kim_init MEAM_LAMMPS_CuiGaoCui_2012_LiSi__MO_557492625287_000 metal unit_conversion_mode

# Set logfile
log output/lmp_T313.15.log

# periodic boundary conditions along all three dimensions
boundary p p p

# Set neighbor skin
variable neigh_skin equal 2.0*${_u_distance}
neighbor ${neigh_skin} bin

# create a supercell with cubic lattice (fcc, bcc, sc, or diamond)
# using 10*10*10 conventional (orthogonal) unit cells
variable latticeconst_converted equal 5.4223007559776315*${_u_distance}
lattice       diamond  ${latticeconst_converted}
region        simbox  block 0 10 0 10 0 10 units lattice
create_box    1 simbox
create_atoms  1 box

variable mass_converted equal 28.0855*${_u_mass}

kim_interactions Si

mass          1 ${mass_converted}

# initial volume
variable      v equal vol        # assign formula
variable      V0 equal ${v}    # evaluate initial value
variable      V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal_times1000 equal ${V0_metal}*1000

print "Initial system volume: ${V0_metal} Angstroms^3"

# set the time step to 0.001 picoseconds
variable timestep_converted equal 0.001*${_u_time}
timestep ${timestep_converted}

variable temp_converted equal 313.15*${_u_temperature}
variable Tdamp_converted equal 0.1*${_u_time}
variable press_converted equal 0.0*${_u_pressure}
variable Pdamp_converted equal 1*${_u_time}

# create initial velocities consistent with the chosen temperature
velocity      all create ${temp_converted} 17 mom yes rot yes

# set NPT ensemble for all atoms
fix           ensemble all npt temp ${temp_converted} ${temp_converted} ${Tdamp_converted} &
              iso ${press_converted} ${press_converted} ${Pdamp_converted}

# compute the time averages of pressure, temperature, and volume, respectively
# ignore the first 5000 timesteps
variable      etotal_metal equal etotal/${_u_energy}
variable      pe_metal equal pe/${_u_energy}
variable      T_metal equal temp/${_u_temperature}
variable      V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance})
variable      P_metal equal press/${_u_pressure}
fix           avgmyTemp  all ave/time 5 20 100 v_T_metal  ave running start 5000
fix           avgmyPress all ave/time 5 20 100 v_P_metal ave running start 5000
fix           avgmyVol   all ave/time 5 20 100 v_V_metal   ave running start 5000

# extract fix quantities into variables so they can be used in if-else logic later.
variable      T equal f_avgmyTemp
variable      P equal f_avgmyPress
variable      V equal f_avgmyVol

# set error bounds for temperature and pressure in original metal units (K and bar)
variable      T_low equal  "313.15 - 0.2"
variable      T_up  equal  "313.15 + 0.2"
variable      P_low equal  "0.0 - 0.2"
variable      P_up  equal  "0.0 + 0.2"

# print to logfile every 1000 timesteps
thermo_style  custom step etotal v_etotal_metal pe v_pe_metal &
              temp v_T_metal vol v_V_metal press v_P_metal
thermo        1000

# Run a simulation for at most 2000*1000 timesteps. At each 1000th time step, check
# whether the temperature and pressure have converged. If yes, break.
label top
variable a loop 2000
run 1000
if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable"
if "${T}>${T_low} && ${T}<${T_up} && ${P}>${P_low} && ${P}<${P_up}" then "jump SELF break"
print "flag: Temp = ${T}, Press = ${P}"
next a
jump SELF top
label break

# Write final averaged volume to file if temperature and volume have converged; otherwise wirte a
# flag to indicate non-convergence.
variable      myStep equal step
if "${myStep} < 2000000" then "print '${V}'  file output/vol_T313.15.out"  &
else  "print 'not_converged'  file output/vol_T313.15.out"

print "LAMMPS calculation completed"
quit 0

# unstable
label unstable
print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation."