# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.634428912401205*${_u_distance} variable latticeconst_converted equal 5.634428912401205*1 lattice fcc ${latticeconst_converted} lattice fcc 5.63442891240121 Lattice spacing in x,y,z = 5.6344289 5.6344289 5.6344289 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (56.344289 56.344289 56.344289) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (56.344289 56.344289 56.344289) create_atoms CPU = 0.001 seconds variable mass_converted equal 83.798*${_u_mass} variable mass_converted equal 83.798*1 kim interactions Kr #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Kr__MO_984281096460_004 pair_coeff * * Kr #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 83.798 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 178875.026769171 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 178875.026769171/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 178875.026769171/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 178875.026769171/(1*1*${_u_distance}) variable V0_metal equal 178875.026769171/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 178875.026769171*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 178875.026769171 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_984281096460_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 = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 7 7 7 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) = 10.2 | 10.2 | 10.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -314.29412 -314.29412 -465.82667 -465.82667 293.15 293.15 178875.03 178875.03 904.84673 904.84673 1000 -37.102967 -37.102967 -188.96422 -188.96422 293.78588 293.78588 378865.58 378865.58 33.192016 33.192016 Loop time of 22.623 on 1 procs for 1000 steps with 4000 atoms Performance: 3.819 ns/day, 6.284 hours/ns, 44.203 timesteps/s, 176.811 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 | 21.602 | 21.602 | 21.602 | 0.0 | 95.49 Neigh | 0.81637 | 0.81637 | 0.81637 | 0.0 | 3.61 Comm | 0.048432 | 0.048432 | 0.048432 | 0.0 | 0.21 Output | 0.00014652 | 0.00014652 | 0.00014652 | 0.0 | 0.00 Modify | 0.13523 | 0.13523 | 0.13523 | 0.0 | 0.60 Other | | 0.02078 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8411 ave 8411 max 8411 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: 799160 ave 799160 max 799160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 799160 Ave neighs/atom = 199.79 Neighbor list builds = 29 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 = ${P}" flag: Temp = 292.450025505515, Press = 22.6811013998495 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.75 | 6.75 | 6.75 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -37.102967 -37.102967 -188.96422 -188.96422 293.78588 293.78588 378865.58 378865.58 33.192016 33.192016 2000 51.85272 51.85272 -101.11537 -101.11537 295.92714 295.92714 695065.84 695065.84 42.206939 42.206939 Loop time of 11.9489 on 1 procs for 1000 steps with 4000 atoms Performance: 7.231 ns/day, 3.319 hours/ns, 83.690 timesteps/s, 334.758 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.28 | 11.28 | 11.28 | 0.0 | 94.40 Neigh | 0.48565 | 0.48565 | 0.48565 | 0.0 | 4.06 Comm | 0.031971 | 0.031971 | 0.031971 | 0.0 | 0.27 Output | 6.0163e-05 | 6.0163e-05 | 6.0163e-05 | 0.0 | 0.00 Modify | 0.13578 | 0.13578 | 0.13578 | 0.0 | 1.14 Other | | 0.01539 | | | 0.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6373 ave 6373 max 6373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 438252 ave 438252 max 438252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 438252 Ave neighs/atom = 109.563 Neighbor list builds = 30 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.980918799861, Press = 28.9840902580884 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.214 | 5.214 | 5.214 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 51.85272 51.85272 -101.11537 -101.11537 295.92714 295.92714 695065.84 695065.84 42.206939 42.206939 3000 117.03219 117.03219 -29.25638 -29.25638 283.00517 283.00517 2437858.4 2437858.4 41.803269 41.803269 Loop time of 6.11882 on 1 procs for 1000 steps with 4000 atoms Performance: 14.120 ns/day, 1.700 hours/ns, 163.430 timesteps/s, 653.721 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2065 | 5.2065 | 5.2065 | 0.0 | 85.09 Neigh | 