# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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 -324.63234 -324.63234 -465.82667 -465.82667 273.15 273.15 178875.03 178875.03 843.11401 843.11401 1000 -62.47482 -62.47482 -204.18309 -204.18309 274.14426 274.14426 353143.47 353143.47 22.681987 22.681987 Loop time of 22.9836 on 1 procs for 1000 steps with 4000 atoms Performance: 3.759 ns/day, 6.384 hours/ns, 43.509 timesteps/s, 174.037 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 | 22.014 | 22.014 | 22.014 | 0.0 | 95.78 Neigh | 0.78472 | 0.78472 | 0.78472 | 0.0 | 3.41 Comm | 0.041547 | 0.041547 | 0.041547 | 0.0 | 0.18 Output | 0.00016692 | 0.00016692 | 0.00016692 | 0.0 | 0.00 Modify | 0.12736 | 0.12736 | 0.12736 | 0.0 | 0.55 Other | | 0.01533 | | | 0.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8686 ave 8686 max 8686 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: 861720 ave 861720 max 861720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 861720 Ave neighs/atom = 215.43 Neighbor list builds = 26 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 = ${P}" flag: Temp = 272.905995543756, Press = 15.1624666475678 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.752 | 6.752 | 6.752 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -62.47482 -62.47482 -204.18309 -204.18309 274.14426 274.14426 353143.47 353143.47 22.681987 22.681987 2000 8.9267648 8.9267648 -131.73285 -131.73285 272.11556 272.11556 544516.6 544516.6 15.929745 15.929745 Loop time of 13.2604 on 1 procs for 1000 steps with 4000 atoms Performance: 6.516 ns/day, 3.683 hours/ns, 75.412 timesteps/s, 301.649 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.683 | 12.683 | 12.683 | 0.0 | 95.64 Neigh | 0.40256 | 0.40256 | 0.40256 | 0.0 | 3.04 Comm | 0.030273 | 0.030273 | 0.030273 | 0.0 | 0.23 Output | 6.8929e-05 | 6.8929e-05 | 6.8929e-05 | 0.0 | 0.00 Modify | 0.13181 | 0.13181 | 0.13181 | 0.0 | 0.99 Other | | 0.01284 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7166 ave 7166 max 7166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560974 ave 560974 max 560974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560974 Ave neighs/atom = 140.2435 Neighbor list builds = 22 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.978413651954, Press = 15.6500779447377 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.599 | 5.599 | 5.599 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 8.9267648 8.9267648 -131.73285 -131.73285 272.11556 272.11556 544516.6 544516.6 15.929745 15.929745 3000 90.540513 90.540513 -54.31839 -54.31839 280.23937 280.23937 1325168.1 1325168.1 45.625784 45.625784 Loop time of 8.33897 on 1 procs for 1000 steps with 4000 atoms Performance: 10.361 ns/day, 2.316 hours/ns, 119.919 timesteps/s, 479.675 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5965 | 7.5965 | 7.5965 | 0.0 | 91.10 Neigh | 0.58024 | 0.58024 | 0.58024 | 0.0 | 6.96 Comm | 0.026964 | 0.026964 | 0.026964 | 0.0 | 0.32 Output | 5.8841e-05 | 5.8841e-05 | 5.8841e-05 | 0.0 | 0.00 Modify | 0.12351 | 0.12351 | 0.12351 | 0.0 | 1.48 Other | | 0.01174 | | | 0.14 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4799 ave 4799 max 4799 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234270 ave 234270 max 234270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234270 Ave neighs/atom = 58.5675 Neighbor list builds = 48 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.893472993146, Press = 23.1365183563245 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.45 | 4.45 | 4.45 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 90.540513 90.540513 -54.31839 -54.31839 280.23937 280.23937 1325168.1 1325168.1 45.625784 45.625784 4000 128.79681 128.79681 -12.921624 -12.921624 274.16392 274.16392 6371538.1 6371538.1 20.115761 20.115761 Loop time of 3.24632 on 1 procs for 1000 steps with 4000 atoms Performance: 26.615 ns/day, 0.902 hours/ns, 308.041 timesteps/s, 1.232 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3785 | 2.3785 | 2.3785 | 0.0 | 73.27 Neigh | 0.71913 | 0.71913 | 0.71913 | 0.0 | 22.15 Comm | 0.020899 | 0.020899 | 0.020899 | 0.0 | 0.64 Output | 4.2379e-05 | 4.2379e-05 | 4.2379e-05 | 0.0 | 0.00 Modify | 0.11662 | 0.11662 | 0.11662 | 0.0 | 3.59 Other | | 0.01112 | | | 0.34 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2512 ave 2512 max 2512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51074 ave 51074 max 51074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51074 Ave neighs/atom = 12.7685 Neighbor list builds = 120 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.793820951859, Press = 26.9640475833229 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 23 23 23 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.727 | 3.727 | 3.727 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 128.79681 128.79681 -12.921624 -12.921624 274.16392 274.16392 6371538.1 6371538.1 20.115761 20.115761 5000 137.46028 137.46028 -4.030257 -4.030257 273.72304 273.72304 35211384 35211384 4.1277999 4.1277999 Loop time of 1.31569 on 1 procs for 1000 steps with 4000 atoms Performance: 65.669 ns/day, 0.365 hours/ns, 760.056 timesteps/s, 3.040 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68629 | 0.68629 | 0.68629 | 0.0 | 52.16 Neigh | 0.48292 | 0.48292 | 0.48292 | 0.0 | 36.70 Comm | 0.017902 | 0.017902 | 0.017902 | 0.0 | 1.36 Output | 2.8904e-05 | 2.8904e-05 | 2.8904e-05 | 0.0 | 0.00 Modify | 0.1168 | 0.1168 | 0.1168 | 0.0 | 8.88 Other | | 0.01176 | | | 0.89 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1276 ave 1276 max 1276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10848 ave 10848 max 10848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10848 Ave neighs/atom = 2.712 Neighbor list builds = 213 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.867556118207, Press = 22.8725287542471 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 40 40 40 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.982 | 3.982 | 3.982 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 137.46028 137.46028 -4.030257 -4.030257 273.72304 273.72304 35211384 35211384 4.1277999 4.1277999 6000 143.09368 143.09368 -1.1364454 -1.1364454 279.02296 279.02296 1.8640639e+08 1.8640639e+08 0.81634739 0.81634739 Loop time of 0.90704 on 1 procs for 1000 steps with 4000 atoms Performance: 95.255 ns/day, 0.252 hours/ns, 1102.488 timesteps/s, 4.410 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31907 | 0.31907 | 0.31907 | 0.0 | 35.18 Neigh | 0.44014 | 0.44014 | 0.44014 | 0.0 | 48.53 Comm | 0.017528 | 0.017528 | 0.017528 | 0.0 | 1.93 Output | 2.8795e-05 | 2.8795e-05 | 2.8795e-05 | 0.0 | 0.00 Modify | 0.11663 | 0.11663 | 0.11663 | 0.0 | 12.86 Other | | 0.01364 | | | 1.50 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 683 ave 683 max 683 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2784 ave 2784 max 2784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2784 Ave neighs/atom = 0.696 Neighbor list builds = 337 Dangerous builds = 0 if "${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 186406391.101882 A^3 has become larger than 178875026.769171 A^3. Aborting calculation. Total wall time: 0:00:50