# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.6150126680731782*${_u_distance} variable latticeconst_converted equal 3.6150126680731782*1 lattice fcc ${latticeconst_converted} lattice fcc 3.61501266807318 Lattice spacing in x,y,z = 3.6150127 3.6150127 3.6150127 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (36.150127 36.150127 36.150127) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.002 seconds variable mass_converted equal 63.546*${_u_mass} variable mass_converted equal 63.546*1 kim_interactions Cu #=== BEGIN kim_interactions ================================== pair_style kim MEAM_LAMMPS_AgrawalMirzaeifar_2021_CuC__MO_028979335952_000 pair_coeff * * Cu #=== END kim_interactions ==================================== mass 1 ${mass_converted} mass 1 63.546 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 47242.1300244323 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47242.1300244323/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 47242.1300244323/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 47242.1300244323/(1*1*${_u_distance}) variable V0_metal equal 47242.1300244323/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 47242.1300244323*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 47242.1300244323 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -14029.144 -14029.144 -14160 -14160 253.15 253.15 47242.13 47242.13 2958.599 2958.599 1000 -13894.374 -13894.374 -14030.526 -14030.526 263.39571 263.39571 47748.422 47748.422 1026.1027 1026.1027 Loop time of 156.304 on 1 procs for 1000 steps with 4000 atoms Performance: 0.553 ns/day, 43.418 hours/ns, 6.398 timesteps/s 68.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 156.01 | 156.01 | 156.01 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039236 | 0.039236 | 0.039236 | 0.0 | 0.03 Output | 4.68e-05 | 4.68e-05 | 4.68e-05 | 0.0 | 0.00 Modify | 0.23555 | 0.23555 | 0.23555 | 0.0 | 0.15 Other | | 0.01823 | | | 0.01 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 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: 536000.0 ave 536000 max 536000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536000 Ave neighs/atom = 134.00000 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13894.374 -13894.374 -14030.526 -14030.526 263.39571 263.39571 47748.422 47748.422 1026.1027 1026.1027 2000 -13901.509 -13901.509 -14036.944 -14036.944 262.00892 262.00892 47767.254 47767.254 -166.499 -166.499 Loop time of 194.12 on 1 procs for 1000 steps with 4000 atoms Performance: 0.445 ns/day, 53.922 hours/ns, 5.151 timesteps/s 57.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 193.78 | 193.78 | 193.78 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.042254 | 0.042254 | 0.042254 | 0.0 | 0.02 Output | 4.46e-05 | 4.46e-05 | 4.46e-05 | 0.0 | 0.00 Modify | 0.25598 | 0.25598 | 0.25598 | 0.0 | 0.13 Other | | 0.03925 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 533848.0 ave 533848 max 533848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533848 Ave neighs/atom = 133.46200 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13901.509 -13901.509 -14036.944 -14036.944 262.00892 262.00892 47767.254 47767.254 -166.499 -166.499 3000 -13898.712 -13898.712 -14027.822 -14027.822 249.7721 249.7721 47782.419 47782.419 6.8238744 6.8238744 Loop time of 225.627 on 1 procs for 1000 steps with 4000 atoms Performance: 0.383 ns/day, 62.674 hours/ns, 4.432 timesteps/s 49.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 225.26 | 225.26 | 225.26 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.077852 | 0.077852 | 0.077852 | 0.0 | 0.03 Output | 4.43e-05 | 4.43e-05 | 4.43e-05 | 0.0 | 0.00 Modify | 0.27445 | 0.27445 | 0.27445 | 0.0 | 0.12 Other | | 0.01916 | | | 0.01 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 534372.0 ave 534372 max 534372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534372 Ave neighs/atom = 133.59300 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13898.712 -13898.712 -14027.822 -14027.822 249.7721 249.7721 47782.419 47782.419 6.8238744 6.8238744 4000 -13901.379 -13901.379 -14032.297 -14032.297 253.27068 253.27068 47773.34 47773.34 -63.519883 -63.519883 Loop time of 232.846 on 1 procs for 1000 steps with 4000 atoms Performance: 0.371 ns/day, 64.679 hours/ns, 4.295 timesteps/s 47.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 232.45 | 232.45 | 232.45 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12793 | 0.12793 | 0.12793 | 0.0 | 0.05 Output | 4.74e-05 | 4.74e-05 | 4.74e-05 | 0.0 | 0.00 Modify | 0.24523 | 0.24523 | 0.24523 | 0.0 | 0.11 Other | | 0.01827 | | | 0.01 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 533516.0 ave 533516 max 533516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533516 Ave neighs/atom = 133.37900 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -13901.379 -13901.379 -14032.297 -14032.297 253.27068 253.27068 47773.34 47773.34 -63.519883 -63.519883 5000 -13897.519 -13897.519 -14029.964 -14029.964 256.22446 256.22446 47792.155 47792.155 -371.27958 -371.27958 Loop time of 232.592 on 1 procs for 1000 steps with 4000 atoms Performance: 0.371 ns/day, 64.609 hours/ns, 4.299 timesteps/s 47.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 232.06 | 232.06 | 232.06 | 0.0 | 99.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.12821 | 0.12821 | 0.12821 | 0.0 | 0.06 Output | 2.86e-05 | 2.86e-05 | 2.86e-05 | 0.0 | 0.00 Modify | 0.36829 | 0.36829 | 0.36829 | 0.0 | 0.16 Other | | 0.03971 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 534134.0 ave 534134 max 534134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 534134 Ave neighs/atom = 133.53350 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.924077704261, Press = -9.5984379409972 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -13897.519 -13897.519 -14029.964 -14029.964 256.22446 256.22446 47792.155 47792.155 -371.27958 -371.27958 6000 -13901.517 -13901.517 -14033.647 -14033.647 255.61449 255.61449 47796.376 47796.376 -819.3175 -819.3175 Loop time of 232.118 on 1 procs for 1000 steps with 4000 atoms Performance: 0.372 ns/day, 64.477 hours/ns, 4.308 timesteps/s 47.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 231.7 | 231.7 | 231.7 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.036973 | 0.036973 | 0.036973 | 0.0 | 0.02 Output | 3.6e-05 | 3.6e-05 | 3.6e-05 | 0.0 | 0.00 Modify | 0.36128 | 0.36128 | 0.36128 | 0.0 | 0.16 Other | | 0.01819 | | | 0.01 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 533820.0 ave 533820 max 533820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533820 Ave neighs/atom = 133.45500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.764904761157, Press = -9.19278674861753 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.370 | 5.370 | 5.370 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -13901.517 -13901.517 -14033.647 -14033.647 255.61449 255.61449 47796.376 47796.376 -819.3175 -819.3175 7000 -13899.584 -13899.584 -14029.289 -14029.289 250.92479 250.92479 47788.784 47788.784 -323.98952 -323.98952 Loop time of 230.184 on 1 procs for 1000 steps with 4000 atoms Performance: 0.375 ns/day, 63.940 hours/ns, 4.344 timesteps/s 48.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 229.62 | 229.62 | 229.62 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.1091 | 0.1091 | 0.1091 | 0.0 | 0.05 Output | 3.51e-05 | 3.51e-05 | 3.51e-05 | 0.0 | 0.00 Modify | 0.43371 | 0.43371 | 0.43371 | 0.0 | 0.19 Other | | 0.01814 | | | 0.01 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 533840.0 ave 533840 max 533840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533840 Ave neighs/atom = 133.46000 Neighbor list builds = 0 Dangerous builds = 0 if "${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 47776.5429140467 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0