# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.614999935030937*${_u_distance} variable latticeconst_converted equal 3.614999935030937*1 lattice fcc ${latticeconst_converted} lattice fcc 3.61499993503094 Lattice spacing in x,y,z = 3.615 3.615 3.615 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (36.15 36.15 36.15) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000466824 secs variable mass_converted equal 63.546*${_u_mass} variable mass_converted equal 63.546*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_FoilesBaskesDaw_1986Universal3_Cu__MO_666348409573_004 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 47241.6308279092 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6308279092/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6308279092/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6308279092/(1*1*${_u_distance}) variable V0_metal equal 47241.6308279092/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 47241.6308279092*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 47241.6308279092 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 6.95 ghost atom cutoff = 6.95 binsize = 3.475, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.95 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -14008.467 -14008.467 -14160 -14160 293.15 293.15 47241.631 47241.631 3426.1478 3426.1478 1000 -13843.385 -13843.385 -14001.663 -14001.663 306.19921 306.19921 48019.908 48019.908 -2254.9691 -2254.9691 Loop time of 20.958 on 1 procs for 1000 steps with 4000 atoms Performance: 4.123 ns/day, 5.822 hours/ns, 47.714 timesteps/s 37.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.335 | 20.335 | 20.335 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059854 | 0.059854 | 0.059854 | 0.0 | 0.29 Output | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.00 Modify | 0.52273 | 0.52273 | 0.52273 | 0.0 | 2.49 Other | | 0.04019 | | | 0.19 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: 536000 ave 536000 max 536000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536000 Ave neighs/atom = 134 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13843.385 -13843.385 -14001.663 -14001.663 306.19921 306.19921 48019.908 48019.908 -2254.9691 -2254.9691 2000 -13857.453 -13857.453 -14007.337 -14007.337 289.95957 289.95957 47880.948 47880.948 917.13663 917.13663 Loop time of 23.457 on 1 procs for 1000 steps with 4000 atoms Performance: 3.683 ns/day, 6.516 hours/ns, 42.631 timesteps/s 38.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.802 | 22.802 | 22.802 | 0.0 | 97.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12999 | 0.12999 | 0.12999 | 0.0 | 0.55 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0.46461 | 0.46461 | 0.46461 | 0.0 | 1.98 Other | | 0.06021 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 517900 ave 517900 max 517900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 517900 Ave neighs/atom = 129.475 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13857.453 -13857.453 -14007.337 -14007.337 289.95957 289.95957 47880.948 47880.948 917.13663 917.13663 3000 -13848.459 -13848.459 -13998.234 -13998.234 289.74938 289.74938 47914.02 47914.02 894.02223 894.02223 Loop time of 22.127 on 1 procs for 1000 steps with 4000 atoms Performance: 3.905 ns/day, 6.146 hours/ns, 45.194 timesteps/s 40.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.673 | 21.673 | 21.673 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.099993 | 0.099993 | 0.099993 | 0.0 | 0.45 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.33388 | 0.33388 | 0.33388 | 0.0 | 1.51 Other | | 0.02022 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5842 ave 5842 max 5842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 520778 ave 520778 max 520778 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 520778 Ave neighs/atom = 130.195 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13848.459 -13848.459 -13998.234 -13998.234 289.74938 289.74938 47914.02 47914.02 894.02223 894.02223 4000 -13857.784 -13857.784 -14004.902 -14004.902 284.60903 284.60903 47926.366 47926.366 -200.07236 -200.07236 Loop time of 22.4291 on 1 procs for 1000 steps with 4000 atoms Performance: 3.852 ns/day, 6.230 hours/ns, 44.585 timesteps/s 39.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.963 | 21.963 | 21.963 | 0.0 | 97.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.099602 | 0.099602 | 0.099602 | 0.0 | 0.44 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0.30631 | 0.30631 | 0.30631 | 0.0 | 1.37 Other | | 0.06002 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518596 ave 518596 max 518596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518596 Ave neighs/atom = 129.649 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -13857.784 -13857.784 -14004.902 -14004.902 284.60903 284.60903 47926.366 47926.366 -200.07236 -200.07236 5000 -13848 -13848 -14003.385 -14003.385 300.6045 300.6045 47914.494 47914.494 442.70512 442.70512 Loop time of 22.3463 on 1 procs for 1000 steps with 4000 atoms Performance: 3.866 ns/day, 6.207 hours/ns, 44.750 timesteps/s 39.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.894 | 21.894 | 21.894 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039835 | 0.039835 | 0.039835 | 0.0 | 0.18 Output | 3.5048e-05 | 3.5048e-05 | 3.5048e-05 | 0.0 | 0.00 Modify | 0.3531 | 0.3531 | 0.3531 | 0.0 | 1.58 Other | | 0.05976 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 519416 ave 519416 max 519416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519416 Ave neighs/atom = 129.854 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 295.8779308161, Press = 2.61125160989479 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -13848 -13848 -14003.385 -14003.385 300.6045 300.6045 47914.494 47914.494 442.70512 442.70512 6000 -13856.323 -13856.323 -14007.983 -14007.983 293.39667 293.39667 47927.966 47927.966 -438.62103 -438.62103 Loop time of 22.2556 on 1 procs for 1000 steps with 4000 atoms Performance: 3.882 ns/day, 6.182 hours/ns, 44.932 timesteps/s 40.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.694 | 21.694 | 21.694 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10044 | 0.10044 | 0.10044 | 0.0 | 0.45 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0.39119 | 0.39119 | 0.39119 | 0.0 | 1.76 Other | | 0.07021 | | | 0.32 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 519368 ave 519368 max 519368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519368 Ave neighs/atom = 129.842 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.320858797826, Press = 3.24095350709095 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -13856.323 -13856.323 -14007.983 -14007.983 293.39667 293.39667 47927.966 47927.966 -438.62103 -438.62103 7000 -13850.495 -13850.495 -14000.371 -14000.371 289.94613 289.94613 47907.948 47907.948 749.59674 749.59674 Loop time of 23.5119 on 1 procs for 1000 steps with 4000 atoms Performance: 3.675 ns/day, 6.531 hours/ns, 42.532 timesteps/s 38.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.973 | 22.973 | 22.973 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079929 | 0.079929 | 0.079929 | 0.0 | 0.34 Output | 5.0068e-05 | 5.0068e-05 | 5.0068e-05 | 0.0 | 0.00 Modify | 0.39816 | 0.39816 | 0.39816 | 0.0 | 1.69 Other | | 0.06031 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 520084 ave 520084 max 520084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 520084 Ave neighs/atom = 130.021 Neighbor list builds = 0 Dangerous builds = 0 if "${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 47925.7514273533 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0