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

# Set neighbor skin
variable neigh_skin equal 2.0*${_u_distance}
variable neigh_skin equal 2.0*1
neighbor ${neigh_skin} bin
neighbor 2 bin

# create a supercell with cubic lattice (fcc, bcc, sc, or diamond)
# using 10*10*10 conventional (orthogonal) unit cells
variable latticeconst_converted equal 6.303511068224907*${_u_distance}
variable latticeconst_converted equal 6.303511068224907*1
lattice       diamond  ${latticeconst_converted}
lattice       diamond  6.30351106822491
Lattice spacing in x,y,z = 6.3035111 6.3035111 6.3035111
region        simbox  block 0 10 0 10 0 10 units lattice
create_box    1 simbox
Created orthogonal box = (0 0 0) to (63.035111 63.035111 63.035111)
  1 by 1 by 1 MPI processor grid
create_atoms  1 box
Created 8000 atoms
  using lattice units in orthogonal box = (0 0 0) to (63.035111 63.035111 63.035111)
  create_atoms CPU = 0.001 seconds

variable mass_converted equal 118.71*${_u_mass}
variable mass_converted equal 118.71*1

kim_interactions Sn

WARNING: 'kim_<command>' has been renamed to 'kim <command>'. Please update your input.

kim interactions Sn
#=== BEGIN kim interactions ==================================
pair_style kim MEAM_LAMMPS_VellaChenStillinger_2017_Sn__MO_316045643888_002
pair_coeff * * Sn
#=== END kim interactions ====================================


mass          1 ${mass_converted}
mass          1 118.71

# initial volume
variable      v equal vol        # assign formula
variable      V0 equal ${v}    # evaluate initial value
variable      V0 equal 250465.295928465    
variable      V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 250465.295928465/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 250465.295928465/(1*${_u_distance}*${_u_distance})
variable      V0_metal equal 250465.295928465/(1*1*${_u_distance})
variable      V0_metal equal 250465.295928465/(1*1*1)
variable      V0_metal_times1000 equal ${V0_metal}*1000
variable      V0_metal_times1000 equal 250465.295928465*1000

print "Initial system volume: ${V0_metal} Angstroms^3"
Initial system volume: 250465.295928465 Angstroms^3

# set the time step to 0.001 picoseconds
variable timestep_converted equal 0.001*${_u_time}
variable timestep_converted equal 0.001*1
timestep ${timestep_converted}
timestep 0.001

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

# create initial velocities consistent with the chosen temperature
velocity      all create ${temp_converted} 17 mom yes rot yes
velocity      all create 313.15 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}
fix           ensemble all npt temp 313.15 ${temp_converted} ${Tdamp_converted}               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 313.15 313.15 ${Tdamp_converted}               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 313.15 313.15 0.1               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 313.15 313.15 0.1               iso 0 ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 313.15 313.15 0.1               iso 0 0 ${Pdamp_converted}
fix           ensemble all npt temp 313.15 313.15 0.1               iso 0 0 1

# compute the time averages of pressure, temperature, and volume, respectively
# ignore the first 5000 timesteps
variable      etotal_metal equal etotal/${_u_energy}
variable      etotal_metal equal etotal/1
variable      pe_metal equal pe/${_u_energy}
variable      pe_metal equal pe/1
variable      T_metal equal temp/${_u_temperature}
variable      T_metal equal temp/1
variable      V_metal equal vol/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V_metal equal vol/(1*${_u_distance}*${_u_distance})
variable      V_metal equal vol/(1*1*${_u_distance})
variable      V_metal equal vol/(1*1*1)
variable      P_metal equal press/${_u_pressure}
variable      P_metal equal press/1
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

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6

@Article{tadmor:elliott:2011,
 author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
 title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
 journal = {{JOM}},
 year =    2011,
 volume =  63,
 number =  17,
 pages =   {17},
 doi =     {10.1007/s11837-011-0102-6}
}

- OpenKIM potential: https://openkim.org/cite/MO_316045643888_002#item-citation

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.307 | 4.307 | 4.307 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
         0  -25432.68      -25432.68      -25756.462     -25756.462      313.15         313.15         250465.3       250465.3       1380.7787      1380.7787    
      1000  -25074.879     -25074.879     -25427.55      -25427.55       341.09011      341.09011      253564.19      253564.19      58.663967      58.663967    
Loop time of 17.3934 on 1 procs for 1000 steps with 8000 atoms

Performance: 4.967 ns/day, 4.831 hours/ns, 57.493 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 17.112     | 17.112     | 17.112     |   0.0 | 98.38
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026677   | 0.026677   | 0.026677   |   0.0 |  0.15
Output  | 0.00018139 | 0.00018139 | 0.00018139 |   0.0 |  0.00
Modify  | 0.23495    | 0.23495    | 0.23495    |   0.0 |  1.35
Other   |            | 0.01919    |            |       |  0.11

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       272000 ave      272000 max      272000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 272000
Ave neighs/atom = 34
Neighbor list builds = 0
Dangerous builds = 0
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}"
flag: Temp = 0, Press = 0
next a
jump SELF top
variable a loop 2000
run 1000
Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      1000  -25074.879     -25074.879     -25427.55      -25427.55       341.09011      341.09011      253564.19      253564.19      58.663967      58.663967    
      2000  -25111.201     -25111.201     -25421.589     -25421.589      300.19538      300.19538      253582.52      253582.52     -62.919893     -62.919893    
Loop time of 21.602 on 1 procs for 1000 steps with 8000 atoms

