# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.299560785293579*${_u_distance} variable latticeconst_converted equal 4.299560785293579*1 lattice fcc ${latticeconst_converted} lattice fcc 4.29956078529358 Lattice spacing in x,y,z = 4.2995608 4.2995608 4.2995608 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (42.995608 42.995608 42.995608) create_atoms CPU = 0.001 seconds variable mass_converted equal 20.1797*${_u_mass} variable mass_converted equal 20.1797*1 kim interactions Ne #=== BEGIN kim interactions ================================== pair_style kim Morse_Shifted_Glyde_1970_Ne__MO_169434419764_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 79482.6392486835 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*${_u_distance}) variable V0_metal equal 79482.6392486835/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 79482.6392486835*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 79482.6392486835 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_169434419764_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 = 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 60.585189 60.585189 -111.62382 -111.62382 333.15 333.15 79482.639 79482.639 2314.2098 2314.2098 1000 164.9037 164.9037 -6.0420966 -6.0420966 330.70623 330.70623 671592.93 671592.93 289.84384 289.84384 Loop time of 6.3081 on 1 procs for 1000 steps with 4000 atoms Performance: 13.697 ns/day, 1.752 hours/ns, 158.526 timesteps/s, 634.105 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 | 5.194 | 5.194 | 5.194 | 0.0 | 82.34 Neigh | 0.9316 | 0.9316 | 0.9316 | 0.0 | 14.77 Comm | 0.031479 | 0.031479 | 0.031479 | 0.0 | 0.50 Output | 8.8396e-05 | 8.8396e-05 | 8.8396e-05 | 0.0 | 0.00 Modify | 0.13504 | 0.13504 | 0.13504 | 0.0 | 2.14 Other | | 0.01592 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3477 ave 3477 max 3477 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: 104286 ave 104286 max 104286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104286 Ave neighs/atom = 26.0715 Neighbor list builds = 80 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 = ${P}" flag: Temp = 330.908790361462, Press = 321.027522059927 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 164.9037 164.9037 -6.0420966 -6.0420966 330.70623 330.70623 671592.93 671592.93 289.84384 289.84384 2000 170.11926 170.11926 -0.94443455 -0.94443455 330.93432 330.93432 3679432.5 3679432.5 50.739777 50.739777 Loop time of 1.65246 on 1 procs for 1000 steps with 4000 atoms Performance: 52.286 ns/day, 0.459 hours/ns, 605.158 timesteps/s, 2.421 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.013 | 1.013 | 1.013 | 0.0 | 61.30 Neigh | 0.47718 | 0.47718 | 0.47718 | 0.0 | 28.88 Comm | 0.01909 | 0.01909 | 0.01909 | 0.0 | 1.16 Output | 3.1759e-05 | 3.1759e-05 | 3.1759e-05 | 0.0 | 0.00 Modify | 0.13104 | 0.13104 | 0.13104 | 0.0 | 7.93 Other | | 0.01212 | | | 0.73 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1719 ave 1719 max 1719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 19530 ave 19530 max 19530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 19530 Ave neighs/atom = 4.8825 Neighbor list builds = 113 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.138131121415, Press = 150.938567384213 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 31 31 31 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.69 | 3.69 | 3.69 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 170.11926 170.11926 -0.94443455 -0.94443455 330.93432 330.93432 3679432.5 3679432.5 50.739777 50.739777 3000 170.99092 170.99092 -0.28179284 -0.28179284 331.33868 331.33868 18655900 18655900 9.8234894 9.8234894 Loop time of 0.864891 on 1 procs for 1000 steps with 4000 atoms Performance: 99.897 ns/day, 0.240 hours/ns, 1156.215 timesteps/s, 4.625 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38991 | 0.38991 | 0.38991 | 0.0 | 45.08 Neigh | 0.31453 | 0.31453 | 0.31453 | 0.0 | 36.37 Comm | 0.016266 | 0.016266 | 0.016266 | 0.0 | 1.88 Output | 3.0707e-05 | 3.0707e-05 | 3.0707e-05 | 0.0 | 0.00 Modify | 0.13131 | 0.13131 | 0.13131 | 0.0 | 15.18 Other | | 0.01284 | | | 1.48 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 952 ave 952 max 952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3782 ave 3782 max 3782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3782 Ave neighs/atom = 0.9455 Neighbor list builds = 175 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.230891809378, Press = 90.7762547109302 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 53 53 53 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.25 | 4.25 | 4.25 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 170.99092 170.99092 -0.28179284 -0.28179284 331.33868 331.33868 18655900 18655900 9.8234894 9.8234894 4000 171.23275 171.23275 -0.023074662 -0.023074662 331.30601 331.30601 90851182 90851182 2.0148961 2.0148961 Loop time of 0.839021 on 1 procs for 1000 steps with 4000 atoms Performance: 102.977 ns/day, 0.233 hours/ns, 1191.865 timesteps/s, 4.767 Matom-step/s 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25734 | 0.25734 | 0.25734 | 0.0 | 30.67 Neigh | 0.4159 | 0.4159 | 0.4159 | 0.0 | 49.57 Comm | 0.017346 | 0.017346 | 0.017346 | 0.0 | 2.07 Output | 5.0314e-05 | 5.0314e-05 | 5.0314e-05 | 0.0 | 0.01 Modify | 0.1333 | 0.1333 | 0.1333 | 0.0 | 15.89 Other | | 0.01509 | | | 1.80 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 574 ave 574 max 574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 862 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 862 Ave neighs/atom = 0.2155 Neighbor list builds = 280 Dangerous builds = 0 if "${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 90851182.1873721 A^3 has become larger than 79482639.2486835 A^3. Aborting calculation. Total wall time: 0:00:09