# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.205006867647171*${_u_distance} variable latticeconst_converted equal 4.205006867647171*1 lattice fcc ${latticeconst_converted} lattice fcc 4.20500686764717 Lattice spacing in x,y,z = 4.2050069 4.2050069 4.2050069 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.050069 42.050069 42.050069) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.050069 42.050069 42.050069) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1122) WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) 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 74353.2794273218 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*1*${_u_distance}) variable V0_metal equal 74353.2794273218/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 74353.2794273218*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 74353.2794273218 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_946046425752_002#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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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) = 7.005 | 7.005 | 7.005 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 39.246108 39.246108 -112.28645 -112.28645 293.15 293.15 74353.279 74353.279 2176.8315 2176.8315 1000 142.99744 142.99744 -7.5232172 -7.5232172 291.19243 291.19243 616311.57 616311.57 276.32919 276.32919 Loop time of 9.01044 on 1 procs for 1000 steps with 4000 atoms Performance: 9.589 ns/day, 2.503 hours/ns, 110.982 timesteps/s, 443.929 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8606 | 7.8606 | 7.8606 | 0.0 | 87.24 Neigh | 0.96293 | 0.96293 | 0.96293 | 0.0 | 10.69 Comm | 0.033642 | 0.033642 | 0.033642 | 0.0 | 0.37 Output | 9.4387e-05 | 9.4387e-05 | 9.4387e-05 | 0.0 | 0.00 Modify | 0.1351 | 0.1351 | 0.1351 | 0.0 | 1.50 Other | | 0.01808 | | | 0.20 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3565 ave 3565 max 3565 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: 114402 ave 114402 max 114402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114402 Ave neighs/atom = 28.6005 Neighbor list builds = 77 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 = ${P}" flag: Temp = 291.12142658209, Press = 302.733870943006 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.948 | 3.948 | 3.948 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 142.99744 142.99744 -7.5232172 -7.5232172 291.19243 291.19243 616311.57 616311.57 276.32919 276.32919 2000 149.14269 149.14269 -1.4742156 -1.4742156 291.37862 291.37862 3346861.5 3346861.5 48.344884 48.344884 Loop time of 2.18936 on 1 procs for 1000 steps with 4000 atoms Performance: 39.464 ns/day, 0.608 hours/ns, 456.755 timesteps/s, 1.827 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5326 | 1.5326 | 1.5326 | 0.0 | 70.00 Neigh | 0.4912 | 0.4912 | 0.4912 | 0.0 | 22.44 Comm | 0.019971 | 0.019971 | 0.019971 | 0.0 | 0.91 Output | 8.0261e-05 | 8.0261e-05 | 8.0261e-05 | 0.0 | 0.00 Modify | 0.1325 | 0.1325 | 0.1325 | 0.0 | 6.05 Other | | 0.01302 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1813 ave 1813 max 1813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21278 ave 21278 max 21278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21278 Ave neighs/atom = 5.3195 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.385825922538, Press = 143.247543526924 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 149.14269 149.14269 -1.4742156 -1.4742156 291.37862 291.37862 3346861.5 3346861.5 48.344884 48.344884 3000 150.37992 150.37992 -0.35886431 -0.35886431 291.61441 291.61441 16968558 16968558 9.4745278 9.4745278 Loop time of 1.01182 on 1 procs for 1000 steps with 4000 atoms Performance: 85.390 ns/day, 0.281 hours/ns, 988.314 timesteps/s, 3.953 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52866 | 0.52866 | 0.52866 | 0.0 | 52.25 Neigh | 0.32154 | 0.32154 | 0.32154 | 0.0 | 31.78 Comm | 0.016508 | 0.016508 | 0.016508 | 0.0 | 1.63 Output | 4.3612e-05 | 4.3612e-05 | 4.3612e-05 | 0.0 | 0.00 Modify | 0.13206 | 0.13206 | 0.13206 | 0.0 | 13.05 Other | | 0.01302 | | | 1.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1017 ave 1017 max 1017 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4206 ave 4206 max 4206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4206 Ave neighs/atom = 1.0515 Neighbor list builds = 170 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 291.464528953625, Press = 86.331244614681 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 51 51 51 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.176 | 4.176 | 4.176 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 150.37992 150.37992 -0.35886431 -0.35886431 291.61441 291.61441 16968558 16968558 9.4745278 9.4745278 4000 150.67359 150.67359 -0.071118831 -0.071118831 291.62586 291.62586 82822057 82822057 1.9431241 1.9431241 Loop time of 0.861386 on 1 procs for 1000 steps with 4000 atoms Performance: 100.303 ns/day, 0.239 hours/ns, 1160.919 timesteps/s, 4.644 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30505 | 0.30505 | 0.30505 | 0.0 | 35.41 Neigh | 0.39208 | 0.39208 | 0.39208 | 0.0 | 45.52 Comm | 0.01659 | 0.01659 | 0.01659 | 0.0 | 1.93 Output | 4.6698e-05 | 4.6698e-05 | 4.6698e-05 | 0.0 | 0.01 Modify | 0.1326 | 0.1326 | 0.1326 | 0.0 | 15.39 Other | | 0.01502 | | | 1.74 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 579 ave 579 max 579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 810 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 810 Ave neighs/atom = 0.2025 Neighbor list builds = 270 Dangerous builds = 0 if "${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 82822057.0432421 A^3 has become larger than 74353279.4273218 A^3. Aborting calculation. Total wall time: 0:00:13