# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.252865672111511*${_u_distance} variable latticeconst_converted equal 5.252865672111511*1 lattice fcc ${latticeconst_converted} lattice fcc 5.25286567211151 Lattice spacing in x,y,z = 5.2528657 5.2528657 5.2528657 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.528657 52.528657 52.528657) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_QuinticSmoothed_Jelinek_1972_Ar__MO_908645784389_002 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) 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 144940.209626461 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*${_u_distance}) variable V0_metal equal 144940.209626461/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 144940.209626461*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 144940.209626461 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_908645784389_002#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 = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -233.43585 -233.43585 -374.63018 -374.63018 273.15 273.15 144940.21 144940.21 1040.513 1040.513 1000 38.57382 38.57382 -102.66665 -102.66665 273.23926 273.23926 415860.32 415860.32 97.017991 97.017991 Loop time of 4.69411 on 1 procs for 1000 steps with 4000 atoms Performance: 18.406 ns/day, 1.304 hours/ns, 213.033 timesteps/s, 852.132 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 | 4.0863 | 4.0863 | 4.0863 | 0.0 | 87.05 Neigh | 0.45176 | 0.45176 | 0.45176 | 0.0 | 9.62 Comm | 0.023352 | 0.023352 | 0.023352 | 0.0 | 0.50 Output | 0.00010027 | 0.00010027 | 0.00010027 | 0.0 | 0.00 Modify | 0.12101 | 0.12101 | 0.12101 | 0.0 | 2.58 Other | | 0.01162 | | | 0.25 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4209 ave 4209 max 4209 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: 167676 ave 167676 max 167676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167676 Ave neighs/atom = 41.919 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 = ${P}" flag: Temp = 272.322407187627, Press = 92.0630239725585 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.846 | 3.846 | 3.846 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 38.57382 38.57382 -102.66665 -102.66665 273.23926 273.23926 415860.32 415860.32 97.017991 97.017991 2000 106.95051 106.95051 -33.004661 -33.004661 270.75277 270.75277 1496433.8 1496433.8 66.317087 66.317087 Loop time of 2.11516 on 1 procs for 1000 steps with 4000 atoms Performance: 40.848 ns/day, 0.588 hours/ns, 472.777 timesteps/s, 1.891 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5491 | 1.5491 | 1.5491 | 0.0 | 73.24 Neigh | 0.41231 | 0.41231 | 0.41231 | 0.0 | 19.49 Comm | 0.018326 | 0.018326 | 0.018326 | 0.0 | 0.87 Output | 7.2986e-05 | 7.2986e-05 | 7.2986e-05 | 0.0 | 0.00 Modify | 0.12452 | 0.12452 | 0.12452 | 0.0 | 5.89 Other | | 0.01085 | | | 0.51 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2513 ave 2513 max 2513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49950 ave 49950 max 49950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49950 Ave neighs/atom = 12.4875 Neighbor list builds = 69 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.779565995723, Press = 88.779432631696 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 23 23 23 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.505 | 3.505 | 3.505 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 106.95051 106.95051 -33.004661 -33.004661 270.75277 270.75277 1496433.8 1496433.8 66.317087 66.317087 3000 133.4304 133.4304 -9.992879 -9.992879 277.46206 277.46206 7793677.5 7793677.5 18.133129 18.133129 Loop time of 1.13214 on 1 procs for 1000 steps with 4000 atoms Performance: 76.316 ns/day, 0.314 hours/ns, 883.283 timesteps/s, 3.533 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59107 | 0.59107 | 0.59107 | 0.0 | 52.21 Neigh | 0.371 | 0.371 | 0.371 | 0.0 | 32.77 Comm | 0.016943 | 0.016943 | 0.016943 | 0.0 | 1.50 Output | 9.5339e-05 | 9.5339e-05 | 9.5339e-05 | 0.0 | 0.01 Modify | 0.14052 | 0.14052 | 0.14052 | 0.0 | 12.41 Other | | 0.01251 | | | 1.11 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1324 ave 1324 max 1324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12084 ave 12084 max 12084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12084 Ave neighs/atom = 3.021 Neighbor list builds = 134 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.838726220145, Press = 65.2801984955181 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 40 40 40 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.76 | 3.76 | 3.76 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 133.4304 133.4304 -9.992879 -9.992879 277.46206 277.46206 7793677.5 7793677.5 18.133129 18.133129 4000 138.78783 138.78783 -2.5739301 -2.5739301 273.47392 273.47392 41353175 41353175 3.5703896 3.5703896 Loop time of 0.844064 on 1 procs for 1000 steps with 4000 atoms Performance: 102.362 ns/day, 0.234 hours/ns, 1184.745 timesteps/s, 4.739 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29873 | 0.29873 | 0.29873 | 0.0 | 35.39 Neigh | 0.36769 | 0.36769 | 0.36769 | 0.0 | 43.56 Comm | 0.01664 | 0.01664 | 0.01664 | 0.0 | 1.97 Output | 5.1446e-05 | 5.1446e-05 | 5.1446e-05 | 0.0 | 0.01 Modify | 0.14637 | 0.14637 | 0.14637 | 0.0 | 17.34 Other | | 0.01459 | | | 1.73 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 699 ave 699 max 699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3194 ave 3194 max 3194 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3194 Ave neighs/atom = 0.7985 Neighbor list builds = 220 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 272.836581172373, Press = 47.0495864015355 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 69 69 69 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 138.78783 138.78783 -2.5739301 -2.5739301 273.47392 273.47392 41353175 41353175 3.5703896 3.5703896 5000 139.20962 139.20962 -0.55263738 -0.55263738 270.37956 270.37956 2.1368575e+08 2.1368575e+08 0.69576053 0.69576053 Loop time of 0.980508 on 1 procs for 1000 steps with 4000 atoms Performance: 88.118 ns/day, 0.272 hours/ns, 1019.880 timesteps/s, 4.080 Matom-step/s 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17267 | 0.17267 | 0.17267 | 0.0 | 17.61 Neigh | 0.65033 | 0.65033 | 0.65033 | 0.0 | 66.33 Comm | 0.015814 | 0.015814 | 0.015814 | 0.0 | 1.61 Output | 4.9473e-05 | 4.9473e-05 | 4.9473e-05 | 0.0 | 0.01 Modify | 0.12636 | 0.12636 | 0.12636 | 0.0 | 12.89 Other | | 0.01528 | | | 1.56 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 776 ave 776 max 776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 776 Ave neighs/atom = 0.194 Neighbor list builds = 355 Dangerous builds = 0 if "${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 213685753.332292 A^3 has become larger than 144940209.626461 A^3. Aborting calculation. Total wall time: 0:00:10