# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.24405661970377*${_u_distance} variable latticeconst_converted equal 4.24405661970377*1 lattice fcc ${latticeconst_converted} lattice fcc 4.24405661970377 Lattice spacing in x,y,z = 4.2440566 4.2440566 4.2440566 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.440566 42.440566 42.440566) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_004 pair_coeff * * Ne #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 20.1797 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 76444.0182483146 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*${_u_distance}) variable V0_metal equal 76444.0182483146/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 76444.0182483146*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 76444.0182483146 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*1 variable Tdamp_converted equal 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_u_pressure} variable press_converted equal 0.0*1 variable Pdamp_converted equal 0.1*${_u_time} variable Pdamp_converted equal 0.1*1 # create initial velocities consistent with the chosen temperature velocity all create ${temp_converted} 17 mom yes rot yes velocity all create 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 1000 fix avgmyPress all ave/time 5 20 100 v_P_metal ave running start 1000 fix avgmyVol all ave/time 5 20 100 v_V_metal ave running start 1000 # 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 "293.15 - 1.0" variable T_up equal "293.15 + 1.0" variable P_low equal "0.0 - 5.0" variable P_up equal "0.0 + 5.0" # 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 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM Project: doi:10.1007/s11837-011-0102-6 @Article{tadmor:elliott:2011, author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker}, title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels}, journal = {{JOM}}, year = 2011, volume = 63, number = 17, pages = {17}, doi = {10.1007/s11837-011-0102-6} } - OpenKIM potential: https://openkim.org/cite/MO_466741694288_004#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.242 | 6.242 | 6.242 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 55.875276 55.875276 -95.657278 -95.657278 293.15 293.15 76444.018 76444.018 2117.2957 2117.2957 1000 144.62055 144.62055 -5.944788 -5.944788 291.27885 291.27885 641541.19 641541.19 271.20755 271.20755 Loop time of 5.7595 on 1 procs for 1000 steps with 4000 atoms Performance: 15.001 ns/day, 1.600 hours/ns, 173.626 timesteps/s, 694.504 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7756 | 4.7756 | 4.7756 | 0.0 | 82.92 Neigh | 0.81115 | 0.81115 | 0.81115 | 0.0 | 14.08 Comm | 0.028158 | 0.028158 | 0.028158 | 0.0 | 0.49 Output | 6.0794e-05 | 6.0794e-05 | 6.0794e-05 | 0.0 | 0.00 Modify | 0.13114 | 0.13114 | 0.13114 | 0.0 | 2.28 Other | | 0.01342 | | | 0.23 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3223 ave 3223 max 3223 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: 88416 ave 88416 max 88416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 88416 Ave neighs/atom = 22.104 Neighbor list builds = 78 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 = ${P}" flag: Temp = 291.054032259029, Press = 290.675968120925 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.576 | 3.576 | 3.576 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 144.62055 144.62055 -5.944788 -5.944788 291.27885 291.27885 641541.19 641541.19 271.20755 271.20755 2000 149.47787 149.47787 -1.2067991 -1.2067991 291.50972 291.50972 3504045.1 3504045.1 46.491102 46.491102 Loop time of 1.62526 on 1 procs for 1000 steps with 4000 atoms Performance: 53.161 ns/day, 0.451 hours/ns, 615.285 timesteps/s, 2.461 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0416 | 1.0416 | 1.0416 | 0.0 | 64.09 Neigh | 0.42136 | 0.42136 | 0.42136 | 0.0 | 25.93 Comm | 0.017996 | 0.017996 | 0.017996 | 0.0 | 1.11 Output | 3.0037e-05 | 3.0037e-05 | 3.0037e-05 | 0.0 | 0.00 Modify | 0.13202 | 0.13202 | 0.13202 | 0.0 | 8.12 Other | | 0.01221 | | | 0.75 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1603 ave 1603 max 1603 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16162 ave 16162 max 16162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16162 Ave neighs/atom = 4.0405 Neighbor list builds = 111 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.377626296665, Press = 138.294262534133 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 33 33 33 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.72 | 3.72 | 3.72 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 149.47787 149.47787 -1.2067991 -1.2067991 291.50972 291.50972 3504045.1 3504045.1 46.491102 46.491102 3000 150.42913 150.42913 -0.28486471 -0.28486471 291.56645 291.56645 17716930 17716930 9.084368 9.084368 Loop time of 0.870097 on 1 procs for 1000 steps with 4000 atoms Performance: 99.299 ns/day, 0.242 hours/ns, 1149.297 timesteps/s, 4.597 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42838 | 0.42838 | 0.42838 | 0.0 | 49.23 Neigh | 0.28224 | 0.28224 | 0.28224 | 0.0 | 32.44 Comm | 0.015123 | 0.015123 | 0.015123 | 0.0 | 1.74 Output | 3.2612e-05 | 3.2612e-05 | 3.2612e-05 | 0.0 | 0.00 Modify | 0.1315 | 0.1315 | 0.1315 | 0.0 | 15.11 Other | | 0.01282 | | | 1.47 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 883 ave 883 max 883 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3094 ave 3094 max 3094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3094 Ave neighs/atom = 0.7735 Neighbor list builds = 171 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.461639821297, Press = 83.2325096140992 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.44 ghost atom cutoff = 9.44 binsize = 4.72, bins = 56 56 56 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.371 | 4.371 | 4.371 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.42913 150.42913 -0.28486471 -0.28486471 291.56645 291.56645 17716930 17716930 9.084368 9.084368 4000 150.46567 150.46567 -0.062007651 -0.062007651 291.206 291.206 86250050 86250050 1.8625461 1.8625461 Loop time of 0.886664 on 1 procs for 1000 steps with 4000 atoms Performance: 97.444 ns/day, 0.246 hours/ns, 1127.823 timesteps/s, 4.511 Matom-step/s 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29958 | 0.29958 | 0.29958 | 0.0 | 33.79 Neigh | 0.42073 | 0.42073 | 0.42073 | 0.0 | 47.45 Comm | 0.017238 | 0.017238 | 0.017238 | 0.0 | 1.94 Output | 6.1785e-05 | 6.1785e-05 | 6.1785e-05 | 0.0 | 0.01 Modify | 0.13395 | 0.13395 | 0.13395 | 0.0 | 15.11 Other | | 0.01511 | | | 1.70 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 536 ave 536 max 536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 686 ave 686 max 686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 686 Ave neighs/atom = 0.1715 Neighbor list builds = 273 Dangerous builds = 0 if "${V_metal}>${V0_metal_times1000}" then "jump SELF unstable" jump SELF unstable print "ERROR: System volume ${V_metal} A^3 has become larger than ${V0_metal_times1000} A^3. Aborting calculation." ERROR: System volume 86250050.0263444 A^3 has become larger than 76444018.2483146 A^3. Aborting calculation. Total wall time: 0:00:09