# Variables that can be adjusted by kim-lammps-preprocessor to switch unit sets for # Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_time equal 1.0 variable _u_pressure equal 1.0 variable _u_temperature equal 1.0 # This line may be swapped out by kim-lammps-preprocessor if running against a Simulator # Model whose atom_style is not 'atomic' atom_style atomic # 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.078000083565712*${_u_distance} variable latticeconst_converted equal 4.078000083565712*1 lattice fcc ${latticeconst_converted} lattice fcc 4.07800008356571 Lattice spacing in x,y,z = 4.078 4.078 4.078 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (40.78 40.78 40.78) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000459909 secs variable mass_converted equal 196.96655*${_u_mass} variable mass_converted equal 196.96655*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_AcklandTichyVitek_1987_Au__MO_104891429740_005 pair_coeff * * Au mass 1 ${mass_converted} mass 1 196.96655 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 67817.4867211144 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 67817.4867211144/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 67817.4867211144/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 67817.4867211144/(1*1*${_u_distance}) variable V0_metal equal 67817.4867211144/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 67817.4867211144*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 67817.4867211144 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*1 variable Tdamp_converted equal 0.1*${_u_time} variable Tdamp_converted equal 0.1*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 1*${_u_time} variable Pdamp_converted equal 1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 5000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 5000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 5000 # 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 "253.15 - 0.2" variable T_up equal "253.15 + 0.2" variable P_low equal "0.0 - 0.2" variable P_up equal "0.0 + 0.2" # 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 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.99451 ghost atom cutoff = 6.99451 binsize = 3.49725, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.99451 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -15025.325 -15025.325 -15156.181 -15156.181 253.15 253.15 67817.487 67817.487 2061.831 2061.831 1000 -14893.306 -14893.306 -15025.223 -15025.223 255.20253 255.20253 69164.119 69164.119 358.4348 358.4348 Loop time of 13.0854 on 1 procs for 1000 steps with 4000 atoms Performance: 6.603 ns/day, 3.635 hours/ns, 76.421 timesteps/s 47.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.641 | 12.641 | 12.641 | 0.0 | 96.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059211 | 0.059211 | 0.059211 | 0.0 | 0.45 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.32586 | 0.32586 | 0.32586 | 0.0 | 2.49 Other | | 0.05964 | | | 0.46 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 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: 312000 ave 312000 max 312000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312000 Ave neighs/atom = 78 Neighbor list builds = 0 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -14893.306 -14893.306 -15025.223 -15025.223 255.20253 255.20253 69164.119 69164.119 358.4348 358.4348 2000 -14902.227 -14902.227 -15034.071 -15034.071 255.0617 255.0617 69068.279 69068.279 637.26779 637.26779 Loop time of 13.2069 on 1 procs for 1000 steps with 4000 atoms Performance: 6.542 ns/day, 3.669 hours/ns, 75.718 timesteps/s 47.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.823 | 12.823 | 12.823 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.080689 | 0.080689 | 0.080689 | 0.0 | 0.61 Output | 4.0054e-05 | 4.0054e-05 | 4.0054e-05 | 0.0 | 0.00 Modify | 0.28346 | 0.28346 | 0.28346 | 0.0 | 2.15 Other | | 0.01955 | | | 0.15 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316530 ave 316530 max 316530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316530 Ave neighs/atom = 79.1325 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -14902.227 -14902.227 -15034.071 -15034.071 255.0617 255.0617 69068.279 69068.279 637.26779 637.26779 3000 -14896.023 -14896.023 -15028.419 -15028.419 256.12919 256.12919 69129.523 69129.523 148.10284 148.10284 Loop time of 14.0872 on 1 procs for 1000 steps with 4000 atoms Performance: 6.133 ns/day, 3.913 hours/ns, 70.987 timesteps/s 45.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.604 | 13.604 | 13.604 | 0.0 | 96.