# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.049998879432679*${_u_distance} variable latticeconst_converted equal 4.049998879432679*1 lattice fcc ${latticeconst_converted} lattice fcc 4.04999887943268 Lattice spacing in x,y,z = 4.0499989 4.0499989 4.0499989 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.499989 40.499989 40.499989) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms create_atoms CPU = 0.001 seconds variable mass_converted equal 26.981538*${_u_mass} variable mass_converted equal 26.981538*1 kim_interactions Al #=== BEGIN kim_interactions ================================== pair_style kim MEAM_LAMMPS_PascuetFernandez_2015_Al__MO_315820974149_000 pair_coeff * * Al #=== END kim_interactions ==================================== 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 66430.0698596988 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 66430.0698596988/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 66430.0698596988/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 66430.0698596988/(1*1*${_u_distance}) variable V0_metal equal 66430.0698596988/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 66430.0698596988*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 66430.0698596988 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 12 12 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) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -13278.089 -13278.089 -13439.96 -13439.96 313.15 313.15 66430.07 66430.07 2602.6968 2602.6968 1000 -13089.834 -13089.834 -13256.313 -13256.313 322.06404 322.06404 68223.394 68223.394 -607.70477 -607.70477 Loop time of 86.6456 on 1 procs for 1000 steps with 4000 atoms Performance: 0.997 ns/day, 24.068 hours/ns, 11.541 timesteps/s 50.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 86.194 | 86.194 | 86.194 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.057135 | 0.057135 | 0.057135 | 0.0 | 0.07 Output | 4.18e-05 | 4.18e-05 | 4.18e-05 | 0.0 | 0.00 Modify | 0.35443 | 0.35443 | 0.35443 | 0.0 | 0.41 Other | | 0.04003 | | | 0.05 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: 312000.0 ave 312000 max 312000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312000 Ave neighs/atom = 78.000000 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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13089.834 -13089.834 -13256.313 -13256.313 322.06404 322.06404 68223.394 68223.394 -607.70477 -607.70477 2000 -13109.897 -13109.897 -13269.249 -13269.249 308.27755 308.27755 67969.693 67969.693 630.06238 630.06238 Loop time of 84.8778 on 1 procs for 1000 steps with 4000 atoms Performance: 1.018 ns/day, 23.577 hours/ns, 11.782 timesteps/s 52.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 84.423 | 84.423 | 84.423 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.11729 | 0.11729 | 0.11729 | 0.0 | 0.14 Output | 4.99e-05 | 4.99e-05 | 4.99e-05 | 0.0 | 0.00 Modify | 0.31797 | 0.31797 | 0.31797 | 0.0 | 0.37 Other | | 0.01915 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320136.0 ave 320136 max 320136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320136 Ave neighs/atom = 80.034000 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -13109.897 -13109.897 -13269.249 -13269.249 308.27755 308.27755 67969.693 67969.693 630.06238 630.06238 3000 -13099.173 -13099.173 -13262.608 -13262.608 316.17663 316.17663 68114.863 68114.863 -109.58756 -109.58756 Loop time of 78.447 on 1 procs for 1000 steps with 4000 atoms Performance: 1.101 ns/day, 21.791 hours/ns, 12.747 timesteps/s 56.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 78.125 | 78.125 | 78.125 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.036891 | 0.036891 | 0.036891 | 0.0 | 0.05 Output | 4.75e-05 | 4.75e-05 | 4.75e-05 | 0.0 | 0.00 Modify | 0.26549 | 0.26549 | 0.26549 | 0.0 | 0.34 Other | | 0.01905 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320688.0 ave 320688 max 320688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320688 Ave neighs/atom = 80.172000 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -13099.173 -13099.173 -13262.608 -13262.608 316.17663 316.17663 68114.863 68114.863 -109.58756 -109.58756 4000 -13106.577 -13106.577 -13267.43 -13267.43 311.18048 311.18048 68056.575 68056.575 -4.3449882 -4.3449882 Loop time of 80.2246 on 1 procs for 1000 steps with 4000 atoms Performance: 1.077 ns/day, 22.285 hours/ns, 12.465 timesteps/s 55.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 79.876 | 79.876 | 79.876 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.057053 | 0.057053 | 0.057053 | 0.0 | 0.07 Output | 4.42e-05 | 4.42e-05 | 4.42e-05 | 0.0 | 0.00 Modify | 0.27236 | 0.27236 | 0.27236 | 0.0 | 0.34 Other | | 0.01925 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320410.0 ave 320410 max 320410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320410 Ave neighs/atom = 80.102500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 0, Press = 0 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -13106.577 -13106.577 -13267.43 -13267.43 311.18048 311.18048 68056.575 68056.575 -4.3449882 -4.3449882 5000 -13099.853 -13099.853 -13264.029 -13264.029 317.60972 317.60972 68091.679 68091.679 5.0491289 5.0491289 Loop time of 81.2581 on 1 procs for 1000 steps with 4000 atoms Performance: 1.063 ns/day, 22.572 hours/ns, 12.306 timesteps/s 54.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 80.88 | 80.88 | 80.88 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.056981 | 0.056981 | 0.056981 | 0.0 | 0.07 Output | 3.47e-05 | 3.47e-05 | 3.47e-05 | 0.0 | 0.00 Modify | 0.30183 | 0.30183 | 0.30183 | 0.0 | 0.37 Other | | 0.01907 | | | 0.02 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320602.0 ave 320602 max 320602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320602 Ave neighs/atom = 80.150500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 315.645156877999, Press = -44.0502307422525 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -13099.853 -13099.853 -13264.029 -13264.029 317.60972 317.60972 68091.679 68091.679 5.0491289 5.0491289 6000 -13107.272 -13107.272 -13270.226 -13270.226 315.24426 315.24426 68091.279 68091.279 -596.66256 -596.66256 Loop time of 76.8189 on 1 procs for 1000 steps with 4000 atoms Performance: 1.125 ns/day, 21.339 hours/ns, 13.018 timesteps/s 57.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 76.404 | 76.404 | 76.404 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03737 | 0.03737 | 0.03737 | 0.0 | 0.05 Output | 3.63e-05 | 3.63e-05 | 3.63e-05 | 0.0 | 0.00 Modify | 0.32793 | 0.32793 | 0.32793 | 0.0 | 0.43 Other | | 0.04975 | | | 0.06 Nlocal: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841.00 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320522.0 ave 320522 max 320522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320522 Ave neighs/atom = 80.130500 Neighbor list builds = 0 Dangerous builds = 0 if "${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 68070.4901416963 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0