# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.430949777364731*${_u_distance} variable latticeconst_converted equal 5.430949777364731*1 lattice diamond ${latticeconst_converted} lattice diamond 5.43094977736473 Lattice spacing in x,y,z = 5.43095 5.43095 5.43095 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (54.3095 54.3095 54.3095) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.000801802 secs variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 # specify which KIM Model to use pair_style kim ThreeBodyCluster_Gong_Gong_1993_Si__MO_407755720412_000 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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 160187.033967556 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160187.033967556/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160187.033967556/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 160187.033967556/(1*1*${_u_distance}) variable V0_metal equal 160187.033967556/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 160187.033967556*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 160187.033967556 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 5.77118 ghost atom cutoff = 5.77118 binsize = 2.88559, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.77118 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 -36837.576 -36837.576 -37120 -37120 273.15 273.15 160187.03 160187.03 1883.1869 1883.1869 1000 -36531.379 -36531.379 -36808.129 -36808.129 267.66228 267.66228 160650.24 160650.24 -496.74785 -496.74785 Loop time of 52.0825 on 1 procs for 1000 steps with 8000 atoms Performance: 1.659 ns/day, 14.467 hours/ns, 19.200 timesteps/s 38.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 51.052 | 51.052 | 51.052 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.091503 | 0.091503 | 0.091503 | 0.0 | 0.18 Output | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 Modify | 0.8239 | 0.8239 | 0.8239 | 0.0 | 1.58 Other | | 0.1151 | | | 0.22 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -36531.379 -36531.379 -36808.129 -36808.129 267.66228 267.66228 160650.24 160650.24 -496.74785 -496.74785 2000 -36561.616 -36561.616 -36844.432 -36844.432 273.52875 273.52875 160611.07 160611.07 -121.05276 -121.05276 Loop time of 59.5012 on 1 procs for 1000 steps with 8000 atoms Performance: 1.452 ns/day, 16.528 hours/ns, 16.806 timesteps/s 37.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.648 | 58.648 | 58.648 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13163 | 0.13163 | 0.13163 | 0.0 | 0.22 Output | 5.3167e-05 | 5.3167e-05 | 5.3167e-05 | 0.0 | 0.00 Modify | 0.64689 | 0.64689 | 0.64689 | 0.0 | 1.09 Other | | 0.07488 | | | 0.13 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 275464 ave 275464 max 275464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275464 Ave neighs/atom = 34.433 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -36561.616 -36561.616 -36844.432 -36844.432 273.52875 273.52875 160611.07 160611.07 -121.05276 -121.05276 3000 -36547.793 -36547.793 -36828.258 -36828.258 271.25539 271.25539 160581.67 160581.67 104.33215 104.33215 Loop time of 59.3112 on 1 procs for 1000 steps with 8000 atoms Performance: 1.457 ns/day, 16.475 hours/ns, 16.860 timesteps/s 37.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.237 | 58.237 | 58.237 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.14748 | 0.14748 | 0.14748 | 0.0 | 0.25 Output | 5.3167e-05 | 5.3167e-05 | 5.3167e-05 | 0.0 | 0.00 Modify | 0.87094 | 0.87094 | 0.87094 | 0.0 | 1.47 Other | | 0.05557 | | | 0.09 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274334 ave 274334 max 274334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274334 Ave neighs/atom = 34.2918 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -36547.793 -36547.793 -36828.258 -36828.258 271.25539 271.25539 160581.67 160581.67 104.33215 104.33215 4000 -36551.971 -36551.971 -36830.958 -36830.958 269.82572 269.82572 160602.77 160602.77 -149.36761 -149.36761 Loop time of 59.0786 on 1 procs for 1000 steps with 8000 atoms Performance: 1.462 ns/day, 16.411 hours/ns, 16.927 timesteps/s 37.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.007 | 58.007 | 58.007 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.091709 | 0.091709 | 0.091709 | 0.0 | 0.16 Output | 4.5776e-05 | 4.5776e-05 | 4.5776e-05 | 0.0 | 0.00 Modify | 0.94512 | 0.94512 | 0.94512 | 0.0 | 1.60 Other | | 0.03482 | | | 0.06 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274752 ave 274752 max 274752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274752 Ave neighs/atom = 34.344 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -36551.971 -36551.971 -36830.958 -36830.958 269.82572 269.82572 160602.77 160602.77 -149.36761 -149.36761 5000 -36554.736 -36554.736 -36836.809 -36836.809 272.81061 272.81061 160581.83 160581.83 129.77121 129.77121 Loop time of 59.4048 on 1 procs for 1000 steps with 8000 atoms Performance: 1.454 ns/day, 16.501 hours/ns, 16.834 timesteps/s 37.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 58.413 | 58.413 | 58.413 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15148 | 0.15148 | 0.15148 | 0.0 | 0.25 Output | 4.2915e-05 | 4.2915e-05 | 4.2915e-05 | 0.0 | 0.00 Modify | 0.74601 | 0.74601 | 0.74601 | 0.0 | 1.26 Other | | 0.09465 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274958 ave 274958 max 274958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274958 Ave neighs/atom = 34.3698 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.582560740501, Press = -36.4053624186309 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -36554.736 -36554.736 -36836.809 -36836.809 272.81061 272.81061 160581.83 160581.83 129.77121 129.77121 6000 -36549.246 -36549.246 -36840.16 -36840.16 281.3619 281.3619 160656.7 160656.7 -388.55928 -388.55928 Loop time of 56.8312 on 1 procs for 1000 steps with 8000 atoms Performance: 1.520 ns/day, 15.786 hours/ns, 17.596 timesteps/s 39.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.822 | 55.822 | 55.822 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13139 | 0.13139 | 0.13139 | 0.0 | 0.23 Output | 4.3154e-05 | 4.3154e-05 | 4.3154e-05 | 0.0 | 0.00 Modify | 0.82304 | 0.82304 | 0.82304 | 0.0 | 1.45 Other | | 0.05505 | | | 0.10 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274650 ave 274650 max 274650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274650 Ave neighs/atom = 34.3312 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.966740369919, Press = 5.09068091543344 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.311 | 4.311 | 4.311 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -36549.246 -36549.246 -36840.16 -36840.16 281.3619 281.3619 160656.7 160656.7 -388.55928 -388.55928 7000 -36554.552 -36554.552 -36839.352 -36839.352 275.44827 275.44827 160452.51 160452.51 976.46603 976.46603 Loop time of 56.3722 on 1 procs for 1000 steps with 8000 atoms Performance: 1.533 ns/day, 15.659 hours/ns, 17.739 timesteps/s 39.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 55.432 | 55.432 | 55.432 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.091277 | 0.091277 | 0.091277 | 0.0 | 0.16 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0.79357 | 0.79357 | 0.79357 | 0.0 | 1.41 Other | | 0.05494 | | | 0.10 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 274520 ave 274520 max 274520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274520 Ave neighs/atom = 34.315 Neighbor list builds = 0 Dangerous builds = 0 if "${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 160594.068895561 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0