# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.976400002837181*${_u_distance} variable latticeconst_converted equal 3.976400002837181*1 lattice fcc ${latticeconst_converted} lattice fcc 3.97640000283718 Lattice spacing in x,y,z = 3.9764 3.9764 3.9764 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (39.764 39.764 39.764) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (39.764 39.764 39.764) create_atoms CPU = 0.001 seconds variable mass_converted equal 195.078*${_u_mass} variable mass_converted equal 195.078*1 kim interactions Pt #=== BEGIN kim interactions ================================== pair_style kim EAM_QuinticClampedSpline_Kim_2021_PtAu__MO_463728687265_001 pair_coeff * * Pt #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 195.078 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 62873.8705103264 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 62873.8705103264/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 62873.8705103264/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 62873.8705103264/(1*1*${_u_distance}) variable V0_metal equal 62873.8705103264/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 62873.8705103264*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 62873.8705103264 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 293.15*${_u_temperature} variable temp_converted equal 293.15*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 293.15 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 293.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 293.15 293.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "293.15 - 1.0" variable T_up equal "293.15 + 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_463728687265_001#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 = 8.65 ghost atom cutoff = 8.65 binsize = 4.325, bins = 10 10 10 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) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -21871.143 -21871.143 -22022.675 -22022.675 293.15 293.15 62873.871 62873.871 2574.2694 2574.2694 1000 -21717.304 -21717.304 -21872.378 -21872.378 300.00142 300.00142 63420.259 63420.259 1765.8144 1765.8144 Loop time of 12.3301 on 1 procs for 1000 steps with 4000 atoms Performance: 7.007 ns/day, 3.425 hours/ns, 81.103 timesteps/s, 324.410 katom-step/s 86.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.131 | 12.131 | 12.131 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.043809 | 0.043809 | 0.043809 | 0.0 | 0.36 Output | 0.00012943 | 0.00012943 | 0.00012943 | 0.0 | 0.00 Modify | 0.13882 | 0.13882 | 0.13882 | 0.0 | 1.13 Other | | 0.0165 | | | 0.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 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: 704000 ave 704000 max 704000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704000 Ave neighs/atom = 176 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 = ${P}" flag: Temp = 293.775553220041, Press = 92.51117811781 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65 ghost atom cutoff = 8.65 binsize = 4.325, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -21717.304 -21717.304 -21872.378 -21872.378 300.00142 300.00142 63420.259 63420.259 1765.8144 1765.8144 2000 -21716.762 -21716.762 -21866.734 -21866.734 290.13033 290.13033 63406.638 63406.638 3055.1612 3055.1612 Loop time of 12.7878 on 1 procs for 1000 steps with 4000 atoms Performance: 6.756 ns/day, 3.552 hours/ns, 78.200 timesteps/s, 312.799 katom-step/s 92.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.604 | 12.604 | 12.604 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.030403 | 0.030403 | 0.030403 | 0.0 | 0.24 Output | 7.3628e-05 | 7.3628e-05 | 7.3628e-05 | 0.0 | 0.00 Modify | 0.13701 | 0.13701 | 0.13701 | 0.0 | 1.07 Other | | 0.01602 | | | 0.13 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 694150 ave 694150 max 694150 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 694150 Ave neighs/atom = 173.5375 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.251147390912, Press = 11.0711102053466 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65 ghost atom cutoff = 8.65 binsize = 4.325, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -21716.762 -21716.762 -21866.734 -21866.734 290.13033 290.13033 63406.638 63406.638 3055.1612 3055.1612 3000 -21705.169 -21705.169 -21861.204 -21861.204 301.86041 301.86041 63437.079 63437.079 2805.7925 2805.7925 Loop time of 11.9782 on 1 procs for 1000 steps with 4000 atoms Performance: 7.213 ns/day, 3.327 hours/ns, 83.485 timesteps/s, 333.941 katom-step/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.813 | 11.813 | 11.813 | 0.0 | 98.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029268 | 0.029268 | 0.029268 | 0.0 | 0.24 Output | 6.427e-05 | 6.427e-05 | 6.427e-05 | 0.0 | 0.00 Modify | 0.1216 | 0.1216 | 0.1216 | 0.0 | 1.02 Other | | 0.01439 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 695098 ave 695098 max 695098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 695098 Ave neighs/atom = 173.7745 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 293.217639803605, Press = 5.54890307939267 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.65 ghost atom cutoff = 8.65 binsize = 4.325, bins = 10 10 10 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 6.244 | 6.244 | 6.244 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -21705.169 -21705.169 -21861.204 -21861.204 301.86041 301.86041 63437.079 63437.079 2805.7925 2805.7925 4000 -21719.326 -21719.326 -21872.844 -21872.844 296.99069 296.99069 63429.513 63429.513 1551.6086 1551.6086 Loop time of 11.9608 on 1 procs for 1000 steps with 4000 atoms Performance: 7.224 ns/day, 3.322 hours/ns, 83.607 timesteps/s, 334.427 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.796 | 11.796 | 11.796 | 0.0 | 98.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.029248 | 0.029248 | 0.029248 | 0.0 | 0.24 Output | 7.2065e-05 | 7.2065e-05 | 7.2065e-05 | 0.0 | 0.00 Modify | 0.121 | 0.121 | 0.121 | 0.0 | 1.01 Other | | 0.01442 | | | 0.12 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8195 ave 8195 max 8195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 694888 ave 694888 max 694888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 694888 Ave neighs/atom = 173.722 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T293.15.out" else "print 'not_converged' file output/vol_T293.15.out" print '${V}' file output/vol_T293.15.out 63486.9747071984 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0