# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.4522535204887386*${_u_distance} variable latticeconst_converted equal 3.4522535204887386*1 lattice bcc ${latticeconst_converted} lattice bcc 3.45225352048874 Lattice spacing in x,y,z = 3.4522535 3.4522535 3.4522535 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (34.522535 34.522535 34.522535) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (34.522535 34.522535 34.522535) create_atoms CPU = 0.000 seconds variable mass_converted equal 6.941*${_u_mass} variable mass_converted equal 6.941*1 kim interactions Li #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style meam/c pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXhXQ2iA/library.meam Li Si /tmp/kim-shared-library-parameter-file-directory-XXXXXXhXQ2iA/LiSi.meam Li #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 6.941 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 41144.1451552659 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 41144.1451552659/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 41144.1451552659/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 41144.1451552659/(1*1*${_u_distance}) variable V0_metal equal 41144.1451552659/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 41144.1451552659*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 41144.1451552659 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/SM_562938628131_000#item-citation CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 11 11 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 10.94 | 10.94 | 10.94 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -3208.5132 -3208.5132 -3294.5961 -3294.5961 333.15 333.15 41144.145 41144.145 2234.7436 2234.7436 1000 -3118.9096 -3118.9096 -3204.1434 -3204.1434 329.86357 329.86357 43177.178 43177.178 -103.53101 -103.53101 Loop time of 22.7594 on 1 procs for 1000 steps with 2000 atoms Performance: 3.796 ns/day, 6.322 hours/ns, 43.938 timesteps/s, 87.876 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 | 22.55 | 22.55 | 22.55 | 0.0 | 99.08 Neigh | 0.12964 | 0.12964 | 0.12964 | 0.0 | 0.57 Comm | 0.013588 | 0.013588 | 0.013588 | 0.0 | 0.06 Output | 7.1104e-05 | 7.1104e-05 | 7.1104e-05 | 0.0 | 0.00 Modify | 0.060165 | 0.060165 | 0.060165 | 0.0 | 0.26 Other | | 0.005512 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3178 ave 3178 max 3178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59578 ave 59578 max 59578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119156 ave 119156 max 119156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119156 Ave neighs/atom = 59.578 Neighbor list builds = 26 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 = ${P}" flag: Temp = 330.036672296253, Press = -25.4326102912752 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -3118.9096 -3118.9096 -3204.1434 -3204.1434 329.86357 329.86357 43177.178 43177.178 -103.53101 -103.53101 2000 -3121.0746 -3121.0746 -3205.2358 -3205.2358 325.71284 325.71284 43243.194 43243.194 -301.91542 -301.91542 Loop time of 23.5751 on 1 procs for 1000 steps with 2000 atoms Performance: 3.665 ns/day, 6.549 hours/ns, 42.418 timesteps/s, 84.835 katom-step/s 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.353 | 23.353 | 23.353 | 0.0 | 99.06 Neigh | 0.13832 | 0.13832 | 0.13832 | 0.0 | 0.59 Comm | 0.013879 | 0.013879 | 0.013879 | 0.0 | 0.06 Output | 6.1525e-05 | 6.1525e-05 | 6.1525e-05 | 0.0 | 0.00 Modify | 0.063632 | 0.063632 | 0.063632 | 0.0 | 0.27 Other | | 0.005758 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3145 ave 3145 max 3145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59614 ave 59614 max 59614 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119228 ave 119228 max 119228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119228 Ave neighs/atom = 59.614 Neighbor list builds = 26 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.269260755851, Press = -5.40006231967934 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -3121.0746 -3121.0746 -3205.2358 -3205.2358 325.71284 325.71284 43243.194 43243.194 -301.91542 -301.91542 3000 -3117.6039 -3117.6039 -3204.9734 -3204.9734 338.12907 338.12907 43084.732 43084.732 219.33958 219.33958 Loop time of 29.0351 on 1 procs for 1000 steps with 2000 atoms Performance: 2.976 ns/day, 8.065 hours/ns, 34.441 timesteps/s, 68.882 katom-step/s 78.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.714 | 28.714 | 28.714 | 0.0 | 98.89 Neigh | 0.19248 | 0.19248 | 0.19248 | 0.0 | 0.66 Comm | 0.021109 | 0.021109 | 0.021109 | 0.0 | 0.07 Output | 6.372e-05 | 6.372e-05 | 6.372e-05 | 0.0 | 0.00 Modify | 0.10092 | 0.10092 | 0.10092 | 0.0 | 0.35 Other | | 0.006878 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3164 ave 3164 max 3164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59523 ave 59523 max 59523 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119046 ave 119046 max 119046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119046 Ave neighs/atom = 59.523 Neighbor list builds = 26 Dangerous builds = 0 if "${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 43145.3285198496 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0