# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.430545687675476*${_u_distance} variable latticeconst_converted equal 5.430545687675476*1 lattice diamond ${latticeconst_converted} lattice diamond 5.43054568767548 Lattice spacing in x,y,z = 5.4305457 5.4305457 5.4305457 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (54.305457 54.305457 54.305457) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (54.305457 54.305457 54.305457) create_atoms CPU = 0.001 seconds variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 kim interactions Si #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style meam/spline pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXH33PL8/Si_1.meam.spline Si Reading meam/spline potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXH33PL8/Si_1.meam.spline with DATE: 2012-02-01 #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 28.0855 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 160151.280490546 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160151.280490546/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160151.280490546/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 160151.280490546/(1*1*${_u_distance}) variable V0_metal equal 160151.280490546/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 160151.280490546*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 160151.280490546 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 313.15*${_u_temperature} variable temp_converted equal 313.15*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 313.15 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 313.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 313.15 313.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "313.15 - 1.0" variable T_up equal "313.15 + 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_622320990752_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 17 17 17 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/spline, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/spline, 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) = 5.69 | 5.69 | 5.69 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -36530.578 -36530.578 -36854.36 -36854.36 313.15 313.15 160151.28 160151.28 2159.4321 2159.4321 1000 -36184.302 -36184.302 -36505.656 -36505.656 310.80188 310.80188 158324.73 158324.73 62.815268 62.815268 Loop time of 64.5135 on 1 procs for 1000 steps with 8000 atoms Performance: 1.339 ns/day, 17.920 hours/ns, 15.501 timesteps/s, 124.005 katom-step/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 64.192 | 64.192 | 64.192 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.027959 | 0.027959 | 0.027959 | 0.0 | 0.04 Output | 0.00014833 | 0.00014833 | 0.00014833 | 0.0 | 0.00 Modify | 0.26691 | 0.26691 | 0.26691 | 0.0 | 0.41 Other | | 0.02616 | | | 0.04 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6725 ave 6725 max 6725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184000 ave 184000 max 184000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 368000 ave 368000 max 368000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 368000 Ave neighs/atom = 46 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 = ${P}" flag: Temp = 313.731277687764, Press = 6.46499641129824 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 5.692 | 5.692 | 5.692 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -36184.302 -36184.302 -36505.656 -36505.656 310.80188 310.80188 158324.73 158324.73 62.815268 62.815268 2000 -36181.926 -36181.926 -36503.903 -36503.903 311.40382 311.40382 158362.69 158362.69 -174.44321 -174.44321 Loop time of 63.3255 on 1 procs for 1000 steps with 8000 atoms Performance: 1.364 ns/day, 17.590 hours/ns, 15.791 timesteps/s, 126.331 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.048 | 63.048 | 63.048 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025682 | 0.025682 | 0.025682 | 0.0 | 0.04 Output | 0.00010478 | 0.00010478 | 0.00010478 | 0.0 | 0.00 Modify | 0.23325 | 0.23325 | 0.23325 | 0.0 | 0.37 Other | | 0.01868 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729 ave 6729 max 6729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195744 ave 195744 max 195744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391488 ave 391488 max 391488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391488 Ave neighs/atom = 48.936 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 158348.874822422 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0