# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.653579071164131*${_u_distance} variable latticeconst_converted equal 5.653579071164131*1 lattice fcc ${latticeconst_converted} lattice fcc 5.65357907116413 Lattice spacing in x,y,z = 5.6535791 5.6535791 5.6535791 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (56.535791 56.535791 56.535791) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (56.535791 56.535791 56.535791) create_atoms CPU = 0.001 seconds variable mass_converted equal 83.798*${_u_mass} variable mass_converted equal 83.798*1 kim interactions Kr #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Kr__MO_995724792024_004 pair_coeff * * Kr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 83.798 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 180705.100868827 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(1*1*${_u_distance}) variable V0_metal equal 180705.100868827/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 180705.100868827*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 180705.100868827 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_995724792024_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 = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 10 10 10 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) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -290.79254 -290.79254 -431.98687 -431.98687 273.15 273.15 180705.1 180705.1 834.57604 834.57604 1000 -37.92309 -37.92309 -175.40805 -175.40805 265.97398 265.97398 377513.89 377513.89 7.826947 7.826947 Loop time of 7.93153 on 1 procs for 1000 steps with 4000 atoms Performance: 10.893 ns/day, 2.203 hours/ns, 126.079 timesteps/s, 504.316 katom-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 | 7.3507 | 7.3507 | 7.3507 | 0.0 | 92.68 Neigh | 0.40632 | 0.40632 | 0.40632 | 0.0 | 5.12 Comm | 0.028195 | 0.028195 | 0.028195 | 0.0 | 0.36 Output | 9.7583e-05 | 9.7583e-05 | 9.7583e-05 | 0.0 | 0.00 Modify | 0.13237 | 0.13237 | 0.13237 | 0.0 | 1.67 Other | | 0.01388 | | | 0.18 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5431 ave 5431 max 5431 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: 296560 ave 296560 max 296560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296560 Ave neighs/atom = 74.14 Neighbor list builds = 29 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 = ${P}" flag: Temp = 272.477623046701, Press = 19.0518746961475 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.707 | 4.707 | 4.707 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -37.92309 -37.92309 -175.40805 -175.40805 265.97398 265.97398 377513.89 377513.89 7.826947 7.826947 2000 44.660981 44.660981 -96.615352 -96.615352 273.30865 273.30865 672502.74 672502.74 37.244012 37.244012 Loop time of 4.89982 on 1 procs for 1000 steps with 4000 atoms Performance: 17.633 ns/day, 1.361 hours/ns, 204.089 timesteps/s, 816.357 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4488 | 4.4488 | 4.4488 | 0.0 | 90.80 Neigh | 0.27903 | 0.27903 | 0.27903 | 0.0 | 5.69 Comm | 0.022324 | 0.022324 | 0.022324 | 0.0 | 0.46 Output | 6.1776e-05 | 6.1776e-05 | 6.1776e-05 | 0.0 | 0.00 Modify | 0.13671 | 0.13671 | 0.13671 | 0.0 | 2.79 Other | | 0.01288 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4231 ave 4231 max 4231 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169082 ave 169082 max 169082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169082 Ave neighs/atom = 42.2705 Neighbor list builds = 29 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.674274471844, Press = 24.6964362825922 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.943 | 3.943 | 3.943 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 44.660981 44.660981 -96.615352 -96.615352 273.30865 273.30865 672502.74 672502.74 37.244012 37.244012 3000 106.80191 106.80191 -29.061755 -29.061755 262.83747 262.83747 2282816.8 2282816.8 39.848265 39.848265 Loop time of 2.78975 on 1 procs for 1000 steps with 4000 atoms Performance: 30.971 ns/day, 0.775 hours/ns, 358.455 timesteps/s, 1.434 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1632 | 2.1632 | 2.1632 | 0.0 | 77.54 Neigh | 0.4584 | 0.4584 | 0.4584 | 0.0 | 16.43 Comm | 0.020091 | 0.020091 | 0.020091 | 0.0 | 0.72 Output | 6.2827e-05 | 6.2827e-05 | 6.2827e-05 | 0.0 | 0.00 Modify | 0.1354 | 0.1354 | 0.1354 | 0.0 | 4.85 Other | | 0.0126 | | | 0.