0.74592 | 0.74592 | 0.74592 | 0.0 | 12.19 Comm | 0.0265 | 0.0265 | 0.0265 | 0.0 | 0.43 Output | 6.8168e-05 | 6.8168e-05 | 6.8168e-05 | 0.0 | 0.00 Modify | 0.12663 | 0.12663 | 0.12663 | 0.0 | 2.07 Other | | 0.01321 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3738 ave 3738 max 3738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126614 ave 126614 max 126614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126614 Ave neighs/atom = 31.6535 Neighbor list builds = 77 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.838772415606, Press = 38.4661076886745 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 17 17 17 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.075 | 4.075 | 4.075 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 117.03219 117.03219 -29.25638 -29.25638 283.00517 283.00517 2437858.4 2437858.4 41.803269 41.803269 4000 144.13326 144.13326 -7.4011685 -7.4011685 293.15363 293.15363 13072137 13072137 11.495287 11.495287 Loop time of 2.14536 on 1 procs for 1000 steps with 4000 atoms Performance: 40.273 ns/day, 0.596 hours/ns, 466.121 timesteps/s, 1.864 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3496 | 1.3496 | 1.3496 | 0.0 | 62.91 Neigh | 0.64377 | 0.64377 | 0.64377 | 0.0 | 30.01 Comm | 0.020393 | 0.020393 | 0.020393 | 0.0 | 0.95 Output | 4.1167e-05 | 4.1167e-05 | 4.1167e-05 | 0.0 | 0.00 Modify | 0.11883 | 0.11883 | 0.11883 | 0.0 | 5.54 Other | | 0.01271 | | | 0.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1898 ave 1898 max 1898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25486 ave 25486 max 25486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25486 Ave neighs/atom = 6.3715 Neighbor list builds = 157 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.783956360602, Press = 34.3019362206525 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 29 29 29 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.789 | 3.789 | 3.789 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 144.13326 144.13326 -7.4011685 -7.4011685 293.15363 293.15363 13072137 13072137 11.495287 11.495287 5000 145.10462 145.10462 -2.4032906 -2.4032906 285.36406 285.36406 71283695 71283695 2.1562953 2.1562953 Loop time of 1.03786 on 1 procs for 1000 steps with 4000 atoms Performance: 83.248 ns/day, 0.288 hours/ns, 963.517 timesteps/s, 3.854 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46176 | 0.46176 | 0.46176 | 0.0 | 44.49 Neigh | 0.4281 | 0.4281 | 0.4281 | 0.0 | 41.25 Comm | 0.017552 | 0.017552 | 0.017552 | 0.0 | 1.69 Output | 6.6856e-05 | 6.6856e-05 | 6.6856e-05 | 0.0 | 0.01 Modify | 0.1174 | 0.1174 | 0.1174 | 0.0 | 11.31 Other | | 0.01298 | | | 1.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 947 ave 947 max 947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 5748 ave 5748 max 5748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5748 Ave neighs/atom = 1.437 Neighbor list builds = 265 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.863865995589, Press = 27.3130813826396 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 51 51 51 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.301 | 4.301 | 4.301 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 145.10462 145.10462 -2.4032906 -2.4032906 285.36406 285.36406 71283695 71283695 2.1562953 2.1562953 6000 155.27541 155.27541 -0.65476488 -0.65476488 301.6575 301.6575 3.7036225e+08 3.7036225e+08 0.44713568 0.44713568 Loop time of 0.962206 on 1 procs for 1000 steps with 4000 atoms Performance: 89.794 ns/day, 0.267 hours/ns, 1039.279 timesteps/s, 4.157 Matom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25915 | 0.25915 | 0.25915 | 0.0 | 26.93 Neigh | 0.55166 | 0.55166 | 0.55166 | 0.0 | 57.33 Comm | 0.018309 | 0.018309 | 0.018309 | 0.0 | 1.90 Output | 4.1839e-05 | 4.1839e-05 | 4.1839e-05 | 0.0 | 0.00 Modify | 0.11721 | 0.11721 | 0.11721 | 0.0 | 12.18 Other | | 0.01584 | | | 1.65 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 508 ave 508 max 508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1624 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1624 Ave neighs/atom = 0.406 Neighbor list builds = 420 Dangerous builds = 0 if "${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 370362246.647833 A^3 has become larger than 178875026.769171 A^3. Aborting calculation. Total wall time: 0:00:45