# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.253563612699509*${_u_distance} variable latticeconst_converted equal 5.253563612699509*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25356361269951 Lattice spacing in x,y,z = 5.2535636 5.2535636 5.2535636 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.535636 52.535636 52.535636) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.535636 52.535636 52.535636) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Jelinek_1972_Ar__MO_831902330215_004 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 144997.99128488 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144997.99128488/(1*1*${_u_distance}) variable V0_metal equal 144997.99128488/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144997.99128488*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144997.99128488 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_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 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 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_831902330215_004#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 -219.68009 -219.68009 -371.21264 -371.21264 293.15 293.15 144997.99 144997.99 1116.254 1116.254 1000 63.202515 63.202515 -88.015302 -88.015302 292.54112 292.54112 472142.42 472142.42 128.38729 128.38729 Loop time of 4.86039 on 1 procs for 1000 steps with 4000 atoms Performance: 17.776 ns/day, 1.350 hours/ns, 205.745 timesteps/s, 822.980 katom-step/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 | 4.1253 | 4.1253 | 4.1253 | 0.0 | 84.88 Neigh | 0.55506 | 0.55506 | 0.55506 | 0.0 | 11.42 Comm | 0.026674 | 0.026674 | 0.026674 | 0.0 | 0.55 Output | 9.6941e-05 | 9.6941e-05 | 9.6941e-05 | 0.0 | 0.00 Modify | 0.14031 | 0.14031 | 0.14031 | 0.0 | 2.89 Other | | 0.01296 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4023 ave 4023 max 4023 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: 149132 ave 149132 max 149132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149132 Ave neighs/atom = 37.283 Neighbor list builds = 46 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 = ${P}" flag: Temp = 293.668620547304, Press = 125.550490332361 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.85 | 3.85 | 3.85 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 63.202515 63.202515 -88.015302 -88.015302 292.54112 292.54112 472142.42 472142.42 128.38729 128.38729 2000 127.83899 127.83899 -25.692722 -25.692722 297.01751 297.01751 1997302.7 1997302.7 66.121954 66.121954 Loop time of 1.93365 on 1 procs for 1000 steps with 4000 atoms Performance: 44.682 ns/day, 0.537 hours/ns, 517.158 timesteps/s, 2.069 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3186 | 1.3186 | 1.3186 | 0.0 | 68.19 Neigh | 0.45294 | 0.45294 | 0.45294 | 0.0 | 23.42 Comm | 0.019173 | 0.019173 | 0.019173 | 0.0 | 0.99 Output | 6.891e-05 | 6.891e-05 | 6.891e-05 | 0.0 | 0.00 Modify | 0.13157 | 0.13157 | 0.13157 | 0.0 | 6.80 Other | | 0.01133 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2234 ave 2234 max 2234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37438 ave 37438 max 37438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37438 Ave neighs/atom = 9.3595 Neighbor list builds = 82 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.972728983765, Press = 104.318440062439 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 25 25 25 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.522 | 3.522 | 3.522 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 127.83899 127.83899 -25.692722 -25.692722 297.01751 297.01751 1997302.7 1997302.7 66.121954 66.121954 3000 145.38659 145.38659 -7.4886992 -7.4886992 295.74762 295.74762 10608227 10608227 14.411643 14.411643 Loop time of 0.887955 on 1 procs for 1000 steps with 4000 atoms Performance: 97.302 ns/day, 0.247 hours/ns, 1126.183 timesteps/s, 4.505 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42268 | 0.42268 | 0.42268 | 0.0 | 47.60 Neigh | 0.31273 | 0.31273 | 0.31273 | 0.0 | 35.22 Comm | 0.014897 | 0.014897 | 0.014897 | 0.0 | 1.68 Output | 4.3772e-05 | 4.3772e-05 | 4.3772e-05 | 0.0 | 0.00 Modify | 0.1261 | 0.1261 | 0.1261 | 0.0 | 14.20 Other | | 0.01151 | | | 1.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1185 ave 1185 max 1185 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 9170 ave 9170 max 9170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 9170 Ave neighs/atom = 2.2925 Neighbor list builds = 148 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.005964639785, Press = 70.8474548259687 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 44 44 44 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.86 | 3.86 | 3.86 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 145.38659 145.38659 -7.4886992 -7.4886992 295.74762 295.74762 10608227 10608227 14.411643 14.411643 4000 150.74382 150.74382 -2.0865822 -2.0865822 295.66078 295.66078 55695567 55695567 2.8895143 2.8895143 Loop time of 0.806884 on 1 procs for 1000 steps with 4000 atoms Performance: 107.079 ns/day, 0.224 hours/ns, 1239.335 timesteps/s, 4.957 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25732 | 0.25732 | 0.25732 | 0.0 | 31.89 Neigh | 0.38212 | 0.38212 | 0.38212 | 0.0 | 47.36 Comm | 0.015321 | 0.015321 | 0.015321 | 0.0 | 1.90 Output | 7.6283e-05 | 7.6283e-05 | 7.6283e-05 | 0.0 | 0.01 Modify | 0.13698 | 0.13698 | 0.13698 | 0.0 | 16.98 Other | | 0.01507 | | | 1.87 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 643 ave 643 max 643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2410 ave 2410 max 2410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2410 Ave neighs/atom = 0.6025 Neighbor list builds = 241 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.996947003974, Press = 50.2720066578467 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 76 76 76 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.434 | 5.434 | 5.434 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 150.74382 150.74382 -2.0865822 -2.0865822 295.66078 295.66078 55695567 55695567 2.8895143 2.8895143 5000 153.52965 153.52965 -0.40384421 -0.40384421 297.79477 297.79477 2.8429967e+08 2.8429967e+08 0.5757429 0.5757429 Loop time of 1.21322 on 1 procs for 1000 steps with 4000 atoms Performance: 71.216 ns/day, 0.337 hours/ns, 824.255 timesteps/s, 3.297 Matom-step/s 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18387 | 0.18387 | 0.18387 | 0.0 | 15.16 Neigh | 0.85622 | 0.85622 | 0.85622 | 0.0 | 70.57 Comm | 0.017836 | 0.017836 | 0.017836 | 0.0 | 1.47 Output | 4.3672e-05 | 4.3672e-05 | 4.3672e-05 | 0.0 | 0.00 Modify | 0.13725 | 0.13725 | 0.13725 | 0.0 | 11.31 Other | | 0.018 | | | 1.48 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 355 ave 355 max 355 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 610 ave 610 max 610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 610 Ave neighs/atom = 0.1525 Neighbor list builds = 389 Dangerous builds = 0 if "${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 284299671.008104 A^3 has become larger than 144997991.28488 A^3. Aborting calculation. Total wall time: 0:00:10