# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.732946127653122*${_u_distance} variable latticeconst_converted equal 4.732946127653122*1 lattice bcc ${latticeconst_converted} lattice bcc 4.73294612765312 Lattice spacing in x,y,z = 4.7329461 4.7329461 4.7329461 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (47.329461 47.329461 47.329461) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (47.329461 47.329461 47.329461) create_atoms CPU = 0.000 seconds variable mass_converted equal 137.327*${_u_mass} variable mass_converted equal 137.327*1 kim interactions Ba #=== BEGIN kim interactions ================================== pair_style kim LJ_ElliottAkerson_2015_Universal__MO_959249795837_003 pair_coeff * * Ba #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 137.327 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 106021.680448174 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 106021.680448174/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 106021.680448174/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 106021.680448174/(1*1*${_u_distance}) variable V0_metal equal 106021.680448174/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 106021.680448174*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 106021.680448174 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_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 = 5 5 5 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) = 9.058 | 9.058 | 9.058 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -30182.358 -30182.358 -30247.769 -30247.769 253.15 253.15 106021.68 106021.68 658.9849 658.9849 1000 -30464.11 -30464.11 -30532.757 -30532.757 265.67378 265.67378 105700.61 105700.61 -782.74325 -782.74325 Loop time of 8.8573 on 1 procs for 1000 steps with 2000 atoms Performance: 9.755 ns/day, 2.460 hours/ns, 112.901 timesteps/s, 225.802 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 | 8.6759 | 8.6759 | 8.6759 | 0.0 | 97.95 Neigh | 0.069241 | 0.069241 | 0.069241 | 0.0 | 0.78 Comm | 0.038277 | 0.038277 | 0.038277 | 0.0 | 0.43 Output | 8.015e-05 | 8.015e-05 | 8.015e-05 | 0.0 | 0.00 Modify | 0.063648 | 0.063648 | 0.063648 | 0.0 | 0.72 Other | | 0.01018 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10699 ave 10699 max 10699 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: 1.3637e+06 ave 1.3637e+06 max 1.3637e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1363702 Ave neighs/atom = 681.851 Neighbor list builds = 2 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 = ${P}" flag: Temp = 262.574242390788, Press = 70.8615117439754 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.68 | 8.68 | 8.68 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -30464.11 -30464.11 -30532.757 -30532.757 265.67378 265.67378 105700.61 105700.61 -782.74325 -782.74325 2000 -30759.719 -30759.719 -30824.867 -30824.867 252.1304 252.1304 105183.54 105183.54 -649.88142 -649.88142 Loop time of 9.56937 on 1 procs for 1000 steps with 2000 atoms Performance: 9.029 ns/day, 2.658 hours/ns, 104.500 timesteps/s, 209.000 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3029 | 9.3029 | 9.3029 | 0.0 | 97.22 Neigh | 0.14824 | 0.14824 | 0.14824 | 0.0 | 1.55 Comm | 0.040566 | 0.040566 | 0.040566 | 0.0 | 0.42 Output | 6.1054e-05 | 6.1054e-05 | 6.1054e-05 | 0.0 | 0.00 Modify | 0.067366 | 0.067366 | 0.067366 | 0.0 | 0.70 Other | | 0.01022 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11030 ave 11030 max 11030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.37073e+06 ave 1.37073e+06 max 1.37073e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1370732 Ave neighs/atom = 685.366 Neighbor list builds = 4 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 257.81618240876, Press = 6.33789499118412 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.682 | 8.682 | 8.682 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -30759.719 -30759.719 -30824.867 -30824.867 252.1304 252.1304 105183.54 105183.54 -649.88142 -649.88142 3000 -30743.203 -30743.203 -30808.095 -30808.095 251.13734 251.13734 105223.46 105223.46 -551.76111 -551.76111 Loop time of 9.30455 on 1 procs for 1000 steps with 2000 atoms Performance: 