# 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 3.8000004738569264*${_u_distance}
variable latticeconst_converted equal 3.8000004738569264*1
lattice       fcc  ${latticeconst_converted}
lattice       fcc  3.80000047385693
Lattice spacing in x,y,z = 3.8000005 3.8000005 3.8000005
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 (38.000005 38.000005 38.000005)
  1 by 1 by 1 MPI processor grid
create_atoms  1 box
Created 4000 atoms
  using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (38.000005 38.000005 38.000005)
  create_atoms CPU = 0.001 seconds

variable mass_converted equal 102.9055*${_u_mass}
variable mass_converted equal 102.9055*1

kim_interactions Rh

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

kim interactions Rh
#=== BEGIN kim interactions ==================================
variable kim_update equal 0
variable kim_periodic equal 1
pair_style adp
pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXgCYqfc/NiRh.adp.txt Rh
#=== END kim interactions ====================================


mass          1 ${mass_converted}
mass          1 102.9055

# initial volume
variable      v equal vol        # assign formula
variable      V0 equal ${v}    # evaluate initial value
variable      V0 equal 54872.0205274848    
variable      V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 54872.0205274848/(${_u_distance}*${_u_distance}*${_u_distance})
variable      V0_metal equal 54872.0205274848/(1*${_u_distance}*${_u_distance})
variable      V0_metal equal 54872.0205274848/(1*1*${_u_distance})
variable      V0_metal equal 54872.0205274848/(1*1*1)
variable      V0_metal_times1000 equal ${V0_metal}*1000
variable      V0_metal_times1000 equal 54872.0205274848*1000

print "Initial system volume: ${V0_metal} Angstroms^3"
Initial system volume: 54872.0205274848 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 293.15*${_u_temperature}
variable temp_converted equal 293.15*1
variable Tdamp_converted equal 0.1*${_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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted}               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 293.15 293.15 ${Tdamp_converted}               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 293.15 293.15 0.1               iso ${press_converted} ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 293.15 293.15 0.1               iso 0 ${press_converted} ${Pdamp_converted}
fix           ensemble all npt temp 293.15 293.15 0.1               iso 0 0 ${Pdamp_converted}
fix           ensemble all npt temp 293.15 293.15 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  "293.15 - 0.2"
variable      T_up  equal  "293.15 + 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/SM_306597220004_000#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 = 8.8454711
  ghost atom cutoff = 8.8454711
  binsize = 4.4227355, bins = 9 9 9
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair adp, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
       0   -22848.467   -22848.467       -23000       -23000       293.15       293.15    54872.021    54872.021    2949.7644    2949.7644 
    1000   -22683.599   -22683.599   -22840.864   -22840.864    304.23968    304.23968     55212.55     55212.55    1156.7548    1156.7548 
Loop time of 80.4445 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.074 ns/day, 22.346 hours/ns, 12.431 timesteps/s
64.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 79.578     | 79.578     | 79.578     |   0.0 | 98.92
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.096019   | 0.096019   | 0.096019   |   0.0 |  0.12
Output  | 0.00043001 | 0.00043001 | 0.00043001 |   0.0 |  0.00
Modify  | 0.65221    | 0.65221    | 0.65221    |   0.0 |  0.81
Other   |            | 0.118      |            |       |  0.15

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        400000.0 ave      400000 max      400000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 400000
Ave neighs/atom = 100.00000
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
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    1000   -22683.599   -22683.599   -22840.864   -22840.864    304.23968    304.23968     55212.55     55212.55    1156.7548    1156.7548 
    2000   -22696.247   -22696.247   -22851.046   -22851.046    299.47049    299.47049    55235.231    55235.231   -718.36174   -718.36174 
Loop time of 68.6856 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.258 ns/day, 19.079 hours/ns, 14.559 timesteps/s
76.3% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 68.035     | 68.035     | 68.035     |   0.0 | 99.05
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.13408    | 0.13408    | 0.13408    |   0.0 |  0.20
Output  | 0.00016913 | 0.00016913 | 0.00016913 |   0.0 |  0.00
Modify  | 0.45137    | 0.45137    | 0.45137    |   0.0 |  0.66
Other   |            | 0.06506    |            |       |  0.09

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        406846.0 ave      406846 max      406846 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 406846
Ave neighs/atom = 101.71150
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
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    2000   -22696.247   -22696.247   -22851.046   -22851.046    299.47049    299.47049    55235.231    55235.231   -718.36174   -718.36174 
    3000   -22691.567   -22691.567   -22845.764   -22845.764    298.30426    298.30426    55248.791    55248.791   -851.50172   -851.50172 
Loop time of 59.7316 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.446 ns/day, 16.592 hours/ns, 16.742 timesteps/s
85.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 59.156     | 59.156     | 59.156     |   0.0 | 99.04
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.074662   | 0.074662   | 0.074662   |   0.0 |  0.12
Output  | 0.00017201 | 0.00017201 | 0.00017201 |   0.0 |  0.00
Modify  | 0.41568    | 0.41568    | 0.41568    |   0.0 |  0.70
Other   |            | 0.08538    |            |       |  0.14

