# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.532111041247845*${_u_distance} variable latticeconst_converted equal 3.532111041247845*1 lattice bcc ${latticeconst_converted} lattice bcc 3.53211104124785 Lattice spacing in x,y,z = 3.532111 3.532111 3.532111 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.32111 35.32111 35.32111) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 2000 atoms using lattice units in orthogonal box = (0 0 0) to (35.32111 35.32111 35.32111) create_atoms CPU = 0.000 seconds variable mass_converted equal 6.941*${_u_mass} variable mass_converted equal 6.941*1 kim interactions Li #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_KimJungLee_2012_LiMg__MO_427397414195_002 pair_coeff * * 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 44065.9406253475 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44065.9406253475/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44065.9406253475/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 44065.9406253475/(1*1*${_u_distance}) variable V0_metal equal 44065.9406253475/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 44065.9406253475*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 44065.9406253475 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 273.15*${_u_temperature} variable temp_converted equal 273.15*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 273.15 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 273.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 273.15 273.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "273.15 - 1.0" variable T_up equal "273.15 + 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_427397414195_002#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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 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) = 3.701 | 3.701 | 3.701 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -3226.1992 -3226.1992 -3296.7787 -3296.7787 273.15 273.15 44065.941 44065.941 1710.7831 1710.7831 1000 -3150.7175 -3150.7175 -3220.6465 -3220.6465 270.63246 270.63246 44473.988 44473.988 145.49561 145.49561 Loop time of 31.2781 on 1 procs for 1000 steps with 2000 atoms Performance: 2.762 ns/day, 8.688 hours/ns, 31.971 timesteps/s, 63.942 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 | 31.09 | 31.09 | 31.09 | 0.0 | 99.40 Neigh | 0.10469 | 0.10469 | 0.10469 | 0.0 | 0.33 Comm | 0.014294 | 0.014294 | 0.014294 | 0.0 | 0.05 Output | 0.00010809 | 0.00010809 | 0.00010809 | 0.0 | 0.00 Modify | 0.063058 | 0.063058 | 0.063058 | 0.0 | 0.20 Other | | 0.006229 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3336 ave 3336 max 3336 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: 120888 ave 120888 max 120888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120888 Ave neighs/atom = 60.444 Neighbor list builds = 22 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 = ${P}" flag: Temp = 273.829088699362, Press = 30.4005393477774 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.704 | 3.704 | 3.704 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -3150.7175 -3150.7175 -3220.6465 -3220.6465 270.63246 270.63246 44473.988 44473.988 145.49561 145.49561 2000 -3149.8266 -3149.8266 -3218.2242 -3218.2242 264.70555 264.70555 44194.24 44194.24 886.59964 886.59964 Loop time of 35.6132 on 1 procs for 1000 steps with 2000 atoms Performance: 2.426 ns/day, 9.893 hours/ns, 28.079 timesteps/s, 56.159 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 35.39 | 35.39 | 35.39 | 0.0 | 99.37 Neigh | 0.12631 | 0.12631 | 0.12631 | 0.0 | 0.35 Comm | 0.016726 | 0.016726 | 0.016726 | 0.0 | 0.05 Output | 6.8529e-05 | 6.8529e-05 | 6.8529e-05 | 0.0 | 0.00 Modify | 0.072871 | 0.072871 | 0.072871 | 0.0 | 0.20 Other | | 0.006938 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3274 ave 3274 max 3274 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121272 ave 121272 max 121272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121272 Ave neighs/atom = 60.636 Neighbor list builds = 22 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.288414148599, Press = 6.36252763139055 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 3.703 | 3.703 | 3.703 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -3149.8266 -3149.8266 -3218.2242 -3218.2242 264.70555 264.70555 44194.24 44194.24 886.59964 886.59964 3000 -3148.6587 -3148.6587 -3218.1412 -3218.1412 268.90427 268.90427 44387.054 44387.054 361.35973 361.35973 Loop time of 38.1209 on 1 procs for 1000 steps with 2000 atoms Performance: 2.266 ns/day, 10.589 hours/ns, 26.232 timesteps/s, 52.465 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.863 | 37.863 | 37.863 | 0.0 | 99.32 Neigh | 0.14997 | 0.14997 | 0.14997 | 0.0 | 0.39 Comm | 0.019441 | 0.019441 | 0.019441 | 0.0 | 0.05 Output | 0.00026677 | 0.00026677 | 0.00026677 | 0.0 | 0.00 Modify | 0.079662 | 0.079662 | 0.079662 | 0.0 | 0.21 Other | | 0.008119 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3335 ave 3335 max 3335 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120986 ave 120986 max 120986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120986 Ave neighs/atom = 60.493 Neighbor list builds = 21 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 44530.2611118864 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0