# 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-XXXXXXm50S8o/library.meam Li Si /tmp/kim-shared-library-parameter-file-directory-XXXXXXm50S8o/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 ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_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/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 -3229.1844 -3229.1844 -3294.5961 -3294.5961 253.15 253.15 41144.145 41144.145 1698.1092 1698.1092 1000 -3162.6311 -3162.6311 -3229.8285 -3229.8285 260.06098 260.06098 42500.577 42500.577 135.76506 135.76506 Loop time of 22.6759 on 1 procs for 1000 steps with 2000 atoms Performance: 3.810 ns/day, 6.299 hours/ns, 44.100 timesteps/s, 88.199 katom-step/s 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.497 | 22.497 | 22.497 | 0.0 | 99.21 Neigh | 0.099921 | 0.099921 | 0.099921 | 0.0 | 0.44 Comm | 0.01309 | 0.01309 | 0.01309 | 0.0 | 0.06 Output | 5.8971e-05 | 5.8971e-05 | 5.8971e-05 | 0.0 | 0.00 Modify | 0.060438 | 0.060438 | 0.060438 | 0.0 | 0.27 Other | | 0.005516 | | | 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: 59608 ave 59608 max 59608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119216 ave 119216 max 119216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119216 Ave neighs/atom = 59.608 Neighbor list builds = 20 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 = ${P}" flag: Temp = 253.843191379124, Press = 12.9671314139369 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -3162.6311 -3162.6311 -3229.8285 -3229.8285 260.06098 260.06098 42500.577 42500.577 135.76506 135.76506 2000 -3164.9392 -3164.9392 -3230.3124 -3230.3124 253.00116 253.00116 42483.344 42483.344 86.81202 86.81202 Loop time of 23.2956 on 1 procs for 1000 steps with 2000 atoms Performance: 3.709 ns/day, 6.471 hours/ns, 42.927 timesteps/s, 85.853 katom-step/s 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.103 | 23.103 | 23.103 | 0.0 | 99.17 Neigh | 0.10805 | 0.10805 | 0.10805 | 0.0 | 0.46 Comm | 0.013935 | 0.013935 | 0.013935 | 0.0 | 0.06 Output | 6.6155e-05 | 6.6155e-05 | 6.6155e-05 | 0.0 | 0.00 Modify | 0.064487 | 0.064487 | 0.064487 | 0.0 | 0.28 Other | | 0.005693 | | | 0.02 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3158 ave 3158 max 3158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59631 ave 59631 max 59631 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119262 ave 119262 max 119262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119262 Ave neighs/atom = 59.631 Neighbor list builds = 21 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 42549.5073549101 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0