# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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 -207.98183 -207.98183 -349.17616 -349.17616 273.15 273.15 144444.44 144444.44 1044.0841 1044.0841 1000 54.217156 54.217156 -86.127438 -86.127438 271.50613 271.50613 485205.97 485205.97 106.15157 106.15157 Loop time of 25.8639 on 1 procs for 1000 steps with 4000 atoms Performance: 3.341 ns/day, 7.184 hours/ns, 38.664 timesteps/s, 154.656 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 | 24.194 | 24.194 | 24.194 | 0.0 | 93.54 Neigh | 1.4833 | 1.4833 | 1.4833 | 0.0 | 5.74 Comm | 0.044122 | 0.044122 | 0.044122 | 0.0 | 0.17 Output | 0.00017376 | 0.00017376 | 0.00017376 | 0.0 | 0.00 Modify | 0.12609 | 0.12609 | 0.12609 | 0.0 | 0.49 Other | | 0.01588 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8022 ave 8022 max 8022 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: 720880 ave 720880 max 720880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 720880 Ave neighs/atom = 180.22 Neighbor list builds = 47 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 = ${P}" flag: Temp = 273.241468796499, Press = 111.542699381204 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 9.138 | 9.138 | 9.138 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 54.217156 54.217156 -86.127438 -86.127438 271.50613 271.50613 485205.97 485205.97 106.15157 106.15157 2000 118.65859 118.65859 -21.83212 -21.83212 271.78881 271.78881 2033985.7 2033985.7 59.629637 59.629637 Loop time of 8.28935 on 1 procs for 1000 steps with 4000 atoms Performance: 10.423 ns/day, 2.303 hours/ns, 120.637 timesteps/s, 482.547 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1668 | 7.1668 | 7.1668 | 0.0 | 86.46 Neigh | 0.95809 | 0.95809 | 0.95809 | 0.0 | 11.56 Comm | 0.028829 | 0.028829 | 0.028829 | 0.0 | 0.35 Output | 5.1787e-05 | 5.1787e-05 | 5.1787e-05 | 0.0 | 0.00 Modify | 0.12326 | 0.12326 | 0.12326 | 0.0 | 1.49 Other | | 0.01231 | | | 0.15 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4249 ave 4249 max 4249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 174504 ave 174504 max 174504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 174504 Ave neighs/atom = 43.626 Neighbor list builds = 82 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.731161680522, Press = 94.9171571778886 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.839 | 6.839 | 6.839 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 118.65859 118.65859 -21.83212 -21.83212 271.78881 271.78881 2033985.7 2033985.7 59.629637 59.629637 3000 136.6473 136.6473 -5.5768049 -5.5768049 275.14218 275.14218 10911772 10911772 13.403796 13.403796 Loop time of 2.63822 on 1 procs for 1000 steps with 4000 atoms Performance: 32.749 ns/day, 0.733 hours/ns, 379.043 timesteps/s, 1.516 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7492 | 1.7492 | 1.7492 | 0.0 | 66.30 Neigh | 0.7371 | 0.7371 | 0.7371 | 0.0 | 27.94 Comm | 0.020815 | 0.020815 | 0.020815 | 0.0 | 0.79 Output | 3.4074e-05 | 3.4074e-05 | 3.4074e-05 | 0.0 | 0.00 Modify | 0.11934 | 0.11934 | 0.11934 | 0.0 | 4.52 Other | | 0.01172 | | | 0.44 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2159 ave 2159 max 2159 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35588 ave 35588 max 35588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35588 Ave neighs/atom = 8.897 Neighbor list builds = 149 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.801649855955, Press = 64.6985754056533 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 26 26 26 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.525 | 6.525 | 6.525 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 136.6473 136.6473 -5.5768049 -5.5768049 275.14218 275.14218 10911772 10911772 13.403796 13.403796 4000 139.05446 139.05446 -1.3821069 -1.3821069 271.68405 271.68405 57618863 57618863 2.5761142 2.5761142 Loop time of 1.16227 on 1 procs for 1000 steps with 4000 atoms Performance: 74.337 ns/day, 0.323 hours/ns, 860.382 timesteps/s, 3.442 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55784 | 0.55784 | 0.55784 | 0.0 | 48.00 Neigh | 0.45568 | 0.45568 | 0.45568 | 0.0 | 39.21 Comm | 0.018473 | 0.018473 | 0.018473 | 0.0 | 1.59 Output | 3.6619e-05 | 3.6619e-05 | 3.6619e-05 | 0.0 | 0.00 Modify | 0.11797 | 0.11797 | 0.11797 | 0.0 | 10.15 Other | | 0.01227 | | | 1.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1137 ave 1137 max 1137 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7860 ave 7860 max 7860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7860 Ave neighs/atom = 1.965 Neighbor list builds = 244 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.704353687095, Press = 45.9125586944062 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 17.3 ghost atom cutoff = 17.3 binsize = 8.65, bins = 45 45 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 139.05446 139.05446 -1.3821069 -1.3821069 271.68405 271.68405 57618863 57618863 2.5761142 2.5761142 5000 140.16896 140.16896 -0.27047615 -0.27047615 271.68962 271.68962 2.9231901e+08 2.9231901e+08 0.51160217 0.51160217 Loop time of 0.933886 on 1 procs for 1000 steps with 4000 atoms Performance: 92.517 ns/day, 0.259 hours/ns, 1070.795 timesteps/s, 4.283 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28063 | 0.28063 | 0.28063 | 0.0 | 30.05 Neigh | 0.50252 | 0.50252 | 0.50252 | 0.0 | 53.81 Comm | 0.018731 | 0.018731 | 0.018731 | 0.0 | 2.01 Output | 6.4541e-05 | 6.4541e-05 | 6.4541e-05 | 0.0 | 0.01 Modify | 0.11742 | 0.11742 | 0.11742 | 0.0 | 12.57 Other | | 0.01452 | | | 1.56 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1864 ave 1864 max 1864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1864 Ave neighs/atom = 0.466 Neighbor list builds = 392 Dangerous builds = 0 if "${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 292319010.251683 A^3 has become larger than 144444444.190373 A^3. Aborting calculation. Total wall time: 0:00:39