data/ADEPT/2.Simulations/modulus_files/in_5.elastic

# Define the finite deformation size. Try several values of this
# variable to verify that results do not depend on it.
variable up equal 2.0e-2
 
# real units, elastic constants in GPa
units		real
variable cfac equal 1.01325e-4
variable cunits string GPa

# Define MD parameters
variable nevery equal 10                  # sampling interval
variable nrepeat equal 10                 # number of samples
variable nfreq equal ${nevery}*${nrepeat} # length of one average
variable nthermo equal ${nfreq}           # interval for thermo output
variable nequil equal 10*${nthermo}       # length of equilibration run
variable nrun equal 3*${nthermo}          # length of equilibrated run
variable temp equal 300.0                 # temperature of initial sample
variable timestep equal 0.25              # timestep (femtoseconds)
variable adiabatic equal 0                # adiabatic (1) or isothermal (2)
variable tdamp equal 100                  # time constant for thermostat
variable seed equal 123457                # seed for thermostat

units        real
dimension 3
boundary p p p
atom_style	 full
pair_style	 lj/cut/coul/long 12.0 12.0
pair_modify  mix arithmetic
bond_style   harmonic
angle_style  harmonic
dihedral_style fourier
improper_style cvff
special_bonds amber
kspace_style pppm 1e-4

read_data eq2_400000.data
change_box all triclinic
velocity	all create ${temp} 87287

# Compute initial state

variable thermostat equal 1
# we must undefine any fix ave/* fix before using reset_timestep
if "$(is_defined(fix,avp))" then "unfix avp"
reset_timestep 0

kspace_style pppm 1.0e-4
neighbor    2.5 bin
neigh_modify  delay 0 every 25 check no

# Setup output

fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
thermo		${nthermo}
thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
thermo_modify norm no

# Setup MD

timestep ${timestep}
fix 4 all nve
if "${thermostat} == 1" then &
   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
run ${nequil}

if "${adiabatic} == 1" &
then "variable thermostat equal 0" &
else "variable thermostat equal 1"

print ${thermostat}

# we must undefine any fix ave/* fix before using reset_timestep
if "$(is_defined(fix,avp))" then "unfix avp"
reset_timestep 0

kspace_style pppm 1.0e-4
neighbor    2.5 bin
neigh_modify  delay 0 every 25 check no

# Setup output

fix avp all ave/time  ${nevery} ${nrepeat} ${nfreq} c_thermo_press mode vector
thermo		${nthermo}
thermo_style custom step temp pe press f_avp[1] f_avp[2] f_avp[3] f_avp[4] f_avp[5] f_avp[6]
thermo_modify norm no

# Setup MD

timestep ${timestep}
fix 4 all nve
if "${thermostat} == 1" then &
   "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
run ${nrun}

variable pxx0 equal f_avp[1]
variable pyy0 equal f_avp[2]
variable pzz0 equal f_avp[3]
variable pxy0 equal f_avp[4]
variable pxz0 equal f_avp[5]
variable pyz0 equal f_avp[6]

variable tmp equal lx
variable lx0 equal ${tmp}
variable tmp equal ly
variable ly0 equal ${tmp}
variable tmp equal lz
variable lz0 equal ${tmp}

# These formulas define the derivatives w.r.t. strain components
# Constants uses $, variables use v_ 
variable d1 equal -(v_pxx1-${pxx0})/(v_delta/v_len0)*${cfac}
variable d2 equal -(v_pyy1-${pyy0})/(v_delta/v_len0)*${cfac}
variable d3 equal -(v_pzz1-${pzz0})/(v_delta/v_len0)*${cfac}
variable d4 equal -(v_pyz1-${pyz0})/(v_delta/v_len0)*${cfac}
variable d5 equal -(v_pxz1-${pxz0})/(v_delta/v_len0)*${cfac}
variable d6 equal -(v_pxy1-${pxy0})/(v_delta/v_len0)*${cfac}

# Write restart
write_restart restart.equil

# uxx Perturbation

variable dir equal 1
include displace.mod

# uyy Perturbation

variable dir equal 2
include displace.mod

# uzz Perturbation

variable dir equal 3
include displace.mod

# uyz Perturbation

variable dir equal 4
include displace.mod

# uxz Perturbation

variable dir equal 5
include displace.mod

# uxy Perturbation

variable dir equal 6
include displace.mod

# Output final values

include post_vrh.mod
clear