# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.266347639262676*${_u_distance} variable latticeconst_converted equal 5.266347639262676*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26634763926268 Lattice spacing in x,y,z = 5.2663476 5.2663476 5.2663476 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.663476 52.663476 52.663476) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958LowCutoff_Ar__MO_720819638419_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 146059.083903987 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*${_u_distance}) variable V0_metal equal 146059.083903987/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 146059.083903987*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 146059.083903987 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_720819638419_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 = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -190.03418 -190.03418 -320.89028 -320.89028 253.15 253.15 146059.08 146059.08 956.93931 956.93931 1000 51.111081 51.111081 -80.056275 -80.056275 253.75214 253.75214 473534.11 473534.11 101.1502 101.1502 Loop time of 7.58471 on 1 procs for 1000 steps with 4000 atoms Performance: 11.391 ns/day, 2.107 hours/ns, 131.844 timesteps/s, 527.377 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 | 6.8165 | 6.8165 | 6.8165 | 0.0 | 89.87 Neigh | 0.59621 | 0.59621 | 0.59621 | 0.0 | 7.86 Comm | 0.028552 | 0.028552 | 0.028552 | 0.0 | 0.38 Output | 7.6323e-05 | 7.6323e-05 | 7.6323e-05 | 0.0 | 0.00 Modify | 0.13085 | 0.13085 | 0.13085 | 0.0 | 1.73 Other | | 0.0125 | | | 0.16 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4591 ave 4591 max 4591 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: 202758 ave 202758 max 202758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202758 Ave neighs/atom = 50.6895 Neighbor list builds = 45 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 = ${P}" flag: Temp = 252.329738494963, Press = 96.4632016334827 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 14 14 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.322 | 4.322 | 4.322 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 51.111081 51.111081 -80.056275 -80.056275 253.75214 253.75214 473534.11 473534.11 101.1502 101.1502 2000 109.22705 109.22705 -21.092291 -21.092291 252.1116 252.1116 1935981.2 1935981.2 57.245869 57.245869 Loop time of 3.16139 on 1 procs for 1000 steps with 4000 atoms Performance: 27.330 ns/day, 0.878 hours/ns, 316.316 timesteps/s, 1.265 Matom-step/s 91.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4487 | 2.4487 | 2.4487 | 0.0 | 77.46 Neigh | 0.54408 | 0.54408 | 0.54408 | 0.0 | 17.21 Comm | 0.019993 | 0.019993 | 0.019993 | 0.0 | 0.63 Output | 4.4464e-05 | 4.4464e-05 | 4.4464e-05 | 0.0 | 0.00 Modify | 0.13661 | 0.13661 | 0.13661 | 0.0 | 4.32 Other | | 0.01198 | | | 0.38 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2533 ave 2533 max 2533 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50938 ave 50938 max 50938 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50938 Ave neighs/atom = 12.7345 Neighbor list builds = 80 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.783899374143, Press = 86.3297237505334 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 23 23 23 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.602 | 3.602 | 3.602 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 109.22705 109.22705 -21.092291 -21.092291 252.1116 252.1116 1935981.2 1935981.2 57.245869 57.245869 3000 118.89927 118.89927 -5.8610446 -5.8610446 241.35729 241.35729 10346673 10346673 12.134796 12.134796 Loop time of 1.2019 on 1 procs for 1000 steps with 4000 atoms Performance: 71.886 ns/day, 0.334 hours/ns, 832.019 timesteps/s, 3.328 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69592 | 0.69592 | 0.69592 | 0.0 | 57.90 Neigh | 0.35363 | 0.35363 | 0.35363 | 0.0 | 29.42 Comm | 0.015804 | 0.015804 | 0.015804 | 0.0 | 1.31 Output | 5.9101e-05 | 5.9101e-05 | 5.9101e-05 | 0.0 | 0.00 Modify | 0.12488 | 0.12488 | 0.12488 | 0.0 | 10.39 Other | | 0.01161 | | | 0.97 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1393 ave 1393 max 1393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11200 ave 11200 max 11200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11200 Ave neighs/atom = 2.8 Neighbor list builds = 145 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.867026902411, Press = 59.6167425208129 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 39 39 39 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.834 | 3.834 | 3.834 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 118.89927 118.89927 -5.8610446 -5.8610446 241.35729 241.35729 10346673 10346673 12.134796 12.134796 4000 128.25379 128.25379 -1.4242695 -1.4242695 250.871 250.871 54699574 54699574 2.4994864 2.4994864 Loop time of 0.965172 on 1 procs for 1000 steps with 4000 atoms Performance: 89.518 ns/day, 0.268 hours/ns, 1036.085 timesteps/s, 4.144 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.394 | 0.394 | 0.394 | 0.0 | 40.82 Neigh | 0.39292 | 0.39292 | 0.39292 | 0.0 | 40.71 Comm | 0.0171 | 0.0171 | 0.0171 | 0.0 | 1.77 Output | 5.0174e-05 | 5.0174e-05 | 5.0174e-05 | 0.0 | 0.01 Modify | 0.14635 | 0.14635 | 0.14635 | 0.0 | 15.16 Other | | 0.01476 | | | 1.53 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 717 ave 717 max 717 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2856 ave 2856 max 2856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2856 Ave neighs/atom = 0.714 Neighbor list builds = 239 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.882849271634, Press = 42.4096309694417 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 68 68 68 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 128.25379 128.25379 -1.4242695 -1.4242695 250.871 250.871 54699574 54699574 2.4994864 2.4994864 5000 131.1354 131.1354 -0.29412824 -0.29412824 254.25934 254.25934 2.7922363e+08 2.7922363e+08 0.49996266 0.49996266 Loop time of 1.17169 on 1 procs for 1000 steps with 4000 atoms Performance: 73.740 ns/day, 0.325 hours/ns, 853.467 timesteps/s, 3.414 Matom-step/s 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24723 | 0.24723 | 0.24723 | 0.0 | 21.10 Neigh | 0.74917 | 0.74917 | 0.74917 | 0.0 | 63.94 Comm | 0.018657 | 0.018657 | 0.018657 | 0.0 | 1.59 Output | 3.5005e-05 | 3.5005e-05 | 3.5005e-05 | 0.0 | 0.00 Modify | 0.13952 | 0.13952 | 0.13952 | 0.0 | 11.91 Other | | 0.01708 | | | 1.46 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 389 ave 389 max 389 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 728 ave 728 max 728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 728 Ave neighs/atom = 0.182 Neighbor list builds = 387 Dangerous builds = 0 if "${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 279223627.180147 A^3 has become larger than 146059083.903987 A^3. Aborting calculation. Total wall time: 0:00:14