# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.246869719028479*${_u_distance} variable latticeconst_converted equal 5.246869719028479*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24686971902848 Lattice spacing in x,y,z = 5.2468697 5.2468697 5.2468697 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.468697 52.468697 52.468697) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.468697 52.468697 52.468697) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 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 144444.444190373 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144444.444190373/(1*1*${_u_distance}) variable V0_metal equal 144444.444190373/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144444.444190373*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144444.444190373 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_398194508715_001#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 = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, 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) = 15.41 | 15.41 | 15.41 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -187.30538 -187.30538 -349.17616 -349.17616 313.15 313.15 144444.44 144444.44 1196.9795 1196.9795 1000 93.448193 93.448193 -68.909964 -68.909964 314.09286 314.09286 590289.28 590289.28 157.7307 157.7307 Loop time of 23.5691 on 1 procs for 1000 steps with 4000 atoms Performance: 3.666 ns/day, 6.547 hours/ns, 42.429 timesteps/s, 169.714 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 | 21.786 | 21.786 | 21.786 | 0.0 | 92.43 Neigh | 1.5995 | 1.5995 | 1.5995 | 0.0 | 6.79 Comm | 0.044346 | 0.044346 | 0.044346 | 0.0 | 0.19 Output | 0.00010355 | 0.00010355 | 0.00010355 | 0.0 | 0.00 Modify | 0.12269 | 0.12269 | 0.12269 | 0.0 | 0.52 Other | | 0.01674 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7315 ave 7315 max 7315 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: 589246 ave 589246 max 589246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 589246 Ave neighs/atom = 147.3115 Neighbor list builds = 56 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 = ${P}" flag: Temp = 313.350774965443, Press = 160.168108776122 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.37 | 8.37 | 8.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 93.448193 93.448193 -68.909964 -68.909964 314.09286 314.09286 590289.28 590289.28 157.7307 157.7307 2000 147.0254 147.0254 -15.690699 -15.690699 314.78532 314.78532 2820493.6 2820493.6 54.664937 54.664937 Loop time of 6.988 on 1 procs for 1000 steps with 4000 atoms Performance: 12.364 ns/day, 1.941 hours/ns, 143.102 timesteps/s, 572.410 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7761 | 5.7761 | 5.7761 | 0.0 | 82.66 Neigh | 1.0352 | 1.0352 | 1.0352 | 0.0 | 14.81 Comm | 0.030184 | 0.030184 | 0.030184 | 0.0 | 0.43 Output | 8.1774e-05 | 8.1774e-05 | 8.1774e-05 | 0.0 | 0.00 Modify | 0.13237 | 0.13237 | 0.13237 | 0.0 | 1.89 Other | | 0.014 | | | 0.20 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3674 ave 3674 max 3674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126712 ave 126712 max 126712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126712 Ave neighs/atom = 31.678 Neighbor list builds = 97 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.144622685398, Press = 109.833044602725 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.845 | 6.845 | 6.845 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 147.0254 147.0254 -15.690699 -15.690699 314.78532 314.78532 2820493.6 2820493.6 54.664937 54.664937 3000 157.4779 157.4779 -3.8389013 -3.8389013 312.0783 312.0783 15152065 15152065 11.085642 11.085642 Loop time of 2.46663 on 1 procs for 1000 steps with 4000 atoms Performance: 35.028 ns/day, 0.685 hours/ns, 405.411 timesteps/s, 1.622 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5336 | 1.5336 | 1.5336 | 0.0 | 62.18 Neigh | 0.76315 | 0.76315 | 0.76315 | 0.0 | 30.94 Comm | 0.023053 | 0.023053 | 0.023053 | 0.0 | 0.93 Output | 6.4811e-05 | 6.4811e-05 | 6.4811e-05 | 0.0 | 0.00 Modify | 0.13382 | 0.13382 | 0.13382 | 0.0 | 5.43 Other | | 0.0129 | | | 0.52 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1919 ave 1919 max 1919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25648 ave 25648 max 25648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25648 Ave neighs/atom = 6.412 Neighbor list builds = 165 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.021327146555, Press = 70.578643641901 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.559 | 6.559 | 6.559 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 157.4779 157.4779 -3.8389013 -3.8389013 312.0783 312.0783 15152065 15152065 11.085642 11.085642 4000 160.79918 160.79918 -0.88780408 -0.88780408 312.79443 312.79443 78941163 78941163 2.1662176 2.1662176 Loop time of 1.0456 on 1 procs for 1000 steps with 4000 atoms Performance: 82.632 ns/day, 0.290 hours/ns, 956.385 timesteps/s, 3.826 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45801 | 0.45801 | 0.45801 | 0.0 | 43.80 Neigh | 0.43954 | 0.43954 | 0.43954 | 0.0 | 42.04 Comm | 0.018089 | 0.018089 | 0.018089 | 0.0 | 1.73 Output | 5.6546e-05 | 5.6546e-05 | 5.6546e-05 | 0.0 | 0.01 Modify | 0.11691 | 0.11691 | 0.11691 | 0.0 | 11.18 Other | | 0.013 | | | 1.24 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1028 ave 1028 max 1028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5662 ave 5662 max 5662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5662 Ave neighs/atom = 1.4155 Neighbor list builds = 272 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.957527882953, Press = 49.5667007103423 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 50 50 50 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.037 | 7.037 | 7.037 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 160.79918 160.79918 -0.88780408 -0.88780408 312.79443 312.79443 78941163 78941163 2.1662176 2.1662176 5000 154.49192 154.49192 -0.22390811 -0.22390811 299.30825 299.30825 3.9579584e+08 3.9579584e+08 0.41701826 0.41701826 Loop time of 0.961599 on 1 procs for 1000 steps with 4000 atoms Performance: 89.850 ns/day, 0.267 hours/ns, 1039.934 timesteps/s, 4.160 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24698 | 0.24698 | 0.24698 | 0.0 | 25.68 Neigh | 0.56302 | 0.56302 | 0.56302 | 0.0 | 58.55 Comm | 0.019197 | 0.019197 | 0.019197 | 0.0 | 2.00 Output | 4.6517e-05 | 4.6517e-05 | 4.6517e-05 | 0.0 | 0.00 Modify | 0.11681 | 0.11681 | 0.11681 | 0.0 | 12.15 Other | | 0.01555 | | | 1.62 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 575 ave 575 max 575 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1332 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1332 Ave neighs/atom = 0.333 Neighbor list builds = 426 Dangerous builds = 0 if "${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 395795837.976368 A^3 has become larger than 144444444.190373 A^3. Aborting calculation. Total wall time: 0:00:35