# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 6.303511068224907*${_u_distance} variable latticeconst_converted equal 6.303511068224907*1 lattice diamond ${latticeconst_converted} lattice diamond 6.30351106822491 Lattice spacing in x,y,z = 6.3035111 6.3035111 6.3035111 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (63.035111 63.035111 63.035111) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.001 seconds variable mass_converted equal 118.71*${_u_mass} variable mass_converted equal 118.71*1 kim_interactions Sn #=== BEGIN kim_interactions ================================== pair_style kim MEAM_LAMMPS_VellaChenStillinger_2017_Sn__MO_316045643888_000 pair_coeff * * 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 250465.295928465 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.295928465/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.295928465/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 250465.295928465/(1*1*${_u_distance}) variable V0_metal equal 250465.295928465/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 250465.295928465*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 250465.295928465 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.307 | 4.307 | 4.307 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 250465.3 250465.3 1380.7787 1380.7787 1000 -25074.879 -25074.879 -25427.55 -25427.55 341.09011 341.09011 253564.19 253564.19 58.663967 58.663967 Loop time of 29.1228 on 1 procs for 1000 steps with 8000 atoms Performance: 2.967 ns/day, 8.090 hours/ns, 34.337 timesteps/s 85.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.558 | 28.558 | 28.558 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.092927 | 0.092927 | 0.092927 | 0.0 | 0.32 Output | 6.42e-05 | 6.42e-05 | 6.42e-05 | 0.0 | 0.00 Modify | 0.43724 | 0.43724 | 0.43724 | 0.0 | 1.50 Other | | 0.03444 | | | 0.12 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272000.0 ave 272000 max 272000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272000 Ave neighs/atom = 34.000000 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -25074.879 -25074.879 -25427.55 -25427.55 341.09011 341.09011 253564.19 253564.19 58.663967 58.663967 2000 -25111.201 -25111.201 -25421.589 -25421.589 300.19538 300.19538 253582.52 253582.52 -62.919893 -62.919893 Loop time of 30.326 on 1 procs for 1000 steps with 8000 atoms Performance: 2.849 ns/day, 8.424 hours/ns, 32.975 timesteps/s 88.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.878 | 29.878 | 29.878 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.052048 | 0.052048 | 0.052048 | 0.0 | 0.17 Output | 6.08e-05 | 6.08e-05 | 6.08e-05 | 0.0 | 0.00 Modify | 0.36098 | 0.36098 | 0.36098 | 0.0 | 1.19 Other | | 0.03484 | | | 0.11 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288868.0 ave 288868 max 288868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288868 Ave neighs/atom = 36.108500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -25111.201 -25111.201 -25421.589 -25421.589 300.19538 300.19538 253582.52 253582.52 -62.919893 -62.919893 3000 -25095.589 -25095.589 -25420.688 -25420.688 314.42315 314.42315 253774.21 253774.21 -187.63199 -187.63199 Loop time of 31.2584 on 1 procs for 1000 steps with 8000 atoms Performance: 2.764 ns/day, 8.683 hours/ns, 31.991 timesteps/s 85.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.799 | 30.799 | 30.799 | 0.0 | 98.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.071343 | 0.071343 | 0.071343 | 0.0 | 0.23 Output | 6.07e-05 | 6.07e-05 | 6.07e-05 | 0.0 | 0.00 Modify | 0.35307 | 0.35307 | 0.35307 | 0.0 | 1.13 Other | | 0.03468 | | | 0.11 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288908.0 ave 288908 max 288908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288908 Ave neighs/atom = 36.113500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -25095.589 -25095.589 -25420.688 -25420.688 314.42315 314.42315 253774.21 253774.21 -187.63199 -187.63199 4000 -25103.961 -25103.961 -25418.134 -25418.134 303.85634 303.85634 253575.47 253575.47 118.78551 118.78551 Loop time of 31.8523 on 1 procs for 1000 steps with 8000 atoms Performance: 2.713 ns/day, 8.848 hours/ns, 31.395 timesteps/s 83.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.387 | 31.387 | 31.387 | 0.0 | 98.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.072994 | 0.072994 | 0.072994 | 0.0 | 0.23 Output | 6.05e-05 | 6.05e-05 | 6.05e-05 | 0.0 | 0.00 Modify | 0.35762 | 0.35762 | 0.35762 | 0.0 | 1.12 Other | | 0.03461 | | | 0.11 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288326.0 ave 288326 max 288326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288326 Ave neighs/atom = 36.040750 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -25103.961 -25103.961 -25418.134 -25418.134 303.85634 303.85634 253575.47 253575.47 118.78551 118.78551 5000 -25100.101 -25100.101 -25424.319 -25424.319 313.5716 313.5716 253485.03 253485.03 191.34335 191.34335 Loop time of 31.3051 on 1 procs for 1000 steps with 8000 atoms Performance: 2.760 ns/day, 8.696 hours/ns, 31.944 timesteps/s 86.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.801 | 30.801 | 30.801 | 0.0 | 98.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.051641 | 0.051641 | 0.051641 | 0.0 | 0.16 Output | 4.61e-05 | 4.61e-05 | 4.61e-05 | 0.0 | 0.00 Modify | 0.39826 | 0.39826 | 0.39826 | 0.0 | 1.27 Other | | 0.0546 | | | 0.17 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288768.0 ave 288768 max 288768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288768 Ave neighs/atom = 36.096000 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 317.004460915743, Press = 76.8003881973843 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -25100.101 -25100.101 -25424.319 -25424.319 313.5716 313.5716 253485.03 253485.03 191.34335 191.34335 6000 -25100.813 -25100.813 -25424.174 -25424.174 312.74289 312.74289 253365.73 253365.73 414.69642 414.69642 Loop time of 30.5146 on 1 procs for 1000 steps with 8000 atoms Performance: 2.831 ns/day, 8.476 hours/ns, 32.771 timesteps/s 88.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 30.105 | 30.105 | 30.105 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.05178 | 0.05178 | 0.05178 | 0.0 | 0.17 Output | 4.71e-05 | 4.71e-05 | 4.71e-05 | 0.0 | 0.00 Modify | 0.32342 | 0.32342 | 0.32342 | 0.0 | 1.06 Other | | 0.03448 | | | 0.11 Nlocal: 8000.00 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725.00 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288798.0 ave 288798 max 288798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288798 Ave neighs/atom = 36.099750 Neighbor list builds = 0 Dangerous builds = 0 if "${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 253609.616879684 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0