# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.5562932789325723*${_u_distance} variable latticeconst_converted equal 3.5562932789325723*1 lattice diamond ${latticeconst_converted} lattice diamond 3.55629327893257 Lattice spacing in x,y,z = 3.5562933 3.5562933 3.5562933 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.562933 35.562933 35.562933) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (35.562933 35.562933 35.562933) create_atoms CPU = 0.001 seconds variable mass_converted equal 12.0107*${_u_mass} variable mass_converted equal 12.0107*1 kim interactions C #=== BEGIN kim interactions ================================== pair_style kim Tersoff_LAMMPS_Tersoff_1994_SiC__MO_794973922560_000 pair_coeff * * C #=== 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 44977.2301895718 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44977.2301895718/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 44977.2301895718/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 44977.2301895718/(1*1*${_u_distance}) variable V0_metal equal 44977.2301895718/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 44977.2301895718*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 44977.2301895718 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 333.15*${_u_temperature} variable temp_converted equal 333.15*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 333.15 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 333.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 333.15 333.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "333.15 - 1.0" variable T_up equal "333.15 + 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_794973922560_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 ghost atom cutoff = 5 binsize = 2.5, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.81 | 10.81 | 10.81 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -59439.447 -59439.447 -59783.908 -59783.908 333.15 333.15 44977.23 44977.23 8180.2514 8180.2514 1000 -59088.468 -59088.468 -59423.868 -59423.868 324.38571 324.38571 45206.898 45206.898 584.38584 584.38584 Loop time of 37.5441 on 1 procs for 1000 steps with 8000 atoms Performance: 2.301 ns/day, 10.429 hours/ns, 26.635 timesteps/s, 213.083 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 | 37.232 | 37.232 | 37.232 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.036711 | 0.036711 | 0.036711 | 0.0 | 0.10 Output | 0.00014109 | 0.00014109 | 0.00014109 | 0.0 | 0.00 Modify | 0.25102 | 0.25102 | 0.25102 | 0.0 | 0.67 Other | | 0.02466 | | | 0.07 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 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: 688000 ave 688000 max 688000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 688000 Ave neighs/atom = 86 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 = ${P}" flag: Temp = 333.137042246985, Press = -22.4095514866314 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5 ghost atom cutoff = 5 binsize = 2.5, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.19 | 11.19 | 11.19 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -59088.468 -59088.468 -59423.868 -59423.868 324.38571 324.38571 45206.898 45206.898 584.38584 584.38584 2000 -59083.447 -59083.447 -59434.222 -59434.222 339.25675 339.25675 45239.789 45239.789 -2552.8176 -2552.8176 Loop time of 40.5 on 1 procs for 1000 steps with 8000 atoms Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s, 197.531 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.167 | 40.167 | 40.167 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.038303 | 0.038303 | 0.038303 | 0.0 | 0.09 Output | 8.7284e-05 | 8.7284e-05 | 8.7284e-05 | 0.0 | 0.00 Modify | 0.26759 | 0.26759 | 0.26759 | 0.0 | 0.66 Other | | 0.02751 | | | 0.07 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 704484 ave 704484 max 704484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 704484 Ave neighs/atom = 88.0605 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.137863981713, Press = -6.47697687414414 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5 ghost atom cutoff = 5 binsize = 2.5, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.19 | 11.19 | 11.19 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -59083.447 -59083.447 -59434.222 -59434.222 339.25675 339.25675 45239.789 45239.789 -2552.8176 -2552.8176 3000 -59081.909 -59081.909 -59442.751 -59442.751 348.99318 348.99318 45258.1 45258.1 -4536.1564 -4536.1564 Loop time of 38.5618 on 1 procs for 1000 steps with 8000 atoms Performance: 2.241 ns/day, 10.712 hours/ns, 25.932 timesteps/s, 207.459 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.251 | 38.251 | 38.251 | 0.0 | 99.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.035403 | 0.035403 | 0.035403 | 0.0 | 0.09 Output | 6.2327e-05 | 6.2327e-05 | 6.2327e-05 | 0.0 | 0.00 Modify | 0.25165 | 0.25165 | 0.25165 | 0.0 | 0.65 Other | | 0.02381 | | | 0.06 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 703208 ave 703208 max 703208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 703208 Ave neighs/atom = 87.901 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 332.930987235755, Press = -8.12746707070799 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5 ghost atom cutoff = 5 binsize = 2.5, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 11.19 | 11.19 | 11.19 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -59081.909 -59081.909 -59442.751 -59442.751 348.99318 348.99318 45258.1 45258.1 -4536.1564 -4536.1564 4000 -59093.863 -59093.863 -59427.93 -59427.93 323.09773 323.09773 45165.222 45165.222 4560.2555 4560.2555 Loop time of 38.3806 on 1 procs for 1000 steps with 8000 atoms Performance: 2.251 ns/day, 10.661 hours/ns, 26.055 timesteps/s, 208.438 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.087 | 38.087 | 38.087 | 0.0 | 99.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.034009 | 0.034009 | 0.034009 | 0.0 | 0.09 Output | 7.0192e-05 | 7.0192e-05 | 7.0192e-05 | 0.0 | 0.00 Modify | 0.24027 | 0.24027 | 0.24027 | 0.0 | 0.63 Other | | 0.01964 | | | 0.05 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 702834 ave 702834 max 702834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 702834 Ave neighs/atom = 87.85425 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T333.15.out" else "print 'not_converged' file output/vol_T333.15.out" print '${V}' file output/vol_T333.15.out 45212.2283413887 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0