# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.24417295455933*${_u_distance} variable latticeconst_converted equal 5.24417295455933*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24417295455933 Lattice spacing in x,y,z = 5.244173 5.244173 5.244173 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.44173 52.44173 52.44173) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958HighCutoff_Ar__MO_242741380554_004 pair_coeff * * Ar #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 39.948 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 144221.835764993 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*${_u_distance}) variable V0_metal equal 144221.835764993/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144221.835764993*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144221.835764993 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_242741380554_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 = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 5 5 5 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) = 24.97 | 24.97 | 24.97 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -223.54259 -223.54259 -354.39869 -354.39869 253.15 253.15 144221.84 144221.84 969.12945 969.12945 1000 26.263364 26.263364 -102.81398 -102.81398 249.70887 249.70887 418081.57 418081.57 73.24998 73.24998 Loop time of 64.9182 on 1 procs for 1000 steps with 4000 atoms Performance: 1.331 ns/day, 18.033 hours/ns, 15.404 timesteps/s, 61.616 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 | 61.811 | 61.811 | 61.811 | 0.0 | 95.21 Neigh | 2.8527 | 2.8527 | 2.8527 | 0.0 | 4.39 Comm | 0.07552 | 0.07552 | 0.07552 | 0.0 | 0.12 Output | 0.00015488 | 0.00015488 | 0.00015488 | 0.0 | 0.00 Modify | 0.15138 | 0.15138 | 0.15138 | 0.0 | 0.23 Other | | 0.02733 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12178 ave 12178 max 12178 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: 1.68761e+06 ave 1.68761e+06 max 1.68761e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1687606 Ave neighs/atom = 421.9015 Neighbor list builds = 41 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 = ${P}" flag: Temp = 252.672349751388, Press = 79.0210234902998 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 7 7 7 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 13.33 | 13.33 | 13.33 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 26.263364 26.263364 -102.81398 -102.81398 249.70887 249.70887 418081.57 418081.57 73.24998 73.24998 2000 102.71551 102.71551 -30.507252 -30.507252 257.72847 257.72847 1454253.6 1454253.6 66.817759 66.817759 Loop time of 25.0821 on 1 procs for 1000 steps with 4000 atoms Performance: 3.445 ns/day, 6.967 hours/ns, 39.869 timesteps/s, 159.477 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.027 | 23.027 | 23.027 | 0.0 | 91.81 Neigh | 1.8274 | 1.8274 | 1.8274 | 0.0 | 7.29 Comm | 0.051384 | 0.051384 | 0.051384 | 0.0 | 0.20 Output | 8.4879e-05 | 8.4879e-05 | 8.4879e-05 | 0.0 | 0.00 Modify | 0.15362 | 0.15362 | 0.15362 | 0.0 | 0.61 Other | | 0.02289 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6678 ave 6678 max 6678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 486508 ave 486508 max 486508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486508 Ave neighs/atom = 121.627 Neighbor list builds = 67 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.659822932533, Press = 79.3815546481431 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.339 | 8.339 | 8.339 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 102.71551 102.71551 -30.507252 -30.507252 257.72847 257.72847 1454253.6 1454253.6 66.817759 66.817759 3000 120.79566 120.79566 -7.6431233 -7.6431233 248.47354 248.47354 7619609.4 7619609.4 16.644162 16.644162 Loop time of 7.10019 on 1 procs for 1000 steps with 4000 atoms Performance: 12.169 ns/day, 1.972 hours/ns, 140.841 timesteps/s, 563.365 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4938 | 5.4938 | 5.4938 | 0.0 | 77.37 Neigh | 1.4095 | 1.4095 | 1.4095 | 0.0 | 19.85 Comm | 0.03467 | 0.03467 | 0.03467 | 0.0 | 0.49 Output | 5.5284e-05 | 5.5284e-05 | 5.5284e-05 | 0.0 | 0.00 Modify | 0.14393 | 0.14393 | 0.14393 | 0.0 | 2.03 Other | | 0.01824 | | | 0.26 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3347 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98570 ave 98570 max 98570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98570 Ave neighs/atom = 24.6425 Neighbor list builds = 133 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.797390032265, Press = 59.5020647033743 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 18 18 18 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.819 | 6.819 | 6.819 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 120.79566 120.79566 -7.6431233 -7.6431233 248.47354 248.47354 7619609.4 7619609.4 16.644162 16.644162 4000 129.68113 129.68113 -1.9242032 -1.9242032 254.59945 254.59945 40705420 40705420 3.3786514 3.3786514 Loop time of 2.51349 on 1 procs for 1000 steps with 4000 atoms Performance: 34.374 ns/day, 0.698 hours/ns, 397.853 timesteps/s, 1.591 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3839 | 1.3839 | 1.3839 | 0.0 | 55.06 Neigh | 0.94564 | 0.94564 | 0.94564 | 0.0 | 37.62 Comm | 0.027711 | 0.027711 | 0.027711 | 0.0 | 1.10 Output | 5.4452e-05 | 5.4452e-05 | 5.4452e-05 | 0.0 | 0.00 Modify | 0.14002 | 0.14002 | 0.14002 | 0.0 | 5.57 Other | | 0.01614 | | | 0.64 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1669 ave 1669 max 1669 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20968 ave 20968 max 20968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20968 Ave neighs/atom = 5.242 Neighbor list builds = 219 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.750628131415, Press = 43.0027743230253 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 32 32 32 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.953 | 6.953 | 6.953 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 129.68113 129.68113 -1.9242032 -1.9242032 254.59945 254.59945 40705420 40705420 3.3786514 3.3786514 5000 131.27705 131.27705 -0.47170069 -0.47170069 254.87689 254.87689 2.1090154e+08 2.1090154e+08 0.66380735 0.66380735 Loop time of 1.47258 on 1 procs for 1000 steps with 4000 atoms Performance: 58.673 ns/day, 0.409 hours/ns, 679.082 timesteps/s, 2.716 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56099 | 0.56099 | 0.56099 | 0.0 | 38.10 Neigh | 0.72756 | 0.72756 | 0.72756 | 0.0 | 49.41 Comm | 0.026823 | 0.026823 | 0.026823 | 0.0 | 1.82 Output | 5.4152e-05 | 5.4152e-05 | 5.4152e-05 | 0.0 | 0.00 Modify | 0.1393 | 0.1393 | 0.1393 | 0.0 | 9.46 Other | | 0.01785 | | | 1.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 913 ave 913 max 913 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4754 ave 4754 max 4754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4754 Ave neighs/atom = 1.1885 Neighbor list builds = 353 Dangerous builds = 0 if "${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 210901543.949458 A^3 has become larger than 144221835.764993 A^3. Aborting calculation. Total wall time: 0:01:41