# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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 -169.35773 -169.35773 -320.89028 -320.89028 293.15 293.15 146059.08 146059.08 1108.1444 1108.1444 1000 89.149801 89.149801 -63.124894 -63.124894 294.58572 294.58572 584741.64 584741.64 145.93257 145.93257 Loop time of 7.00856 on 1 procs for 1000 steps with 4000 atoms Performance: 12.328 ns/day, 1.947 hours/ns, 142.683 timesteps/s, 570.730 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 | 6.1713 | 6.1713 | 6.1713 | 0.0 | 88.05 Neigh | 0.6653 | 0.6653 | 0.6653 | 0.0 | 9.49 Comm | 0.029085 | 0.029085 | 0.029085 | 0.0 | 0.41 Output | 0.00011957 | 0.00011957 | 0.00011957 | 0.0 | 0.00 Modify | 0.12752 | 0.12752 | 0.12752 | 0.0 | 1.82 Other | | 0.0152 | | | 0.22 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4176 ave 4176 max 4176 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: 162776 ave 162776 max 162776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162776 Ave neighs/atom = 40.694 Neighbor list builds = 55 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 = ${P}" flag: Temp = 293.026210200812, Press = 146.886296567353 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.942 | 3.942 | 3.942 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 89.149801 89.149801 -63.124894 -63.124894 294.58572 294.58572 584741.64 584741.64 145.93257 145.93257 2000 136.44798 136.44798 -14.596189 -14.596189 292.20519 292.20519 2777633.5 2777633.5 51.713033 51.713033 Loop time of 2.46981 on 1 procs for 1000 steps with 4000 atoms Performance: 34.982 ns/day, 0.686 hours/ns, 404.889 timesteps/s, 1.620 Matom-step/s 92.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7719 | 1.7719 | 1.7719 | 0.0 | 71.74 Neigh | 0.5335 | 0.5335 | 0.5335 | 0.0 | 21.60 Comm | 0.018653 | 0.018653 | 0.018653 | 0.0 | 0.76 Output | 6.2858e-05 | 6.2858e-05 | 6.2858e-05 | 0.0 | 0.00 Modify | 0.13357 | 0.13357 | 0.13357 | 0.0 | 5.41 Other | | 0.01214 | | | 0.49 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2220 ave 2220 max 2220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36248 ave 36248 max 36248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36248 Ave neighs/atom = 9.062 Neighbor list builds = 96 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.776164940212, Press = 102.314788959287 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 26 26 26 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.629 | 3.629 | 3.629 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 136.44798 136.44798 -14.596189 -14.596189 292.20519 292.20519 2777633.5 2777633.5 51.713033 51.713033 3000 145.53378 145.53378 -3.8985118 -3.8985118 289.0869 289.0869 14901401 14901401 10.354803 10.354803 Loop time of 1.12079 on 1 procs for 1000 steps with 4000 atoms Performance: 77.089 ns/day, 0.311 hours/ns, 892.231 timesteps/s, 3.569 Matom-step/s 89.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61555 | 0.61555 | 0.61555 | 0.0 | 54.92 Neigh | 0.3471 | 0.3471 | 0.3471 | 0.0 | 30.97 Comm | 0.014773 | 0.014773 | 0.014773 | 0.0 | 1.32 Output | 4.7338e-05 | 4.7338e-05 | 4.7338e-05 | 0.0 | 0.00 Modify | 0.13137 | 0.13137 | 0.13137 | 0.0 | 11.72 Other | | 0.01195 | | | 1.07 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1195 ave 1195 max 1195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7764 ave 7764 max 7764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7764 Ave neighs/atom = 1.941 Neighbor list builds = 165 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.811253991086, Press = 65.9441819743048 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 44 44 44 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.956 | 3.956 | 3.956 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 145.53378 145.53378 -3.8985118 -3.8985118 289.0869 289.0869 14901401 14901401 10.354803 10.354803 4000 148.51668 148.51668 -0.94803813 -0.94803813 289.14963 289.14963 77766646 77766646 2.0347766 2.0347766 Loop time of 0.780838 on 1 procs for 1000 steps with 4000 atoms Performance: 110.650 ns/day, 0.217 hours/ns, 1280.676 timesteps/s, 5.123 Matom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28034 | 0.28034 | 0.28034 | 0.0 | 35.90 Neigh | 0.35434 | 0.35434 | 0.35434 | 0.0 | 45.38 Comm | 0.015547 | 0.015547 | 0.015547 | 0.0 | 1.99 Output | 4.5977e-05 | 4.5977e-05 | 4.5977e-05 | 0.0 | 0.01 Modify | 0.11751 | 0.11751 | 0.11751 | 0.0 | 15.05 Other | | 0.01306 | | | 1.67 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 645 ave 645 max 645 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1948 ave 1948 max 1948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1948 Ave neighs/atom = 0.487 Neighbor list builds = 269 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 292.855522958773, Press = 46.340091900754 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.23 ghost atom cutoff = 11.23 binsize = 5.615, bins = 77 77 77 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.607 | 5.607 | 5.607 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 148.51668 148.51668 -0.94803813 -0.94803813 289.14963 289.14963 77766646 77766646 2.0347766 2.0347766 5000 153.6734 153.6734 -0.25678449 -0.25678449 297.78838 297.78838 3.8974455e+08 3.8974455e+08 0.42079687 0.42079687 Loop time of 1.23279 on 1 procs for 1000 steps with 4000 atoms Performance: 70.085 ns/day, 0.342 hours/ns, 811.169 timesteps/s, 3.245 Matom-step/s 94.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19681 | 0.19681 | 0.19681 | 0.0 | 15.96 Neigh | 0.87923 | 0.87923 | 0.87923 | 0.0 | 71.32 Comm | 0.021074 | 0.021074 | 0.021074 | 0.0 | 1.71 Output | 6.5613e-05 | 6.5613e-05 | 6.5613e-05 | 0.0 | 0.01 Modify | 0.11927 | 0.11927 | 0.11927 | 0.0 | 9.67 Other | | 0.01634 | | | 1.33 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 380 ave 380 max 380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 468 ave 468 max 468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 468 Ave neighs/atom = 0.117 Neighbor list builds = 422 Dangerous builds = 0 if "${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 389744550.243973 A^3 has become larger than 146059083.903987 A^3. Aborting calculation. Total wall time: 0:00:12