# 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 4.049998879432679*${_u_distance}
variable latticeconst_converted equal 4.049998879432679*1
lattice       fcc  ${latticeconst_converted}
lattice       fcc  4.04999887943268
Lattice spacing in x,y,z = 4.0499989 4.0499989 4.0499989
region        simbox  block 0 10 0 10 0 10 units lattice
create_box    1 simbox
Created orthogonal box = (0 0 0) to (40.499989 40.499989 40.499989)
  1 by 1 by 1 MPI processor grid
create_atoms  1 box
Created 4000 atoms
  using lattice units in orthogonal box = (0 0 0) to (40.499989 40.499989 40.499989)
  create_atoms CPU = 0.001 seconds

variable mass_converted equal 26.981538*${_u_mass}
variable mass_converted equal 26.981538*1

kim_interactions Al

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

kim interactions Al
#=== BEGIN kim interactions ==================================
pair_style kim MEAM_LAMMPS_PascuetFernandez_2015_Al__MO_315820974149_002
pair_coeff * * Al
#=== END kim interactions ====================================


mass          1 ${mass_converted}
mass          1 26.981538

# initial volume
variable      v equal vol        # assign formula
variable      V0 equal ${v}    # evaluate initial value
variable      V0 equal 66430.0698596988    
variable      V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 66430.0698596988/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 66430.0698596988/(1*${_u_distance}*${_u_distance})
variable      V0_metal equal 66430.0698596988/(1*1*${_u_distance})
variable      V0_metal equal 66430.0698596988/(1*1*1)
variable      V0_metal_times1000 equal ${V0_metal}*1000
variable      V0_metal_times1000 equal 66430.0698596988*1000

print "Initial system volume: ${V0_metal} Angstroms^3"
Initial system volume: 66430.0698596988 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_315820974149_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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
         0  -13278.089     -13278.089     -13439.96      -13439.96       313.15         313.15         66430.07       66430.07       2602.6968      2602.6968    
      1000  -13089.834     -13089.834     -13256.313     -13256.313      322.06404      322.06404      68223.394      68223.394     -607.70477     -607.70477    
Loop time of 35.8898 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.407 ns/day, 9.969 hours/ns, 27.863 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 35.728     | 35.728     | 35.728     |   0.0 | 99.55
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.023342   | 0.023342   | 0.023342   |   0.0 |  0.07
Output  | 0.00018212 | 0.00018212 | 0.00018212 |   0.0 |  0.00
Modify  | 0.12434    | 0.12434    | 0.12434    |   0.0 |  0.35
Other   |            | 0.01407    |            |       |  0.04

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       312000 ave      312000 max      312000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 312000
Ave neighs/atom = 78
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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      1000  -13089.834     -13089.834     -13256.313     -13256.313      322.06404      322.06404      68223.394      68223.394     -607.70477     -607.70477    
      2000  -13109.897     -13109.897     -13269.249     -13269.249      308.27755      308.27755      67969.693      67969.693      630.06238      630.06238    
Loop time of 38.4962 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.244 ns/day, 10.693 hours/ns, 25.977 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    | 38.334     | 38.334     | 38.334     |   0.0 | 99.58
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.023155   | 0.023155   | 0.023155   |   0.0 |  0.06
Output  | 0.00017828 | 0.00017828 | 0.00017828 |   0.0 |  0.00
Modify  | 0.12612    | 0.12612    | 0.12612    |   0.0 |  0.33
Other   |            | 0.01273    |            |       |  0.03

