Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/USER/qtb/alpha_quartz_qtb/alpha_quartz_qtb.in
d1bbe9546c02lammm-devel

Last Change
Raw File

alpha_quartz_qtb.in
View Options

## This script first constructs an alpha quartz structure of a given size. It then uses fix qtb to equilibrate the computational cell to the specified temperature and pressure.
variable x_rep equal 2 #x-direction replication number
variable y_rep equal 2 #y-direction replication number
variable z_rep equal 2 #z-direction replication number
variable cut_off equal 10.0 #Cut-off distance for the Buckingham term (Angstrom in metal units)
variable pressure equal 1.03125 #Initial state pressure (bar in metal units)
variable temperature equal 300.0 #Initial state quantum temperature (K in metal units)
variable delta_t equal 1.0e-3 #MD timestep length (ps in metal units)
variable damp_qtb equal 1 #1/gamma where gamma is the friction coefficient in quantum thermal bath (ps in metal units)
## This part defines units, alpha-quartz crystal, and atomic information
#General
units metal
dimension 3
boundary p p p
atom_style charge
#Lattice
lattice custom 1.0 &
a1 4.916000 0.000000 0.000000 &
a2 -2.45800 4.257381 0.000000 &
a3 0.000000 0.000000 5.405400 &
&
basis 0.469700 0.000000 0.000000 &
basis 0.000000 0.469700 0.666667 &
basis 0.530300 0.530300 0.333333 &
&
basis 0.413500 0.266900 0.119100 &
basis 0.266900 0.413500 0.547567 &
basis 0.733100 0.146600 0.785767 &
basis 0.586500 0.853400 0.214233 &
basis 0.853400 0.586500 0.452433 &
basis 0.146600 0.733100 0.880900 #American Mineralogist 65 920 1980 (Space Group 154)
#Computational Cell
region orthorhombic_unit_cell block 0 4.916000 0 8.514762 0 5.405400 units box
create_box 2 orthorhombic_unit_cell
create_atoms 1 box &
basis 1 1 &
basis 2 1 &
basis 3 1 &
basis 4 2 &
basis 5 2 &
basis 6 2 &
basis 7 2 &
basis 8 2 &
basis 9 2
replicate ${x_rep} ${y_rep} ${z_rep}
#Atomic Information
mass 1 28.085500
mass 2 15.999400
set type 1 charge +2.4
set type 2 charge -1.2
## This part implements the BKS pair potential with a cut-off distance for the Buckingham term. Long range Coulomb interactions are evaluated with the pppm method.
#Pair Potentials
pair_style buck/coul/long ${cut_off} #BKS interaction, PRL 64 1955 (1990)
pair_coeff 1 1 0.0 1.0 0.0
pair_coeff 1 2 18003.757200 0.205205 133.538100
pair_coeff 2 2 1388.773000 0.362319 175.000000
pair_modify shift yes
kspace_style pppm 1.0e-4
#Neighbor style
neighbor 2.0 bin
neigh_modify check yes every 1 delay 0 page 100000 one 2000
## This part equilibrates your crystal to a pressure of ${pressure}(unit pressure) and a temperature of ${temperature}(unit temperatureture) with quantum nuclear effects
variable p_damp equal ${delta_t}*1000 #Recommended pressure damping parameter in fix nph
fix scapegoat_qtb all nph iso ${pressure} ${pressure} ${p_damp} #NPH does the time integration
fix quartz_qtb all qtb temp ${temperature} damp ${damp_qtb} seed 35082 f_max 120.00 N_f 100 #Change f_max (THz) if your Debye frequency is higher
thermo_style custom step temp press etotal vol lx ly lz pxx pyy pzz pxy pyz pxz
thermo 100
run 20000 # 20 ps
unfix quartz_qtb
unfix scapegoat_qtb
c4science · Help