# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.56523135304451*${_u_distance} variable latticeconst_converted equal 3.56523135304451*1 lattice diamond ${latticeconst_converted} lattice diamond 3.56523135304451 Lattice spacing in x,y,z = 3.5652314 3.5652314 3.5652314 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.652314 35.652314 35.652314) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (35.652314 35.652314 35.652314) create_atoms CPU = 0.001 seconds variable mass_converted equal 12.0107*${_u_mass} variable mass_converted equal 12.0107*1 kim interactions C #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style lcbop pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXfQU7MW/C.lcbop C Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXfQU7MW/C.lcbop with DATE: 2012-05-22 #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 12.0107 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 45317.2086511454 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45317.2086511454/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45317.2086511454/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 45317.2086511454/(1*1*${_u_distance}) variable V0_metal equal 45317.2086511454/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 45317.2086511454*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 45317.2086511454 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/SM_469631949122_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 = 8.6 ghost atom cutoff = 8.6 binsize = 4.3, bins = 9 9 9 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lcbop, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -58523.08 -58523.08 -58805.504 -58805.504 273.15 273.15 45317.209 45317.209 6657.1466 6657.1466 1000 -58253.057 -58253.057 -58528.701 -58528.701 266.59267 266.59267 45543.426 45543.426 212.98881 212.98881 Loop time of 83.2658 on 1 procs for 1000 steps with 8000 atoms Performance: 1.038 ns/day, 23.129 hours/ns, 12.010 timesteps/s, 96.078 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 | 82.882 | 82.882 | 82.882 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.071592 | 0.071592 | 0.071592 | 0.0 | 0.09 Output | 0.00017477 | 0.00017477 | 0.00017477 | 0.0 | 0.00 Modify | 0.27621 | 0.27621 | 0.27621 | 0.0 | 0.33 Other | | 0.03554 | | | 0.04 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17695 ave 17695 max 17695 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: 3.712e+06 ave 3.712e+06 max 3.712e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3712000 Ave neighs/atom = 464 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 = ${P}" flag: Temp = 273.183579700832, Press = 34.9278758627104 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -58253.057 -58253.057 -58528.701 -58528.701 266.59267 266.59267 45543.426 45543.426 212.98881 212.98881 2000 -58251.138 -58251.138 -58532.467 -58532.467 272.09109 272.09109 45587.16 45587.16 -3957.7062 -3957.7062 Loop time of 88.1049 on 1 procs for 1000 steps with 8000 atoms Performance: 0.981 ns/day, 24.474 hours/ns, 11.350 timesteps/s, 90.801 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 87.714 | 87.714 | 87.714 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.071187 | 0.071187 | 0.071187 | 0.0 | 0.08 Output | 0.00010717 | 0.00010717 | 0.00010717 | 0.0 | 0.00 Modify | 0.28404 | 0.28404 | 0.28404 | 0.0 | 0.32 Other | | 0.03556 | | | 0.04 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17695 ave 17695 max 17695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.70875e+06 ave 3.70875e+06 max 3.70875e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3708752 Ave neighs/atom = 463.594 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 273.041233052135, Press = -5.60543988684067 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -58251.138 -58251.138 -58532.467 -58532.467 272.09109 272.09109 45587.16 45587.16 -3957.7062 -3957.7062 3000 -58250.369 -58250.369 -58533.877 -58533.877 274.1986 274.1986 45549.922 45549.922 -335.44651 -335.44651 Loop time of 85.5447 on 1 procs for 1000 steps with 8000 atoms Performance: 1.010 ns/day, 23.762 hours/ns, 11.690 timesteps/s, 93.518 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 85.16 | 85.16 | 85.16 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.06861 | 0.06861 | 0.06861 | 0.0 | 0.08 Output | 0.0001037 | 0.0001037 | 0.0001037 | 0.0 | 0.00 Modify | 0.28151 | 0.28151 | 0.28151 | 0.0 | 0.33 Other | | 0.03474 | | | 0.04 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17695 ave 17695 max 17695 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 3.7081e+06 ave 3.7081e+06 max 3.7081e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3708100 Ave neighs/atom = 463.5125 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T273.15.out" else "print 'not_converged' file output/vol_T273.15.out" print '${V}' file output/vol_T273.15.out 45547.5853816863 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0