# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.742339283227921*${_u_distance} variable latticeconst_converted equal 3.742339283227921*1 lattice bcc ${latticeconst_converted} lattice bcc 3.74233928322792 Lattice spacing in x,y,z = 3.7423393 3.7423393 3.7423393 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (37.423393 37.423393 37.423393) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (37.423393 37.423393 37.423393) create_atoms CPU = 0.000 seconds variable mass_converted equal 180.9479*${_u_mass} variable mass_converted equal 180.9479*1 kim interactions Ta #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Ta #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 180.9479 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 52411.848285638 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 52411.848285638/(1*1*${_u_distance}) variable V0_metal equal 52411.848285638/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 52411.848285638*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 52411.848285638 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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 = 4 4 4 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) = 17.04 | 17.04 | 17.04 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -63647.989 -63647.989 -63734.072 -63734.072 333.15 333.15 52411.848 52411.848 1754.0549 1754.0549 1000 -64807.831 -64807.831 -64894.571 -64894.571 335.69154 335.69154 52043.219 52043.219 -7067.7176 -7067.7176 Loop time of 11.2834 on 1 procs for 1000 steps with 2000 atoms Performance: 7.657 ns/day, 3.134 hours/ns, 88.625 timesteps/s, 177.251 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 | 10.978 | 10.978 | 10.978 | 0.0 | 97.29 Neigh | 0.16603 | 0.16603 | 0.16603 | 0.0 | 1.47 Comm | 0.056857 | 0.056857 | 0.056857 | 0.0 | 0.50 Output | 8.8796e-05 | 8.8796e-05 | 8.8796e-05 | 0.0 | 0.00 Modify | 0.066236 | 0.066236 | 0.066236 | 0.0 | 0.59 Other | | 0.01619 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16531 ave 16531 max 16531 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: 2.78987e+06 ave 2.78987e+06 max 2.78987e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2789872 Ave neighs/atom = 1394.936 Neighbor list builds = 3 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 = ${P}" flag: Temp = 344.220310763098, Press = -62.3885269281831 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -64807.831 -64807.831 -64894.571 -64894.571 335.69154 335.69154 52043.219 52043.219 -7067.7176 -7067.7176 2000 -64892.937 -64892.937 -64980.242 -64980.242 337.88012 337.88012 51950.284 51950.284 5404.311 5404.311 Loop time of 11.0842 on 1 procs for 1000 steps with 2000 atoms Performance: 7.795 ns/day, 3.079 hours/ns, 90.219 timesteps/s, 180.438 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.89 | 10.89 | 10.89 | 0.0 | 98.25 Neigh | 0.055984 | 0.055984 | 0.055984 | 0.0 | 0.51 Comm | 0.056381 | 0.056381 | 0.056381 | 0.0 | 0.51 Output | 4.3952e-05 | 4.3952e-05 | 4.3952e-05 | 0.0 | 0.00 Modify | 0.066268 | 0.066268 | 0.066268 | 0.0 | 0.60 Other | | 0.01544 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16543 ave 16543 max 16543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79421e+06 ave 2.79421e+06 max 2.79421e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2794206 Ave neighs/atom = 1397.103 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 335.818955640024, Press = 23.0543966724126 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -64892.937 -64892.937 -64980.242 -64980.242 337.88012 337.88012 51950.284 51950.284 5404.311 5404.311 3000 -64953.824 -64953.824 -65039.958 -65039.958 333.34888 333.34888 51962.258 51962.258 -5798.5183 -5798.5183 Loop time of 11.0648 on 1 procs for 1000 steps with 2000 atoms Performance: 7.809 ns/day, 3.074 hours/ns, 90.377 timesteps/s, 180.753 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.872 | 10.872 | 10.872 | 0.0 | 98.26 Neigh | 0.055859 | 0.055859 | 0.055859 | 0.0 | 0.50 Comm | 0.05599 | 0.05599 | 0.05599 | 0.0 | 0.51 Output | 7.4139e-05 | 7.4139e-05 | 7.4139e-05 | 0.0 | 0.00 Modify | 0.065409 | 0.065409 | 0.065409 | 0.0 | 0.59 Other | | 0.0154 | | | 0.14 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16539 ave 16539 max 16539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79076e+06 ave 2.79076e+06 max 2.79076e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2790758 Ave neighs/atom = 1395.379 Neighbor list builds = 1 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 335.257179109459, Press = -2.10104627377701 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -64953.824 -64953.824 -65039.958 -65039.958 333.34888 333.34888 51962.258 51962.258 -5798.5183 -5798.5183 4000 -64948.994 -64948.994 -65037.887 -65037.887 344.02556 344.02556 51925.012 51925.012 5937.2435 5937.2435 Loop time of 11.1389 on 1 procs for 1000 steps with 2000 atoms Performance: 7.757 ns/day, 3.094 hours/ns, 89.775 timesteps/s, 179.551 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.992 | 10.992 | 10.992 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.059401 | 0.059401 | 0.059401 | 0.0 | 0.53 Output | 5.4723e-05 | 5.4723e-05 | 5.4723e-05 | 0.0 | 0.00 Modify | 0.069318 | 0.069318 | 0.069318 | 0.0 | 0.62 Other | | 0.01852 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16547 ave 16547 max 16547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.78982e+06 ave 2.78982e+06 max 2.78982e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2789820 Ave neighs/atom = 1394.91 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 334.53482047756, Press = 8.45859728871658 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -64948.994 -64948.994 -65037.887 -65037.887 344.02556 344.02556 51925.012 51925.012 5937.2435 5937.2435 5000 -64957.056 -64957.056 -65039.512 -65039.512 319.11008 319.11008 51953.771 51953.771 -2911.8608 -2911.8608 Loop time of 11.3754 on 1 procs for 1000 steps with 2000 atoms Performance: 7.595 ns/day, 3.160 hours/ns, 87.909 timesteps/s, 175.817 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.228 | 11.228 | 11.228 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060243 | 0.060243 | 0.060243 | 0.0 | 0.53 Output | 6.7697e-05 | 6.7697e-05 | 6.7697e-05 | 0.0 | 0.00 Modify | 0.069104 | 0.069104 | 0.069104 | 0.0 | 0.61 Other | | 0.01823 | | | 0.16 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16540 ave 16540 max 16540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79259e+06 ave 2.79259e+06 max 2.79259e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2792586 Ave neighs/atom = 1396.293 Neighbor list builds = 0 Dangerous builds = 0 if "${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 51953.2929047483 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0