# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.24417295455933*${_u_distance} variable latticeconst_converted equal 5.24417295455933*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24417295455933 Lattice spacing in x,y,z = 5.244173 5.244173 5.244173 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ar__MO_242741380554_004 pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 144221.835764993 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144221.835764993*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144221.835764993 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_242741380554_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 = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 5 5 5 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) = 24.97 | 24.97 | 24.97 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -202.86614 -202.86614 -354.39869 -354.39869 293.15 293.15 144221.84 144221.84 1122.2608 1122.2608 1000 71.407061 71.407061 -80.541373 -80.541373 293.95455 293.95455 521834.68 521834.68 129.54422 129.54422 Loop time of 58.9758 on 1 procs for 1000 steps with 4000 atoms Performance: 1.465 ns/day, 16.382 hours/ns, 16.956 timesteps/s, 67.824 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 | 55.578 | 55.578 | 55.578 | 0.0 | 94.24 Neigh | 3.1442 | 3.1442 | 3.1442 | 0.0 | 5.33 Comm | 0.07481 | 0.07481 | 0.07481 | 0.0 | 0.13 Output | 0.00015268 | 0.00015268 | 0.00015268 | 0.0 | 0.00 Modify | 0.1532 | 0.1532 | 0.1532 | 0.0 | 0.26 Other | | 0.02502 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10941 ave 10941 max 10941 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: 1.36776e+06 ave 1.36776e+06 max 1.36776e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1367758 Ave neighs/atom = 341.9395 Neighbor list builds = 50 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 = ${P}" flag: Temp = 292.753238523975, Press = 131.782568851944 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 71.407061 71.407061 -80.541373 -80.541373 293.95455 293.95455 521834.68 521834.68 129.54422 129.54422 2000 130.4919 130.4919 -19.829324 -19.829324 290.8066 290.8066 2307801.8 2307801.8 57.010055 57.010055 Loop time of 18.3452 on 1 procs for 1000 steps with 4000 atoms Performance: 4.710 ns/day, 5.096 hours/ns, 54.510 timesteps/s, 218.041 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.284 | 16.284 | 16.284 | 0.0 | 88.76 Neigh | 1.8482 | 1.8482 | 1.8482 | 0.0 | 10.07 Comm | 0.046472 | 0.046472 | 0.046472 | 0.0 | 0.25 Output | 7.5942e-05 | 7.5942e-05 | 7.5942e-05 | 0.0 | 0.00 Modify | 0.14874 | 0.14874 | 0.14874 | 0.0 | 0.81 Other | | 0.01785 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5478 ave 5478 max 5478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 308264 ave 308264 max 308264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308264 Ave neighs/atom = 77.066 Neighbor list builds = 87 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.681958738879, Press = 102.892939272737 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.955 | 7.955 | 7.955 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 130.4919 130.4919 -19.829324 -19.829324 290.8066 290.8066 2307801.8 2307801.8 57.010055 57.010055 3000 146.01011 146.01011 -4.6535241 -4.6535241 291.46901 291.46901 12401722 12401722 12.510844 12.510844 Loop time of 5.02312 on 1 procs for 1000 steps with 4000 atoms Performance: 17.200 ns/day, 1.395 hours/ns, 199.080 timesteps/s, 796.319 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5424 | 3.5424 | 3.5424 | 0.0 | 70.52 Neigh | 1.2944 | 1.2944 | 1.2944 | 0.0 | 25.77 Comm | 0.031382 | 0.031382 | 0.031382 | 0.0 | 0.62 Output | 4.9954e-05 | 4.9954e-05 | 4.9954e-05 | 0.0 | 0.00 Modify | 0.14017 | 0.14017 | 0.14017 | 0.0 | 2.79 Other | | 0.01476 | | | 0.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2669 ave 2669 max 2669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61152 ave 61152 max 61152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61152 Ave neighs/atom = 15.288 Neighbor list builds = 155 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.84159642762, Press = 68.3777572689297 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 22 22 22 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.842 | 6.842 | 6.842 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 146.01011 146.01011 -4.6535241 -4.6535241 291.46901 291.46901 12401722 12401722 12.510844 12.510844 4000 146.83319 146.83319 -1.1178022 -1.1178022 286.22123 286.22123 65235168 65235168 2.4048148 2.4048148 Loop time of 2.01657 on 1 procs for 1000 steps with 4000 atoms Performance: 42.845 ns/day, 0.560 hours/ns, 495.892 timesteps/s, 1.984 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0069 | 1.0069 | 1.0069 | 0.0 | 49.93 Neigh | 0.82925 | 0.82925 | 0.82925 | 0.0 | 41.12 Comm | 0.026962 | 0.026962 | 0.026962 | 0.0 | 1.34 Output | 4.7179e-05 | 4.7179e-05 | 4.7179e-05 | 0.0 | 0.00 Modify | 0.13796 | 0.13796 | 0.13796 | 0.0 | 6.84 Other | | 0.01546 | | | 0.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1453 ave 1453 max 1453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13168 ave 13168 max 13168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13168 Ave neighs/atom = 3.292 Neighbor list builds = 253 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.784979894252, Press = 48.304321409429 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 37 37 37 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.041 | 7.041 | 7.041 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 146.83319 146.83319 -1.1178022 -1.1178022 286.22123 286.22123 65235168 65235168 2.4048148 2.4048148 5000 151.66177 151.66177 -0.27561553 -0.27561553 293.93318 293.93318 3.3043576e+08 3.3043576e+08 0.49029274 0.49029274 Loop time of 1.39326 on 1 procs for 1000 steps with 4000 atoms Performance: 62.013 ns/day, 0.387 hours/ns, 717.740 timesteps/s, 2.871 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47734 | 0.47734 | 0.47734 | 0.0 | 34.26 Neigh | 0.73213 | 0.73213 | 0.73213 | 0.0 | 52.55 Comm | 0.027669 | 0.027669 | 0.027669 | 0.0 | 1.99 Output | 4.6708e-05 | 4.6708e-05 | 4.6708e-05 | 0.0 | 0.00 Modify | 0.13765 | 0.13765 | 0.13765 | 0.0 | 9.88 Other | | 0.01842 | | | 1.32 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 802 ave 802 max 802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3052 ave 3052 max 3052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3052 Ave neighs/atom = 0.763 Neighbor list builds = 405 Dangerous builds = 0 if "${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 330435758.607063 A^3 has become larger than 144221835.764993 A^3. Aborting calculation. Total wall time: 0:01:26