# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.457114815711976*${_u_distance} variable latticeconst_converted equal 5.457114815711976*1 lattice diamond ${latticeconst_converted} lattice diamond 5.45711481571198 Lattice spacing in x,y,z = 5.45711 5.45711 5.45711 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (54.5711 54.5711 54.5711) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.000780821 secs variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 # specify which KIM Model to use pair_style kim SW_LeeHwang_2012GGA_Si__MO_040570764911_000 pair_coeff * * Si mass 1 ${mass_converted} mass 1 28.0855 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 162513.436448064 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 162513.436448064/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 162513.436448064/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 162513.436448064/(1*1*${_u_distance}) variable V0_metal equal 162513.436448064/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 162513.436448064*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 162513.436448064 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 5.78935 ghost atom cutoff = 5.78935 binsize = 2.89467, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.78935 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -22394.938 -22394.938 -22718.72 -22718.72 313.15 313.15 162513.44 162513.44 2128.0551 2128.0551 1000 -22042.247 -22042.247 -22359.544 -22359.544 306.87799 306.87799 163611.11 163611.11 315.60232 315.60232 Loop time of 90.704 on 1 procs for 1000 steps with 8000 atoms Performance: 0.953 ns/day, 25.196 hours/ns, 11.025 timesteps/s 43.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 89.555 | 89.555 | 89.555 | 0.0 | 98.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.19336 | 0.19336 | 0.19336 | 0.0 | 0.21 Output | 5.4121e-05 | 5.4121e-05 | 5.4121e-05 | 0.0 | 0.00 Modify | 0.83923 | 0.83923 | 0.83923 | 0.0 | 0.93 Other | | 0.1159 | | | 0.13 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 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: 272000 ave 272000 max 272000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272000 Ave neighs/atom = 34 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -22042.247 -22042.247 -22359.544 -22359.544 306.87799 306.87799 163611.11 163611.11 315.60232 315.60232 2000 -22079.256 -22079.256 -22403.352 -22403.352 313.45355 313.45355 163708.55 163708.55 -372.84909 -372.84909 Loop time of 98.5738 on 1 procs for 1000 steps with 8000 atoms Performance: 0.877 ns/day, 27.382 hours/ns, 10.145 timesteps/s 44.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 97.662 | 97.662 | 97.662 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1931 | 0.1931 | 0.1931 | 0.0 | 0.20 Output | 4.4823e-05 | 4.4823e-05 | 4.4823e-05 | 0.0 | 0.00 Modify | 0.62273 | 0.62273 | 0.62273 | 0.0 | 0.63 Other | | 0.09579 | | | 0.10 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275750 ave 275750 max 275750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275750 Ave neighs/atom = 34.4688 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -22079.256 -22079.256 -22403.352 -22403.352 313.45355 313.45355 163708.55 163708.55 -372.84909 -372.84909 3000 -22056.807 -22056.807 -22384.461 -22384.461 316.89562 316.89562 163785.74 163785.74 -470.55563 -470.55563 Loop time of 94.5538 on 1 procs for 1000 steps with 8000 atoms Performance: 0.914 ns/day, 26.265 hours/ns, 10.576 timesteps/s 46.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 93.643 | 93.643 | 93.643 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15372 | 0.15372 | 0.15372 | 0.0 | 0.16 Output | 5.2929e-05 | 5.2929e-05 | 5.2929e-05 | 0.0 | 0.00 Modify | 0.70004 | 0.70004 | 0.70004 | 0.0 | 0.74 Other | | 0.05661 | | | 0.06 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275024 ave 275024 max 275024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275024 Ave neighs/atom = 34.378 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -22056.807 -22056.807 -22384.461 -22384.461 316.89562 316.89562 163785.74 163785.74 -470.55563 -470.55563 4000 -22069.308 -22069.308 -22403.733 -22403.733 323.44375 323.44375 163701.21 163701.21 -121.12315 -121.12315 Loop time of 93.992 on 1 procs for 1000 steps with 8000 atoms Performance: 0.919 ns/day, 26.109 hours/ns, 10.639 timesteps/s 46.