# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_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_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 -280.45431 -280.45431 -431.98687 -431.98687 293.15 293.15 180705.1 180705.1 895.68356 895.68356 1000 -13.456598 -13.456598 -161.19614 -161.19614 285.81216 285.81216 407417.56 407417.56 22.780709 22.780709 Loop time of 8.27026 on 1 procs for 1000 steps with 4000 atoms Performance: 10.447 ns/day, 2.297 hours/ns, 120.915 timesteps/s, 483.661 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 | 7.6118 | 7.6118 | 7.6118 | 0.0 | 92.04 Neigh | 0.46904 | 0.46904 | 0.46904 | 0.0 | 5.67 Comm | 0.031285 | 0.031285 | 0.031285 | 0.0 | 0.38 Output | 0.00011616 | 0.00011616 | 0.00011616 | 0.0 | 0.00 Modify | 0.14005 | 0.14005 | 0.14005 | 0.0 | 1.69 Other | | 0.01801 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5240 ave 5240 max 5240 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: 275924 ave 275924 max 275924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275924 Ave neighs/atom = 68.981 Neighbor list builds = 32 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 = ${P}" flag: Temp = 292.368040677142, Press = 29.1969033151785 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.324 | 4.324 | 4.324 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13.456598 -13.456598 -161.19614 -161.19614 285.81216 285.81216 407417.56 407417.56 22.780709 22.780709 2000 77.679503 77.679503 -72.676017 -72.676017 290.87295 290.87295 881279.31 881279.31 51.527318 51.527318 Loop time of 4.65064 on 1 procs for 1000 steps with 4000 atoms Performance: 18.578 ns/day, 1.292 hours/ns, 215.024 timesteps/s, 860.096 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1107 | 4.1107 | 4.1107 | 0.0 | 88.39 Neigh | 0.35902 | 0.35902 | 0.35902 | 0.0 | 7.72 Comm | 0.023955 | 0.023955 | 0.023955 | 0.0 | 0.52 Output | 7.0322e-05 | 7.0322e-05 | 7.0322e-05 | 0.0 | 0.00 Modify | 0.14136 | 0.14136 | 0.14136 | 0.0 | 3.04 Other | | 0.01552 | | | 0.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788 ave 3788 max 3788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129846 ave 129846 max 129846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129846 Ave neighs/atom = 32.4615 Neighbor list builds = 39 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.084875254371, Press = 40.6782725247014 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.95 | 3.95 | 3.95 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 77.679503 77.679503 -72.676017 -72.676017 290.87295 290.87295 881279.31 881279.31 51.527318 51.527318 3000 133.57789 133.57789 -17.898398 -17.898398 293.04114 293.04114 3803349.9 3803349.9 33.979972 33.979972 Loop time of 2.33156 on 1 procs for 1000 steps with 4000 atoms Performance: 37.057 ns/day, 0.648 hours/ns, 428.897 timesteps/s, 1.716 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6452 | 1.6452 | 1.6452 | 0.0 | 70.56 Neigh | 0.51578 | 0.51578 | 0.51578 | 0.0 | 22.12 Comm | 0.020972 | 0.020972 | 0.020972 | 0.0 | 0.90 Output | 7.0963e-05 | 7.0963e-05 | 7.0963e-05 | 0.0 | 0.00 Modify | 0.13588 | 0.13588 | 0.13588 | 0.0 | 5.83 Other | | 0.01366 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2079 ave 2079 max 2079 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31808 ave 31808 max 31808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31808 Ave neighs/atom = 7.952 Neighbor list builds = 99 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.757178060249, Press = 45.6466429368891 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.639 | 3.639 | 3.639 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 133.57789 133.57789 -17.898398 -17.898398 293.04114 293.04114 3803349.9 3803349.9 33.979972 33.979972 4000 145.33951 145.33951 -4.9996087 -4.9996087 290.84122 290.84122 20902534 20902534 7.3182905 7.3182905 Loop time of 1.20233 on 1 procs for 1000 steps with 4000 atoms Performance: 71.860 ns/day, 0.334 hours/ns, 831.717 timesteps/s, 3.327 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62445 | 0.62445 | 0.62445 | 0.0 | 51.94 Neigh | 0.40908 | 0.40908 | 0.40908 | 0.0 | 34.02 Comm | 0.019319 | 0.019319 | 0.019319 | 0.0 | 1.61 Output | 5.0034e-05 | 5.0034e-05 | 5.0034e-05 | 0.0 | 0.00 Modify | 0.13512 | 0.13512 | 0.13512 | 0.0 | 11.24 Other | | 0.01431 | | | 1.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1099 ave 1099 max 1099 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7034 ave 7034 max 7034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7034 Ave neighs/atom = 1.7585 Neighbor list builds = 183 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.881387418109, Press = 36.6796711893453 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 47 47 47 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.043 | 4.043 | 4.043 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 145.33951 145.33951 -4.9996087 -4.9996087 290.84122 290.84122 20902534 20902534 7.3182905 7.3182905 5000 149.50967 149.50967 -1.445664 -1.445664 292.03332 292.03332 1.1185693e+08 1.1185693e+08 1.4180654 1.4180654 Loop time of 1.00079 on 1 procs for 1000 steps with 4000 atoms Performance: 86.332 ns/day, 0.278 hours/ns, 999.209 timesteps/s, 3.997 Matom-step/s 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36313 | 0.36313 | 0.36313 | 0.0 | 36.28 Neigh | 0.46752 | 0.46752 | 0.46752 | 0.0 | 46.72 Comm | 0.020051 | 0.020051 | 0.020051 | 0.0 | 2.00 Output | 5.2128e-05 | 5.2128e-05 | 5.2128e-05 | 0.0 | 0.01 Modify | 0.13403 | 0.13403 | 0.13403 | 0.0 | 13.39 Other | | 0.01601 | | | 1.60 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 580 ave 580 max 580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1868 ave 1868 max 1868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1868 Ave neighs/atom = 0.467 Neighbor list builds = 295 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.936134254303, Press = 28.6130957674393 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 81 81 81 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.929 | 5.929 | 5.929 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 149.50967 149.50967 -1.445664 -1.445664 292.03332 292.03332 1.1185693e+08 1.1185693e+08 1.4180654 1.4180654 6000 152.9277 152.9277 -0.32040728 -0.32040728 296.46886 296.46886 5.7347879e+08 5.7347879e+08 0.28426204 0.28426204 Loop time of 1.78467 on 1 procs for 1000 steps with 4000 atoms Performance: 48.412 ns/day, 0.496 hours/ns, 560.327 timesteps/s, 2.241 Matom-step/s 96.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28825 | 0.28825 | 0.28825 | 0.0 | 16.15 Neigh | 1.2952 | 1.2952 | 1.2952 | 0.0 | 72.58 Comm | 0.028402 | 0.028402 | 0.028402 | 0.0 | 1.59 Output | 7.969e-05 | 7.969e-05 | 7.969e-05 | 0.0 | 0.00 Modify | 0.1493 | 0.1493 | 0.1493 | 0.0 | 8.37 Other | | 0.0234 | | | 1.31 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 303 ave 303 max 303 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522 Ave neighs/atom = 0.1305 Neighbor list builds = 463 Dangerous builds = 0 if "${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 573478790.714501 A^3 has become larger than 180705100.868827 A^3. Aborting calculation. Total wall time: 0:00:19