# 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 ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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 -63653.157 -63653.157 -63734.072 -63734.072 313.15 313.15 52411.848 52411.848 1648.7383 1648.7383 1000 -64816.26 -64816.26 -64896.648 -64896.648 311.1104 311.1104 52020.506 52020.506 -803.07754 -803.07754 Loop time of 12.1125 on 1 procs for 1000 steps with 2000 atoms Performance: 7.133 ns/day, 3.365 hours/ns, 82.560 timesteps/s, 165.119 katom-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 | 11.786 | 11.786 | 11.786 | 0.0 | 97.30 Neigh | 0.17112 | 0.17112 | 0.17112 | 0.0 | 1.41 Comm | 0.064767 | 0.064767 | 0.064767 | 0.0 | 0.53 Output | 0.00010099 | 0.00010099 | 0.00010099 | 0.0 | 0.00 Modify | 0.072557 | 0.072557 | 0.072557 | 0.0 | 0.60 Other | | 0.01799 | | | 0.15 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: 2.79046e+06 ave 2.79046e+06 max 2.79046e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2790460 Ave neighs/atom = 1395.23 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 = ${P}" flag: Temp = 325.50727077039, Press = 56.131793645743 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -64816.26 -64816.26 -64896.648 -64896.648 311.1104 311.1104 52020.506 52020.506 -803.07754 -803.07754 2000 -64951.473 -64951.473 -65022.797 -65022.797 276.03163 276.03163 51972.364 51972.364 -8182.3635 -8182.3635 Loop time of 11.344 on 1 procs for 1000 steps with 2000 atoms Performance: 7.616 ns/day, 3.151 hours/ns, 88.152 timesteps/s, 176.304 katom-step/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.015 | 11.015 | 11.015 | 0.0 | 97.10 Neigh | 0.16872 | 0.16872 | 0.16872 | 0.0 | 1.49 Comm | 0.062577 | 0.062577 | 0.062577 | 0.0 | 0.55 Output | 4.9392e-05 | 4.9392e-05 | 4.9392e-05 | 0.0 | 0.00 Modify | 0.077731 | 0.077731 | 0.077731 | 0.0 | 0.69 Other | | 0.01983 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16551 ave 16551 max 16551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79399e+06 ave 2.79399e+06 max 2.79399e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2793994 Ave neighs/atom = 1396.997 Neighbor list builds = 3 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 316.755859637283, Press = -19.9520435560995 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -64951.473 -64951.473 -65022.797 -65022.797 276.03163 276.03163 51972.364 51972.364 -8182.3635 -8182.3635 3000 -64978.602 -64978.602 -65058.887 -65058.887 310.71191 310.71191 51942.55 51942.55 -1756.2719 -1756.2719 Loop time of 11.0568 on 1 procs for 1000 steps with 2000 atoms Performance: 7.814 ns/day, 3.071 hours/ns, 90.442 timesteps/s, 180.885 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.907 | 10.907 | 10.907 | 0.0 | 98.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.060625 | 0.060625 | 0.060625 | 0.0 | 0.55 Output | 4.9612e-05 | 4.9612e-05 | 4.9612e-05 | 0.0 | 0.00 Modify | 0.070091 | 0.070091 | 0.070091 | 0.0 | 0.63 Other | | 0.01902 | | | 0.17 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16528 ave 16528 max 16528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79156e+06 ave 2.79156e+06 max 2.79156e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2791564 Ave neighs/atom = 1395.782 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 315.419481125986, Press = -2.92151622642749 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -64978.602 -64978.602 -65058.887 -65058.887 310.71191 310.71191 51942.55 51942.55 -1756.2719 -1756.2719 4000 -64965.383 -64965.383 -65042.164 -65042.164 297.15344 297.15344 51982.945 51982.945 -12528.34 -12528.34 Loop time of 11.1913 on 1 procs for 1000 steps with 2000 atoms Performance: 7.720 ns/day, 3.109 hours/ns, 89.355 timesteps/s, 178.710 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.035 | 11.035 | 11.035 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.063279 | 0.063279 | 0.063279 | 0.0 | 0.57 Output | 6.7086e-05 | 6.7086e-05 | 6.7086e-05 | 0.0 | 0.00 Modify | 0.072842 | 0.072842 | 0.072842 | 0.0 | 0.65 Other | | 0.02035 | | | 0.18 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16553 ave 16553 max 16553 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79277e+06 ave 2.79277e+06 max 2.79277e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2792772 Ave neighs/atom = 1396.386 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 314.622850069813, Press = -10.5285441362157 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -64965.383 -64965.383 -65042.164 -65042.164 297.15344 297.15344 51982.945 51982.945 -12528.34 -12528.34 5000 -64960.678 -64960.678 -65036.836 -65036.836 294.73962 294.73962 51989.848 51989.848 -14918.443 -14918.443 Loop time of 11.1231 on 1 procs for 1000 steps with 2000 atoms Performance: 7.768 ns/day, 3.090 hours/ns, 89.903 timesteps/s, 179.806 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.97 | 10.97 | 10.97 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.062281 | 0.062281 | 0.062281 | 0.0 | 0.56 Output | 3.6258e-05 | 3.6258e-05 | 3.6258e-05 | 0.0 | 0.00 Modify | 0.070579 | 0.070579 | 0.070579 | 0.0 | 0.63 Other | | 0.01973 | | | 0.18 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16526 ave 16526 max 16526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79117e+06 ave 2.79117e+06 max 2.79117e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2791172 Ave neighs/atom = 1395.586 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 314.238704667796, Press = -9.05638861937386 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 17.31 | 17.31 | 17.31 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -64960.678 -64960.678 -65036.836 -65036.836 294.73962 294.73962 51989.848 51989.848 -14918.443 -14918.443 6000 -64969.092 -64969.092 -65046.435 -65046.435 299.32679 299.32679 51967.114 51967.114 -8530.6926 -8530.6926 Loop time of 11.1635 on 1 procs for 1000 steps with 2000 atoms Performance: 7.740 ns/day, 3.101 hours/ns, 89.578 timesteps/s, 179.156 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.003 | 11.003 | 11.003 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06658 | 0.06658 | 0.06658 | 0.0 | 0.60 Output | 5.0084e-05 | 5.0084e-05 | 5.0084e-05 | 0.0 | 0.00 Modify | 0.071644 | 0.071644 | 0.071644 | 0.0 | 0.64 Other | | 0.0217 | | | 0.19 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16517 ave 16517 max 16517 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.79007e+06 ave 2.79007e+06 max 2.79007e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2790072 Ave neighs/atom = 1395.036 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 51950.3507606583 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0