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2554 ave 2554 max 2554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51680 ave 51680 max 51680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51680 Ave neighs/atom = 12.92 Neighbor list builds = 74 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.656224995854, Press = 34.1016406951962 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 23 23 23 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.602 | 3.602 | 3.602 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 106.80191 106.80191 -29.061755 -29.061755 262.83747 262.83747 2282816.8 2282816.8 39.848265 39.848265 4000 135.18282 135.18282 -7.3090365 -7.3090365 275.66017 275.66017 12159995 12159995 11.585556 11.585556 Loop time of 1.38502 on 1 procs for 1000 steps with 4000 atoms Performance: 62.382 ns/day, 0.385 hours/ns, 722.011 timesteps/s, 2.888 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79779 | 0.79779 | 0.79779 | 0.0 | 57.60 Neigh | 0.42297 | 0.42297 | 0.42297 | 0.0 | 30.54 Comm | 0.0177 | 0.0177 | 0.0177 | 0.0 | 1.28 Output | 4.3311e-05 | 4.3311e-05 | 4.3311e-05 | 0.0 | 0.00 Modify | 0.13338 | 0.13338 | 0.13338 | 0.0 | 9.63 Other | | 0.01314 | | | 0.95 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1325 ave 1325 max 1325 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11164 ave 11164 max 11164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11164 Ave neighs/atom = 2.791 Neighbor list builds = 152 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.722232945895, Press = 31.1468372557546 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 39 39 39 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.834 | 3.834 | 3.834 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 135.18282 135.18282 -7.3090365 -7.3090365 275.66017 275.66017 12159995 12159995 11.585556 11.585556 5000 139.468 139.468 -2.3476293 -2.3476293 274.35195 274.35195 66234667 66234667 2.2276876 2.2276876 Loop time of 0.964434 on 1 procs for 1000 steps with 4000 atoms Performance: 89.586 ns/day, 0.268 hours/ns, 1036.878 timesteps/s, 4.148 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40234 | 0.40234 | 0.40234 | 0.0 | 41.72 Neigh | 0.39673 | 0.39673 | 0.39673 | 0.0 | 41.14 Comm | 0.017605 | 0.017605 | 0.017605 | 0.0 | 1.83 Output | 4.3001e-05 | 4.3001e-05 | 4.3001e-05 | 0.0 | 0.00 Modify | 0.13293 | 0.13293 | 0.13293 | 0.0 | 13.78 Other | | 0.01479 | | | 1.53 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 675 ave 675 max 675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2822 ave 2822 max 2822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2822 Ave neighs/atom = 0.7055 Neighbor list builds = 259 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.676696242984, Press = 24.9204890500641 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 68 68 68 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 139.468 139.468 -2.3476293 -2.3476293 274.35195 274.35195 66234667 66234667 2.2276876 2.2276876 6000 137.72146 137.72146 -0.57955815 -0.57955815 267.55271 267.55271 3.4451891e+08 3.4451891e+08 0.42657849 0.42657849 Loop time of 1.21944 on 1 procs for 1000 steps with 4000 atoms Performance: 70.852 ns/day, 0.339 hours/ns, 820.051 timesteps/s, 3.280 Matom-step/s 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30255 | 0.30255 | 0.30255 | 0.0 | 24.81 Neigh | 0.74224 | 0.74224 | 0.74224 | 0.0 | 60.87 Comm | 0.022351 | 0.022351 | 0.022351 | 0.0 | 1.83 Output | 4.4814e-05 | 4.4814e-05 | 4.4814e-05 | 0.0 | 0.00 Modify | 0.13421 | 0.13421 | 0.13421 | 0.0 | 11.01 Other | | 0.01804 | | | 1.48 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 351 ave 351 max 351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 808 Ave neighs/atom = 0.202 Neighbor list builds = 414 Dangerous builds = 0 if "${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 344518910.824684 A^3 has become larger than 180705100.868827 A^3. Aborting calculation. Total wall time: 0:00:19