# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.128871455788613*${_u_distance} variable latticeconst_converted equal 4.128871455788613*1 lattice fcc ${latticeconst_converted} lattice fcc 4.12887145578861 Lattice spacing in x,y,z = 4.12887 4.12887 4.12887 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (41.2887 41.2887 41.2887) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.000458002 secs variable mass_converted equal 26.981538*${_u_mass} variable mass_converted equal 26.981538*1 # specify which KIM Model to use pair_style kim EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003 WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) pair_coeff * * Al mass 1 ${mass_converted} mass 1 26.981538 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 70387.264381338 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 70387.264381338/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 70387.264381338/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 70387.264381338/(1*1*${_u_distance}) variable V0_metal equal 70387.264381338/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 70387.264381338*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 70387.264381338 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.1 iso 0 0 1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 0.2" variable T_up equal "273.15 + 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 = 9.2 ghost atom cutoff = 9.2 binsize = 4.6, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.241 | 6.241 | 6.241 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -14715.379 -14715.379 -14856.574 -14856.574 273.15 273.15 70387.264 70387.264 2142.6279 2142.6279 1000 -14561.941 -14561.941 -14704.003 -14704.003 274.82874 274.82874 71140.615 71140.615 1443.987 1443.987 Loop time of 70.675 on 1 procs for 1000 steps with 4000 atoms Performance: 1.222 ns/day, 19.632 hours/ns, 14.149 timesteps/s 37.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.03 | 70.03 | 70.03 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13356 | 0.13356 | 0.13356 | 0.0 | 0.19 Output | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 Modify | 0.44928 | 0.44928 | 0.44928 | 0.0 | 0.64 Other | | 0.06168 | | | 0.09 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: 704000 ave 704000 max 704000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704000 Ave neighs/atom = 176 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -14561.941 -14561.941 -14704.003 -14704.003 274.82874 274.82874 71140.615 71140.615 1443.987 1443.987 2000 -14573.545 -14573.545 -14714.54 -14714.54 272.76378 272.76378 71178.088 71178.088 302.13543 302.13543 Loop time of 72.0638 on 1 procs for 1000 steps with 4000 atoms Performance: 1.199 ns/day, 20.018 hours/ns, 13.877 timesteps/s 38.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 71.278 | 71.278 | 71.278 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15396 | 0.15396 | 0.15396 | 0.0 | 0.21 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.53001 | 0.53001 | 0.53001 | 0.0 | 0.74 Other | | 0.1014 | | | 0.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 735160 ave 735160 max 735160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 735160 Ave neighs/atom = 183.79 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -14573.545 -14573.545 -14714.54 -14714.54 272.76378 272.76378 71178.088 71178.088 302.13543 302.13543 3000 -14568.08 -14568.08 -14711.795 -14711.795 278.02592 278.02592 71211.213 71211.213 88.743266 88.743266 Loop time of 71.2699 on 1 procs for 1000 steps with 4000 atoms Performance: 1.212 ns/day, 19.797 hours/ns, 14.031 timesteps/s 38.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.578 | 70.578 | 70.578 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15328 | 0.15328 | 0.15328 | 0.0 | 0.22 Output | 4.4107e-05 | 4.4107e-05 | 4.4107e-05 | 0.0 | 0.00 Modify | 0.47741 | 0.47741 | 0.47741 | 0.0 | 0.67 Other | | 0.06135 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 734060 ave 734060 max 734060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 734060 Ave neighs/atom = 183.515 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -14568.08 -14568.08 -14711.795 -14711.795 278.02592 278.02592 71211.213 71211.213 88.743266 88.743266 4000 -14570.306 -14570.306 -14709.572 -14709.572 269.41895 269.41895 71198.382 71198.382 375.25635 375.25635 Loop time of 70.4693 on 1 procs for 1000 steps with 4000 atoms Performance: 1.226 ns/day, 19.575 hours/ns, 14.191 timesteps/s 39.