# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.653579071164131*${_u_distance} variable latticeconst_converted equal 5.653579071164131*1 lattice fcc ${latticeconst_converted} lattice fcc 5.65357907116413 Lattice spacing in x,y,z = 5.6535791 5.6535791 5.6535791 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (56.535791 56.535791 56.535791) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (56.535791 56.535791 56.535791) create_atoms CPU = 0.001 seconds variable mass_converted equal 83.798*${_u_mass} variable mass_converted equal 83.798*1 kim interactions Kr #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Kr__MO_995724792024_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 180705.100868827 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 180705.100868827/(1*1*${_u_distance}) variable V0_metal equal 180705.100868827/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 180705.100868827*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 180705.100868827 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_995724792024_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 = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, 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) = 5.481 | 5.481 | 5.481 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -259.77786 -259.77786 -431.98687 -431.98687 333.15 333.15 180705.1 180705.1 1017.8986 1017.8986 1000 37.761367 37.761367 -134.62894 -134.62894 333.50074 333.50074 478923 478923 64.823088 64.823088 Loop time of 7.37265 on 1 procs for 1000 steps with 4000 atoms Performance: 11.719 ns/day, 2.048 hours/ns, 135.637 timesteps/s, 542.546 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6989 | 6.6989 | 6.6989 | 0.0 | 90.86 Neigh | 0.49653 | 0.49653 | 0.49653 | 0.0 | 6.73 Comm | 0.028543 | 0.028543 | 0.028543 | 0.0 | 0.39 Output | 8.5551e-05 | 8.5551e-05 | 8.5551e-05 | 0.0 | 0.00 Modify | 0.13492 | 0.13492 | 0.13492 | 0.0 | 1.83 Other | | 0.0137 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4902 ave 4902 max 4902 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: 237668 ave 237668 max 237668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237668 Ave neighs/atom = 59.417 Neighbor list builds = 38 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 = ${P}" flag: Temp = 334.35237827353, Press = 67.8922461555361 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.325 | 4.325 | 4.325 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 37.761367 37.761367 -134.62894 -134.62894 333.50074 333.50074 478923 478923 64.823088 64.823088 2000 133.18999 133.18999 -40.902041 -40.902041 336.79283 336.79283 1480950.3 1480950.3 75.808781 75.808781 Loop time of 3.65605 on 1 procs for 1000 steps with 4000 atoms Performance: 23.632 ns/day, 1.016 hours/ns, 273.519 timesteps/s, 1.094 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0187 | 3.0187 | 3.0187 | 0.0 | 82.57 Neigh | 0.46559 | 0.46559 | 0.46559 | 0.0 | 12.73 Comm | 0.021847 | 0.021847 | 0.021847 | 0.0 | 0.60 Output | 4.5996e-05 | 4.5996e-05 | 4.5996e-05 | 0.0 | 0.00 Modify | 0.13723 | 0.13723 | 0.13723 | 0.0 | 3.75 Other | | 0.01263 | | | 0.35 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3039 ave 3039 max 3039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77538 ave 77538 max 77538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77538 Ave neighs/atom = 19.3845 Neighbor list builds = 62 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.845354560084, Press = 75.2869635713783 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 20 20 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.581 | 3.581 | 3.581 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 133.18999 133.18999 -40.902041 -40.902041 336.79283 336.79283 1480950.3 1480950.3 75.808781 75.808781 3000 162.94691 162.94691 -9.6312932 -9.6312932 333.86424 333.86424 7699344.8 7699344.8 21.951778 21.951778 Loop time of 1.67076 on 1 procs for 1000 steps with 4000 atoms Performance: 51.713 ns/day, 0.464 hours/ns, 598.529 timesteps/s, 2.394 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0304 | 1.0304 | 1.0304 | 0.0 | 61.67 Neigh | 0.47435 | 0.47435 | 0.47435 | 0.0 | 28.39 Comm | 0.018722 | 0.018722 | 0.018722 | 0.0 | 1.12 Output | 4.5285e-05 | 4.5285e-05 | 4.5285e-05 | 0.0 | 0.00 Modify | 0.13433 | 0.13433 | 0.13433 | 0.0 | 8.04 Other | | 0.01289 | | | 0.77 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1634 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16182 ave 16182 max 16182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16182 Ave neighs/atom = 4.0455 Neighbor list builds = 135 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.708955763248, Press = 61.4093184852388 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 34 34 34 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.737 | 3.737 | 3.737 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 162.94691 162.94691 -9.6312932 -9.6312932 333.86424 333.86424 7699344.8 7699344.8 21.951778 21.951778 4000 169.4166 169.4166 -2.8557947 -2.8557947 333.27263 333.27263 41867348 41867348 4.2880345 4.2880345 Loop time of 0.984916 on 1 procs for 1000 steps with 4000 atoms Performance: 87.723 ns/day, 0.274 hours/ns, 1015.315 timesteps/s, 4.061 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45336 | 0.45336 | 0.45336 | 0.0 | 46.03 Neigh | 0.36584 | 0.36584 | 0.36584 | 0.0 | 37.14 Comm | 0.017256 | 0.017256 | 0.017256 | 0.0 | 1.75 Output | 3.6298e-05 | 3.6298e-05 | 3.6298e-05 | 0.0 | 0.00 Modify | 0.1343 | 0.1343 | 0.1343 | 0.0 | 13.64 Other | | 0.01413 | | | 1.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 855 ave 855 max 855 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3818 ave 3818 max 3818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3818 Ave neighs/atom = 0.9545 Neighbor list builds = 222 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.765285096046, Press = 45.0813652457178 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.91 ghost atom cutoff = 11.91 binsize = 5.955, bins = 59 59 59 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.505 | 4.505 | 4.505 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 169.4166 169.4166 -2.8557947 -2.8557947 333.27263 333.27263 41867348 41867348 4.2880345 4.2880345 5000 174.04587 174.04587 -0.81971206 -0.81971206 338.28933 338.28933 2.1811418e+08 2.1811418e+08 0.85141188 0.85141188 Loop time of 1.06147 on 1 procs for 1000 steps with 4000 atoms Performance: 81.396 ns/day, 0.295 hours/ns, 942.086 timesteps/s, 3.768 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31554 | 0.31554 | 0.31554 | 0.0 | 29.73 Neigh | 0.57389 | 0.57389 | 0.57389 | 0.0 | 54.06 Comm | 0.020527 | 0.020527 | 0.020527 | 0.0 | 1.93 Output | 4.1778e-05 | 4.1778e-05 | 4.1778e-05 | 0.0 | 0.00 Modify | 0.13456 | 0.13456 | 0.13456 | 0.0 | 12.68 Other | | 0.01693 | | | 1.59 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 480 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 990 ave 990 max 990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 990 Ave neighs/atom = 0.2475 Neighbor list builds = 364 Dangerous builds = 0 if "${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 218114180.167995 A^3 has become larger than 180705100.868827 A^3. Aborting calculation. Total wall time: 0:00:14