# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.262299403548241*${_u_distance} variable latticeconst_converted equal 5.262299403548241*1 lattice fcc ${latticeconst_converted} lattice fcc 5.26229940354824 Lattice spacing in x,y,z = 5.2622994 5.2622994 5.2622994 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (52.622994 52.622994 52.622994) create_atoms CPU = 0.001 seconds variable mass_converted equal 39.948*${_u_mass} variable mass_converted equal 39.948*1 kim interactions Ar #=== BEGIN kim interactions ================================== pair_style kim Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_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 145722.516377902 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*${_u_distance}) variable V0_metal equal 145722.516377902/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 145722.516377902*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 145722.516377902 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_071460865933_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 0 171.98225 171.98225 -0.2267577 -0.2267577 333.15 333.15 145722.52 145722.52 1262.2585 1262.2585 1000 172.59441 172.59441 1.4365711 1.4365711 331.11644 331.11644 1055208.6 1055208.6 176.68929 176.68929 Loop time of 5.08294 on 1 procs for 1000 steps with 4000 atoms Performance: 16.998 ns/day, 1.412 hours/ns, 196.736 timesteps/s, 786.946 katom-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 | 4.1809 | 4.1809 | 4.1809 | 0.0 | 82.25 Neigh | 0.72544 | 0.72544 | 0.72544 | 0.0 | 14.27 Comm | 0.027923 | 0.027923 | 0.027923 | 0.0 | 0.55 Output | 0.0001042 | 0.0001042 | 0.0001042 | 0.0 | 0.00 Modify | 0.13238 | 0.13238 | 0.13238 | 0.0 | 2.60 Other | | 0.0162 | | | 0.32 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2913 ave 2913 max 2913 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: 64046 ave 64046 max 64046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64046 Ave neighs/atom = 16.0115 Neighbor list builds = 82 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 = ${P}" flag: Temp = 331.123583637437, Press = 192.943483741447 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.491 | 3.491 | 3.491 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 172.59441 172.59441 1.4365711 1.4365711 331.11644 331.11644 1055208.6 1055208.6 176.68929 176.68929 2000 171.47307 171.47307 0.228702 0.228702 331.28384 331.28384 5915955.9 5915955.9 31.009997 31.009997 Loop time of 1.3977 on 1 procs for 1000 steps with 4000 atoms Performance: 61.816 ns/day, 0.388 hours/ns, 715.462 timesteps/s, 2.862 Matom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82832 | 0.82832 | 0.82832 | 0.0 | 59.26 Neigh | 0.40415 | 0.40415 | 0.40415 | 0.0 | 28.92 Comm | 0.018879 | 0.018879 | 0.018879 | 0.0 | 1.35 Output | 7.2526e-05 | 7.2526e-05 | 7.2526e-05 | 0.0 | 0.01 Modify | 0.133 | 0.133 | 0.133 | 0.0 | 9.52 Other | | 0.01327 | | | 0.95 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1468 ave 1468 max 1468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11484 ave 11484 max 11484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11484 Ave neighs/atom = 2.871 Neighbor list builds = 127 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.223287039424, Press = 92.424405814445 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 36 36 36 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.676 | 3.676 | 3.676 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 171.47307 171.47307 0.228702 0.228702 331.28384 331.28384 5915955.9 5915955.9 31.009997 31.009997 3000 171.33731 171.33731 0.058635931 0.058635931 331.3502 331.3502 30672581 30672581 5.9698371 5.9698371 Loop time of 0.829246 on 1 procs for 1000 steps with 4000 atoms Performance: 104.191 ns/day, 0.230 hours/ns, 1205.914 timesteps/s, 4.824 Matom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34726 | 0.34726 | 0.34726 | 0.0 | 41.88 Neigh | 0.31752 | 0.31752 | 0.31752 | 0.0 | 38.29 Comm | 0.01749 | 0.01749 | 0.01749 | 0.0 | 2.11 Output | 5.6646e-05 | 5.6646e-05 | 5.6646e-05 | 0.0 | 0.01 Modify | 0.13292 | 0.13292 | 0.13292 | 0.0 | 16.03 Other | | 0.01401 | | | 1.69 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 809 ave 809 max 809 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2304 ave 2304 max 2304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2304 Ave neighs/atom = 0.576 Neighbor list builds = 204 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 331.270620625324, Press = 55.5855195731189 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.15 ghost atom cutoff = 10.15 binsize = 5.075, bins = 62 62 62 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 171.33731 171.33731 0.058635931 0.058635931 331.3502 331.3502 30672581 30672581 5.9698371 5.9698371 4000 171.30802 171.30802 0.0079472638 0.0079472638 331.3916 331.3916 1.5213603e+08 1.5213603e+08 1.2028346 1.2028346 Loop time of 0.921593 on 1 procs for 1000 steps with 4000 atoms Performance: 93.751 ns/day, 0.256 hours/ns, 1085.077 timesteps/s, 4.340 Matom-step/s 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23782 | 0.23782 | 0.23782 | 0.0 | 25.81 Neigh | 0.51479 | 0.51479 | 0.51479 | 0.0 | 55.86 Comm | 0.018168 | 0.018168 | 0.018168 | 0.0 | 1.97 Output | 7.7726e-05 | 7.7726e-05 | 7.7726e-05 | 0.0 | 0.01 Modify | 0.1346 | 0.1346 | 0.1346 | 0.0 | 14.61 Other | | 0.01614 | | | 1.75 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 462 ave 462 max 462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 444 ave 444 max 444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 444 Ave neighs/atom = 0.111 Neighbor list builds = 309 Dangerous builds = 0 if "${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 152136026.842098 A^3 has become larger than 145722516.377902 A^3. Aborting calculation. Total wall time: 0:00:08