# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.266347639262676*${_u_distance} variable latticeconst_converted equal 5.266347639262676*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26634763926268 Lattice spacing in x,y,z = 5.2663476 5.2663476 5.2663476 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_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 146059.083903987 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 146059.083903987*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 146059.083903987 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_720819638419_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 = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -159.0195 -159.0195 -320.89028 -320.89028 313.15 313.15 146059.08 146059.08 1183.747 1183.747 1000 104.08798 104.08798 -57.255231 -57.255231 312.12938 312.12938 636153.82 636153.82 162.00796 162.00796 Loop time of 7.16751 on 1 procs for 1000 steps with 4000 atoms Performance: 12.054 ns/day, 1.991 hours/ns, 139.518 timesteps/s, 558.074 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 | 6.2623 | 6.2623 | 6.2623 | 0.0 | 87.37 Neigh | 0.72812 | 0.72812 | 0.72812 | 0.0 | 10.16 Comm | 0.029532 | 0.029532 | 0.029532 | 0.0 | 0.41 Output | 7.7435e-05 | 7.7435e-05 | 7.7435e-05 | 0.0 | 0.00 Modify | 0.13361 | 0.13361 | 0.13361 | 0.0 | 1.86 Other | | 0.01386 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4041 ave 4041 max 4041 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: 148894 ave 148894 max 148894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 148894 Ave neighs/atom = 37.2235 Neighbor list builds = 59 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 = ${P}" flag: Temp = 311.263930495319, Press = 164.272678121832 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 16 16 16 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.946 | 3.946 | 3.946 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 104.08798 104.08798 -57.255231 -57.255231 312.12938 312.12938 636153.82 636153.82 162.00796 162.00796 2000 147.6067 147.6067 -12.935788 -12.935788 310.58032 310.58032 3146628.8 3146628.8 49.968213 49.968213 Loop time of 2.44687 on 1 procs for 1000 steps with 4000 atoms Performance: 35.310 ns/day, 0.680 hours/ns, 408.685 timesteps/s, 1.635 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7384 | 1.7384 | 1.7384 | 0.0 | 71.05 Neigh | 0.5421 | 0.5421 | 0.5421 | 0.0 | 22.15 Comm | 0.020181 | 0.020181 | 0.020181 | 0.0 | 0.82 Output | 5.1066e-05 | 5.1066e-05 | 5.1066e-05 | 0.0 | 0.00 Modify | 0.13384 | 0.13384 | 0.13384 | 0.0 | 5.47 Other | | 0.0123 | | | 0.50 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2109 ave 2109 max 2109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32212 ave 32212 max 32212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32212 Ave neighs/atom = 8.053 Neighbor list builds = 102 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.380542444096, Press = 107.62600624212 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 27 27 27 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.64 | 3.64 | 3.64 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 147.6067 147.6067 -12.935788 -12.935788 310.58032 310.58032 3146628.8 3146628.8 49.968213 49.968213 3000 159.13347 159.13347 -3.45925 -3.45925 314.54664 314.54664 16846108 16846108 10.056897 10.056897 Loop time of 0.993191 on 1 procs for 1000 steps with 4000 atoms Performance: 86.992 ns/day, 0.276 hours/ns, 1006.856 timesteps/s, 4.027 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52223 | 0.52223 | 0.52223 | 0.0 | 52.58 Neigh | 0.32228 | 0.32228 | 0.32228 | 0.0 | 32.45 Comm | 0.015267 | 0.015267 | 0.015267 | 0.0 | 1.54 Output | 4.4514e-05 | 4.4514e-05 | 4.4514e-05 | 0.0 | 0.00 Modify | 0.12123 | 0.12123 | 0.12123 | 0.0 | 12.21 Other | | 0.01213 | | | 1.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1152 ave 1152 max 1152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 6936 ave 6936 max 6936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6936 Ave neighs/atom = 1.734 Neighbor list builds = 173 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.577120482075, Press = 68.2319775360867 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 46 46 46 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.013 | 4.013 | 4.013 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 159.13347 159.13347 -3.45925 -3.45925 314.54664 314.54664 16846108 16846108 10.056897 10.056897 4000 155.96573 155.96573 -0.71716447 -0.71716447 303.11368 303.11368 87168721 87168721 1.9083126 1.9083126 Loop time of 0.78318 on 1 procs for 1000 steps with 4000 atoms Performance: 110.319 ns/day, 0.218 hours/ns, 1276.846 timesteps/s, 5.107 Matom-step/s 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26744 | 0.26744 | 0.26744 | 0.0 | 34.15 Neigh | 0.36848 | 0.36848 | 0.36848 | 0.0 | 47.05 Comm | 0.014422 | 0.014422 | 0.014422 | 0.0 | 1.84 Output | 4.6027e-05 | 4.6027e-05 | 4.6027e-05 | 0.0 | 0.01 Modify | 0.11907 | 0.11907 | 0.11907 | 0.0 | 15.20 Other | | 0.01372 | | | 1.75 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 631 ave 631 max 631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1622 ave 1622 max 1622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1622 Ave neighs/atom = 0.4055 Neighbor list builds = 279 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.658567961208, Press = 47.8062214418993 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 79 79 79 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.764 | 5.764 | 5.764 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 155.96573 155.96573 -0.71716447 -0.71716447 303.11368 303.11368 87168721 87168721 1.9083126 1.9083126 5000 159.58455 159.58455 -0.20341883 -0.20341883 309.12067 309.12067 4.3513511e+08 4.3513511e+08 0.39143623 0.39143623 Loop time of 1.2277 on 1 procs for 1000 steps with 4000 atoms Performance: 70.376 ns/day, 0.341 hours/ns, 814.531 timesteps/s, 3.258 Matom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18805 | 0.18805 | 0.18805 | 0.0 | 15.32 Neigh | 0.8886 | 0.8886 | 0.8886 | 0.0 | 72.38 Comm | 0.017 | 0.017 | 0.017 | 0.0 | 1.38 Output | 5.9722e-05 | 5.9722e-05 | 5.9722e-05 | 0.0 | 0.00 Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 9.61 Other | | 0.01603 | | | 1.31 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 371 ave 371 max 371 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 370 ave 370 max 370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370 Ave neighs/atom = 0.0925 Neighbor list builds = 435 Dangerous builds = 0 if "${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 435135105.882165 A^3 has become larger than 146059083.903987 A^3. Aborting calculation. Total wall time: 0:00:12