# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.292160376906395*${_u_distance} variable latticeconst_converted equal 5.292160376906395*1 lattice fcc ${latticeconst_converted} lattice fcc 5.29216037690639 Lattice spacing in x,y,z = 5.2921604 5.2921604 5.2921604 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.921604 52.921604 52.921604) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Smoothed_Bernardes_1958_Ar__MO_764178710049_001 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 148217.331689156 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*${_u_distance}) variable V0_metal equal 148217.331689156/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 148217.331689156*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 148217.331689156 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 0.01*${_u_time} variable Tdamp_converted equal 0.01*1 variable press_converted equal 0.0*${_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 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 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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_764178710049_001#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 = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 11 11 11 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -121.15997 -121.15997 -283.03075 -283.03075 313.15 313.15 148217.33 148217.33 1166.51 1166.51 1000 120.86827 120.86827 -42.982544 -42.982544 316.9805 316.9805 716815.09 716815.09 169.91285 169.91285 Loop time of 5.37478 on 1 procs for 1000 steps with 4000 atoms Performance: 16.075 ns/day, 1.493 hours/ns, 186.054 timesteps/s, 744.216 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5986 | 4.5986 | 4.5986 | 0.0 | 85.56 Neigh | 0.6212 | 0.6212 | 0.6212 | 0.0 | 11.56 Comm | 0.023826 | 0.023826 | 0.023826 | 0.0 | 0.44 Output | 5.5834e-05 | 5.5834e-05 | 5.5834e-05 | 0.0 | 0.00 Modify | 0.11927 | 0.11927 | 0.11927 | 0.0 | 2.22 Other | | 0.01188 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3517 ave 3517 max 3517 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: 107482 ave 107482 max 107482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107482 Ave neighs/atom = 26.8705 Neighbor list builds = 64 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 = ${P}" flag: Temp = 313.490184688259, Press = 171.47653305508 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.857 | 3.857 | 3.857 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 120.86827 120.86827 -42.982544 -42.982544 316.9805 316.9805 716815.09 716815.09 169.91285 169.91285 2000 152.51937 152.51937 -10.079057 -10.079057 314.55768 314.55768 3677185.7 3677185.7 43.818431 43.818431 Loop time of 1.74756 on 1 procs for 1000 steps with 4000 atoms Performance: 49.440 ns/day, 0.485 hours/ns, 572.227 timesteps/s, 2.289 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1724 | 1.1724 | 1.1724 | 0.0 | 67.09 Neigh | 0.42802 | 0.42802 | 0.42802 | 0.0 | 24.49 Comm | 0.016932 | 0.016932 | 0.016932 | 0.0 | 0.97 Output | 5.7508e-05 | 5.7508e-05 | 5.7508e-05 | 0.0 | 0.00 Modify | 0.11929 | 0.11929 | 0.11929 | 0.0 | 6.83 Other | | 0.01083 | | | 0.62 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1856 ave 1856 max 1856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22846 ave 22846 max 22846 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22846 Ave neighs/atom = 5.7115 Neighbor list builds = 109 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.684715035237, Press = 102.812080531105 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 30 30 30 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.58 | 3.58 | 3.58 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 152.51937 152.51937 -10.079057 -10.079057 314.55768 314.55768 3677185.7 3677185.7 43.818431 43.818431 3000 155.50657 155.50657 -2.5899648 -2.5899648 305.84847 305.84847 19506209 19506209 8.4481899 8.4481899 Loop time of 0.841509 on 1 procs for 1000 steps with 4000 atoms Performance: 102.673 ns/day, 0.234 hours/ns, 1188.341 timesteps/s, 4.753 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.419 | 0.419 | 0.419 | 0.0 | 49.79 Neigh | 0.2813 | 0.2813 | 0.2813 | 0.0 | 33.43 Comm | 0.013915 | 0.013915 | 0.013915 | 0.0 | 1.65 Output | 3.9104e-05 | 3.9104e-05 | 3.9104e-05 | 0.0 | 0.00 Modify | 0.11594 | 0.11594 | 0.11594 | 0.0 | 13.78 Other | | 0.01132 | | | 1.35 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 990 ave 990 max 990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5144 ave 5144 max 5144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5144 Ave neighs/atom = 1.286 Neighbor list builds = 179 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.650432300431, Press = 64.1395885329909 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 52 52 52 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.116 | 4.116 | 4.116 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 155.50657 155.50657 -2.5899648 -2.5899648 305.84847 305.84847 19506209 19506209 8.4481899 8.4481899 4000 159.8416 159.8416 -0.62771892 -0.62771892 310.43878 310.43878 1.0000175e+08 1.0000175e+08 1.7030585 1.7030585 Loop time of 0.780266 on 1 procs for 1000 steps with 4000 atoms Performance: 110.731 ns/day, 0.217 hours/ns, 1281.614 timesteps/s, 5.126 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24244 | 0.24244 | 0.24244 | 0.0 | 31.07 Neigh | 0.39537 | 0.39537 | 0.39537 | 0.0 | 50.67 Comm | 0.013707 | 0.013707 | 0.013707 | 0.0 | 1.76 Output | 4.7109e-05 | 4.7109e-05 | 4.7109e-05 | 0.0 | 0.01 Modify | 0.11587 | 0.11587 | 0.11587 | 0.0 | 14.85 Other | | 0.01284 | | | 1.65 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 529 ave 529 max 529 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1244 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1244 Ave neighs/atom = 0.311 Neighbor list builds = 288 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.62043779189, Press = 44.825363199802 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 89 89 89 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.575 | 6.575 | 6.575 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 159.8416 159.8416 -0.62771892 -0.62771892 310.43878 310.43878 1.0000175e+08 1.0000175e+08 1.7030585 1.7030585 5000 161.56577 161.56577 -0.13802395 -0.13802395 312.82696 312.82696 4.9569004e+08 4.9569004e+08 0.34817563 0.34817563 Loop time of 1.47464 on 1 procs for 1000 steps with 4000 atoms Performance: 58.591 ns/day, 0.410 hours/ns, 678.132 timesteps/s, 2.713 Matom-step/s 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18282 | 0.18282 | 0.18282 | 0.0 | 12.40 Neigh | 1.1354 | 1.1354 | 1.1354 | 0.0 | 76.99 Comm | 0.022087 | 0.022087 | 0.022087 | 0.0 | 1.50 Output | 5.6697e-05 | 5.6697e-05 | 5.6697e-05 | 0.0 | 0.00 Modify | 0.11844 | 0.11844 | 0.11844 | 0.0 | 8.03 Other | | 0.01589 | | | 1.08 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 282 ave 282 max 282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 242 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242 Ave neighs/atom = 0.0605 Neighbor list builds = 447 Dangerous builds = 0 if "${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 495690040.616123 A^3 has become larger than 148217331.689156 A^3. Aborting calculation. Total wall time: 0:00:10