# 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 ${latticeconst_converted} lattice diamond 6.30351104587317 Lattice spacing in x,y,z = 6.30351 6.30351 6.30351 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (63.0351 63.0351 63.0351) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms create_atoms CPU = 0.000849962 secs variable mass_converted equal 118.71*${_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-XXXXXXxRv4YL/library_VellaChen_Sn-2.meam Sn /tmp/kim-simulator-model-parameter-file-directory-XXXXXXxRv4YL/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 ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_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 = 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 -25494.717 -25494.717 -25756.462 -25756.462 253.15 253.15 250465.29 250465.29 1116.224 1116.224 1000 -25206.9 -25206.9 -25491.132 -25491.132 274.89831 274.89831 253317.66 253317.66 -546.10013 -546.10013 Loop time of 18.3896 on 1 procs for 1000 steps with 8000 atoms Performance: 4.698 ns/day, 5.108 hours/ns, 54.379 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 | 18.014 | 18.014 | 18.014 | 0.0 | 97.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.049184 | 0.049184 | 0.049184 | 0.0 | 0.27 Output | 5.0068e-05 | 5.0068e-05 | 5.0068e-05 | 0.0 | 0.00 Modify | 0.29304 | 0.29304 | 0.29304 | 0.0 | 1.59 Other | | 0.03301 | | | 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.46 | 14.46 | 14.46 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -25206.9 -25206.9 -25491.132 -25491.132 274.89831 274.89831 253317.66 253317.66 -546.10013 -546.10013 2000 -25236.197 -25236.197 -25493.027 -25493.027 248.39704 248.39704 252941.49 252941.49 -88.280559 -88.280559 Loop time of 18.1187 on 1 procs for 1000 steps with 8000 atoms Performance: 4.769 ns/day, 5.033 hours/ns, 55.192 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.764 | 17.764 | 17.764 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.044974 | 0.044974 | 0.044974 | 0.0 | 0.25 Output | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.00 Modify | 0.27905 | 0.27905 | 0.27905 | 0.0 | 1.54 Other | | 0.03044 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143434 ave 143434 max 143434 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286868 ave 286868 max 286868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286868 Ave neighs/atom = 35.8585 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -25236.197 -25236.197 -25493.027 -25493.027 248.39704 248.39704 252941.49 252941.49 -88.280559 -88.280559 3000 -25224.358 -25224.358 -25487.331 -25487.331 254.33763 254.33763 252950.61 252950.61 115.56647 115.56647 Loop time of 18.0954 on 1 procs for 1000 steps with 8000 atoms Performance: 4.775 ns/day, 5.026 hours/ns, 55.263 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.744 | 17.744 | 17.744 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.043538 | 0.043538 | 0.043538 | 0.0 | 0.24 Output | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 0.00 Modify | 0.27735 | 0.27735 | 0.27735 | 0.0 | 1.53 Other | | 0.03021 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143921 ave 143921 max 143921 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287842 ave 287842 max 287842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287842 Ave neighs/atom = 35.9802 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -25224.358 -25224.358 -25487.331 -25487.331 254.33763 254.33763 252950.61 252950.61 115.56647 115.56647 4000 -25228.507 -25228.507 -25492.649 -25492.649 255.46772 255.46772 253133.65 253133.65 -250.94955 -250.94955 Loop time of 17.453 on 1 procs for 1000 steps with 8000 atoms Performance: 4.950 ns/day, 4.848 hours/ns, 57.297 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.112 | 17.112 | 17.112 | 0.0 | 98.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.041937 | 0.041937 | 0.041937 | 0.0 | 0.24 Output | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.00 Modify | 0.27004 | 0.27004 | 0.27004 | 0.0 | 1.55 Other | | 0.02864 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143832 ave 143832 max 143832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287664 ave 287664 max 287664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287664 Ave neighs/atom = 35.958 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -25228.507 -25228.507 -25492.649 -25492.649 255.46772 255.46772 253133.65 253133.65 -250.94955 -250.94955 5000 -25228.734 -25228.734 -25480.544 -25480.544 243.5408 243.5408 252838.22 252838.22 309.79975 309.79975 Loop time of 17.8676 on 1 procs for 1000 steps with 8000 atoms Performance: 4.836 ns/day, 4.963 hours/ns, 55.967 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.521 | 17.521 | 17.521 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.042513 | 0.042513 | 0.042513 | 0.0 | 0.24 Output | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 Modify | 0.27464 | 0.27464 | 0.27464 | 0.0 | 1.54 Other | | 0.02947 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143460 ave 143460 max 143460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 286920 ave 286920 max 286920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 286920 Ave neighs/atom = 35.865 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.615616521612, Press = -146.745453196101 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -25228.734 -25228.734 -25480.544 -25480.544 243.5408 243.5408 252838.22 252838.22 309.79975 309.79975 6000 -25228.247 -25228.247 -25489.207 -25489.207 252.3905 252.3905 253043.99 253043.99 -78.278138 -78.278138 Loop time of 17.2963 on 1 procs for 1000 steps with 8000 atoms Performance: 4.995 ns/day, 4.805 hours/ns, 57.816 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.95 | 16.95 | 16.95 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.041765 | 0.041765 | 0.041765 | 0.0 | 0.24 Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.00 Modify | 0.27517 | 0.27517 | 0.27517 | 0.0 | 1.59 Other | | 0.02911 | | | 0.17 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144149 ave 144149 max 144149 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 288298 ave 288298 max 288298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 288298 Ave neighs/atom = 36.0373 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.150753718822, Press = 4.75151298963863 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -25228.247 -25228.247 -25489.207 -25489.207 252.3905 252.3905 253043.99 253043.99 -78.278138 -78.278138 7000 -25224.291 -25224.291 -25488.254 -25488.254 255.29463 255.29463 253081.71 253081.71 -74.041185 -74.041185 Loop time of 16.8423 on 1 procs for 1000 steps with 8000 atoms Performance: 5.130 ns/day, 4.678 hours/ns, 59.374 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.501 | 16.501 | 16.501 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.040203 | 0.040203 | 0.040203 | 0.0 | 0.24 Output | 4.0054e-05 | 4.0054e-05 | 4.0054e-05 | 0.0 | 0.00 Modify | 0.27311 | 0.27311 | 0.27311 | 0.0 | 1.62 Other | | 0.02779 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143666 ave 143666 max 143666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287332 ave 287332 max 287332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287332 Ave neighs/atom = 35.9165 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 253.063684671134, Press = -8.12017953834129 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 14.48 | 14.48 | 14.48 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -25224.291 -25224.291 -25488.254 -25488.254 255.29463 255.29463 253081.71 253081.71 -74.041185 -74.041185 8000 -25228.545 -25228.545 -25486.329 -25486.329 249.31924 249.31924 252926.09 252926.09 101.30981 101.30981 Loop time of 16.7253 on 1 procs for 1000 steps with 8000 atoms Performance: 5.166 ns/day, 4.646 hours/ns, 59.790 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.386 | 16.386 | 16.386 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039722 | 0.039722 | 0.039722 | 0.0 | 0.24 Output | 3.7193e-05 | 3.7193e-05 | 3.7193e-05 | 0.0 | 0.00 Modify | 0.27199 | 0.27199 | 0.27199 | 0.0 | 1.63 Other | | 0.02738 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143559 ave 143559 max 143559 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287118 ave 287118 max 287118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287118 Ave neighs/atom = 35.8897 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 252987.700261246 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0