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 69.937 | 69.937 | 69.937 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.15367 | 0.15367 | 0.15367 | 0.0 | 0.22 Output | 6.2943e-05 | 6.2943e-05 | 6.2943e-05 | 0.0 | 0.00 Modify | 0.297 | 0.297 | 0.297 | 0.0 | 0.42 Other | | 0.08139 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 733874 ave 733874 max 733874 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 733874 Ave neighs/atom = 183.469 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -14570.306 -14570.306 -14709.572 -14709.572 269.41895 269.41895 71198.382 71198.382 375.25635 375.25635 5000 -14569.18 -14569.18 -14711.721 -14711.721 275.7553 275.7553 71220.257 71220.257 -101.16054 -101.16054 Loop time of 71.3818 on 1 procs for 1000 steps with 4000 atoms Performance: 1.210 ns/day, 19.828 hours/ns, 14.009 timesteps/s 38.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.79 | 70.79 | 70.79 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11382 | 0.11382 | 0.11382 | 0.0 | 0.16 Output | 3.2902e-05 | 3.2902e-05 | 3.2902e-05 | 0.0 | 0.00 Modify | 0.43706 | 0.43706 | 0.43706 | 0.0 | 0.61 Other | | 0.04131 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 733646 ave 733646 max 733646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 733646 Ave neighs/atom = 183.411 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 275.952691401506, Press = 204.317098460127 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -14569.18 -14569.18 -14711.721 -14711.721 275.7553 275.7553 71220.257 71220.257 -101.16054 -101.16054 6000 -14568.772 -14568.772 -14709.518 -14709.518 272.28149 272.28149 71265.183 71265.183 -681.14566 -681.14566 Loop time of 70.7632 on 1 procs for 1000 steps with 4000 atoms Performance: 1.221 ns/day, 19.656 hours/ns, 14.132 timesteps/s 38.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.22 | 70.22 | 70.22 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.13352 | 0.13352 | 0.13352 | 0.0 | 0.19 Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.00 Modify | 0.36797 | 0.36797 | 0.36797 | 0.0 | 0.52 Other | | 0.04126 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 733696 ave 733696 max 733696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 733696 Ave neighs/atom = 183.424 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.630619727136, Press = 24.6769249892887 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 6000 -14568.772 -14568.772 -14709.518 -14709.518 272.28149 272.28149 71265.183 71265.183 -681.14566 -681.14566 7000 -14571.669 -14571.669 -14710.406 -14710.406 268.39712 268.39712 71350.249 71350.249 -1986.12 -1986.12 Loop time of 65.3787 on 1 procs for 1000 steps with 4000 atoms Performance: 1.322 ns/day, 18.161 hours/ns, 15.296 timesteps/s 42.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 64.891 | 64.891 | 64.891 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.16 Output | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 Modify | 0.32221 | 0.32221 | 0.32221 | 0.0 | 0.49 Other | | 0.06149 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 733186 ave 733186 max 733186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 733186 Ave neighs/atom = 183.297 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.113035463471, Press = 8.77486728624405 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 6.243 | 6.243 | 6.243 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 7000 -14571.669 -14571.669 -14710.406 -14710.406 268.39712 268.39712 71350.249 71350.249 -1986.12 -1986.12 8000 -14568.5 -14568.5 -14709.141 -14709.141 272.08146 272.08146 71280.581 71280.581 -878.23354 -878.23354 Loop time of 62.9197 on 1 procs for 1000 steps with 4000 atoms Performance: 1.373 ns/day, 17.478 hours/ns, 15.893 timesteps/s 43.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 62.189 | 62.189 | 62.189 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.10437 | 0.10437 | 0.10437 | 0.0 | 0.17 Output | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.00 Modify | 0.6034 | 0.6034 | 0.6034 | 0.0 | 0.96 Other | | 0.0225 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 732310 ave 732310 max 732310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 732310 Ave neighs/atom = 183.077 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 71215.1704706381 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0