# Reset timestep and Write restart commands
#***********************************************************************

reset_timestep 0 									# This resets the timestep to 0.

restart ${restart_freq} SiO2_1500_atoms_5000K 						# Write a restart file every ${restart_freq} steps
restart 10000 SiO2_1500_atoms_5000K 						


# Specify pair wise coefficient for short range forces
#***********************************************************************

pair_coeff 1 1 1843388098006.800 0.046 580.902 	     # Si-Si
pair_coeff 1 2 1157587.838 	 0.161 1067.657      # Si-O
pair_coeff 2 2 149032.853        0.276 1962.280	     # O-O

# Intialize velocities
#***********************************************************************

velocity all create ${T} 12345 dist gaussian mom yes
velocity all create 5000 12345 dist gaussian mom yes

# Specify timestep
#***********************************************************************

timestep ${time_step}
timestep 1

# Thermostating and Barostating the system
#***********************************************************************

fix 	NPT all npt temp ${T} ${T} 100 iso 1.0 1.0 1000
fix 	NPT all npt temp 5000 ${T} 100 iso 1.0 1.0 1000
fix 	NPT all npt temp 5000 5000 100 iso 1.0 1.0 1000

# Property Calculation & Dumping
#***********************************************************************

thermo ${th_freq}
thermo 10000


variable T equal temp
variable P equal press
variable rho equal density

compute 1 all ke
compute 2 all pe


fix 1 all print 1000 """{"timestep": $(step), "pe": $(pe), "ke": $(ke), "temp": $T, "Pressure": $P, "Density": ${rho}}""" title "" file output.json screen no


# Output file writing
#***********************************************************************

thermo_style custom step cpu cpuremain spcpu ke pe etotal temp press density
thermo_modify flush yes

# Run Details
#***********************************************************************
run ${run_steps}
run 10000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.29631569
  grid = 24 24 24
  stencil order = 5
  estimated absolute RMS force accuracy = 0.018297351
  estimated relative force accuracy = 5.510193e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 29791 13824
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair buck/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 44.7 | 44.7 | 44.7 Mbytes
   Step          CPU          CPULeft         S/CPU          KinEng         PotEng         TotEng          Temp          Press         Density    
         0   0              0              0              22341.171     -309127.45     -286786.28      5000           382050.02      1.6745156    
     10000   596.01584      0              16.778077      22464.464     -379874.29     -357409.83      5027.5932     -6926.336       1.9861507    
Loop time of 596.017 on 40 procs for 10000 steps with 1500 atoms

Performance: 1.450 ns/day, 16.556 hours/ns, 16.778 timesteps/s
99.7% CPU use with 1 MPI tasks x 40 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 360.01     | 360.01     | 360.01     |   0.0 | 60.40
Bond    | 0.0032685  | 0.0032685  | 0.0032685  |   0.0 |  0.00
Kspace  | 97.506     | 97.506     | 97.506     |   0.0 | 16.36
Neigh   | 29.472     | 29.472     | 29.472     |   0.0 |  4.94
Comm    | 1.649      | 1.649      | 1.649      |   0.0 |  0.28
Output  | 0.0070031  | 0.0070031  | 0.0070031  |   0.0 |  0.00
Modify  | 106.98     | 106.98     | 106.98     |   0.0 | 17.95
Other   |            | 0.3911     |            |       |  0.07

Nlocal:           1500 ave        1500 max        1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           7502 ave        7502 max        7502 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         323818 ave      323818 max      323818 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 323818
Ave neighs/atom = 215.87867
Ave special neighs/atom = 0
Neighbor list builds = 611
Dangerous builds = 19

Total wall time: 0:09:56