# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 5.429000049829484*${_u_distance} variable latticeconst_converted equal 5.429000049829484*1 lattice diamond ${latticeconst_converted} lattice diamond 5.42900004982948 Lattice spacing in x,y,z = 5.429 5.429 5.429 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (54.29 54.29 54.29) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (54.29 54.29 54.29) create_atoms CPU = 0.001 seconds variable mass_converted equal 28.0855*${_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 tersoff/mod pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXX2MW1av/Si.tersoff.mod Si Reading tersoff/mod potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXX2MW1av/Si.tersoff.mod with DATE: 2013-07-26 #=== 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 160014.572995028 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160014.572995028/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 160014.572995028/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 160014.572995028/(1*1*${_u_distance}) variable V0_metal equal 160014.572995028/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 160014.572995028*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 160014.572995028 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_773333226968_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 = 5.3 ghost atom cutoff = 5.3 binsize = 2.65, bins = 21 21 21 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tersoff/mod, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.102 | 4.102 | 4.102 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -36778.249 -36778.249 -37039.994 -37039.994 253.15 253.15 160014.57 160014.57 1747.1759 1747.1759 1000 -36499.56 -36499.56 -36769.194 -36769.194 260.77963 260.77963 160772.69 160772.69 234.77397 234.77397 Loop time of 15.4482 on 1 procs for 1000 steps with 8000 atoms Performance: 5.593 ns/day, 4.291 hours/ns, 64.733 timesteps/s, 517.860 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 | 15.164 | 15.164 | 15.164 | 0.0 | 98.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.021435 | 0.021435 | 0.021435 | 0.0 | 0.14 Output | 0.00010539 | 0.00010539 | 0.00010539 | 0.0 | 0.00 Modify | 0.24157 | 0.24157 | 0.24157 | 0.0 | 1.56 Other | | 0.02058 | | | 0.13 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4995 ave 4995 max 4995 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: 224000 ave 224000 max 224000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224000 Ave neighs/atom = 28 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 = ${P}" flag: Temp = 253.725066348691, Press = -23.5230157252551 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 4.103 | 4.103 | 4.103 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -36499.56 -36499.56 -36769.194 -36769.194 260.77963 260.77963 160772.69 160772.69 234.77397 234.77397 2000 -36512.89 -36512.89 -36770.587 -36770.587 249.23463 249.23463 160887.9 160887.9 -591.3988 -591.3988 Loop time of 16.3434 on 1 procs for 1000 steps with 8000 atoms Performance: 5.287 ns/day, 4.540 hours/ns, 61.187 timesteps/s, 489.494 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.048 | 16.048 | 16.048 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.02011 | 0.02011 | 0.02011 | 0.0 | 0.12 Output | 7.9058e-05 | 7.9058e-05 | 7.9058e-05 | 0.0 | 0.00 Modify | 0.25621 | 0.25621 | 0.25621 | 0.0 | 1.57 Other | | 0.0191 | | | 0.12 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5001 ave 5001 max 5001 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225434 ave 225434 max 225434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225434 Ave neighs/atom = 28.17925 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 160798.283745527 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0