# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.235186479985714*${_u_distance} variable latticeconst_converted equal 5.235186479985714*1 lattice fcc ${latticeconst_converted} lattice fcc 5.23518647998571 Lattice spacing in x,y,z = 5.2351865 5.2351865 5.2351865 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.351865 52.351865 52.351865) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1122) 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 143481.684999044 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*${_u_distance}) variable V0_metal equal 143481.684999044/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 143481.684999044*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 143481.684999044 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_946046425752_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 -210.40147 -210.40147 -341.25757 -341.25757 253.15 253.15 143481.68 143481.68 974.12929 974.12929 1000 41.875727 41.875727 -89.575219 -89.575219 254.30077 254.30077 430090.96 430090.96 89.306833 89.306833 Loop time of 7.05211 on 1 procs for 1000 steps with 4000 atoms Performance: 12.252 ns/day, 1.959 hours/ns, 141.802 timesteps/s, 567.206 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3823 | 6.3823 | 6.3823 | 0.0 | 90.50 Neigh | 0.49482 | 0.49482 | 0.49482 | 0.0 | 7.02 Comm | 0.026676 | 0.026676 | 0.026676 | 0.0 | 0.38 Output | 0.00012467 | 0.00012467 | 0.00012467 | 0.0 | 0.00 Modify | 0.13477 | 0.13477 | 0.13477 | 0.0 | 1.91 Other | | 0.01337 | | | 0.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4154 ave 4154 max 4154 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: 163436 ave 163436 max 163436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163436 Ave neighs/atom = 40.859 Neighbor list builds = 42 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 = ${P}" flag: Temp = 254.226534233398, Press = 90.183855228364 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.846 | 3.846 | 3.846 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 41.875727 41.875727 -89.575219 -89.575219 254.30077 254.30077 430090.96 430090.96 89.306833 89.306833 2000 104.33267 104.33267 -26.162404 -26.162404 252.45157 252.45157 1639828.7 1639828.7 61.85788 61.85788 Loop time of 2.70265 on 1 procs for 1000 steps with 4000 atoms Performance: 31.969 ns/day, 0.751 hours/ns, 370.008 timesteps/s, 1.480 Matom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1351 | 2.1351 | 2.1351 | 0.0 | 79.00 Neigh | 0.41423 | 0.41423 | 0.41423 | 0.0 | 15.33 Comm | 0.018814 | 0.018814 | 0.018814 | 0.0 | 0.70 Output | 6.8979e-05 | 6.8979e-05 | 6.8979e-05 | 0.0 | 0.00 Modify | 0.12271 | 0.12271 | 0.12271 | 0.0 | 4.54 Other | | 0.0117 | | | 0.43 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2376 ave 2376 max 2376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45088 ave 45088 max 45088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45088 Ave neighs/atom = 11.272 Neighbor list builds = 74 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.869332973283, Press = 85.8477114881069 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 24 24 24 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.513 | 3.513 | 3.513 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 104.33267 104.33267 -26.162404 -26.162404 252.45157 252.45157 1639828.7 1639828.7 61.85788 61.85788 3000 123.84727 123.84727 -7.3788218 -7.3788218 253.86578 253.86578 8590030.9 8590030.9 15.108936 15.108936 Loop time of 1.1293 on 1 procs for 1000 steps with 4000 atoms Performance: 76.507 ns/day, 0.314 hours/ns, 885.502 timesteps/s, 3.542 Matom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6831 | 0.6831 | 0.6831 | 0.0 | 60.49 Neigh | 0.3015 | 0.3015 | 0.3015 | 0.0 | 26.70 Comm | 0.014305 | 0.014305 | 0.014305 | 0.0 | 1.27 Output | 6.1606e-05 | 6.1606e-05 | 6.1606e-05 | 0.0 | 0.01 Modify | 0.11934 | 0.11934 | 0.11934 | 0.0 | 10.57 Other | | 0.01099 | | | 0.97 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1245 ave 1245 max 1245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 10704 ave 10704 max 10704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 10704 Ave neighs/atom = 2.676 Neighbor list builds = 138 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.73535548242, Press = 61.2568886663093 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 41 41 41 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.783 | 3.783 | 3.783 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 123.84727 123.84727 -7.3788218 -7.3788218 253.86578 253.86578 8590030.9 8590030.9 15.108936 15.108936 4000 124.8467 124.8467 -2.053031 -2.053031 245.49614 245.49614 45700075 45700075 2.8970707 2.8970707 Loop time of 0.756576 on 1 procs for 1000 steps with 4000 atoms Performance: 114.199 ns/day, 0.210 hours/ns, 1321.744 timesteps/s, 5.287 Matom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30879 | 0.30879 | 0.30879 | 0.0 | 40.81 Neigh | 0.30384 | 0.30384 | 0.30384 | 0.0 | 40.16 Comm | 0.013154 | 0.013154 | 0.013154 | 0.0 | 1.74 Output | 6.6264e-05 | 6.6264e-05 | 6.6264e-05 | 0.0 | 0.01 Modify | 0.11836 | 0.11836 | 0.11836 | 0.0 | 15.64 Other | | 0.01237 | | | 1.63 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 670 ave 670 max 670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2756 ave 2756 max 2756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2756 Ave neighs/atom = 0.689 Neighbor list builds = 227 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 252.797005448185, Press = 43.9029743022279 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 71 71 71 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.082 | 5.082 | 5.082 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 124.8467 124.8467 -2.053031 -2.053031 245.49614 245.49614 45700075 45700075 2.8970707 2.8970707 5000 130.83337 130.83337 -0.47938892 -0.47938892 254.03344 254.03344 2.3445863e+08 2.3445863e+08 0.59471317 0.59471317 Loop time of 1.17203 on 1 procs for 1000 steps with 4000 atoms Performance: 73.718 ns/day, 0.326 hours/ns, 853.219 timesteps/s, 3.413 Matom-step/s 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22151 | 0.22151 | 0.22151 | 0.0 | 18.90 Neigh | 0.77717 | 0.77717 | 0.77717 | 0.0 | 66.31 Comm | 0.017895 | 0.017895 | 0.017895 | 0.0 | 1.53 Output | 8.0682e-05 | 8.0682e-05 | 8.0682e-05 | 0.0 | 0.01 Modify | 0.13875 | 0.13875 | 0.13875 | 0.0 | 11.84 Other | | 0.01663 | | | 1.42 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 386 ave 386 max 386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 716 ave 716 max 716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 716 Ave neighs/atom = 0.179 Neighbor list builds = 368 Dangerous builds = 0 if "${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 234458633.306684 A^3 has become larger than 143481684.999044 A^3. Aborting calculation. Total wall time: 0:00:13