

    NPT simulation of MIL-53(Al) using a QuickFF force field.

    If the pressure is high enough (for instance 2000 atm),

    a phase transition from large pore to narrow pore is observed

#########################################

#General settings

#########################################

units           real

atom_style      full

boundary        p p p

dielectric      1

#########################################

#Force field and system specification

#########################################

special_bonds   lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000

pair_style      mm3/switch3/coulgauss/long  12.0000  4.0000

pair_modify     table 16 # Accuracy of the table used for real space electrostatics

pair_modify     mix arithmetic

pair_modify     tail no

bond_style      harmonic

angle_style     hybrid cosine/periodic cross harmonic cosine/squared

dihedral_style  fourier

improper_style  distharm

box tilt large

read_data       lammps.data       # Data file location

kspace_style    pppm 0.0000001      # Ewald accuracy

neighbor        2.0 multi

neigh_modify    every 2 delay 4 check yes

#########################################

#Output settings

#########################################

thermo 100       # Provide output every n steps

thermo_style 	custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press

thermo_modify	line multi format float %20.12f

#########################################

#Sampling options

#########################################

timestep 0.5 # in femtosecond

velocity all create 0.0 5 # initial temperature in Kelvin and random seed

fix 1 all npt temp 300.0 300.0 100.0 tri 2000.0 2000.0 1000.0 tchain 3 mtk yes nreset 1000

fix_modify 1 energy yes # Add thermo/barostat contributions to energy

run 10000

#########################################

#General settings

#########################################

units           real

atom_style      full

boundary        p p p

dielectric      1

#########################################

#Force field and system specification

#########################################

special_bonds   lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000

pair_style      mm3/switch3/coulgauss/long  12.0000  4.0000

pair_modify     table 16 # Accuracy of the table used for real space electrostatics

pair_modify     mix arithmetic

pair_modify     tail no

bond_style      mm3

angle_style     hybrid cross mm3

dihedral_style  fourier

improper_style  distharm

box tilt large

read_data       lammps.data       # Data file location

kspace_style    pppm 0.0000001      # Ewald accuracy

neighbor        2.0 multi

neigh_modify    every 2 delay 4 check yes

#########################################

#Output settings

#########################################

thermo 10       # Provide output every n steps

thermo_style 	custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press

thermo_modify	line multi format float %20.12f

#########################################

#Sampling options

#########################################

timestep 0.5 # in femtosecond

velocity all create 0.0 5 # initial temperature in Kelvin and random seed

fix 1 all npt temp 300.0 300.0 100.0 tri 1.0 1.0 1000.0 tchain 3 mtk yes nreset 1000

fix_modify 1 energy yes # Add thermo/barostat contributions to energy

run 100