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        405974.0 ave      405974 max      405974 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 405974
Ave neighs/atom = 101.49350
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
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    3000   -22691.567   -22691.567   -22845.764   -22845.764    298.30426    298.30426    55248.791    55248.791   -851.50172   -851.50172 
    4000   -22693.132   -22693.132   -22847.966   -22847.966    299.53815    299.53815    55271.411    55271.411   -1980.8686   -1980.8686 
Loop time of 52.7254 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.639 ns/day, 14.646 hours/ns, 18.966 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    | 52.249     | 52.249     | 52.249     |   0.0 | 99.10
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.075898   | 0.075898   | 0.075898   |   0.0 |  0.14
Output  | 0.00037477 | 0.00037477 | 0.00037477 |   0.0 |  0.00
Modify  | 0.3456     | 0.3456     | 0.3456     |   0.0 |  0.66
Other   |            | 0.0546     |            |       |  0.10

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        406087.0 ave      406087 max      406087 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 406087
Ave neighs/atom = 101.52175
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
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    4000   -22693.132   -22693.132   -22847.966   -22847.966    299.53815    299.53815    55271.411    55271.411   -1980.8686   -1980.8686 
    5000   -22693.987   -22693.987   -22847.746   -22847.746    297.45761    297.45761    55245.321    55245.321    -974.6334    -974.6334 
Loop time of 52.4474 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.647 ns/day, 14.569 hours/ns, 19.067 timesteps/s
98.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 51.971     | 51.971     | 51.971     |   0.0 | 99.09
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.074281   | 0.074281   | 0.074281   |   0.0 |  0.14
Output  | 0.00013686 | 0.00013686 | 0.00013686 |   0.0 |  0.00
Modify  | 0.34876    | 0.34876    | 0.34876    |   0.0 |  0.66
Other   |            | 0.05371    |            |       |  0.10

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        405630.0 ave      405630 max      405630 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 405630
Ave neighs/atom = 101.40750
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 = 294.707875795261, Press = -180.218856384924
next a
jump SELF top
variable a loop 2000
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    5000   -22693.987   -22693.987   -22847.746   -22847.746    297.45761    297.45761    55245.321    55245.321    -974.6334    -974.6334 
    6000   -22691.156   -22691.156   -22843.295   -22843.295    294.32304    294.32304    55176.535    55176.535    2742.6398    2742.6398 
Loop time of 53.052 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.629 ns/day, 14.737 hours/ns, 18.849 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 52.567     | 52.567     | 52.567     |   0.0 | 99.09
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.075446   | 0.075446   | 0.075446   |   0.0 |  0.14
Output  | 0.00012269 | 0.00012269 | 0.00012269 |   0.0 |  0.00
Modify  | 0.35518    | 0.35518    | 0.35518    |   0.0 |  0.67
Other   |            | 0.05389    |            |       |  0.10

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        406055.0 ave      406055 max      406055 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 406055
Ave neighs/atom = 101.51375
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 = 292.718699076944, Press = 6.65914521590872
next a
jump SELF top
variable a loop 2000
run 1000
Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes
Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 
    6000   -22691.156   -22691.156   -22843.295   -22843.295    294.32304    294.32304    55176.535    55176.535    2742.6398    2742.6398 
    7000    -22695.34    -22695.34   -22843.733   -22843.733     287.0753     287.0753     55235.41     55235.41   -151.24697   -151.24697 
Loop time of 52.209 on 1 procs for 1000 steps with 4000 atoms

Performance: 1.655 ns/day, 14.502 hours/ns, 19.154 timesteps/s
97.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 51.738     | 51.738     | 51.738     |   0.0 | 99.10
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.07409    | 0.07409    | 0.07409    |   0.0 |  0.14
Output  | 0.00013277 | 0.00013277 | 0.00013277 |   0.0 |  0.00
Modify  | 0.34259    | 0.34259    | 0.34259    |   0.0 |  0.66
Other   |            | 0.05427    |            |       |  0.10

Nlocal:        4000.00 ave        4000 max        4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        8195.00 ave        8195 max        8195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        406622.0 ave      406622 max      406622 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 406622
Ave neighs/atom = 101.65550
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_T293.15.out"  else  "print 'not_converged'  file output/vol_T293.15.out"
print '${V}'  file output/vol_T293.15.out
55230.8922679688

print "LAMMPS calculation completed"
LAMMPS calculation completed
quit 0