# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.266347639262676*${_u_distance} variable latticeconst_converted equal 5.266347639262676*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26634763926268 Lattice spacing in x,y,z = 5.2663476 5.2663476 5.2663476 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_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 146059.083903987 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 146059.083903987*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 146059.083903987 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_720819638419_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 = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -148.68128 -148.68128 -320.89028 -320.89028 333.15 333.15 146059.08 146059.08 1259.3496 1259.3496 1000 119.46827 119.46827 -52.722731 -52.722731 333.11517 333.11517 685213.9 685213.9 175.53647 175.53647 Loop time of 6.30849 on 1 procs for 1000 steps with 4000 atoms Performance: 13.696 ns/day, 1.752 hours/ns, 158.517 timesteps/s, 634.067 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4663 | 5.4663 | 5.4663 | 0.0 | 86.65 Neigh | 0.68141 | 0.68141 | 0.68141 | 0.0 | 10.80 Comm | 0.027133 | 0.027133 | 0.027133 | 0.0 | 0.43 Output | 9.9617e-05 | 9.9617e-05 | 9.9617e-05 | 0.0 | 0.00 Modify | 0.12043 | 0.12043 | 0.12043 | 0.0 | 1.91 Other | | 0.01308 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3902 ave 3902 max 3902 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: 137674 ave 137674 max 137674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137674 Ave neighs/atom = 34.4185 Neighbor list builds = 63 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 = ${P}" flag: Temp = 333.351216687629, Press = 181.936537479498 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.945 | 3.945 | 3.945 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 119.46827 119.46827 -52.722731 -52.722731 333.11517 333.11517 685213.9 685213.9 175.53647 175.53647 2000 160.78161 160.78161 -11.926466 -11.926466 334.11549 334.11549 3474549.9 3474549.9 49.008446 49.008446 Loop time of 2.0251 on 1 procs for 1000 steps with 4000 atoms Performance: 42.665 ns/day, 0.563 hours/ns, 493.802 timesteps/s, 1.975 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.406 | 1.406 | 1.406 | 0.0 | 69.43 Neigh | 0.47292 | 0.47292 | 0.47292 | 0.0 | 23.35 Comm | 0.017773 | 0.017773 | 0.017773 | 0.0 | 0.88 Output | 6.7276e-05 | 6.7276e-05 | 6.7276e-05 | 0.0 | 0.00 Modify | 0.11735 | 0.11735 | 0.11735 | 0.0 | 5.79 Other | | 0.01102 | | | 0.54 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2062 ave 2062 max 2062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29264 ave 29264 max 29264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29264 Ave neighs/atom = 7.316 Neighbor list builds = 106 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.926573408996, Press = 112.050114330048 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.639 | 3.639 | 3.639 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 160.78161 160.78161 -11.926466 -11.926466 334.11549 334.11549 3474549.9 3474549.9 49.008446 49.008446 3000 168.35087 168.35087 -3.0222047 -3.0222047 331.53283 331.53283 18484613 18484613 9.7119658 9.7119658 Loop time of 1.12361 on 1 procs for 1000 steps with 4000 atoms Performance: 76.895 ns/day, 0.312 hours/ns, 889.987 timesteps/s, 3.560 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57511 | 0.57511 | 0.57511 | 0.0 | 51.18 Neigh | 0.37255 | 0.37255 | 0.37255 | 0.0 | 33.16 Comm | 0.018428 | 0.018428 | 0.018428 | 0.0 | 1.64 Output | 7.2757e-05 | 7.2757e-05 | 7.2757e-05 | 0.0 | 0.01 Modify | 0.14406 | 0.14406 | 0.14406 | 0.0 | 12.82 Other | | 0.01339 | | | 1.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1089 ave 1089 max 1089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6372 ave 6372 max 6372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6372 Ave neighs/atom = 1.593 Neighbor list builds = 176 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.851478449684, Press = 70.2184783739151 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 48 48 48 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.075 | 4.075 | 4.075 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 168.35087 168.35087 -3.0222047 -3.0222047 331.53283 331.53283 18484613 18484613 9.7119658 9.7119658 4000 172.17894 172.17894 -0.73174723 -0.73174723 334.50745 334.50745 95143411 95143411 1.9289381 1.9289381 Loop time of 0.968117 on 1 procs for 1000 steps with 4000 atoms Performance: 89.245 ns/day, 0.269 hours/ns, 1032.933 timesteps/s, 4.132 Matom-step/s 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31743 | 0.31743 | 0.31743 | 0.0 | 32.79 Neigh | 0.47092 | 0.47092 | 0.47092 | 0.0 | 48.64 Comm | 0.01797 | 0.01797 | 0.01797 | 0.0 | 1.86 Output | 4.7379e-05 | 4.7379e-05 | 4.7379e-05 | 0.0 | 0.00 Modify | 0.14596 | 0.14596 | 0.14596 | 0.0 | 15.08 Other | | 0.01579 | | | 1.63 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 622 ave 622 max 622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1474 ave 1474 max 1474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1474 Ave neighs/atom = 0.3685 Neighbor list builds = 287 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.821958016162, Press = 49.1121601526982 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 82 82 82 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.015 | 6.015 | 6.015 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 172.17894 172.17894 -0.73174723 -0.73174723 334.50745 334.50745 95143411 95143411 1.9289381 1.9289381 5000 171.37565 171.37565 -0.10488217 -0.10488217 331.74072 331.74072 4.7279193e+08 4.7279193e+08 0.38683035 0.38683035 Loop time of 1.44026 on 1 procs for 1000 steps with 4000 atoms Performance: 59.989 ns/day, 0.400 hours/ns, 694.317 timesteps/s, 2.777 Matom-step/s 94.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20033 | 0.20033 | 0.20033 | 0.0 | 13.91 Neigh | 1.0763 | 1.0763 | 1.0763 | 0.0 | 74.73 Comm | 0.018423 | 0.018423 | 0.018423 | 0.0 | 1.28 Output | 4.3371e-05 | 4.3371e-05 | 4.3371e-05 | 0.0 | 0.00 Modify | 0.12796 | 0.12796 | 0.12796 | 0.0 | 8.88 Other | | 0.01726 | | | 1.20 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 346 ave 346 max 346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 374 ave 374 max 374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 374 Ave neighs/atom = 0.0935 Neighbor list builds = 445 Dangerous builds = 0 if "${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 472791929.925025 A^3 has become larger than 146059083.903987 A^3. Aborting calculation. Total wall time: 0:00:12