# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_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_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 -293.61766 -293.61766 -465.82667 -465.82667 333.15 333.15 178875.03 178875.03 1028.3122 1028.3122 1000 13.095675 13.095675 -160.35687 -160.35687 335.55571 335.55571 440477.94 440477.94 57.536592 57.536592 Loop time of 21.7684 on 1 procs for 1000 steps with 4000 atoms Performance: 3.969 ns/day, 6.047 hours/ns, 45.938 timesteps/s, 183.753 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.599 | 20.599 | 20.599 | 0.0 | 94.63 Neigh | 0.96601 | 0.96601 | 0.96601 | 0.0 | 4.44 Comm | 0.047072 | 0.047072 | 0.047072 | 0.0 | 0.22 Output | 0.0001372 | 0.0001372 | 0.0001372 | 0.0 | 0.00 Modify | 0.13538 | 0.13538 | 0.13538 | 0.0 | 0.62 Other | | 0.0204 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7827 ave 7827 max 7827 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: 692224 ave 692224 max 692224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692224 Ave neighs/atom = 173.056 Neighbor list builds = 35 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 = ${P}" flag: Temp = 333.941376041867, Press = 50.9113374311934 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.985 | 5.985 | 5.985 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 13.095675 13.095675 -160.35687 -160.35687 335.55571 335.55571 440477.94 440477.94 57.536592 57.536592 2000 113.39282 113.39282 -58.218616 -58.218616 331.99395 331.99395 1165483.8 1165483.8 77.498962 77.498962 Loop time of 9.42976 on 1 procs for 1000 steps with 4000 atoms Performance: 9.162 ns/day, 2.619 hours/ns, 106.047 timesteps/s, 424.189 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5423 | 8.5423 | 8.5423 | 0.0 | 90.59 Neigh | 0.69765 | 0.69765 | 0.69765 | 0.0 | 7.40 Comm | 0.032029 | 0.032029 | 0.032029 | 0.0 | 0.34 Output | 9.2514e-05 | 9.2514e-05 | 9.2514e-05 | 0.0 | 0.00 Modify | 0.13928 | 0.13928 | 0.13928 | 0.0 | 1.48 Other | | 0.0184 | | | 0.20 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5119 ave 5119 max 5119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 262700 ave 262700 max 262700 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 262700 Ave neighs/atom = 65.675 Neighbor list builds = 51 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.771976462205, Press = 63.7716693654177 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 13 13 13 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.448 | 4.448 | 4.448 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 113.39282 113.39282 -58.218616 -58.218616 331.99395 331.99395 1165483.8 1165483.8 77.498962 77.498962 3000 155.27255 155.27255 -13.449845 -13.449845 326.40491 326.40491 5809100.2 5809100.2 27.298991 27.298991 Loop time of 3.56181 on 1 procs for 1000 steps with 4000 atoms Performance: 24.257 ns/day, 0.989 hours/ns, 280.757 timesteps/s, 1.123 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6318 | 2.6318 | 2.6318 | 0.0 | 73.89 Neigh | 0.76474 | 0.76474 | 0.76474 | 0.0 | 21.47 Comm | 0.023652 | 0.023652 | 0.023652 | 0.0 | 0.66 Output | 4.0055e-05 | 4.0055e-05 | 4.0055e-05 | 0.0 | 0.00 Modify | 0.12683 | 0.12683 | 0.12683 | 0.0 | 3.56 Other | | 0.01473 | | | 0.41 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2599 ave 2599 max 2599 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54364 ave 54364 max 54364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54364 Ave neighs/atom = 13.591 Neighbor list builds = 120 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.768477962726, Press = 59.1057340012419 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 22 22 22 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.719 | 3.719 | 3.719 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 155.27255 155.27255 -13.449845 -13.449845 326.40491 326.40491 5809100.2 5809100.2 27.298991 27.298991 4000 168.06675 168.06675 -3.7742886 -3.7742886 332.43813 332.43813 31716277 31716277 5.6195186 5.6195186 Loop time of 1.36762 on 1 procs for 1000 steps with 4000 atoms Performance: 63.176 ns/day, 0.380 hours/ns, 731.200 timesteps/s, 2.925 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72332 | 0.72332 | 0.72332 | 0.0 | 52.89 Neigh | 0.49402 | 0.49402 | 0.49402 | 0.0 | 36.12 Comm | 0.019071 | 0.019071 | 0.019071 | 0.0 | 1.39 Output | 4.1649e-05 | 4.1649e-05 | 4.1649e-05 | 0.0 | 0.00 Modify | 0.11826 | 0.11826 | 0.11826 | 0.0 | 8.65 Other | | 0.01291 | | | 0.94 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1397 ave 1397 max 1397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11236 ave 11236 max 11236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11236 Ave neighs/atom = 2.809 Neighbor list builds = 208 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.771291246596, Press = 44.5441110187594 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 39 39 39 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.96 | 3.96 | 3.96 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 168.06675 168.06675 -3.7742886 -3.7742886 332.43813 332.43813 31716277 31716277 5.6195186 5.6195186 5000 170.35563 170.35563 -1.0160145 -1.0160145 331.53007 331.53007 1.6679483e+08 1.6679483e+08 1.0890716 1.0890716 Loop time of 0.893201 on 1 procs for 1000 steps with 4000 atoms Performance: 96.731 ns/day, 0.248 hours/ns, 1119.569 timesteps/s, 4.478 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32515 | 0.32515 | 0.32515 | 0.0 | 36.40 Neigh | 0.41922 | 0.41922 | 0.41922 | 0.0 | 46.93 Comm | 0.017376 | 0.017376 | 0.017376 | 0.0 | 1.95 Output | 3.9694e-05 | 3.9694e-05 | 3.9694e-05 | 0.0 | 0.00 Modify | 0.11729 | 0.11729 | 0.11729 | 0.0 | 13.13 Other | | 0.01413 | | | 1.58 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 711 ave 711 max 711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2856 ave 2856 max 2856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2856 Ave neighs/atom = 0.714 Neighbor list builds = 320 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.842040970148, Press = 34.3492934673175 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 67 67 67 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.054 | 5.054 | 5.054 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 170.35563 170.35563 -1.0160145 -1.0160145 331.53007 331.53007 1.6679483e+08 1.6679483e+08 1.0890716 1.0890716 6000 172.08309 172.08309 -0.28800127 -0.28800127 333.46357 333.46357 8.432479e+08 8.432479e+08 0.21815177 0.21815177 Loop time of 1.15929 on 1 procs for 1000 steps with 4000 atoms Performance: 74.528 ns/day, 0.322 hours/ns, 862.597 timesteps/s, 3.450 Matom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2131 | 0.2131 | 0.2131 | 0.0 | 18.38 Neigh | 0.78783 | 0.78783 | 0.78783 | 0.0 | 67.96 Comm | 0.022561 | 0.022561 | 0.022561 | 0.0 | 1.95 Output | 5.313e-05 | 5.313e-05 | 5.313e-05 | 0.0 | 0.00 Modify | 0.11816 | 0.11816 | 0.11816 | 0.0 | 10.19 Other | | 0.01759 | | | 1.52 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 405 ave 405 max 405 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 780 ave 780 max 780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 780 Ave neighs/atom = 0.195 Neighbor list builds = 500 Dangerous builds = 0 if "${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 843247897.868761 A^3 has become larger than 178875026.769171 A^3. Aborting calculation. Total wall time: 0:00:38