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 93.253 | 93.253 | 93.253 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.092965 | 0.092965 | 0.092965 | 0.0 | 0.10 Output | 5.2929e-05 | 5.2929e-05 | 5.2929e-05 | 0.0 | 0.00 Modify | 0.58948 | 0.58948 | 0.58948 | 0.0 | 0.63 Other | | 0.05611 | | | 0.06 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275132 ave 275132 max 275132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275132 Ave neighs/atom = 34.3915 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -22069.308 -22069.308 -22403.733 -22403.733 323.44375 323.44375 163701.21 163701.21 -121.12315 -121.12315 5000 -22066.255 -22066.255 -22394.564 -22394.564 317.52822 317.52822 163607.23 163607.23 183.91671 183.91671 Loop time of 88.257 on 1 procs for 1000 steps with 8000 atoms Performance: 0.979 ns/day, 24.516 hours/ns, 11.331 timesteps/s 49.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 87.426 | 87.426 | 87.426 | 0.0 | 99.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13467 | 0.13467 | 0.13467 | 0.0 | 0.15 Output | 4.3154e-05 | 4.3154e-05 | 4.3154e-05 | 0.0 | 0.00 Modify | 0.65914 | 0.65914 | 0.65914 | 0.0 | 0.75 Other | | 0.03693 | | | 0.04 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274644 ave 274644 max 274644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274644 Ave neighs/atom = 34.3305 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 314.889944743862, Press = 238.362475766131 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -22066.255 -22066.255 -22394.564 -22394.564 317.52822 317.52822 163607.23 163607.23 183.91671 183.91671 6000 -22062.53 -22062.53 -22391.315 -22391.315 317.9883 317.9883 163441.09 163441.09 904.76536 904.76536 Loop time of 87.102 on 1 procs for 1000 steps with 8000 atoms Performance: 0.992 ns/day, 24.195 hours/ns, 11.481 timesteps/s 50.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 86.275 | 86.275 | 86.275 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.073443 | 0.073443 | 0.073443 | 0.0 | 0.08 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.69656 | 0.69656 | 0.69656 | 0.0 | 0.80 Other | | 0.0569 | | | 0.07 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275022 ave 275022 max 275022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275022 Ave neighs/atom = 34.3777 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.591780030799, Press = 17.3097873422498 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -22062.53 -22062.53 -22391.315 -22391.315 317.9883 317.9883 163441.09 163441.09 904.76536 904.76536 7000 -22071.558 -22071.558 -22391.142 -22391.142 309.08962 309.08962 163524.25 163524.25 500.40099 500.40099 Loop time of 86.9302 on 1 procs for 1000 steps with 8000 atoms Performance: 0.994 ns/day, 24.147 hours/ns, 11.503 timesteps/s 50.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 86.168 | 86.168 | 86.168 | 0.0 | 99.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11747 | 0.11747 | 0.11747 | 0.0 | 0.14 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0.56804 | 0.56804 | 0.56804 | 0.0 | 0.65 Other | | 0.07685 | | | 0.09 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275442 ave 275442 max 275442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275442 Ave neighs/atom = 34.4303 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.127220638118, Press = -5.1300134259512 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -22071.558 -22071.558 -22391.142 -22391.142 309.08962 309.08962 163524.25 163524.25 500.40099 500.40099 8000 -22059.949 -22059.949 -22386.875 -22386.875 316.19051 316.19051 163732.26 163732.26 -203.17613 -203.17613 Loop time of 104.991 on 1 procs for 1000 steps with 8000 atoms Performance: 0.823 ns/day, 29.164 hours/ns, 9.525 timesteps/s 41.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 103.82 | 103.82 | 103.82 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1548 | 0.1548 | 0.1548 | 0.0 | 0.15 Output | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 Modify | 0.95654 | 0.95654 | 0.95654 | 0.0 | 0.91 Other | | 0.056 | | | 0.05 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275026 ave 275026 max 275026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275026 Ave neighs/atom = 34.3783 Neighbor list builds = 0 Dangerous builds = 0 if "${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 163661.105306436 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0