# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_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_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 -303.95589 -303.95589 -465.82667 -465.82667 313.15 313.15 178875.03 178875.03 966.57946 966.57946 1000 -15.433311 -15.433311 -174.09198 -174.09198 306.93596 306.93596 408555.41 408555.41 30.435041 30.435041 Loop time of 22.1206 on 1 procs for 1000 steps with 4000 atoms Performance: 3.906 ns/day, 6.145 hours/ns, 45.207 timesteps/s, 180.827 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 | 20.992 | 20.992 | 20.992 | 0.0 | 94.90 Neigh | 0.92919 | 0.92919 | 0.92919 | 0.0 | 4.20 Comm | 0.046133 | 0.046133 | 0.046133 | 0.0 | 0.21 Output | 0.00019722 | 0.00019722 | 0.00019722 | 0.0 | 0.00 Modify | 0.13346 | 0.13346 | 0.13346 | 0.0 | 0.60 Other | | 0.01997 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8122 ave 8122 max 8122 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: 744732 ave 744732 max 744732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 744732 Ave neighs/atom = 186.183 Neighbor list builds = 32 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 = ${P}" flag: Temp = 313.54579834676, Press = 36.7060344297284 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.366 | 6.366 | 6.366 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -15.433311 -15.433311 -174.09198 -174.09198 306.93596 306.93596 408555.41 408555.41 30.435041 30.435041 2000 83.202017 83.202017 -78.225742 -78.225742 312.29295 312.29295 889777.86 889777.86 59.428735 59.428735 Loop time of 10.6498 on 1 procs for 1000 steps with 4000 atoms Performance: 8.113 ns/day, 2.958 hours/ns, 93.899 timesteps/s, 375.596 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8845 | 9.8845 | 9.8845 | 0.0 | 92.81 Neigh | 0.57937 | 0.57937 | 0.57937 | 0.0 | 5.44 Comm | 0.031347 | 0.031347 | 0.031347 | 0.0 | 0.29 Output | 5.7919e-05 | 5.7919e-05 | 5.7919e-05 | 0.0 | 0.00 Modify | 0.13781 | 0.13781 | 0.13781 | 0.0 | 1.29 Other | | 0.01671 | | | 0.16 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5719 ave 5719 max 5719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338348 ave 338348 max 338348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338348 Ave neighs/atom = 84.587 Neighbor list builds = 40 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.794274203517, Press = 44.8656243049433 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.831 | 4.831 | 4.831 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 83.202017 83.202017 -78.225742 -78.225742 312.29295 312.29295 889777.86 889777.86 59.428735 59.428735 3000 143.54703 143.54703 -18.549974 -18.549974 313.58765 313.58765 3915384.6 3915384.6 36.228707 36.228707 Loop time of 4.94546 on 1 procs for 1000 steps with 4000 atoms Performance: 17.471 ns/day, 1.374 hours/ns, 202.206 timesteps/s, 808.822 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.929 | 3.929 | 3.929 | 0.0 | 79.45 Neigh | 0.83869 | 0.83869 | 0.83869 | 0.0 | 16.96 Comm | 0.026721 | 0.026721 | 0.026721 | 0.0 | 0.54 Output | 4.7078e-05 | 4.7078e-05 | 4.7078e-05 | 0.0 | 0.00 Modify | 0.1364 | 0.1364 | 0.1364 | 0.0 | 2.76 Other | | 0.01458 | | | 0.29 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3088 ave 3088 max 3088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80612 ave 80612 max 80612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80612 Ave neighs/atom = 20.153 Neighbor list builds = 100 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.960291433638, Press = 49.8806633017906 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 20 20 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 143.54703 143.54703 -18.549974 -18.549974 313.58765 313.58765 3915384.6 3915384.6 36.228707 36.228707 4000 157.01303 157.01303 -4.9624162 -4.9624162 313.35247 313.35247 21546666 21546666 7.6857922 7.6857922 Loop time of 1.81263 on 1 procs for 1000 steps with 4000 atoms Performance: 47.666 ns/day, 0.504 hours/ns, 551.685 timesteps/s, 2.207 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0339 | 1.0339 | 1.0339 | 0.0 | 57.04 Neigh | 0.61697 | 0.61697 | 0.61697 | 0.0 | 34.04 Comm | 0.020501 | 0.020501 | 0.020501 | 0.0 | 1.13 Output | 6.2487e-05 | 6.2487e-05 | 6.2487e-05 | 0.0 | 0.00 Modify | 0.12799 | 0.12799 | 0.12799 | 0.0 | 7.06 Other | | 0.01322 | | | 0.73 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1579 ave 1579 max 1579 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16302 ave 16302 max 16302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16302 Ave neighs/atom = 4.0755 Neighbor list builds = 185 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.986276211705, Press = 39.8075112888756 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 34 34 34 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.863 | 3.863 | 3.863 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 157.01303 157.01303 -4.9624162 -4.9624162 313.35247 313.35247 21546666 21546666 7.6857922 7.6857922 5000 159.97497 159.97497 -1.5341798 -1.5341798 312.4504 312.4504 1.152232e+08 1.152232e+08 1.477396 1.477396 Loop time of 0.948967 on 1 procs for 1000 steps with 4000 atoms Performance: 91.046 ns/day, 0.264 hours/ns, 1053.777 timesteps/s, 4.215 Matom-step/s 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37809 | 0.37809 | 0.37809 | 0.0 | 39.84 Neigh | 0.42136 | 0.42136 | 0.42136 | 0.0 | 44.40 Comm | 0.017861 | 0.017861 | 0.017861 | 0.0 | 1.88 Output | 9.9006e-05 | 9.9006e-05 | 9.9006e-05 | 0.0 | 0.01 Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 12.43 Other | | 0.01362 | | | 1.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 827 ave 827 max 827 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3864 ave 3864 max 3864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3864 Ave neighs/atom = 0.966 Neighbor list builds = 297 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.920670786345, Press = 31.0127806014377 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16.5 ghost atom cutoff = 16.5 binsize = 8.25, bins = 59 59 59 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.631 | 4.631 | 4.631 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 159.97497 159.97497 -1.5341798 -1.5341798 312.4504 312.4504 1.152232e+08 1.152232e+08 1.477396 1.477396 6000 158.97275 158.97275 -0.32679017 -0.32679017 308.17576 308.17576 5.884369e+08 5.884369e+08 0.28808526 0.28808526 Loop time of 1.33981 on 1 procs for 1000 steps with 4000 atoms Performance: 64.487 ns/day, 0.372 hours/ns, 746.373 timesteps/s, 2.985 Matom-step/s 86.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28672 | 0.28672 | 0.28672 | 0.0 | 21.40 Neigh | 0.84485 | 0.84485 | 0.84485 | 0.0 | 63.06 Comm | 0.024036 | 0.024036 | 0.024036 | 0.0 | 1.79 Output | 5.0575e-05 | 5.0575e-05 | 5.0575e-05 | 0.0 | 0.00 Modify | 0.16549 | 0.16549 | 0.16549 | 0.0 | 12.35 Other | | 0.01868 | | | 1.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 454 ave 454 max 454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1052 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1052 Ave neighs/atom = 0.263 Neighbor list builds = 464 Dangerous builds = 0 if "${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 588436898.227876 A^3 has become larger than 178875026.769171 A^3. Aborting calculation. Total wall time: 0:00:42