# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.426835507154466*${_u_distance} variable latticeconst_converted equal 5.426835507154466*1 lattice diamond ${latticeconst_converted} lattice diamond 5.42683550715447 Lattice spacing in x,y,z = 5.4268355 5.4268355 5.4268355 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (54.268355 54.268355 54.268355) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (54.268355 54.268355 54.268355) create_atoms CPU = 0.001 seconds variable mass_converted equal 28.0855*${_u_mass} variable mass_converted equal 28.0855*1 kim interactions Si #=== BEGIN kim interactions ================================== pair_style kim ThreeBodyBondOrder_KDS_KhorDasSarma_1988_Si__MO_722489435928_000 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Si #=== 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 159823.255831311 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 159823.255831311/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 159823.255831311/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 159823.255831311/(1*1*${_u_distance}) variable V0_metal equal 159823.255831311/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 159823.255831311*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 159823.255831311 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/MO_722489435928_000#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 = 5.4656875 ghost atom cutoff = 5.4656875 binsize = 2.7328438, bins = 20 20 20 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) = 4.314 | 4.314 | 4.314 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -37599.862 -37599.862 -37923.644 -37923.644 313.15 313.15 159823.26 159823.26 2163.8756 2163.8756 1000 -37269.227 -37269.227 -37593.85 -37593.85 313.96307 313.96307 161121.11 161121.11 -596.58409 -596.58409 Loop time of 28.9617 on 1 procs for 1000 steps with 8000 atoms Performance: 2.983 ns/day, 8.045 hours/ns, 34.528 timesteps/s, 276.227 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.625 | 28.625 | 28.625 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032795 | 0.032795 | 0.032795 | 0.0 | 0.11 Output | 8.5541e-05 | 8.5541e-05 | 8.5541e-05 | 0.0 | 0.00 Modify | 0.27061 | 0.27061 | 0.27061 | 0.0 | 0.93 Other | | 0.03287 | | | 0.11 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: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272000 ave 272000 max 272000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272000 Ave neighs/atom = 34 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 = ${P}" flag: Temp = 312.708591177337, Press = -6.77240838084348 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.4656875 ghost atom cutoff = 5.4656875 binsize = 2.7328438, bins = 20 20 20 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.309 | 4.309 | 4.309 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -37269.227 -37269.227 -37593.85 -37593.85 313.96307 313.96307 161121.11 161121.11 -596.58409 -596.58409 2000 -37211.938 -37211.938 -37541.218 -37541.218 318.46702 318.46702 161222.61 161222.61 160.21465 160.21465 Loop time of 33.0125 on 1 procs for 1000 steps with 8000 atoms Performance: 2.617 ns/day, 9.170 hours/ns, 30.292 timesteps/s, 242.333 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 32.656 | 32.656 | 32.656 | 0.0 | 98.92 Neigh | 0.009466 | 0.009466 | 0.009466 | 0.0 | 0.03 Comm | 0.02988 | 0.02988 | 0.02988 | 0.0 | 0.09 Output | 0.00011969 | 0.00011969 | 0.00011969 | 0.0 | 0.00 Modify | 0.28985 | 0.28985 | 0.28985 | 0.0 | 0.88 Other | | 0.02717 | | | 0.08 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6068 ave 6068 max 6068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 253628 ave 253628 max 253628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253628 Ave neighs/atom = 31.7035 Neighbor list builds = 1 Dangerous builds = 0 if "${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 161074.705199536 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0