# NOTE: This script can be modified for different atomic structures, 
# units, etc. See in.elastic for more info.
#
# Define MD parameters
# These can be modified by the user
# These settings replicate the 1477~K benchmark of
# Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
# Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265

# set log file

variable logsuffix index ortho
log log.elastic.${logsuffix}

# select temperature and pressure (lattice constant)

variable temp index 1477.0                 # temperature of initial sample
variable a index 5.457                     # lattice constant

# select sampling parameters, important for speed/convergence

variable nthermo index 1500               # interval for thermo output
variable nevery index 10                  # stress sampling interval
variable neveryborn index 100             # Born sampling interval
variable timestep index 0.000766          # timestep
variable nlat index 3                     # number of lattice unit cells

# other settings

variable mass1 index 28.06                # mass
variable tdamp index 0.01                 # time constant for thermostat
variable seed index 123457                # seed for thermostat
variable thermostat index 1               # 0 if NVE, 1 if NVT
variable delta index 1.0e-6               # Born numdiff strain magnitude 

# hard-coded rules-of-thumb for run length, etc.

variable nfreq equal ${nthermo}           # interval for averaging output
variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
variable nequil equal 10*${nthermo}       # length of equilibration run
variable nrun equal 100*${nthermo}        # length of equilibrated run

# this generates a general triclinic cell
# conforming to LAMMPS cell (upper triangular)

units		metal
box 		tilt large

# unit lattice vectors are
# a1 = (a1x 0 0)
# a2 = (a2x a2y 0)
# a3 = (a3x a3y a3z)

variable        a1x index 1
variable 	a2x index 0
variable 	a2y index 1
variable 	a3x index 0
variable 	a3y index 0
variable	a3z index 1
variable	atmp equal $a
variable 	l index $a
variable	basis index "basis 0    0    0  basis 0.25 0.25 0.25 basis 0    0.5  0.5 basis 0.25 0.75 0.75 basis 0.5  0    0.5 basis 0.75 0.25 0.75 basis 0.5  0.5  0 basis 0.75 0.75 0.25"
lattice         custom ${l}             &
                a1 ${a1x}      0      0 &
                a2 ${a2x} ${a2y}      0 &
                a3 ${a3x} ${a3y} ${a3z} &
                ${basis}    &
		spacing 1 1 1

region		box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}

create_box	1 box
create_atoms	1 box
mass 1 ${mass1}
replicate ${nlat} ${nlat} ${nlat}
velocity	all create ${temp} 87287