# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.235186479985714*${_u_distance} variable latticeconst_converted equal 5.235186479985714*1 lattice fcc ${latticeconst_converted} lattice fcc 5.23518647998571 Lattice spacing in x,y,z = 5.2351865 5.2351865 5.2351865 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1122) 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 143481.684999044 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 143481.684999044*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 143481.684999044 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_946046425752_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 -169.04857 -169.04857 -341.25757 -341.25757 333.15 333.15 143481.68 143481.68 1281.9718 1281.9718 1000 114.07391 114.07391 -57.225848 -57.225848 331.39099 331.39099 636737.16 636737.16 176.24357 176.24357 Loop time of 6.10194 on 1 procs for 1000 steps with 4000 atoms Performance: 14.159 ns/day, 1.695 hours/ns, 163.882 timesteps/s, 655.529 katom-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 | 5.3489 | 5.3489 | 5.3489 | 0.0 | 87.66 Neigh | 0.59058 | 0.59058 | 0.59058 | 0.0 | 9.68 Comm | 0.025067 | 0.025067 | 0.025067 | 0.0 | 0.41 Output | 6.2667e-05 | 6.2667e-05 | 6.2667e-05 | 0.0 | 0.00 Modify | 0.12388 | 0.12388 | 0.12388 | 0.0 | 2.03 Other | | 0.0134 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3543 ave 3543 max 3543 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: 110646 ave 110646 max 110646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110646 Ave neighs/atom = 27.6615 Neighbor list builds = 60 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 = ${P}" flag: Temp = 330.988633036221, Press = 183.935920963899 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.851 | 3.851 | 3.851 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 114.07391 114.07391 -57.225848 -57.225848 331.39099 331.39099 636737.16 636737.16 176.24357 176.24357 2000 159.83802 159.83802 -13.43356 -13.43356 335.20562 335.20562 3187048.2 3187048.2 53.474212 53.474212 Loop time of 1.86176 on 1 procs for 1000 steps with 4000 atoms Performance: 46.408 ns/day, 0.517 hours/ns, 537.126 timesteps/s, 2.149 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3167 | 1.3167 | 1.3167 | 0.0 | 70.72 Neigh | 0.39982 | 0.39982 | 0.39982 | 0.0 | 21.48 Comm | 0.016865 | 0.016865 | 0.016865 | 0.0 | 0.91 Output | 3.5336e-05 | 3.5336e-05 | 3.5336e-05 | 0.0 | 0.00 Modify | 0.11741 | 0.11741 | 0.11741 | 0.0 | 6.31 Other | | 0.01091 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1885 ave 1885 max 1885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23880 ave 23880 max 23880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23880 Ave neighs/atom = 5.97 Neighbor list builds = 102 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.383778784418, Press = 116.725530997872 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.566 | 3.566 | 3.566 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.83802 159.83802 -13.43356 -13.43356 335.20562 335.20562 3187048.2 3187048.2 53.474212 53.474212 3000 168.70238 168.70238 -3.5267364 -3.5267364 333.1889 333.1889 17029219 17029219 10.512537 10.512537 Loop time of 0.856046 on 1 procs for 1000 steps with 4000 atoms Performance: 100.929 ns/day, 0.238 hours/ns, 1168.162 timesteps/s, 4.673 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43922 | 0.43922 | 0.43922 | 0.0 | 51.31 Neigh | 0.27477 | 0.27477 | 0.27477 | 0.0 | 32.10 Comm | 0.01382 | 0.01382 | 0.01382 | 0.0 | 1.61 Output | 4.7079e-05 | 4.7079e-05 | 4.7079e-05 | 0.0 | 0.01 Modify | 0.11669 | 0.11669 | 0.11669 | 0.0 | 13.63 Other | | 0.0115 | | | 1.34 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1029 ave 1029 max 1029 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5348 ave 5348 max 5348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5348 Ave neighs/atom = 1.337 Neighbor list builds = 171 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.620953920476, Press = 73.6312726631226 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 51 51 51 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.08 | 4.08 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 168.70238 168.70238 -3.5267364 -3.5267364 333.1889 333.1889 17029219 17029219 10.512537 10.512537 4000 171.38733 171.38733 -0.81077521 -0.81077521 333.12891 333.12891 88070978 88070978 2.0862728 2.0862728 Loop time of 0.751062 on 1 procs for 1000 steps with 4000 atoms Performance: 115.037 ns/day, 0.209 hours/ns, 1331.449 timesteps/s, 5.326 Matom-step/s 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22644 | 0.22644 | 0.22644 | 0.0 | 30.15 Neigh | 0.38034 | 0.38034 | 0.38034 | 0.0 | 50.64 Comm | 0.01384 | 0.01384 | 0.01384 | 0.0 | 1.84 Output | 3.6478e-05 | 3.6478e-05 | 3.6478e-05 | 0.0 | 0.00 Modify | 0.11707 | 0.11707 | 0.11707 | 0.0 | 15.59 Other | | 0.01333 | | | 1.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 556 ave 556 max 556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1268 ave 1268 max 1268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1268 Ave neighs/atom = 0.317 Neighbor list builds = 278 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.75457464087, Press = 51.5497871949782 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 88 88 88 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.475 | 6.475 | 6.475 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 171.38733 171.38733 -0.81077521 -0.81077521 333.12891 333.12891 88070978 88070978 2.0862728 2.0862728 5000 172.64014 172.64014 -0.16323312 -0.16323312 334.29985 334.29985 4.3891129e+08 4.3891129e+08 0.41969415 0.41969415 Loop time of 1.58524 on 1 procs for 1000 steps with 4000 atoms Performance: 54.503 ns/day, 0.440 hours/ns, 630.818 timesteps/s, 2.523 Matom-step/s 92.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16088 | 0.16088 | 0.16088 | 0.0 | 10.15 Neigh | 1.2672 | 1.2672 | 1.2672 | 0.0 | 79.93 Comm | 0.022622 | 0.022622 | 0.022622 | 0.0 | 1.43 Output | 5.1467e-05 | 5.1467e-05 | 5.1467e-05 | 0.0 | 0.00 Modify | 0.1182 | 0.1182 | 0.1182 | 0.0 | 7.46 Other | | 0.01633 | | | 1.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 320 ave 320 max 320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 304 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304 Ave neighs/atom = 0.076 Neighbor list builds = 433 Dangerous builds = 0 if "${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 438911289.202592 A^3 has become larger than 143481684.999044 A^3. Aborting calculation. Total wall time: 0:00:11