# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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 -270.11609 -270.11609 -431.98687 -431.98687 313.15 313.15 180705.1 180705.1 956.79109 956.79109 1000 10.026698 10.026698 -147.76215 -147.76215 305.25323 305.25323 441144.6 441144.6 34.87435 34.87435 Loop time of 7.5784 on 1 procs for 1000 steps with 4000 atoms Performance: 11.401 ns/day, 2.105 hours/ns, 131.954 timesteps/s, 527.816 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 | 6.9246 | 6.9246 | 6.9246 | 0.0 | 91.37 Neigh | 0.47002 | 0.47002 | 0.47002 | 0.0 | 6.20 Comm | 0.029234 | 0.029234 | 0.029234 | 0.0 | 0.39 Output | 8.1894e-05 | 8.1894e-05 | 8.1894e-05 | 0.0 | 0.00 Modify | 0.138 | 0.138 | 0.138 | 0.0 | 1.82 Other | | 0.01646 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5044 ave 5044 max 5044 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: 255844 ave 255844 max 255844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255844 Ave neighs/atom = 63.961 Neighbor list builds = 35 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 = ${P}" flag: Temp = 312.285498385226, Press = 44.3489596512832 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.322 | 4.322 | 4.322 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 10.026698 10.026698 -147.76215 -147.76215 305.25323 305.25323 441144.6 441144.6 34.87435 34.87435 2000 108.29195 108.29195 -54.437893 -54.437893 314.81192 314.81192 1148146.7 1148146.7 72.027985 72.027985 Loop time of 4.03835 on 1 procs for 1000 steps with 4000 atoms Performance: 21.395 ns/day, 1.122 hours/ns, 247.626 timesteps/s, 990.503 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4595 | 3.4595 | 3.4595 | 0.0 | 85.67 Neigh | 0.40919 | 0.40919 | 0.40919 | 0.0 | 10.13 Comm | 0.021878 | 0.021878 | 0.021878 | 0.0 | 0.54 Output | 6.2948e-05 | 6.2948e-05 | 6.2948e-05 | 0.0 | 0.00 Modify | 0.13525 | 0.13525 | 0.13525 | 0.0 | 3.35 Other | | 0.01249 | | | 0.31 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3406 ave 3406 max 3406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100410 ave 100410 max 100410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100410 Ave neighs/atom = 25.1025 Neighbor list builds = 50 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.578337421264, Press = 57.9152578180441 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.952 | 3.952 | 3.952 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 108.29195 108.29195 -54.437893 -54.437893 314.81192 314.81192 1148146.7 1148146.7 72.027985 72.027985 3000 149.88876 149.88876 -12.708996 -12.708996 314.55638 314.55638 5688296 5688296 26.694245 26.694245 Loop time of 1.88985 on 1 procs for 1000 steps with 4000 atoms Performance: 45.718 ns/day, 0.525 hours/ns, 529.143 timesteps/s, 2.117 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.231 | 1.231 | 1.231 | 0.0 | 65.14 Neigh | 0.49408 | 0.49408 | 0.49408 | 0.0 | 26.14 Comm | 0.018984 | 0.018984 | 0.018984 | 0.0 | 1.00 Output | 3.183e-05 | 3.183e-05 | 3.183e-05 | 0.0 | 0.00 Modify | 0.13306 | 0.13306 | 0.13306 | 0.0 | 7.04 Other | | 0.01269 | | | 0.67 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1803 ave 1803 max 1803 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21674 ave 21674 max 21674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21674 Ave neighs/atom = 5.4185 Neighbor list builds = 119 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.52127296907, Press = 54.5678897482158 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 149.88876 149.88876 -12.708996 -12.708996 314.55638 314.55638 5688296 5688296 26.694245 26.694245 4000 158.56294 158.56294 -3.8528927 -3.8528927 314.20444 314.20444 31185056 31185056 5.364114 5.364114 Loop time of 1.04514 on 1 procs for 1000 steps with 4000 atoms Performance: 82.668 ns/day, 0.290 hours/ns, 956.806 timesteps/s, 3.827 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49937 | 0.49937 | 0.49937 | 0.0 | 47.78 Neigh | 0.38153 | 0.38153 | 0.38153 | 0.0 | 36.50 Comm | 0.017607 | 0.017607 | 0.017607 | 0.0 | 1.68 Output | 3.5277e-05 | 3.5277e-05 | 3.5277e-05 | 0.0 | 0.00 Modify | 0.13273 | 0.13273 | 0.13273 | 0.0 | 12.70 Other | | 0.01387 | | | 1.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 941 ave 941 max 941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4890 ave 4890 max 4890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4890 Ave neighs/atom = 1.2225 Neighbor list builds = 208 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.634749701168, Press = 41.2790561404542 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 53 53 53 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.25 | 4.25 | 4.25 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 158.56294 158.56294 -3.8528927 -3.8528927 314.20444 314.20444 31185056 31185056 5.364114 5.364114 5000 158.82052 158.82052 -1.1427762 -1.1427762 309.45984 309.45984 1.6399194e+08 1.6399194e+08 1.0325084 1.0325084 Loop time of 0.972704 on 1 procs for 1000 steps with 4000 atoms Performance: 88.825 ns/day, 0.270 hours/ns, 1028.062 timesteps/s, 4.112 Matom-step/s 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31756 | 0.31756 | 0.31756 | 0.0 | 32.65 Neigh | 0.48823 | 0.48823 | 0.48823 | 0.0 | 50.19 Comm | 0.017287 | 0.017287 | 0.017287 | 0.0 | 1.78 Output | 4.1188e-05 | 4.1188e-05 | 4.1188e-05 | 0.0 | 0.00 Modify | 0.13364 | 0.13364 | 0.13364 | 0.0 | 13.74 Other | | 0.01595 | | | 1.64 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 514 ave 514 max 514 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1324 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1324 Ave neighs/atom = 0.331 Neighbor list builds = 317 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.601848543039, Press = 31.8496770375861 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 92 92 92 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.984 | 6.984 | 6.984 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 158.82052 158.82052 -1.1427762 -1.1427762 309.45984 309.45984 1.6399194e+08 1.6399194e+08 1.0325084 1.0325084 6000 162.47663 162.47663 -0.18258902 -0.18258902 314.67529 314.67529 8.3080941e+08 8.3080941e+08 0.20913438 0.20913438 Loop time of 1.82706 on 1 procs for 1000 steps with 4000 atoms Performance: 47.289 ns/day, 0.508 hours/ns, 547.328 timesteps/s, 2.189 Matom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2745 | 0.2745 | 0.2745 | 0.0 | 15.02 Neigh | 1.3651 | 1.3651 | 1.3651 | 0.0 | 74.71 Comm | 0.022955 | 0.022955 | 0.022955 | 0.0 | 1.26 Output | 4.5786e-05 | 4.5786e-05 | 4.5786e-05 | 0.0 | 0.00 Modify | 0.1427 | 0.1427 | 0.1427 | 0.0 | 7.81 Other | | 0.02179 | | | 1.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 282 ave 282 max 282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 374 ave 374 max 374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374 Ave neighs/atom = 0.0935 Neighbor list builds = 496 Dangerous builds = 0 if "${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 830809411.841023 A^3 has become larger than 180705100.868827 A^3. Aborting calculation. Total wall time: 0:00:17