# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.089999961853028*${_u_distance} variable latticeconst_converted equal 4.089999961853028*1 lattice fcc ${latticeconst_converted} lattice fcc 4.08999996185303 Lattice spacing in x,y,z = 4.09 4.09 4.09 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (40.9 40.9 40.9) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000448942 secs variable mass_converted equal 107.8682*${_u_mass} variable mass_converted equal 107.8682*1 # specify which KIM Model to use pair_style kim EAM_Dynamo_FoilesBaskesDaw_1986Universal3_Ag__MO_626948998302_000 pair_coeff * * Ag mass 1 ${mass_converted} mass 1 107.8682 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 68417.927085621 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 68417.927085621/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 68417.927085621/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 68417.927085621/(1*1*${_u_distance}) variable V0_metal equal 68417.927085621/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 68417.927085621*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 68417.927085621 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 0.2" variable T_up equal "313.15 + 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 = 7.55 ghost atom cutoff = 7.55 binsize = 3.775, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -11238.129 -11238.129 -11400 -11400 313.15 313.15 68417.927 68417.927 2527.0431 2527.0431 1000 -11054.982 -11054.982 -11220.949 -11220.949 321.07357 321.07357 69798.681 69798.681 -414.13317 -414.13317 Loop time of 19.8446 on 1 procs for 1000 steps with 4000 atoms Performance: 4.354 ns/day, 5.512 hours/ns, 50.392 timesteps/s 36.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.251 | 19.251 | 19.251 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.09809 | 0.09809 | 0.09809 | 0.0 | 0.49 Output | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.00 Modify | 0.43582 | 0.43582 | 0.43582 | 0.0 | 2.20 Other | | 0.05964 | | | 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: 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -11054.982 -11054.982 -11220.949 -11220.949 321.07357 321.07357 69798.681 69798.681 -414.13317 -414.13317 2000 -11076.606 -11076.606 -11236.778 -11236.778 309.86315 309.86315 69551.713 69551.713 1491.8701 1491.8701 Loop time of 21.5803 on 1 procs for 1000 steps with 4000 atoms Performance: 4.004 ns/day, 5.995 hours/ns, 46.339 timesteps/s 36.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.005 | 21.005 | 21.005 | 0.0 | 97.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098355 | 0.098355 | 0.098355 | 0.0 | 0.46 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.45744 | 0.45744 | 0.45744 | 0.0 | 2.12 Other | | 0.01988 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366996 ave 366996 max 366996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366996 Ave neighs/atom = 91.749 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -11076.606 -11076.606 -11236.778 -11236.778 309.86315 309.86315 69551.713 69551.713 1491.8701 1491.8701 3000 -11065.248 -11065.248 -11227.581 -11227.581 314.04485 314.04485 69818.513 69818.513 -1370.3306 -1370.3306 Loop time of 22.3253 on 1 procs for 1000 steps with 4000 atoms Performance: 3.870 ns/day, 6.201 hours/ns, 44.792 timesteps/s 35.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.854 | 21.854 | 21.854 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.098 | 0.098 | 0.098 | 0.0 | 0.44 Output | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 Modify | 0.29698 | 0.29698 | 0.29698 | 0.0 | 1.33 Other | | 0.07584 | | | 0.34 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 367376 ave 367376 max 367376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 367376 Ave neighs/atom = 91.844 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -11065.248 -11065.248 -11227.581 -11227.581 314.04485 314.04485 69818.513 69818.513 -1370.3306 -1370.3306 4000 -11072.417 -11072.417 -11234.837 -11234.837 314.21248 314.21248 69698.032 69698.032 -319.7649 -319.7649 Loop time of 21.9773 on 1 procs for 1000 steps with 4000 atoms Performance: 3.931 ns/day, 6.105 hours/ns, 45.501 timesteps/s 35.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.38 | 21.38 | 21.38 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.16107 | 0.16107 | 0.16107 | 0.0 | 0.73 Output | 4.2915e-05 | 4.2915e-05 | 4.2915e-05 | 0.0 | 0.00 Modify | 0.39644 | 0.39644 | 0.39644 | 0.0 | 1.80 Other | | 0.0397 | | | 0.18 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 365508 ave 365508 max 365508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365508 Ave neighs/atom = 91.377 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -11072.417 -11072.417 -11234.837 -11234.837 314.21248 314.21248 69698.032 69698.032 -319.7649 -319.7649 5000 -11066.384 -11066.384 -11231.871 -11231.871 320.14725 320.14725 69655.693 69655.693 622.37716 622.37716 Loop time of 21.7083 on 1 procs for 1000 steps with 4000 atoms Performance: 3.980 ns/day, 6.030 hours/ns, 46.065 timesteps/s 36.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.18 | 21.18 | 21.18 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13759 | 0.13759 | 0.13759 | 0.0 | 0.63 Output | 5.0068e-05 | 5.0068e-05 | 5.0068e-05 | 0.0 | 0.00 Modify | 0.33099 | 0.33099 | 0.33099 | 0.0 | 1.52 Other | | 0.05958 | | | 0.27 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 365872 ave 365872 max 365872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365872 Ave neighs/atom = 91.468 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 316.109494332925, Press = 491.913877593649 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -11066.384 -11066.384 -11231.871 -11231.871 320.14725 320.14725 69655.693 69655.693 622.37716 622.37716 6000 -11071.404 -11071.404 -11232.732 -11232.732 312.09859 312.09859 69702.225 69702.225 -248.93393 -248.93393 Loop time of 21.4136 on 1 procs for 1000 steps with 4000 atoms Performance: 4.035 ns/day, 5.948 hours/ns, 46.699 timesteps/s 36.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.975 | 20.975 | 20.975 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.077662 | 0.077662 | 0.077662 | 0.0 | 0.36 Output | 3.3855e-05 | 3.3855e-05 | 3.3855e-05 | 0.0 | 0.00 Modify | 0.32118 | 0.32118 | 0.32118 | 0.0 | 1.50 Other | | 0.03976 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366638 ave 366638 max 366638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366638 Ave neighs/atom = 91.6595 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.776890221755, Press = 30.0978843582814 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.606 | 4.606 | 4.606 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -11071.404 -11071.404 -11232.732 -11232.732 312.09859 312.09859 69702.225 69702.225 -248.93393 -248.93393 7000 -11068.395 -11068.395 -11229.609 -11229.609 311.87853 311.87853 69675.696 69675.696 456.31748 456.31748 Loop time of 21.9689 on 1 procs for 1000 steps with 4000 atoms Performance: 3.933 ns/day, 6.102 hours/ns, 45.519 timesteps/s 35.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.2 | 21.2 | 21.2 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10746 | 0.10746 | 0.10746 | 0.0 | 0.49 Output | 4.1008e-05 | 4.1008e-05 | 4.1008e-05 | 0.0 | 0.00 Modify | 0.56148 | 0.56148 | 0.56148 | 0.0 | 2.56 Other | | 0.09986 | | | 0.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 365992 ave 365992 max 365992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 365992 Ave neighs/atom = 91.498 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 69694.5606627842 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0