# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.666074258089072*${_u_distance} variable latticeconst_converted equal 5.666074258089072*1 lattice fcc ${latticeconst_converted} lattice fcc 5.66607425808907 Lattice spacing in x,y,z = 5.6660743 5.6660743 5.6660743 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (56.660743 56.660743 56.660743) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (56.660743 56.660743 56.660743) create_atoms CPU = 0.001 seconds variable mass_converted equal 232.0381*${_u_mass} variable mass_converted equal 232.0381*1 kim interactions Th #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Th #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 232.0381 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 181905.900235895 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 181905.900235895/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 181905.900235895/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 181905.900235895/(1*1*${_u_distance}) variable V0_metal equal 181905.900235895/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 181905.900235895*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 181905.900235895 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 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) = 18.26 | 18.26 | 18.26 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -76852.239 -76852.239 -77024.448 -77024.448 333.15 333.15 181905.9 181905.9 1011.3015 1011.3015 1000 -76680.53 -76680.53 -76852.045 -76852.045 331.80854 331.80854 182201.61 182201.61 27.06808 27.06808 Loop time of 19.095 on 1 procs for 1000 steps with 4000 atoms Performance: 4.525 ns/day, 5.304 hours/ns, 52.370 timesteps/s, 209.479 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 | 18.867 | 18.867 | 18.867 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.067805 | 0.067805 | 0.067805 | 0.0 | 0.36 Output | 0.00013225 | 0.00013225 | 0.00013225 | 0.0 | 0.00 Modify | 0.13789 | 0.13789 | 0.13789 | 0.0 | 0.72 Other | | 0.02235 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 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: 3.16e+06 ave 3.16e+06 max 3.16e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3160000 Ave neighs/atom = 790 Neighbor list builds = 0 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 = ${P}" flag: Temp = 332.447733070611, Press = 135.957731965888 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.51 | 18.51 | 18.51 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -76680.53 -76680.53 -76852.045 -76852.045 331.80854 331.80854 182201.61 182201.61 27.06808 27.06808 2000 -76674.852 -76674.852 -76848.841 -76848.841 336.59372 336.59372 182289.22 182289.22 -2448.3363 -2448.3363 Loop time of 22.8204 on 1 procs for 1000 steps with 4000 atoms Performance: 3.786 ns/day, 6.339 hours/ns, 43.820 timesteps/s, 175.281 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.581 | 22.581 | 22.581 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.069498 | 0.069498 | 0.069498 | 0.0 | 0.30 Output | 7.4029e-05 | 7.4029e-05 | 7.4029e-05 | 0.0 | 0.00 Modify | 0.14666 | 0.14666 | 0.14666 | 0.0 | 0.64 Other | | 0.02353 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.15849e+06 ave 3.15849e+06 max 3.15849e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3158488 Ave neighs/atom = 789.622 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.997405953442, Press = 18.9325732553113 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.51 | 18.51 | 18.51 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -76674.852 -76674.852 -76848.841 -76848.841 336.59372 336.59372 182289.22 182289.22 -2448.3363 -2448.3363 3000 -76682.799 -76682.799 -76850.928 -76850.928 325.25765 325.25765 182198.86 182198.86 153.08615 153.08615 Loop time of 23.2029 on 1 procs for 1000 steps with 4000 atoms Performance: 3.724 ns/day, 6.445 hours/ns, 43.098 timesteps/s, 172.392 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.966 | 22.966 | 22.966 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.068667 | 0.068667 | 0.068667 | 0.0 | 0.30 Output | 7.448e-05 | 7.448e-05 | 7.448e-05 | 0.0 | 0.00 Modify | 0.14553 | 0.14553 | 0.14553 | 0.0 | 0.63 Other | | 0.02224 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.15847e+06 ave 3.15847e+06 max 3.15847e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3158474 Ave neighs/atom = 789.6185 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.076255005975, Press = 19.3519427472613 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.51 | 18.51 | 18.51 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -76682.799 -76682.799 -76850.928 -76850.928 325.25765 325.25765 182198.86 182198.86 153.08615 153.08615 4000 -76685.412 -76685.412 -76853.982 -76853.982 326.11011 326.11011 182173.49 182173.49 776.86548 776.86548 Loop time of 22.9895 on 1 procs for 1000 steps with 4000 atoms Performance: 3.758 ns/day, 6.386 hours/ns, 43.498 timesteps/s, 173.992 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.754 | 22.754 | 22.754 | 0.0 | 98.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06831 | 0.06831 | 0.06831 | 0.0 | 0.30 Output | 7.1694e-05 | 7.1694e-05 | 7.1694e-05 | 0.0 | 0.00 Modify | 0.1445 | 0.1445 | 0.1445 | 0.0 | 0.63 Other | | 0.02232 | | | 0.10 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.15828e+06 ave 3.15828e+06 max 3.15828e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3158278 Ave neighs/atom = 789.5695 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.058989332599, Press = 9.13438796044497 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.51 | 18.51 | 18.51 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -76685.412 -76685.412 -76853.982 -76853.982 326.11011 326.11011 182173.49 182173.49 776.86548 776.86548 5000 -76668.809 -76668.809 -76843.541 -76843.541 338.03187 338.03187 182221.67 182221.67 -139.77016 -139.77016 Loop time of 22.2479 on 1 procs for 1000 steps with 4000 atoms Performance: 3.884 ns/day, 6.180 hours/ns, 44.948 timesteps/s, 179.792 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.023 | 22.023 | 22.023 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.065168 | 0.065168 | 0.065168 | 0.0 | 0.29 Output | 6.397e-05 | 6.397e-05 | 6.397e-05 | 0.0 | 0.00 Modify | 0.13965 | 0.13965 | 0.13965 | 0.0 | 0.63 Other | | 0.01983 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.15874e+06 ave 3.15874e+06 max 3.15874e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3158744 Ave neighs/atom = 789.686 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.980155739616, Press = 5.28276953291079 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 18.51 | 18.51 | 18.51 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -76668.809 -76668.809 -76843.541 -76843.541 338.03187 338.03187 182221.67 182221.67 -139.77016 -139.77016 6000 -76684.92 -76684.92 -76852.638 -76852.638 324.46211 324.46211 182309.42 182309.42 -3266.244 -3266.244 Loop time of 21.9193 on 1 procs for 1000 steps with 4000 atoms Performance: 3.942 ns/day, 6.089 hours/ns, 45.622 timesteps/s, 182.488 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.699 | 21.699 | 21.699 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.064244 | 0.064244 | 0.064244 | 0.0 | 0.29 Output | 6.1776e-05 | 6.1776e-05 | 6.1776e-05 | 0.0 | 0.00 Modify | 0.13695 | 0.13695 | 0.13695 | 0.0 | 0.62 Other | | 0.0189 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17437 ave 17437 max 17437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.15838e+06 ave 3.15838e+06 max 3.15838e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3158378 Ave neighs/atom = 789.5945 Neighbor list builds = 0 Dangerous builds = 0 if "${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" jump SELF break # Write final averaged volume to file if temperature and volume have converged; otherwise wirte a # flag to indicate non-convergence. variable myStep equal step if "${myStep} < 2000000" then "print '${V}' file output/vol_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 182203.683083438 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0