# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.252865672111511*${_u_distance} variable latticeconst_converted equal 5.252865672111511*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25286567211151 Lattice spacing in x,y,z = 5.2528657 5.2528657 5.2528657 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_QuinticSmoothed_Jelinek_1972_Ar__MO_908645784389_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) 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 144940.209626461 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144940.209626461*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144940.209626461 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_908645784389_002#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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -202.42117 -202.42117 -374.63018 -374.63018 333.15 333.15 144940.21 144940.21 1269.0716 1269.0716 1000 99.692602 99.692602 -73.070527 -73.070527 334.22199 334.22199 564418.47 564418.47 170.49855 170.49855 Loop time of 4.41879 on 1 procs for 1000 steps with 4000 atoms Performance: 19.553 ns/day, 1.227 hours/ns, 226.306 timesteps/s, 905.225 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 | 3.722 | 3.722 | 3.722 | 0.0 | 84.23 Neigh | 0.54116 | 0.54116 | 0.54116 | 0.0 | 12.25 Comm | 0.023171 | 0.023171 | 0.023171 | 0.0 | 0.52 Output | 8.6562e-05 | 8.6562e-05 | 8.6562e-05 | 0.0 | 0.00 Modify | 0.12093 | 0.12093 | 0.12093 | 0.0 | 2.74 Other | | 0.01146 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3741 ave 3741 max 3741 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: 124752 ave 124752 max 124752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124752 Ave neighs/atom = 31.188 Neighbor list builds = 54 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 = ${P}" flag: Temp = 332.290602965891, Press = 172.438267195716 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.853 | 3.853 | 3.853 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 99.692602 99.692602 -73.070527 -73.070527 334.22199 334.22199 564418.47 564418.47 170.49855 170.49855 2000 152.36735 152.36735 -19.243537 -19.243537 331.9929 331.9929 2677128.8 2677128.8 58.778398 58.778398 Loop time of 1.82162 on 1 procs for 1000 steps with 4000 atoms Performance: 47.430 ns/day, 0.506 hours/ns, 548.962 timesteps/s, 2.196 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1784 | 1.1784 | 1.1784 | 0.0 | 64.69 Neigh | 0.47476 | 0.47476 | 0.47476 | 0.0 | 26.06 Comm | 0.019577 | 0.019577 | 0.019577 | 0.0 | 1.07 Output | 7.6774e-05 | 7.6774e-05 | 7.6774e-05 | 0.0 | 0.00 Modify | 0.13689 | 0.13689 | 0.13689 | 0.0 | 7.51 Other | | 0.01196 | | | 0.66 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2026 ave 2026 max 2026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28590 ave 28590 max 28590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28590 Ave neighs/atom = 7.1475 Neighbor list builds = 94 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.212501290846, Press = 119.228524563538 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 28 28 28 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.555 | 3.555 | 3.555 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 152.36735 152.36735 -19.243537 -19.243537 331.9929 331.9929 2677128.8 2677128.8 58.778398 58.778398 3000 168.29629 168.29629 -5.1278621 -5.1278621 335.50079 335.50079 14369176 14369176 12.380263 12.380263 Loop time of 0.904163 on 1 procs for 1000 steps with 4000 atoms Performance: 95.558 ns/day, 0.251 hours/ns, 1105.996 timesteps/s, 4.424 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41576 | 0.41576 | 0.41576 | 0.0 | 45.98 Neigh | 0.32472 | 0.32472 | 0.32472 | 0.0 | 35.91 Comm | 0.016097 | 0.016097 | 0.016097 | 0.0 | 1.78 Output | 4.1998e-05 | 4.1998e-05 | 4.1998e-05 | 0.0 | 0.00 Modify | 0.13494 | 0.13494 | 0.13494 | 0.0 | 14.92 Other | | 0.0126 | | | 1.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1082 ave 1082 max 1082 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6512 ave 6512 max 6512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6512 Ave neighs/atom = 1.628 Neighbor list builds = 163 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.661463159012, Press = 76.9273871480138 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 48 48 48 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.978 | 3.978 | 3.978 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 168.29629 168.29629 -5.1278621 -5.1278621 335.50079 335.50079 14369176 14369176 12.380263 12.380263 4000 165.55033 165.55033 -1.2605423 -1.2605423 322.70694 322.70694 74793706 74793706 2.3611365 2.3611365 Loop time of 0.692317 on 1 procs for 1000 steps with 4000 atoms Performance: 124.798 ns/day, 0.192 hours/ns, 1444.426 timesteps/s, 5.778 Matom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19233 | 0.19233 | 0.19233 | 0.0 | 27.78 Neigh | 0.35786 | 0.35786 | 0.35786 | 0.0 | 51.69 Comm | 0.013612 | 0.013612 | 0.013612 | 0.0 | 1.97 Output | 4.0987e-05 | 4.0987e-05 | 4.0987e-05 | 0.0 | 0.01 Modify | 0.11619 | 0.11619 | 0.11619 | 0.0 | 16.78 Other | | 0.01228 | | | 1.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 619 ave 619 max 619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1580 ave 1580 max 1580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1580 Ave neighs/atom = 0.395 Neighbor list builds = 267 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.623867101922, Press = 54.0664289004591 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 84 84 84 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.096 | 6.096 | 6.096 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 165.55033 165.55033 -1.2605423 -1.2605423 322.70694 322.70694 74793706 74793706 2.3611365 2.3611365 5000 174.96854 174.96854 -0.2492886 -0.2492886 338.97077 338.97077 3.7601695e+08 3.7601695e+08 0.49682696 0.49682696 Loop time of 1.25047 on 1 procs for 1000 steps with 4000 atoms Performance: 69.094 ns/day, 0.347 hours/ns, 799.701 timesteps/s, 3.199 Matom-step/s 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14063 | 0.14063 | 0.14063 | 0.0 | 11.25 Neigh | 0.95714 | 0.95714 | 0.95714 | 0.0 | 76.54 Comm | 0.02056 | 0.02056 | 0.02056 | 0.0 | 1.64 Output | 5.0765e-05 | 5.0765e-05 | 5.0765e-05 | 0.0 | 0.00 Modify | 0.11712 | 0.11712 | 0.11712 | 0.0 | 9.37 Other | | 0.01496 | | | 1.20 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 353 ave 353 max 353 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366 ave 366 max 366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366 Ave neighs/atom = 0.0915 Neighbor list builds = 421 Dangerous builds = 0 if "${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 376016951.945094 A^3 has become larger than 144940209.626461 A^3. Aborting calculation. Total wall time: 0:00:09