# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.9946083426475534*${_u_distance} variable latticeconst_converted equal 3.9946083426475534*1 lattice fcc ${latticeconst_converted} lattice fcc 3.99460834264755 Lattice spacing in x,y,z = 3.99461 3.99461 3.99461 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (39.9461 39.9461 39.9461) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000527859 secs variable mass_converted equal 26.981538*${_u_mass} variable mass_converted equal 26.981538*1 # specify which KIM Model to use pair_style kim EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001 pair_coeff * * Al mass 1 ${mass_converted} mass 1 26.981538 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 63741.5491299752 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 63741.5491299752/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 63741.5491299752/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 63741.5491299752/(1*1*${_u_distance}) variable V0_metal equal 63741.5491299752/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 63741.5491299752*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 63741.5491299752 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 0.2" variable T_up equal "333.15 + 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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 -12967.249 -12967.249 -13139.458 -13139.458 333.15 333.15 63741.549 63741.549 2885.713 2885.713 1000 -12777.021 -12777.021 -12949.53 -12949.53 333.72986 333.72986 65547.678 65547.678 420.37102 420.37102 Loop time of 67.8125 on 1 procs for 1000 steps with 4000 atoms Performance: 1.274 ns/day, 18.837 hours/ns, 14.747 timesteps/s 41.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 67.194 | 67.194 | 67.194 | 0.0 | 99.09 Neigh | 0.05621 | 0.05621 | 0.05621 | 0.0 | 0.08 Comm | 0.099462 | 0.099462 | 0.099462 | 0.0 | 0.15 Output | 4.0054e-05 | 4.0054e-05 | 4.0054e-05 | 0.0 | 0.00 Modify | 0.44236 | 0.44236 | 0.44236 | 0.0 | 0.65 Other | | 0.02033 | | | 0.03 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: 468916 ave 468916 max 468916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468916 Ave neighs/atom = 117.229 Neighbor list builds = 1 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -12777.021 -12777.021 -12949.53 -12949.53 333.72986 333.72986 65547.678 65547.678 420.37102 420.37102 2000 -12794.397 -12794.397 -12963.081 -12963.081 326.33019 326.33019 65573.961 65573.961 -275.72201 -275.72201 Loop time of 66.4318 on 1 procs for 1000 steps with 4000 atoms Performance: 1.301 ns/day, 18.453 hours/ns, 15.053 timesteps/s 43.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 65.975 | 65.975 | 65.975 | 0.0 | 99.31 Neigh | 0.037298 | 0.037298 | 0.037298 | 0.0 | 0.06 Comm | 0.059443 | 0.059443 | 0.059443 | 0.0 | 0.09 Output | 3.6955e-05 | 3.6955e-05 | 3.6955e-05 | 0.0 | 0.00 Modify | 0.32065 | 0.32065 | 0.32065 | 0.0 | 0.48 Other | | 0.03973 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463134 ave 463134 max 463134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463134 Ave neighs/atom = 115.784 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -12794.397 -12794.397 -12963.081 -12963.081 326.33019 326.33019 65573.961 65573.961 -275.72201 -275.72201 3000 -12784.996 -12784.996 -12961.109 -12961.109 340.70225 340.70225 65623.991 65623.991 -296.44369 -296.44369 Loop time of 68.084 on 1 procs for 1000 steps with 4000 atoms Performance: 1.269 ns/day, 18.912 hours/ns, 14.688 timesteps/s 41.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 67.568 | 67.568 | 67.568 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.070886 | 0.070886 | 0.070886 | 0.0 | 0.10 Output | 4.1008e-05 | 4.1008e-05 | 4.1008e-05 | 0.0 | 0.00 Modify | 0.42537 | 0.42537 | 0.42537 | 0.0 | 0.62 Other | | 0.01958 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463266 ave 463266 max 463266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463266 Ave neighs/atom = 115.817 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -12784.996 -12784.996 -12961.109 -12961.109 340.70225 340.70225 65623.991 65623.991 -296.44369 -296.44369 4000 -12790.076 -12790.076 -12961.09 -12961.09 330.83686 330.83686 65559.639 65559.639 -53.391311 -53.391311 Loop time of 69.2902 on 1 procs for 1000 steps with 4000 atoms Performance: 1.247 ns/day, 19.247 hours/ns, 14.432 timesteps/s 41.