# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.126234233379364*${_u_distance} variable latticeconst_converted equal 6.126234233379364*1 lattice fcc ${latticeconst_converted} lattice fcc 6.12623423337936 Lattice spacing in x,y,z = 6.12623 6.12623 6.12623 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (61.2623 61.2623 61.2623) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000496864 secs variable mass_converted equal 87.62*${_u_mass} variable mass_converted equal 87.62*1 # specify which KIM Model to use pair_style kim Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Sr__MO_801083489225_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) pair_coeff * * Sr mass 1 ${mass_converted} mass 1 87.62 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 229922.140227974 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 229922.140227974/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 229922.140227974/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 229922.140227974/(1*1*${_u_distance}) variable V0_metal equal 229922.140227974/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 229922.140227974*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 229922.140227974 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 0.2" variable T_up equal "253.15 + 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 = 14.2649 ghost atom cutoff = 14.2649 binsize = 7.13245, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 14.2649 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -6271.555 -6271.555 -6402.4111 -6402.4111 253.15 253.15 229922.14 229922.14 607.8979 607.8979 1000 -6126.5391 -6126.5391 -6260.7098 -6260.7098 259.56228 259.56228 235064.54 235064.54 -121.22529 -121.22529 Loop time of 16.0357 on 1 procs for 1000 steps with 4000 atoms Performance: 5.388 ns/day, 4.454 hours/ns, 62.361 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.712 | 15.712 | 15.712 | 0.0 | 97.98 Neigh | 0.10978 | 0.10978 | 0.10978 | 0.0 | 0.68 Comm | 0.049146 | 0.049146 | 0.049146 | 0.0 | 0.31 Output | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.00 Modify | 0.14571 | 0.14571 | 0.14571 | 0.0 | 0.91 Other | | 0.01865 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 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: 813322 ave 813322 max 813322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 813322 Ave neighs/atom = 203.331 Neighbor list builds = 5 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -6126.5391 -6126.5391 -6260.7098 -6260.7098 259.56228 259.56228 235064.54 235064.54 -121.22529 -121.22529 2000 -6132.8078 -6132.8078 -6267.994 -6267.994 261.52676 261.52676 234976.43 234976.43 -160.3151 -160.3151 Loop time of 18.2115 on 1 procs for 1000 steps with 4000 atoms Performance: 4.744 ns/day, 5.059 hours/ns, 54.910 timesteps/s 91.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.845 | 17.845 | 17.845 | 0.0 | 97.99 Neigh | 0.12544 | 0.12544 | 0.12544 | 0.0 | 0.69 Comm | 0.061823 | 0.061823 | 0.061823 | 0.0 | 0.34 Output | 0.002635 | 0.002635 | 0.002635 | 0.0 | 0.01 Modify | 0.15257 | 0.15257 | 0.15257 | 0.0 | 0.84 Other | | 0.02434 | | | 0.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 815862 ave 815862 max 815862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815862 Ave neighs/atom = 203.965 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -6132.8078 -6132.8078 -6267.994 -6267.994 261.52676 261.52676 234976.43 234976.43 -160.3151 -160.3151 3000 -6142.3273 -6142.3273 -6271.6737 -6271.6737 250.22938 250.22938 234584.48 234584.48 -30.908938 -30.908938 Loop time of 16.0838 on 1 procs for 1000 steps with 4000 atoms Performance: 5.372 ns/day, 4.468 hours/ns, 62.174 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.761 | 15.761 | 15.761 | 0.0 | 97.99 Neigh | 0.11122 | 0.11122 | 0.11122 | 0.0 | 0.69 Comm | 0.048633 | 0.048633 | 0.048633 | 0.0 | 0.30 Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.00 Modify | 0.14427 | 0.14427 | 0.14427 | 0.0 | 0.90 Other | | 0.01869 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 815832 ave 815832 max 815832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815832 Ave neighs/atom = 203.958 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -6142.3273 -6142.3273 -6271.6737 -6271.6737 250.22938 250.22938 234584.48 234584.48 -30.908938 -30.908938 4000 -6142.4865 -6142.4865 -6271.939 -6271.939 250.4346 250.4346 234319.04 234319.04 82.147246 82.147246 Loop time of 15.8996 on 1 procs for 1000 steps with 4000 atoms Performance: 5.434 ns/day, 4.417 hours/ns, 62.894 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.579 | 15.579 | 15.579 | 0.0 | 97.98 Neigh | 0.11098 | 0.11098 | 0.11098 | 0.0 | 0.70 Comm | 0.047568 | 0.047568 | 0.047568 | 0.0 | 0.30 Output | 3.6001e-05 | 3.6001e-05 | 3.6001e-05 | 0.0 | 0.00 Modify | 0.14447 | 0.14447 | 0.14447 | 0.0 | 0.91 Other | | 0.01802 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 814684 ave 814684 max 814684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 814684 Ave neighs/atom = 203.671 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -6142.4865 -6142.4865 -6271.939 -6271.939 250.4346 250.4346 234319.04 234319.04 82.147246 82.147246 5000 -6131.2854 -6131.2854 -6265.4567 -6265.4567 259.56334 259.56334 234797.22 234797.22 -43.553038 -43.553038 Loop time of 15.6208 on 1 procs for 1000 steps with 4000 atoms Performance: 5.531 ns/day, 4.339 hours/ns, 64.017 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.307 | 15.307 | 15.307 | 0.0 | 97.99 Neigh | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.66 Comm | 0.047281 | 0.047281 | 0.047281 | 0.0 | 0.30 Output | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 Modify | 0.14506 | 0.14506 | 0.14506 | 0.0 | 0.93 Other | | 0.01775 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 814402 ave 814402 max 814402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 814402 Ave neighs/atom = 203.601 Neighbor list builds = 5 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 255.124781185318, Press = -68.9894378054331 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.623 | 6.623 | 6.623 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -6131.2854 -6131.2854 -6265.4567 -6265.4567 259.56334 259.56334 234797.22 234797.22 -43.553038 -43.553038 6000 -6142.6894 -6142.6894 -6271.3985 -6271.3985 248.99657 248.99657 234905.9 234905.9 -190.09011 -190.09011 Loop time of 15.6634 on 1 procs for 1000 steps with 4000 atoms Performance: 5.516 ns/day, 4.351 hours/ns, 63.843 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.36 | 15.36 | 15.36 | 0.0 | 98.06 Neigh | 0.092855 | 0.092855 | 0.092855 | 0.0 | 0.59 Comm | 0.047395 | 0.047395 | 0.047395 | 0.0 | 0.30 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.14563 | 0.14563 | 0.14563 | 0.0 | 0.93 Other | | 0.01785 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 814820 ave 814820 max 814820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 814820 Ave neighs/atom = 203.705 Neighbor list builds = 5 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 234601.859863584 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0