Performance: 4.000 ns/day, 6.001 hours/ns, 46.292 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.322     | 21.322     | 21.322     |   0.0 | 98.70
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026569   | 0.026569   | 0.026569   |   0.0 |  0.12
Output  | 9.036e-05  | 9.036e-05  | 9.036e-05  |   0.0 |  0.00
Modify  | 0.23371    | 0.23371    | 0.23371    |   0.0 |  1.08
Other   |            | 0.01941    |            |       |  0.09

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       288868 ave      288868 max      288868 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288868
Ave neighs/atom = 36.1085
Neighbor list builds = 0
Dangerous builds = 0
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}"
flag: Temp = 0, Press = 0
next a
jump SELF top
variable a loop 2000
run 1000
Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      2000  -25111.201     -25111.201     -25421.589     -25421.589      300.19538      300.19538      253582.52      253582.52     -62.919893     -62.919893    
      3000  -25095.589     -25095.589     -25420.688     -25420.688      314.42315      314.42315      253774.21      253774.21     -187.63199     -187.63199    
Loop time of 21.6494 on 1 procs for 1000 steps with 8000 atoms

Performance: 3.991 ns/day, 6.014 hours/ns, 46.191 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.37      | 21.37      | 21.37      |   0.0 | 98.71
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026697   | 0.026697   | 0.026697   |   0.0 |  0.12
Output  | 7.951e-05  | 7.951e-05  | 7.951e-05  |   0.0 |  0.00
Modify  | 0.23383    | 0.23383    | 0.23383    |   0.0 |  1.08
Other   |            | 0.01897    |            |       |  0.09

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       288908 ave      288908 max      288908 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288908
Ave neighs/atom = 36.1135
Neighbor list builds = 0
Dangerous builds = 0
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}"
flag: Temp = 0, Press = 0
next a
jump SELF top
variable a loop 2000
run 1000
Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      3000  -25095.589     -25095.589     -25420.688     -25420.688      314.42315      314.42315      253774.21      253774.21     -187.63199     -187.63199    
      4000  -25103.961     -25103.961     -25418.134     -25418.134      303.85634      303.85634      253575.47      253575.47      118.78551      118.78551    
Loop time of 21.6208 on 1 procs for 1000 steps with 8000 atoms

Performance: 3.996 ns/day, 6.006 hours/ns, 46.252 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.341     | 21.341     | 21.341     |   0.0 | 98.71
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026528   | 0.026528   | 0.026528   |   0.0 |  0.12
Output  | 8.4569e-05 | 8.4569e-05 | 8.4569e-05 |   0.0 |  0.00
Modify  | 0.23416    | 0.23416    | 0.23416    |   0.0 |  1.08
Other   |            | 0.01868    |            |       |  0.09

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       288326 ave      288326 max      288326 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288326
Ave neighs/atom = 36.04075
Neighbor list builds = 0
Dangerous builds = 0
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}"
flag: Temp = 0, Press = 0
next a
jump SELF top
variable a loop 2000
run 1000
Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      4000  -25103.961     -25103.961     -25418.134     -25418.134      303.85634      303.85634      253575.47      253575.47      118.78551      118.78551    
      5000  -25100.101     -25100.101     -25424.319     -25424.319      313.5716       313.5716       253485.03      253485.03      191.34335      191.34335    
Loop time of 21.6723 on 1 procs for 1000 steps with 8000 atoms

Performance: 3.987 ns/day, 6.020 hours/ns, 46.142 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.392     | 21.392     | 21.392     |   0.0 | 98.71
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026559   | 0.026559   | 0.026559   |   0.0 |  0.12
Output  | 6.2768e-05 | 6.2768e-05 | 6.2768e-05 |   0.0 |  0.00
Modify  | 0.23502    | 0.23502    | 0.23502    |   0.0 |  1.08
Other   |            | 0.01867    |            |       |  0.09

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       288768 ave      288768 max      288768 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288768
Ave neighs/atom = 36.096
Neighbor list builds = 0
Dangerous builds = 0
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}"
flag: Temp = 317.004460915756, Press = 76.800388201829
next a
jump SELF top
variable a loop 2000
run 1000
Generated 0 of 0 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 = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 19 19 19
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 6.8
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      5000  -25100.101     -25100.101     -25424.319     -25424.319      313.5716       313.5716       253485.03      253485.03      191.34335      191.34335    
      6000  -25100.813     -25100.813     -25424.174     -25424.174      312.74289      312.74289      253365.73      253365.73      414.69642      414.69642    
Loop time of 21.6285 on 1 procs for 1000 steps with 8000 atoms

Performance: 3.995 ns/day, 6.008 hours/ns, 46.235 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 21.342     | 21.342     | 21.342     |   0.0 | 98.68
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.026606   | 0.026606   | 0.026606   |   0.0 |  0.12
Output  | 6.1726e-05 | 6.1726e-05 | 6.1726e-05 |   0.0 |  0.00
Modify  | 0.24071    | 0.24071    | 0.24071    |   0.0 |  1.11
Other   |            | 0.01872    |            |       |  0.09

Nlocal:           8000 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           6725 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       288798 ave      288798 max      288798 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288798
Ave neighs/atom = 36.09975
Neighbor list builds = 0
Dangerous builds = 0
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"
jump SELF 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 '${V}'  file output/vol_T313.15.out
253609.616879683

print "LAMMPS calculation completed"
LAMMPS calculation completed
quit 0