# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.615000084042549*${_u_distance} variable latticeconst_converted equal 3.615000084042549*1 lattice fcc ${latticeconst_converted} lattice fcc 3.61500008404255 Lattice spacing in x,y,z = 3.615 3.615 3.615 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (36.15 36.15 36.15) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000452042 secs variable mass_converted equal 63.546*${_u_mass} variable mass_converted equal 63.546*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_AcklandTichyVitek_1987_Cu__MO_179025990738_005 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 47241.6366698609 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6366698609/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6366698609/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 47241.6366698609/(1*1*${_u_distance}) variable V0_metal equal 47241.6366698609/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 47241.6366698609*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 47241.6366698609 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 0.1*${_u_time} variable Tdamp_converted equal 0.1*1 variable press_converted equal 0.0*${_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 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 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 0.2" variable T_up equal "273.15 + 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 = 6.42745 ghost atom cutoff = 6.42745 binsize = 3.21373, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.42745 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 -13936.218 -13936.218 -14077.412 -14077.412 273.15 273.15 47241.637 47241.637 3193.581 3193.581 1000 -13787.644 -13787.644 -13935.572 -13935.572 286.17723 286.17723 48144.554 48144.554 783.42688 783.42688 Loop time of 17.4119 on 1 procs for 1000 steps with 4000 atoms Performance: 4.962 ns/day, 4.837 hours/ns, 57.432 timesteps/s 36.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.816 | 16.816 | 16.816 | 0.0 | 96.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.058324 | 0.058324 | 0.058324 | 0.0 | 0.33 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.47777 | 0.47777 | 0.47777 | 0.0 | 2.74 Other | | 0.05963 | | | 0.34 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: 344000 ave 344000 max 344000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344000 Ave neighs/atom = 86 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13787.644 -13787.644 -13935.572 -13935.572 286.17723 286.17723 48144.554 48144.554 783.42688 783.42688 2000 -13798.58 -13798.58 -13937.306 -13937.306 268.37424 268.37424 48069.645 48069.645 2628.5399 2628.5399 Loop time of 17.6046 on 1 procs for 1000 steps with 4000 atoms Performance: 4.908 ns/day, 4.890 hours/ns, 56.803 timesteps/s 36.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.988 | 16.988 | 16.988 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079907 | 0.079907 | 0.079907 | 0.0 | 0.45 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0.51707 | 0.51707 | 0.51707 | 0.0 | 2.94 Other | | 0.01945 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340782 ave 340782 max 340782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340782 Ave neighs/atom = 85.1955 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13798.58 -13798.58 -13937.306 -13937.306 268.37424 268.37424 48069.645 48069.645 2628.5399 2628.5399 3000 -13797.227 -13797.227 -13936.076 -13936.076 268.61289 268.61289 48163.295 48163.295 -178.38359 -178.38359 Loop time of 16.777 on 1 procs for 1000 steps with 4000 atoms Performance: 5.150 ns/day, 4.660 hours/ns, 59.605 timesteps/s 38.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.281 | 16.281 | 16.281 | 0.0 | 97.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.058452 | 0.058452 | 0.058452 | 0.0 | 0.35 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0.3578 | 0.3578 | 0.3578 | 0.0 | 2.13 Other | | 0.07981 | | | 0.48 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 341000 ave 341000 max 341000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341000 Ave neighs/atom = 85.25 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13797.227 -13797.227 -13936.076 -13936.076 268.61289 268.61289 48163.295 48163.295 -178.38359 -178.38359 4000 -13796.265 -13796.265 -13939.893 -13939.893 277.85976 277.85976 48137.55 48137.55 117.23337 117.23337 Loop time of 17.2174 on 1 procs for 1000 steps with 4000 atoms Performance: 5.018 ns/day, 4.783 hours/ns, 58.081 timesteps/s 37.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.723 | 16.723 | 16.723 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098166 | 0.098166 | 0.098166 | 0.0 | 0.57 Output | 4.2915e-05 | 4.2915e-05 | 4.2915e-05 | 0.0 | 0.00 Modify | 0.37704 | 0.37704 | 0.37704 | 0.0 | 2.19 Other | | 0.01937 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340724 ave 340724 max 340724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340724 Ave neighs/atom = 85.181 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -13796.265 -13796.265 -13939.893 -13939.893 277.85976 277.85976 48137.55 48137.55 117.23337 117.23337 5000 -13797.933 -13797.933 -13935.396 -13935.396 265.93023 265.93023 48134.673 48134.673 1061.2503 1061.2503 Loop time of 17.8473 on 1 procs for 1000 steps with 4000 atoms Performance: 4.841 ns/day, 4.958 hours/ns, 56.031 timesteps/s 36.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.232 | 17.232 | 17.232 | 0.0 | 96.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.05832 | 0.05832 | 0.05832 | 0.0 | 0.33 Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.00 Modify | 0.49774 | 0.49774 | 0.49774 | 0.0 | 2.79 Other | | 0.05956 | | | 0.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340908 ave 340908 max 340908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340908 Ave neighs/atom = 85.227 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.049685021667, Press = -129.93852382219 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -13797.933 -13797.933 -13935.396 -13935.396 265.93023 265.93023 48134.673 48134.673 1061.2503 1061.2503 6000 -13794.758 -13794.758 -13936.774 -13936.774 274.74034 274.74034 48142.117 48142.117 633.36112 633.36112 Loop time of 16.6706 on 1 procs for 1000 steps with 4000 atoms Performance: 5.183 ns/day, 4.631 hours/ns, 59.986 timesteps/s 39.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.135 | 16.135 | 16.135 | 0.0 | 96.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.079526 | 0.079526 | 0.079526 | 0.0 | 0.48 Output | 3.314e-05 | 3.314e-05 | 3.314e-05 | 0.0 | 0.00 Modify | 0.40326 | 0.40326 | 0.40326 | 0.0 | 2.42 Other | | 0.0529 | | | 0.32 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340674 ave 340674 max 340674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340674 Ave neighs/atom = 85.1685 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.91616874422, Press = 7.91009500541836 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.609 | 4.609 | 4.609 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -13794.758 -13794.758 -13936.774 -13936.774 274.74034 274.74034 48142.117 48142.117 633.36112 633.36112 7000 -13798.637 -13798.637 -13942.395 -13942.395 278.10809 278.10809 48061.743 48061.743 2373.983 2373.983 Loop time of 17.0601 on 1 procs for 1000 steps with 4000 atoms Performance: 5.064 ns/day, 4.739 hours/ns, 58.616 timesteps/s 37.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.45 | 16.45 | 16.45 | 0.0 | 96.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11842 | 0.11842 | 0.11842 | 0.0 | 0.69 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0.45247 | 0.45247 | 0.45247 | 0.0 | 2.65 Other | | 0.03951 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 340820 ave 340820 max 340820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 340820 Ave neighs/atom = 85.205 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 48153.2063516046 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0