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059772 | 0.059772 | 0.059772 | 0.0 | 0.42 Output | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.00 Modify | 0.38384 | 0.38384 | 0.38384 | 0.0 | 2.72 Other | | 0.03988 | | | 0.28 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316404 ave 316404 max 316404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316404 Ave neighs/atom = 79.101 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -14896.023 -14896.023 -15028.419 -15028.419 256.12919 256.12919 69129.523 69129.523 148.10284 148.10284 4000 -14904.027 -14904.027 -15031.534 -15031.534 246.67223 246.67223 69114.571 69114.571 -165.90578 -165.90578 Loop time of 10.4988 on 1 procs for 1000 steps with 4000 atoms Performance: 8.230 ns/day, 2.916 hours/ns, 95.249 timesteps/s 59.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.121 | 10.121 | 10.121 | 0.0 | 96.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.099575 | 0.099575 | 0.099575 | 0.0 | 0.95 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.25587 | 0.25587 | 0.25587 | 0.0 | 2.44 Other | | 0.02217 | | | 0.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316418 ave 316418 max 316418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316418 Ave neighs/atom = 79.1045 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -14904.027 -14904.027 -15031.534 -15031.534 246.67223 246.67223 69114.571 69114.571 -165.90578 -165.90578 5000 -14896.611 -14896.611 -15029.204 -15029.204 256.5093 256.5093 69164.847 69164.847 -806.91357 -806.91357 Loop time of 13.0482 on 1 procs for 1000 steps with 4000 atoms Performance: 6.622 ns/day, 3.625 hours/ns, 76.639 timesteps/s 48.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.669 | 12.669 | 12.669 | 0.0 | 97.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039816 | 0.039816 | 0.039816 | 0.0 | 0.31 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.2796 | 0.2796 | 0.2796 | 0.0 | 2.14 Other | | 0.05965 | | | 0.46 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316378 ave 316378 max 316378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316378 Ave neighs/atom = 79.0945 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.140403892606, Press = 20.4259180254905 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -14896.611 -14896.611 -15029.204 -15029.204 256.5093 256.5093 69164.847 69164.847 -806.91357 -806.91357 6000 -14903.017 -14903.017 -15031.931 -15031.931 249.39403 249.39403 69067.589 69067.589 955.62989 955.62989 Loop time of 14.7502 on 1 procs for 1000 steps with 4000 atoms Performance: 5.858 ns/day, 4.097 hours/ns, 67.795 timesteps/s 43.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.215 | 14.215 | 14.215 | 0.0 | 96.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12013 | 0.12013 | 0.12013 | 0.0 | 0.81 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0.37524 | 0.37524 | 0.37524 | 0.0 | 2.54 Other | | 0.03971 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316272 ave 316272 max 316272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316272 Ave neighs/atom = 79.068 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.58001209991, Press = -6.57025194794369 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -14903.017 -14903.017 -15031.931 -15031.931 249.39403 249.39403 69067.589 69067.589 955.62989 955.62989 7000 -14898.931 -14898.931 -15029.97 -15029.97 253.50306 253.50306 69198.853 69198.853 -2086.9257 -2086.9257 Loop time of 13.4624 on 1 procs for 1000 steps with 4000 atoms Performance: 6.418 ns/day, 3.740 hours/ns, 74.281 timesteps/s 47.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.008 | 13.008 | 13.008 | 0.0 | 96.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10031 | 0.10031 | 0.10031 | 0.0 | 0.75 Output | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.00 Modify | 0.31369 | 0.31369 | 0.31369 | 0.0 | 2.33 Other | | 0.0399 | | | 0.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316480 ave 316480 max 316480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316480 Ave neighs/atom = 79.12 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.216992955984, Press = -6.41009483470273 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -14898.931 -14898.931 -15029.97 -15029.97 253.50306 253.50306 69198.853 69198.853 -2086.9257 -2086.9257 8000 -14901.7 -14901.7 -15033.788 -15033.788 255.53385 255.53385 69080.105 69080.105 295.34502 295.34502 Loop time of 13.2756 on 1 procs for 1000 steps with 4000 atoms Performance: 6.508 ns/day, 3.688 hours/ns, 75.326 timesteps/s 48.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.832 | 12.832 | 12.832 | 0.0 | 96.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.08011 | 0.08011 | 0.08011 | 0.0 | 0.60 Output | 3.4809e-05 | 3.4809e-05 | 3.4809e-05 | 0.0 | 0.00 Modify | 0.32374 | 0.32374 | 0.32374 | 0.0 | 2.44 Other | | 0.03999 | | | 0.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 316268 ave 316268 max 316268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316268 Ave neighs/atom = 79.067 Neighbor list builds = 0 Dangerous builds = 0 if "${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" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 69111.0041931402 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0