# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_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_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 -213.20436 -213.20436 -354.39869 -354.39869 273.15 273.15 144221.84 144221.84 1045.6951 1045.6951 1000 49.769698 49.769698 -90.779509 -90.779509 271.90197 271.90197 469055.58 469055.58 100.29702 100.29702 Loop time of 61.2644 on 1 procs for 1000 steps with 4000 atoms Performance: 1.410 ns/day, 17.018 hours/ns, 16.323 timesteps/s, 65.291 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 | 57.953 | 57.953 | 57.953 | 0.0 | 94.59 Neigh | 3.0554 | 3.0554 | 3.0554 | 0.0 | 4.99 Comm | 0.075439 | 0.075439 | 0.075439 | 0.0 | 0.12 Output | 0.00014605 | 0.00014605 | 0.00014605 | 0.0 | 0.00 Modify | 0.15396 | 0.15396 | 0.15396 | 0.0 | 0.25 Other | | 0.02684 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11514 ave 11514 max 11514 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: 1.5077e+06 ave 1.5077e+06 max 1.5077e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1507704 Ave neighs/atom = 376.926 Neighbor list builds = 46 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 = ${P}" flag: Temp = 273.277471306567, Press = 106.131069781463 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 12.56 | 12.56 | 12.56 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 49.769698 49.769698 -90.779509 -90.779509 271.90197 271.90197 469055.58 469055.58 100.29702 100.29702 2000 116.96277 116.96277 -23.402985 -23.402985 271.54707 271.54707 1904022.2 1904022.2 61.822489 61.822489 Loop time of 20.9784 on 1 procs for 1000 steps with 4000 atoms Performance: 4.119 ns/day, 5.827 hours/ns, 47.668 timesteps/s, 190.672 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.893 | 18.893 | 18.893 | 0.0 | 90.06 Neigh | 1.8548 | 1.8548 | 1.8548 | 0.0 | 8.84 Comm | 0.049995 | 0.049995 | 0.049995 | 0.0 | 0.24 Output | 8.4399e-05 | 8.4399e-05 | 8.4399e-05 | 0.0 | 0.00 Modify | 0.1583 | 0.1583 | 0.1583 | 0.0 | 0.75 Other | | 0.02232 | | | 0.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5973 ave 5973 max 5973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 372504 ave 372504 max 372504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372504 Ave neighs/atom = 93.126 Neighbor list builds = 79 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.655469351195, Press = 93.9449119387984 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.956 | 7.956 | 7.956 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 116.96277 116.96277 -23.402985 -23.402985 271.54707 271.54707 1904022.2 1904022.2 61.822489 61.822489 3000 134.45254 134.45254 -6.0301894 -6.0301894 271.77336 271.77336 10162956 10162956 13.943362 13.943362 Loop time of 5.71741 on 1 procs for 1000 steps with 4000 atoms Performance: 15.112 ns/day, 1.588 hours/ns, 174.904 timesteps/s, 699.617 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1881 | 4.1881 | 4.1881 | 0.0 | 73.25 Neigh | 1.3356 | 1.3356 | 1.3356 | 0.0 | 23.36 Comm | 0.032829 | 0.032829 | 0.032829 | 0.0 | 0.57 Output | 4.9433e-05 | 4.9433e-05 | 4.9433e-05 | 0.0 | 0.00 Modify | 0.14356 | 0.14356 | 0.14356 | 0.0 | 2.51 Other | | 0.01723 | | | 0.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2917 ave 2917 max 2917 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74662 ave 74662 max 74662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74662 Ave neighs/atom = 18.6655 Neighbor list builds = 147 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.670583492134, Press = 64.9759841651729 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 20 20 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.829 | 6.829 | 6.829 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 134.45254 134.45254 -6.0301894 -6.0301894 271.77336 271.77336 10162956 10162956 13.943362 13.943362 4000 136.44067 136.44067 -1.5021773 -1.5021773 266.85979 266.85979 53785564 53785564 2.7025765 2.7025765 Loop time of 2.1718 on 1 procs for 1000 steps with 4000 atoms Performance: 39.783 ns/day, 0.603 hours/ns, 460.447 timesteps/s, 1.842 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1226 | 1.1226 | 1.1226 | 0.0 | 51.69 Neigh | 0.87008 | 0.87008 | 0.87008 | 0.0 | 40.06 Comm | 0.02726 | 0.02726 | 0.02726 | 0.0 | 1.26 Output | 4.3882e-05 | 4.3882e-05 | 4.3882e-05 | 0.0 | 0.00 Modify | 0.13628 | 0.13628 | 0.13628 | 0.0 | 6.27 Other | | 0.01549 | | | 0.71 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1590 ave 1590 max 1590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15968 ave 15968 max 15968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15968 Ave neighs/atom = 3.992 Neighbor list builds = 242 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.661869581735, Press = 46.2408144165655 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21.9 ghost atom cutoff = 21.9 binsize = 10.95, bins = 35 35 35 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 7.003 | 7.003 | 7.003 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 136.44067 136.44067 -1.5021773 -1.5021773 266.85979 266.85979 53785564 53785564 2.7025765 2.7025765 5000 140.48721 140.48721 -0.32279189 -0.32279189 272.4065 272.4065 2.7459463e+08 2.7459463e+08 0.54629149 0.54629149 Loop time of 1.39835 on 1 procs for 1000 steps with 4000 atoms Performance: 61.787 ns/day, 0.388 hours/ns, 715.130 timesteps/s, 2.861 Matom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49637 | 0.49637 | 0.49637 | 0.0 | 35.50 Neigh | 0.71907 | 0.71907 | 0.71907 | 0.0 | 51.42 Comm | 0.027918 | 0.027918 | 0.027918 | 0.0 | 2.00 Output | 4.4303e-05 | 4.4303e-05 | 4.4303e-05 | 0.0 | 0.00 Modify | 0.13676 | 0.13676 | 0.13676 | 0.0 | 9.78 Other | | 0.01818 | | | 1.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 811 ave 811 max 811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3802 ave 3802 max 3802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3802 Ave neighs/atom = 0.9505 Neighbor list builds = 390 Dangerous builds = 0 if "${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 274594630.064448 A^3 has become larger than 144221835.764993 A^3. Aborting calculation. Total wall time: 0:01:31