# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.5612920299172397*${_u_distance} variable latticeconst_converted equal 3.5612920299172397*1 lattice diamond ${latticeconst_converted} lattice diamond 3.56129202991724 Lattice spacing in x,y,z = 3.561292 3.561292 3.561292 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.61292 35.61292 35.61292) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (35.61292 35.61292 35.61292) create_atoms CPU = 0.001 seconds variable mass_converted equal 12.0107*${_u_mass} variable mass_converted equal 12.0107*1 kim interactions C #=== BEGIN kim interactions ================================== pair_style kim EDIP_LAMMPS_JiangMorganSzlufarska_2012_SiC__MO_667792548433_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 45167.1578417994 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45167.1578417994/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45167.1578417994/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 45167.1578417994/(1*1*${_u_distance}) variable V0_metal equal 45167.1578417994/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 45167.1578417994*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 45167.1578417994 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_667792548433_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 = 4.941586 ghost atom cutoff = 4.941586 binsize = 2.470793, bins = 15 15 15 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) = 8.652 | 8.652 | 8.652 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -58650.051 -58650.051 -58994.512 -58994.512 333.15 333.15 45167.158 45167.158 8145.815 8145.815 1000 -58294.653 -58294.653 -58634.044 -58634.044 328.24616 328.24616 45376.484 45376.484 -2369.0424 -2369.0424 Loop time of 14.7835 on 1 procs for 1000 steps with 8000 atoms Performance: 5.844 ns/day, 4.107 hours/ns, 67.643 timesteps/s, 541.144 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 | 14.489 | 14.489 | 14.489 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.032863 | 0.032863 | 0.032863 | 0.0 | 0.22 Output | 9.2944e-05 | 9.2944e-05 | 9.2944e-05 | 0.0 | 0.00 Modify | 0.23956 | 0.23956 | 0.23956 | 0.0 | 1.62 Other | | 0.02165 | | | 0.15 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 = ${P}" flag: Temp = 332.267132389901, Press = -189.230748944639 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.941586 ghost atom cutoff = 4.941586 binsize = 2.470793, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.904 | 8.904 | 8.904 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -58294.653 -58294.653 -58634.044 -58634.044 328.24616 328.24616 45376.484 45376.484 -2369.0424 -2369.0424 2000 -58292.803 -58292.803 -58634.641 -58634.641 330.61336 330.61336 45342.408 45342.408 1117.6101 1117.6101 Loop time of 21.1051 on 1 procs for 1000 steps with 8000 atoms Performance: 4.094 ns/day, 5.863 hours/ns, 47.382 timesteps/s, 379.055 katom-step/s 74.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.683 | 20.683 | 20.683 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.036946 | 0.036946 | 0.036946 | 0.0 | 0.18 Output | 7.8588e-05 | 7.8588e-05 | 7.8588e-05 | 0.0 | 0.00 Modify | 0.35136 | 0.35136 | 0.35136 | 0.0 | 1.66 Other | | 0.03414 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 688460 ave 688460 max 688460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 688460 Ave neighs/atom = 86.0575 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 333.271558414184, Press = -9.21765257541784 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.941586 ghost atom cutoff = 4.941586 binsize = 2.470793, bins = 15 15 15 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 8.904 | 8.904 | 8.904 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -58292.803 -58292.803 -58634.641 -58634.641 330.61336 330.61336 45342.408 45342.408 1117.6101 1117.6101 3000 -58297.187 -58297.187 -58643.109 -58643.109 334.56327 334.56327 45347.964 45347.964 545.54184 545.54184 Loop time of 15.2572 on 1 procs for 1000 steps with 8000 atoms Performance: 5.663 ns/day, 4.238 hours/ns, 65.543 timesteps/s, 524.342 katom-step/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.949 | 14.949 | 14.949 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.033495 | 0.033495 | 0.033495 | 0.0 | 0.22 Output | 8.2946e-05 | 8.2946e-05 | 8.2946e-05 | 0.0 | 0.00 Modify | 0.25041 | 0.25041 | 0.25041 | 0.0 | 1.64 Other | | 0.02436 | | | 0.16 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8601 ave 8601 max 8601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 688420 ave 688420 max 688420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 688420 Ave neighs/atom = 86.0525 Neighbor list builds = 0 Dangerous builds = 0 if "${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 45353.6679798466 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0