# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.6148132324218762*${_u_distance} variable latticeconst_converted equal 3.6148132324218762*1 lattice fcc ${latticeconst_converted} lattice fcc 3.61481323242188 Lattice spacing in x,y,z = 3.61481 3.61481 3.61481 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (36.1481 36.1481 36.1481) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000506163 secs variable mass_converted equal 63.546*${_u_mass} variable mass_converted equal 63.546*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_ZhouWadleyJohnson_2001_Cu__MO_380822813353_000 pair_coeff * * Cu mass 1 ${mass_converted} mass 1 63.546 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 47234.3115910894 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47234.3115910894/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47234.3115910894/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 47234.3115910894/(1*1*${_u_distance}) variable V0_metal equal 47234.3115910894/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 47234.3115910894*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 47234.3115910894 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 0.2" variable T_up equal "293.15 + 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -14007.682 -14007.682 -14159.214 -14159.214 293.15 293.15 47234.312 47234.312 3426.6485 3426.6485 1000 -13840.955 -13840.955 -14005.73 -14005.73 318.76726 318.76726 47717.165 47717.165 -2328.2827 -2328.2827 Loop time of 119.942 on 1 procs for 1000 steps with 4000 atoms Performance: 0.720 ns/day, 33.317 hours/ns, 8.337 timesteps/s 38.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 119.24 | 119.24 | 119.24 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.28293 | 0.28293 | 0.28293 | 0.0 | 0.24 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.36415 | 0.36415 | 0.36415 | 0.0 | 0.30 Other | | 0.05474 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13969 ave 13969 max 13969 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: 1.832e+06 ave 1.832e+06 max 1.832e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1832000 Ave neighs/atom = 458 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13840.955 -13840.955 -14005.73 -14005.73 318.76726 318.76726 47717.165 47717.165 -2328.2827 -2328.2827 2000 -13856.279 -13856.279 -14005.37 -14005.37 288.4253 288.4253 47582.535 47582.535 710.65053 710.65053 Loop time of 124.721 on 1 procs for 1000 steps with 4000 atoms Performance: 0.693 ns/day, 34.645 hours/ns, 8.018 timesteps/s 37.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 124.02 | 124.02 | 124.02 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1651 | 0.1651 | 0.1651 | 0.0 | 0.13 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.4916 | 0.4916 | 0.4916 | 0.0 | 0.39 Other | | 0.04456 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13905 ave 13905 max 13905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85181e+06 ave 1.85181e+06 max 1.85181e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1851808 Ave neighs/atom = 462.952 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13856.279 -13856.279 -14005.37 -14005.37 288.4253 288.4253 47582.535 47582.535 710.65053 710.65053 3000 -13849.062 -13849.062 -14003.072 -14003.072 297.94261 297.94261 47617.51 47617.51 64.634909 64.634909 Loop time of 112.787 on 1 procs for 1000 steps with 4000 atoms Performance: 0.766 ns/day, 31.330 hours/ns, 8.866 timesteps/s 41.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 112.21 | 112.21 | 112.21 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.18448 | 0.18448 | 0.18448 | 0.0 | 0.16 Output | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 Modify | 0.37227 | 0.37227 | 0.37227 | 0.0 | 0.33 Other | | 0.02451 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13905 ave 13905 max 13905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85953e+06 ave 1.85953e+06 max 1.85953e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1859532 Ave neighs/atom = 464.883 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13849.062 -13849.062 -14003.072 -14003.072 297.94261 297.94261 47617.51 47617.51 64.634909 64.634909 4000 -13854.127 -13854.127 -14005.366 -14005.366 292.58337 292.58337 47632.965 47632.965 -591.76341 -591.76341 Loop time of 93.9792 on 1 procs for 1000 steps with 4000 atoms Performance: 0.919 ns/day, 26.105 hours/ns, 10.641 timesteps/s 50.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 93.476 | 93.476 | 93.476 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14594 | 0.14594 | 0.14594 | 0.0 | 0.16 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.33056 | 0.33056 | 0.33056 | 0.0 | 0.35 Other | | 0.02704 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13867 ave 13867 max 13867 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85787e+06 ave 1.85787e+06 max 1.85787e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1857872 Ave neighs/atom = 464.468 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -13854.127 -13854.127 -14005.366 -14005.366 292.58337 292.58337 47632.965 47632.965 -591.76341 -591.76341 5000 -13849.71 -13849.71 -14002.843 -14002.843 296.24674 296.24674 47598.299 47598.299 592.30437 592.30437 Loop time of 78.2522 on 1 procs for 1000 steps with 4000 atoms Performance: 1.104 ns/day, 21.737 hours/ns, 12.779 timesteps/s 60.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 77.859 | 77.859 | 77.859 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10575 | 0.10575 | 0.10575 | 0.0 | 0.14 Output | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 Modify | 0.24253 | 0.24253 | 0.24253 | 0.0 | 0.31 Other | | 0.04466 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13886 ave 13886 max 13886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85693e+06 ave 1.85693e+06 max 1.85693e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1856934 Ave neighs/atom = 464.233 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 294.988276615932, Press = 342.63827521529 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -13849.71 -13849.71 -14002.843 -14002.843 296.24674 296.24674 47598.299 47598.299 592.30437 592.30437 6000 -13853.75 -13853.75 -14007.163 -14007.163 296.78903 296.78903 47657.712 47657.712 -1213.7173 -1213.7173 Loop time of 91.318 on 1 procs for 1000 steps with 4000 atoms Performance: 0.946 ns/day, 25.366 hours/ns, 10.951 timesteps/s 50.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 90.547 | 90.547 | 90.547 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.24358 | 0.24358 | 0.24358 | 0.0 | 0.27 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0.48318 | 0.48318 | 0.48318 | 0.0 | 0.53 Other | | 0.04422 | | | 0.05 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13885 ave 13885 max 13885 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85851e+06 ave 1.85851e+06 max 1.85851e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1858514 Ave neighs/atom = 464.628 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.366243931667, Press = 3.13422969320542 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 13.12 | 13.12 | 13.12 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -13853.75 -13853.75 -14007.163 -14007.163 296.78903 296.78903 47657.712 47657.712 -1213.7173 -1213.7173 7000 -13849.307 -13849.307 -14005.051 -14005.051 301.29709 301.29709 47564.539 47564.539 1420.4576 1420.4576 Loop time of 92.6299 on 1 procs for 1000 steps with 4000 atoms Performance: 0.933 ns/day, 25.731 hours/ns, 10.796 timesteps/s 50.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 92.068 | 92.068 | 92.068 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.21394 | 0.21394 | 0.21394 | 0.0 | 0.23 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.26394 | 0.26394 | 0.26394 | 0.0 | 0.28 Other | | 0.08441 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13898 ave 13898 max 13898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.85536e+06 ave 1.85536e+06 max 1.85536e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1855364 Ave neighs/atom = 463.841 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 47617.6305591604 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0