# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.248509056866169*${_u_distance} variable latticeconst_converted equal 5.248509056866169*1 lattice fcc ${latticeconst_converted} lattice fcc 5.24850905686617 Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.485091 52.485091 52.485091) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_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 144579.877647162 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*${_u_distance}) variable V0_metal equal 144579.877647162/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144579.877647162*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144579.877647162 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_126566794224_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 = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, 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) = 10.2 | 10.2 | 10.2 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -173.81303 -173.81303 -346.02203 -346.02203 333.15 333.15 144579.88 144579.88 1272.2349 1272.2349 1000 111.59714 111.59714 -62.48462 -62.48462 336.77297 336.77297 637722.39 637722.39 175.01601 175.01601 Loop time of 17.6478 on 1 procs for 1000 steps with 4000 atoms Performance: 4.896 ns/day, 4.902 hours/ns, 56.664 timesteps/s, 226.657 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 | 16.136 | 16.136 | 16.136 | 0.0 | 91.43 Neigh | 1.3308 | 1.3308 | 1.3308 | 0.0 | 7.54 Comm | 0.039529 | 0.039529 | 0.039529 | 0.0 | 0.22 Output | 0.00011004 | 0.00011004 | 0.00011004 | 0.0 | 0.00 Modify | 0.12659 | 0.12659 | 0.12659 | 0.0 | 0.72 Other | | 0.015 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6058 ave 6058 max 6058 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: 389110 ave 389110 max 389110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389110 Ave neighs/atom = 97.2775 Neighbor list builds = 60 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 = ${P}" flag: Temp = 333.226355057581, Press = 179.077948723544 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.834 | 4.834 | 4.834 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 111.59714 111.59714 -62.48462 -62.48462 336.77297 336.77297 637722.39 637722.39 175.01601 175.01601 2000 159.63482 159.63482 -13.618935 -13.618935 335.17113 335.17113 3148563.3 3148563.3 54.01311 54.01311 Loop time of 5.43283 on 1 procs for 1000 steps with 4000 atoms Performance: 15.903 ns/day, 1.509 hours/ns, 184.066 timesteps/s, 736.264 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3083 | 4.3083 | 4.3083 | 0.0 | 79.30 Neigh | 0.9408 | 0.9408 | 0.9408 | 0.0 | 17.32 Comm | 0.027732 | 0.027732 | 0.027732 | 0.0 | 0.51 Output | 6.7215e-05 | 6.7215e-05 | 6.7215e-05 | 0.0 | 0.00 Modify | 0.14215 | 0.14215 | 0.14215 | 0.0 | 2.62 Other | | 0.01378 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3071 ave 3071 max 3071 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82784 ave 82784 max 82784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82784 Ave neighs/atom = 20.696 Neighbor list builds = 102 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.527820465546, Press = 115.00241845561 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 19 19 19 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.7 | 3.7 | 3.7 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 159.63482 159.63482 -13.618935 -13.618935 335.17113 335.17113 3148563.3 3148563.3 54.01311 54.01311 3000 167.75343 167.75343 -3.5101077 -3.5101077 331.32093 331.32093 16844734 16844734 10.580235 10.580235 Loop time of 1.65375 on 1 procs for 1000 steps with 4000 atoms Performance: 52.245 ns/day, 0.459 hours/ns, 604.685 timesteps/s, 2.419 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96662 | 0.96662 | 0.96662 | 0.0 | 58.45 Neigh | 0.5384 | 0.5384 | 0.5384 | 0.0 | 32.56 Comm | 0.01861 | 0.01861 | 0.01861 | 0.0 | 1.13 Output | 4.5947e-05 | 4.5947e-05 | 4.5947e-05 | 0.0 | 0.00 Modify | 0.11828 | 0.11828 | 0.11828 | 0.0 | 7.15 Other | | 0.0118 | | | 0.71 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1618 ave 1618 max 1618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 16726 ave 16726 max 16726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 16726 Ave neighs/atom = 4.1815 Neighbor list builds = 172 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.464067685588, Press = 72.8584408399681 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 34 34 34 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.863 | 3.863 | 3.863 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 167.75343 167.75343 -3.5101077 -3.5101077 331.32093 331.32093 16844734 16844734 10.580235 10.580235 4000 170.48019 170.48019 -0.8009025 -0.8009025 331.35489 331.35489 86822995 86822995 2.0905953 2.0905953 Loop time of 1.02944 on 1 procs for 1000 steps with 4000 atoms Performance: 83.929 ns/day, 0.286 hours/ns, 971.403 timesteps/s, 3.886 Matom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41709 | 0.41709 | 0.41709 | 0.0 | 40.52 Neigh | 0.44478 | 0.44478 | 0.44478 | 0.0 | 43.21 Comm | 0.019581 | 0.019581 | 0.019581 | 0.0 | 1.90 Output | 4.8702e-05 | 4.8702e-05 | 4.8702e-05 | 0.0 | 0.00 Modify | 0.13173 | 0.13173 | 0.13173 | 0.0 | 12.80 Other | | 0.01621 | | | 1.57 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 883 ave 883 max 883 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3708 ave 3708 max 3708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3708 Ave neighs/atom = 0.927 Neighbor list builds = 276 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.097320980553, Press = 51.03855794287 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 15.5 ghost atom cutoff = 15.5 binsize = 7.75, bins = 58 58 58 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.585 | 4.585 | 4.585 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 170.48019 170.48019 -0.8009025 -0.8009025 331.35489 331.35489 86822995 86822995 2.0905953 2.0905953 5000 171.1426 171.1426 -0.1562768 -0.1562768 331.38929 331.38929 4.3174967e+08 4.3174967e+08 0.42285023 0.42285023 Loop time of 1.00234 on 1 procs for 1000 steps with 4000 atoms Performance: 86.198 ns/day, 0.278 hours/ns, 997.660 timesteps/s, 3.991 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23627 | 0.23627 | 0.23627 | 0.0 | 23.57 Neigh | 0.60736 | 0.60736 | 0.60736 | 0.0 | 60.59 Comm | 0.021615 | 0.021615 | 0.021615 | 0.0 | 2.16 Output | 4.2399e-05 | 4.2399e-05 | 4.2399e-05 | 0.0 | 0.00 Modify | 0.12132 | 0.12132 | 0.12132 | 0.0 | 12.10 Other | | 0.01574 | | | 1.57 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 531 ave 531 max 531 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 910 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 910 Ave neighs/atom = 0.2275 Neighbor list builds = 431 Dangerous builds = 0 if "${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 431749665.135684 A^3 has become larger than 144579877.647162 A^3. Aborting calculation. Total wall time: 0:00:27