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 68.82 | 68.82 | 68.82 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.057842 | 0.057842 | 0.057842 | 0.0 | 0.08 Output | 3.6955e-05 | 3.6955e-05 | 3.6955e-05 | 0.0 | 0.00 Modify | 0.39305 | 0.39305 | 0.39305 | 0.0 | 0.57 Other | | 0.0193 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 462664 ave 462664 max 462664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462664 Ave neighs/atom = 115.666 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -12790.076 -12790.076 -12961.09 -12961.09 330.83686 330.83686 65559.639 65559.639 -53.391311 -53.391311 5000 -12789.456 -12789.456 -12961.751 -12961.751 333.31607 333.31607 65486.514 65486.514 473.91908 473.91908 Loop time of 68.8293 on 1 procs for 1000 steps with 4000 atoms Performance: 1.255 ns/day, 19.119 hours/ns, 14.529 timesteps/s 41.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 68.376 | 68.376 | 68.376 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.058104 | 0.058104 | 0.058104 | 0.0 | 0.08 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.35627 | 0.35627 | 0.35627 | 0.0 | 0.52 Other | | 0.03915 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463538 ave 463538 max 463538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463538 Ave neighs/atom = 115.885 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 334.463454340023, Press = 129.311366934949 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -12789.456 -12789.456 -12961.751 -12961.751 333.31607 333.31607 65486.514 65486.514 473.91908 473.91908 6000 -12786.649 -12786.649 -12958.098 -12958.098 331.67951 331.67951 65491.62 65491.62 477.6892 477.6892 Loop time of 75.8006 on 1 procs for 1000 steps with 4000 atoms Performance: 1.140 ns/day, 21.056 hours/ns, 13.193 timesteps/s 37.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 75.295 | 75.295 | 75.295 | 0.0 | 99.33 Neigh | 0.031631 | 0.031631 | 0.031631 | 0.0 | 0.04 Comm | 0.078709 | 0.078709 | 0.078709 | 0.0 | 0.10 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.31643 | 0.31643 | 0.31643 | 0.0 | 0.42 Other | | 0.07919 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463702 ave 463702 max 463702 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463702 Ave neighs/atom = 115.925 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.573972464737, Press = 55.6545564631444 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -12786.649 -12786.649 -12958.098 -12958.098 331.67951 331.67951 65491.62 65491.62 477.6892 477.6892 7000 -12789.967 -12789.967 -12963.094 -12963.094 334.92616 334.92616 65657.58 65657.58 -673.72153 -673.72153 Loop time of 73.8696 on 1 procs for 1000 steps with 4000 atoms Performance: 1.170 ns/day, 20.519 hours/ns, 13.537 timesteps/s 38.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 73.177 | 73.177 | 73.177 | 0.0 | 99.06 Neigh | 0.06973 | 0.06973 | 0.06973 | 0.0 | 0.09 Comm | 0.058939 | 0.058939 | 0.058939 | 0.0 | 0.08 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0.44456 | 0.44456 | 0.44456 | 0.0 | 0.60 Other | | 0.1191 | | | 0.16 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 464756 ave 464756 max 464756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 464756 Ave neighs/atom = 116.189 Neighbor list builds = 3 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.107802053745, Press = 27.8808611467523 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.369 | 5.369 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -12789.967 -12789.967 -12963.094 -12963.094 334.92616 334.92616 65657.58 65657.58 -673.72153 -673.72153 8000 -12781.753 -12781.753 -12955.682 -12955.682 336.47701 336.47701 65715.18 65715.18 -694.21603 -694.21603 Loop time of 70.7905 on 1 procs for 1000 steps with 4000 atoms Performance: 1.221 ns/day, 19.664 hours/ns, 14.126 timesteps/s 39.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.336 | 70.336 | 70.336 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.077603 | 0.077603 | 0.077603 | 0.0 | 0.11 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.31738 | 0.31738 | 0.31738 | 0.0 | 0.45 Other | | 0.05925 | | | 0.08 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 461948 ave 461948 max 461948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461948 Ave neighs/atom = 115.487 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 65557.7248885578 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0