# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.303511045873165*${_u_distance} variable latticeconst_converted equal 6.303511045873165*1 lattice diamond ${latticeconst_converted} lattice diamond 6.30351104587317 Lattice spacing in x,y,z = 6.30351 6.30351 6.30351 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (63.0351 63.0351 63.0351) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.000874043 secs variable mass_converted equal 118.71*${_u_mass} variable mass_converted equal 118.71*1 kim_interactions Sn #=== BEGIN kim_interactions ================================== pair_style meam/c pair_coeff * * /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlszgGL/library_VellaChen_Sn-2.meam Sn /tmp/kim-simulator-model-parameter-file-directory-XXXXXXlszgGL/Sn_VellaChen-2.meam Sn #=== END kim_interactions ==================================== mass 1 ${mass_converted} mass 1 118.71 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 250465.293264076 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.293264076/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.293264076/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.293264076/(1*1*${_u_distance}) variable V0_metal equal 250465.293264076/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 250465.293264076*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 250465.293264076 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 19 19 19 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 14.29 | 14.29 | 14.29 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -25432.68 -25432.68 -25756.462 -25756.462 313.15 313.15 250465.29 250465.29 1380.7834 1380.7834 1000 -25074.879 -25074.879 -25427.55 -25427.55 341.09011 341.09011 253564.19 253564.19 58.663777 58.663777 Loop time of 17.7262 on 1 procs for 1000 steps with 8000 atoms Performance: 4.874 ns/day, 4.924 hours/ns, 56.414 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.361 | 17.361 | 17.361 | 0.0 | 97.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.047615 | 0.047615 | 0.047615 | 0.0 | 0.27 Output | 7.391e-05 | 7.391e-05 | 7.391e-05 | 0.0 | 0.00 Modify | 0.28544 | 0.28544 | 0.28544 | 0.0 | 1.61 Other | | 0.03229 | | | 0.18 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: 136000 ave 136000 max 136000 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.49 | 14.49 | 14.49 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -25074.879 -25074.879 -25427.55 -25427.55 341.09011 341.09011 253564.19 253564.19 58.663777 58.663777 2000 -25111.201 -25111.201 -25421.589 -25421.589 300.19538 300.19538 253582.52 253582.52 -62.919846 -62.919846 Loop time of 18.3491 on 1 procs for 1000 steps with 8000 atoms Performance: 4.709 ns/day, 5.097 hours/ns, 54.499 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.995 | 17.995 | 17.995 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045208 | 0.045208 | 0.045208 | 0.0 | 0.25 Output | 4.7922e-05 | 4.7922e-05 | 4.7922e-05 | 0.0 | 0.00 Modify | 0.27868 | 0.27868 | 0.27868 | 0.0 | 1.52 Other | | 0.0298 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144434 ave 144434 max 144434 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288868 ave 288868 max 288868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288868 Ave neighs/atom = 36.1085 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.49 | 14.49 | 14.49 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -25111.201 -25111.201 -25421.589 -25421.589 300.19538 300.19538 253582.52 253582.52 -62.919846 -62.919846 3000 -25095.589 -25095.589 -25420.688 -25420.688 314.42315 314.42315 253774.21 253774.21 -187.63183 -187.63183 Loop time of 18.3976 on 1 procs for 1000 steps with 8000 atoms Performance: 4.696 ns/day, 5.110 hours/ns, 54.355 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.042 | 18.042 | 18.042 | 0.0 | 98.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.044591 | 0.044591 | 0.044591 | 0.0 | 0.24 Output | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.00 Modify | 0.28004 | 0.28004 | 0.28004 | 0.0 | 1.52 Other | | 0.0307 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144454 ave 144454 max 144454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288908 ave 288908 max 288908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288908 Ave neighs/atom = 36.1135 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.49 | 14.49 | 14.49 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -25095.589 -25095.589 -25420.688 -25420.688 314.42315 314.42315 253774.21 253774.21 -187.63183 -187.63183 4000 -25103.961 -25103.961 -25418.134 -25418.134 303.85634 303.85634 253575.47 253575.47 118.78564 118.78564 Loop time of 17.9115 on 1 procs for 1000 steps with 8000 atoms Performance: 4.824 ns/day, 4.975 hours/ns, 55.830 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.557 | 17.557 | 17.557 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.045357 | 0.045357 | 0.045357 | 0.0 | 0.25 Output | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 Modify | 0.27822 | 0.27822 | 0.27822 | 0.0 | 1.55 Other | | 0.03066 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144163 ave 144163 max 144163 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288326 ave 288326 max 288326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288326 Ave neighs/atom = 36.0408 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.49 | 14.49 | 14.49 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -25103.961 -25103.961 -25418.134 -25418.134 303.85634 303.85634 253575.47 253575.47 118.78564 118.78564 5000 -25100.101 -25100.101 -25424.319 -25424.319 313.5716 313.5716 253485.03 253485.03 191.3434 191.3434 Loop time of 17.5754 on 1 procs for 1000 steps with 8000 atoms Performance: 4.916 ns/day, 4.882 hours/ns, 56.898 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.228 | 17.228 | 17.228 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.043925 | 0.043925 | 0.043925 | 0.0 | 0.25 Output | 3.6955e-05 | 3.6955e-05 | 3.6955e-05 | 0.0 | 0.00 Modify | 0.27349 | 0.27349 | 0.27349 | 0.0 | 1.56 Other | | 0.02963 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144384 ave 144384 max 144384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288768 ave 288768 max 288768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288768 Ave neighs/atom = 36.096 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 317.00446076956, Press = 76.800294067429 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.49 | 14.49 | 14.49 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -25100.101 -25100.101 -25424.319 -25424.319 313.5716 313.5716 253485.03 253485.03 191.3434 191.3434 6000 -25100.813 -25100.813 -25424.174 -25424.174 312.74289 312.74289 253365.73 253365.73 414.69629 414.69629 Loop time of 17.5787 on 1 procs for 1000 steps with 8000 atoms Performance: 4.915 ns/day, 4.883 hours/ns, 56.887 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.223 | 17.223 | 17.223 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.044669 | 0.044669 | 0.044669 | 0.0 | 0.25 Output | 5.2929e-05 | 5.2929e-05 | 5.2929e-05 | 0.0 | 0.00 Modify | 0.28091 | 0.28091 | 0.28091 | 0.0 | 1.60 Other | | 0.03003 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144399 ave 144399 max 144399 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288798 ave 288798 max 288798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288798 Ave neighs/atom = 36.0998 Neighbor list builds = 0 Dangerous builds = 0 if "${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 253609.616881163 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0