# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.248509056866169*${_u_distance} variable latticeconst_converted equal 5.248509056866169*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24850905686617 Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_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 144579.877647162 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144579.877647162*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144579.877647162 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_126566794224_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 = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 7 7 7 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) = 10.2 | 10.2 | 10.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -194.48948 -194.48948 -346.02203 -346.02203 293.15 293.15 144579.88 144579.88 1119.4828 1119.4828 1000 75.872797 75.872797 -75.847787 -75.847787 293.51376 293.51376 537296.87 537296.87 134.04727 134.04727 Loop time of 18.6231 on 1 procs for 1000 steps with 4000 atoms Performance: 4.639 ns/day, 5.173 hours/ns, 53.697 timesteps/s, 214.787 katom-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 | 17.182 | 17.182 | 17.182 | 0.0 | 92.26 Neigh | 1.2582 | 1.2582 | 1.2582 | 0.0 | 6.76 Comm | 0.04027 | 0.04027 | 0.04027 | 0.0 | 0.22 Output | 0.00015065 | 0.00015065 | 0.00015065 | 0.0 | 0.00 Modify | 0.12564 | 0.12564 | 0.12564 | 0.0 | 0.67 Other | | 0.01709 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6558 ave 6558 max 6558 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: 463670 ave 463670 max 463670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463670 Ave neighs/atom = 115.9175 Neighbor list builds = 52 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 = ${P}" flag: Temp = 293.101054651133, Press = 136.486370642666 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.216 | 5.216 | 5.216 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 75.872797 75.872797 -75.847787 -75.847787 293.51376 293.51376 537296.87 537296.87 134.04727 134.04727 2000 132.77273 132.77273 -18.451529 -18.451529 292.55359 292.55359 2417461.6 2417461.6 56.671918 56.671918 Loop time of 5.6345 on 1 procs for 1000 steps with 4000 atoms Performance: 15.334 ns/day, 1.565 hours/ns, 177.478 timesteps/s, 709.912 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6714 | 4.6714 | 4.6714 | 0.0 | 82.91 Neigh | 0.79911 | 0.79911 | 0.79911 | 0.0 | 14.18 Comm | 0.02583 | 0.02583 | 0.02583 | 0.0 | 0.46 Output | 9.4557e-05 | 9.4557e-05 | 9.4557e-05 | 0.0 | 0.00 Modify | 0.12421 | 0.12421 | 0.12421 | 0.0 | 2.20 Other | | 0.0139 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3445 ave 3445 max 3445 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106902 ave 106902 max 106902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106902 Ave neighs/atom = 26.7255 Neighbor list builds = 89 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.636780064219, Press = 102.726673238435 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.078 | 4.078 | 4.078 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 132.77273 132.77273 -18.451529 -18.451529 292.55359 292.55359 2417461.6 2417461.6 56.671918 56.671918 3000 145.90964 145.90964 -4.4789693 -4.4789693 290.93697 290.93697 13017570 13017570 12.058856 12.058856 Loop time of 1.90776 on 1 procs for 1000 steps with 4000 atoms Performance: 45.289 ns/day, 0.530 hours/ns, 524.176 timesteps/s, 2.097 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1771 | 1.1771 | 1.1771 | 0.0 | 61.70 Neigh | 0.57989 | 0.57989 | 0.57989 | 0.0 | 30.40 Comm | 0.019488 | 0.019488 | 0.019488 | 0.0 | 1.02 Output | 4.7338e-05 | 4.7338e-05 | 4.7338e-05 | 0.0 | 0.00 Modify | 0.11936 | 0.11936 | 0.11936 | 0.0 | 6.26 Other | | 0.01187 | | | 0.62 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1791 ave 1791 max 1791 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21852 ave 21852 max 21852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21852 Ave neighs/atom = 5.463 Neighbor list builds = 158 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.696576737272, Press = 67.7336738135623 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 31 31 31 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 145.90964 145.90964 -4.4789693 -4.4789693 290.93697 290.93697 13017570 13017570 12.058856 12.058856 4000 151.31218 151.31218 -1.0139829 -1.0139829 294.6853 294.6853 68490764 68490764 2.3523428 2.3523428 Loop time of 0.974552 on 1 procs for 1000 steps with 4000 atoms Performance: 88.656 ns/day, 0.271 hours/ns, 1026.112 timesteps/s, 4.104 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42961 | 0.42961 | 0.42961 | 0.0 | 44.08 Neigh | 0.39666 | 0.39666 | 0.39666 | 0.0 | 40.70 Comm | 0.01746 | 0.01746 | 0.01746 | 0.0 | 1.79 Output | 4.8031e-05 | 4.8031e-05 | 4.8031e-05 | 0.0 | 0.00 Modify | 0.11782 | 0.11782 | 0.11782 | 0.0 | 12.09 Other | | 0.01295 | | | 1.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4988 ave 4988 max 4988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4988 Ave neighs/atom = 1.247 Neighbor list builds = 259 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.834965703907, Press = 47.7850738886267 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 53 53 53 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.376 | 4.376 | 4.376 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 151.31218 151.31218 -1.0139829 -1.0139829 294.6853 294.6853 68490764 68490764 2.3523428 2.3523428 5000 153.34754 153.34754 -0.29354209 -0.29354209 297.22909 297.22909 3.4658348e+08 3.4658348e+08 0.47268014 0.47268014 Loop time of 0.941121 on 1 procs for 1000 steps with 4000 atoms Performance: 91.805 ns/day, 0.261 hours/ns, 1062.563 timesteps/s, 4.250 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24065 | 0.24065 | 0.24065 | 0.0 | 25.57 Neigh | 0.54802 | 0.54802 | 0.54802 | 0.0 | 58.23 Comm | 0.019969 | 0.019969 | 0.019969 | 0.0 | 2.12 Output | 4.5115e-05 | 4.5115e-05 | 4.5115e-05 | 0.0 | 0.00 Modify | 0.11723 | 0.11723 | 0.11723 | 0.0 | 12.46 Other | | 0.01521 | | | 1.62 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 542 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1198 ave 1198 max 1198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1198 Ave neighs/atom = 0.2995 Neighbor list builds = 410 Dangerous builds = 0 if "${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 346583477.223354 A^3 has become larger than 144579877.647162 A^3. Aborting calculation. Total wall time: 0:00:28