# 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 = (0.0000000 0.0000000 0.0000000) 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 = (0.0000000 0.0000000 0.0000000) to (63.035111 63.035111 63.035111)
  create_atoms CPU = 0.006 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_001
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_001#item-citation

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

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 109.788 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.787 ns/day, 30.497 hours/ns, 9.109 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 108.07     | 108.07     | 108.07     |   0.0 | 98.43
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21374    | 0.21374    | 0.21374    |   0.0 |  0.19
Output  | 0.00040135 | 0.00040135 | 0.00040135 |   0.0 |  0.00
Modify  | 1.3392     | 1.3392     | 1.3392     |   0.0 |  1.22
Other   |            | 0.166      |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      272000.0 ave      272000 max      272000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 272000
Ave neighs/atom = 34.000000
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
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 113.067 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.764 ns/day, 31.408 hours/ns, 8.844 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 111.36     | 111.36     | 111.36     |   0.0 | 98.49
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21173    | 0.21173    | 0.21173    |   0.0 |  0.19
Output  | 0.0002666  | 0.0002666  | 0.0002666  |   0.0 |  0.00
Modify  | 1.3343     | 1.3343     | 1.3343     |   0.0 |  1.18
Other   |            | 0.1656     |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      288868.0 ave      288868 max      288868 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288868
Ave neighs/atom = 36.108500
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
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 114.766 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.753 ns/day, 31.879 hours/ns, 8.713 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 113.03     | 113.03     | 113.03     |   0.0 | 98.49
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21089    | 0.21089    | 0.21089    |   0.0 |  0.18
Output  | 0.00026249 | 0.00026249 | 0.00026249 |   0.0 |  0.00
Modify  | 1.3579     | 1.3579     | 1.3579     |   0.0 |  1.18
Other   |            | 0.1672     |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      288908.0 ave      288908 max      288908 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288908
Ave neighs/atom = 36.113500
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
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 113.792 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.759 ns/day, 31.609 hours/ns, 8.788 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 112.06     | 112.06     | 112.06     |   0.0 | 98.48
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21462    | 0.21462    | 0.21462    |   0.0 |  0.19
Output  | 0.00026486 | 0.00026486 | 0.00026486 |   0.0 |  0.00
Modify  | 1.3509     | 1.3509     | 1.3509     |   0.0 |  1.19
Other   |            | 0.1676     |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      288326.0 ave      288326 max      288326 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288326
Ave neighs/atom = 36.040750
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
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 114.243 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.756 ns/day, 31.734 hours/ns, 8.753 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 112.51     | 112.51     | 112.51     |   0.0 | 98.48
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21233    | 0.21233    | 0.21233    |   0.0 |  0.19
Output  | 0.00021967 | 0.00021967 | 0.00021967 |   0.0 |  0.00
Modify  | 1.3537     | 1.3537     | 1.3537     |   0.0 |  1.18
Other   |            | 0.1671     |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      288768.0 ave      288768 max      288768 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288768
Ave neighs/atom = 36.096000
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
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 113.64 on 1 procs for 1000 steps with 8000 atoms

Performance: 0.760 ns/day, 31.567 hours/ns, 8.800 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 111.89     | 111.89     | 111.89     |   0.0 | 98.46
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.21292    | 0.21292    | 0.21292    |   0.0 |  0.19
Output  | 0.0002153  | 0.0002153  | 0.0002153  |   0.0 |  0.00
Modify  | 1.3707     | 1.3707     | 1.3707     |   0.0 |  1.21
Other   |            | 0.1667     |            |       |  0.15

Nlocal:        8000.00 ave        8000 max        8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6725.00 ave        6725 max        6725 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      288798.0 ave      288798 max      288798 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 288798
Ave neighs/atom = 36.099750
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