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       320136 ave      320136 max      320136 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 320136
Ave neighs/atom = 80.034
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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      2000  -13109.897     -13109.897     -13269.249     -13269.249      308.27755      308.27755      67969.693      67969.693      630.06238      630.06238    
      3000  -13099.173     -13099.173     -13262.608     -13262.608      316.17663      316.17663      68114.863      68114.863     -109.58756     -109.58756    
Loop time of 37.7181 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.291 ns/day, 10.477 hours/ns, 26.512 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    | 37.559     | 37.559     | 37.559     |   0.0 | 99.58
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.022974   | 0.022974   | 0.022974   |   0.0 |  0.06
Output  | 0.0001134  | 0.0001134  | 0.0001134  |   0.0 |  0.00
Modify  | 0.12324    | 0.12324    | 0.12324    |   0.0 |  0.33
Other   |            | 0.01315    |            |       |  0.03

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       320688 ave      320688 max      320688 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 320688
Ave neighs/atom = 80.172
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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      3000  -13099.173     -13099.173     -13262.608     -13262.608      316.17663      316.17663      68114.863      68114.863     -109.58756     -109.58756    
      4000  -13106.577     -13106.577     -13267.43      -13267.43       311.18048      311.18048      68056.575      68056.575     -4.3449882     -4.3449882    
Loop time of 38.4449 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.247 ns/day, 10.679 hours/ns, 26.011 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 38.281     | 38.281     | 38.281     |   0.0 | 99.58
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.02408    | 0.02408    | 0.02408    |   0.0 |  0.06
Output  | 0.00017082 | 0.00017082 | 0.00017082 |   0.0 |  0.00
Modify  | 0.12563    | 0.12563    | 0.12563    |   0.0 |  0.33
Other   |            | 0.01351    |            |       |  0.04

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       320410 ave      320410 max      320410 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 320410
Ave neighs/atom = 80.1025
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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      4000  -13106.577     -13106.577     -13267.43      -13267.43       311.18048      311.18048      68056.575      68056.575     -4.3449882     -4.3449882    
      5000  -13099.853     -13099.853     -13264.029     -13264.029      317.60972      317.60972      68091.679      68091.679      5.0491289      5.0491289    
Loop time of 38.2336 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.260 ns/day, 10.620 hours/ns, 26.155 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 38.076     | 38.076     | 38.076     |   0.0 | 99.59
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.022746   | 0.022746   | 0.022746   |   0.0 |  0.06
Output  | 6.1226e-05 | 6.1226e-05 | 6.1226e-05 |   0.0 |  0.00
Modify  | 0.12296    | 0.12296    | 0.12296    |   0.0 |  0.32
Other   |            | 0.01181    |            |       |  0.03

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       320602 ave      320602 max      320602 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 320602
Ave neighs/atom = 80.1505
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 = 315.64515687793, Press = -44.0502307653753
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 = 7
  ghost atom cutoff = 7
  binsize = 3.5, bins = 12 12 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 7
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.61 | 4.61 | 4.61 Mbytes
   Step         TotEng     v_etotal_metal     PotEng       v_pe_metal        Temp        v_T_metal        Volume       v_V_metal        Press        v_P_metal   
      5000  -13099.853     -13099.853     -13264.029     -13264.029      317.60972      317.60972      68091.679      68091.679      5.0491289      5.0491289    
      6000  -13107.272     -13107.272     -13270.226     -13270.226      315.24426      315.24426      68091.279      68091.279     -596.66256     -596.66256    
Loop time of 37.6107 on 1 procs for 1000 steps with 4000 atoms

Performance: 2.297 ns/day, 10.447 hours/ns, 26.588 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 37.452     | 37.452     | 37.452     |   0.0 | 99.58
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.02208    | 0.02208    | 0.02208    |   0.0 |  0.06
Output  | 7.409e-05  | 7.409e-05  | 7.409e-05  |   0.0 |  0.00
Modify  | 0.12541    | 0.12541    | 0.12541    |   0.0 |  0.33
Other   |            | 0.01153    |            |       |  0.03

Nlocal:           4000 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5841 ave        5841 max        5841 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:       320522 ave      320522 max      320522 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 320522
Ave neighs/atom = 80.1305
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
68070.4901416965

print "LAMMPS calculation completed"
LAMMPS calculation completed
quit 0