# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.262299403548241*${_u_distance} variable latticeconst_converted equal 5.262299403548241*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26229940354824 Lattice spacing in x,y,z = 5.2622994 5.2622994 5.2622994 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 145722.516377902 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 145722.516377902*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 145722.516377902 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # 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 "253.15 - 1.0" variable T_up equal "253.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # 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 Project: doi: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_071460865933_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 = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 130.62934 130.62934 -0.2267577 -0.2267577 253.15 253.15 145722.52 145722.52 959.14973 959.14973 1000 131.08909 131.08909 1.0286437 1.0286437 251.61075 251.61075 1055867.4 1055867.4 134.27558 134.27558 Loop time of 5.057 on 1 procs for 1000 steps with 4000 atoms Performance: 17.085 ns/day, 1.405 hours/ns, 197.746 timesteps/s, 790.982 katom-step/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 | 4.17 | 4.17 | 4.17 | 0.0 | 82.46 Neigh | 0.71841 | 0.71841 | 0.71841 | 0.0 | 14.21 Comm | 0.026164 | 0.026164 | 0.026164 | 0.0 | 0.52 Output | 7.96e-05 | 7.96e-05 | 7.96e-05 | 0.0 | 0.00 Modify | 0.1285 | 0.1285 | 0.1285 | 0.0 | 2.54 Other | | 0.0138 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2894 ave 2894 max 2894 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: 62934 ave 62934 max 62934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62934 Ave neighs/atom = 15.7335 Neighbor list builds = 82 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 = ${P}" flag: Temp = 251.6041693391, Press = 146.586147790171 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.491 | 3.491 | 3.491 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 131.08909 131.08909 1.0286437 1.0286437 251.61075 251.61075 1055867.4 1055867.4 134.27558 134.27558 2000 130.27401 130.27401 0.14983308 0.14983308 251.73404 251.73404 5929132.3 5929132.3 23.52147 23.52147 Loop time of 1.38509 on 1 procs for 1000 steps with 4000 atoms Performance: 62.379 ns/day, 0.385 hours/ns, 721.973 timesteps/s, 2.888 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81957 | 0.81957 | 0.81957 | 0.0 | 59.17 Neigh | 0.40333 | 0.40333 | 0.40333 | 0.0 | 29.12 Comm | 0.018207 | 0.018207 | 0.018207 | 0.0 | 1.31 Output | 5.4702e-05 | 5.4702e-05 | 5.4702e-05 | 0.0 | 0.00 Modify | 0.13135 | 0.13135 | 0.13135 | 0.0 | 9.48 Other | | 0.01258 | | | 0.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1451 ave 1451 max 1451 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11404 ave 11404 max 11404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11404 Ave neighs/atom = 2.851 Neighbor list builds = 127 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.681440714695, Press = 70.2610418823636 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 36 36 36 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 130.27401 130.27401 0.14983308 0.14983308 251.73404 251.73404 5929132.3 5929132.3 23.52147 23.52147 3000 130.20417 130.20417 0.055684911 0.055684911 251.78107 251.78107 30733462 30733462 4.5268724 4.5268724 Loop time of 0.821323 on 1 procs for 1000 steps with 4000 atoms Performance: 105.196 ns/day, 0.228 hours/ns, 1217.548 timesteps/s, 4.870 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33919 | 0.33919 | 0.33919 | 0.0 | 41.30 Neigh | 0.31908 | 0.31908 | 0.31908 | 0.0 | 38.85 Comm | 0.016378 | 0.016378 | 0.016378 | 0.0 | 1.99 Output | 3.6268e-05 | 3.6268e-05 | 3.6268e-05 | 0.0 | 0.00 Modify | 0.13273 | 0.13273 | 0.13273 | 0.0 | 16.16 Other | | 0.0139 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 849 ave 849 max 849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2194 ave 2194 max 2194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2194 Ave neighs/atom = 0.5485 Neighbor list builds = 203 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 251.719445215444, Press = 42.242299795767 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 62 62 62 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 130.20417 130.20417 0.055684911 0.055684911 251.78107 251.78107 30733462 30733462 4.5268724 4.5268724 4000 130.16954 130.16954 0.004165563 0.004165563 251.81374 251.81374 1.5240086e+08 1.5240086e+08 0.91239359 0.91239359 Loop time of 0.923752 on 1 procs for 1000 steps with 4000 atoms Performance: 93.532 ns/day, 0.257 hours/ns, 1082.541 timesteps/s, 4.330 Matom-step/s 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23994 | 0.23994 | 0.23994 | 0.0 | 25.97 Neigh | 0.51385 | 0.51385 | 0.51385 | 0.0 | 55.63 Comm | 0.017978 | 0.017978 | 0.017978 | 0.0 | 1.95 Output | 3.707e-05 | 3.707e-05 | 3.707e-05 | 0.0 | 0.00 Modify | 0.13523 | 0.13523 | 0.13523 | 0.0 | 14.64 Other | | 0.01672 | | | 1.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 484 ave 484 max 484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 458 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458 Ave neighs/atom = 0.1145 Neighbor list builds = 308 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 152400861.805841 A^3 has become larger than 145722516.377902 A^3. Aborting calculation. Total wall time: 0:00:08