9.286 ns/day, 2.585 hours/ns, 107.474 timesteps/s, 214.949 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.1887 | 9.1887 | 9.1887 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039164 | 0.039164 | 0.039164 | 0.0 | 0.42 Output | 4.7199e-05 | 4.7199e-05 | 4.7199e-05 | 0.0 | 0.00 Modify | 0.066692 | 0.066692 | 0.066692 | 0.0 | 0.72 Other | | 0.009919 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11028 ave 11028 max 11028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.37037e+06 ave 1.37037e+06 max 1.37037e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1370374 Ave neighs/atom = 685.187 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 255.470003057984, Press = -3.38824626282497 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.682 | 8.682 | 8.682 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -30743.203 -30743.203 -30808.095 -30808.095 251.13734 251.13734 105223.46 105223.46 -551.76111 -551.76111 4000 -30752.451 -30752.451 -30817.788 -30817.788 252.86148 252.86148 105153.14 105153.14 1275.1807 1275.1807 Loop time of 9.05553 on 1 procs for 1000 steps with 2000 atoms Performance: 9.541 ns/day, 2.515 hours/ns, 110.430 timesteps/s, 220.860 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.9429 | 8.9429 | 8.9429 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03815 | 0.03815 | 0.03815 | 0.0 | 0.42 Output | 5.0665e-05 | 5.0665e-05 | 5.0665e-05 | 0.0 | 0.00 Modify | 0.064845 | 0.064845 | 0.064845 | 0.0 | 0.72 Other | | 0.009565 | | | 0.11 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11063 ave 11063 max 11063 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.36992e+06 ave 1.36992e+06 max 1.36992e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1369922 Ave neighs/atom = 684.961 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.707110969811, Press = 3.24903567967892 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.682 | 8.682 | 8.682 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -30752.451 -30752.451 -30817.788 -30817.788 252.86148 252.86148 105153.14 105153.14 1275.1807 1275.1807 5000 -30743.614 -30743.614 -30808.632 -30808.632 251.62807 251.62807 105278.61 105278.61 -2271.6793 -2271.6793 Loop time of 8.819 on 1 procs for 1000 steps with 2000 atoms Performance: 9.797 ns/day, 2.450 hours/ns, 113.392 timesteps/s, 226.783 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7092 | 8.7092 | 8.7092 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.037375 | 0.037375 | 0.037375 | 0.0 | 0.42 Output | 3.6589e-05 | 3.6589e-05 | 3.6589e-05 | 0.0 | 0.00 Modify | 0.063274 | 0.063274 | 0.063274 | 0.0 | 0.72 Other | | 0.009116 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11024 ave 11024 max 11024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.37169e+06 ave 1.37169e+06 max 1.37169e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1371688 Ave neighs/atom = 685.844 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 254.221514717568, Press = 1.32313832727185 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.682 | 8.682 | 8.682 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 5000 -30743.614 -30743.614 -30808.632 -30808.632 251.62807 251.62807 105278.61 105278.61 -2271.6793 -2271.6793 6000 -30744.786 -30744.786 -30807.319 -30807.319 242.00798 242.00798 105201.61 105201.61 595.60878 595.60878 Loop time of 9.20075 on 1 procs for 1000 steps with 2000 atoms Performance: 9.391 ns/day, 2.556 hours/ns, 108.687 timesteps/s, 217.374 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0865 | 9.0865 | 9.0865 | 0.0 | 98.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038934 | 0.038934 | 0.038934 | 0.0 | 0.42 Output | 4.6627e-05 | 4.6627e-05 | 4.6627e-05 | 0.0 | 0.00 Modify | 0.065918 | 0.065918 | 0.065918 | 0.0 | 0.72 Other | | 0.009395 | | | 0.10 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11025 ave 11025 max 11025 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.36786e+06 ave 1.36786e+06 max 1.36786e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1367864 Ave neighs/atom = 683.932 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 105239.660692723 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0