# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.566999986767769*${_u_distance} variable latticeconst_converted equal 3.566999986767769*1 lattice diamond ${latticeconst_converted} lattice diamond 3.56699998676777 Lattice spacing in x,y,z = 3.567 3.567 3.567 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.67 35.67 35.67) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8000 atoms using lattice units in orthogonal box = (0 0 0) to (35.67 35.67 35.67) create_atoms CPU = 0.001 seconds variable mass_converted equal 12.0107*${_u_mass} variable mass_converted equal 12.0107*1 kim interactions C #=== BEGIN kim interactions ================================== pair_style kim MEAM_LAMMPS_LiyanageKimHouze_2014_FeC__MO_075279800195_002 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 45384.6847579196 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45384.6847579196/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 45384.6847579196/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 45384.6847579196/(1*1*${_u_distance}) variable V0_metal equal 45384.6847579196/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 45384.6847579196*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 45384.6847579196 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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_075279800195_002#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 11 11 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) = 11.89 | 11.89 | 11.89 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -58636.218 -58636.218 -58960 -58960 313.15 313.15 45384.685 45384.685 7620.1516 7620.1516 1000 -58293.95 -58293.95 -58625.014 -58625.014 320.19323 320.19323 45727.68 45727.68 5319.4893 5319.4893 Loop time of 110.4 on 1 procs for 1000 steps with 8000 atoms Performance: 0.783 ns/day, 30.667 hours/ns, 9.058 timesteps/s, 72.464 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 | 110.03 | 110.03 | 110.03 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.054875 | 0.054875 | 0.054875 | 0.0 | 0.05 Output | 0.00016502 | 0.00016502 | 0.00016502 | 0.0 | 0.00 Modify | 0.27877 | 0.27877 | 0.27877 | 0.0 | 0.25 Other | | 0.03517 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817 ave 12817 max 12817 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: 1.52e+06 ave 1.52e+06 max 1.52e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1520000 Ave neighs/atom = 190 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 = ${P}" flag: Temp = 313.291749284044, Press = 48.3758605833671 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -58293.95 -58293.95 -58625.014 -58625.014 320.19323 320.19323 45727.68 45727.68 5319.4893 5319.4893 2000 -58290.73 -58290.73 -58613.418 -58613.418 312.09185 312.09185 45797.032 45797.032 -464.00786 -464.00786 Loop time of 127.585 on 1 procs for 1000 steps with 8000 atoms Performance: 0.677 ns/day, 35.440 hours/ns, 7.838 timesteps/s, 62.703 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 127.21 | 127.21 | 127.21 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.052494 | 0.052494 | 0.052494 | 0.0 | 0.04 Output | 8.8556e-05 | 8.8556e-05 | 8.8556e-05 | 0.0 | 0.00 Modify | 0.28499 | 0.28499 | 0.28499 | 0.0 | 0.22 Other | | 0.03366 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817 ave 12817 max 12817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.51967e+06 ave 1.51967e+06 max 1.51967e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1519672 Ave neighs/atom = 189.959 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.065812346748, Press = -9.83452651356003 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -58290.73 -58290.73 -58613.418 -58613.418 312.09185 312.09185 45797.032 45797.032 -464.00786 -464.00786 3000 -58298.133 -58298.133 -58620.331 -58620.331 311.61839 311.61839 45797.699 45797.699 -1275.2917 -1275.2917 Loop time of 123.32 on 1 procs for 1000 steps with 8000 atoms Performance: 0.701 ns/day, 34.256 hours/ns, 8.109 timesteps/s, 64.872 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 122.96 | 122.96 | 122.96 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.050851 | 0.050851 | 0.050851 | 0.0 | 0.04 Output | 8.8566e-05 | 8.8566e-05 | 8.8566e-05 | 0.0 | 0.00 Modify | 0.27774 | 0.27774 | 0.27774 | 0.0 | 0.23 Other | | 0.03285 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817 ave 12817 max 12817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.51941e+06 ave 1.51941e+06 max 1.51941e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1519414 Ave neighs/atom = 189.92675 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.175161969789, Press = -8.06782797794805 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 3000 -58298.133 -58298.133 -58620.331 -58620.331 311.61839 311.61839 45797.699 45797.699 -1275.2917 -1275.2917 4000 -58295.265 -58295.265 -58620.418 -58620.418 314.47657 314.47657 45830.616 45830.616 -4286.1349 -4286.1349 Loop time of 122.272 on 1 procs for 1000 steps with 8000 atoms Performance: 0.707 ns/day, 33.964 hours/ns, 8.179 timesteps/s, 65.428 katom-step/s 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 121.92 | 121.92 | 121.92 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.050458 | 0.050458 | 0.050458 | 0.0 | 0.04 Output | 9.09e-05 | 9.09e-05 | 9.09e-05 | 0.0 | 0.00 Modify | 0.26815 | 0.26815 | 0.26815 | 0.0 | 0.22 Other | | 0.03258 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817 ave 12817 max 12817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.51942e+06 ave 1.51942e+06 max 1.51942e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1519422 Ave neighs/atom = 189.92775 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 313.166055211051, Press = -7.45539780290136 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 4000 -58295.265 -58295.265 -58620.418 -58620.418 314.47657 314.47657 45830.616 45830.616 -4286.1349 -4286.1349 5000 -58292.325 -58292.325 -58620.72 -58620.72 317.61176 317.61176 45820.896 45820.896 -3304.6377 -3304.6377 Loop time of 121.858 on 1 procs for 1000 steps with 8000 atoms Performance: 0.709 ns/day, 33.849 hours/ns, 8.206 timesteps/s, 65.650 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 121.51 | 121.51 | 121.51 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.050055 | 0.050055 | 0.050055 | 0.0 | 0.04 Output | 0.0001475 | 0.0001475 | 0.0001475 | 0.0 | 0.00 Modify | 0.26308 | 0.26308 | 0.26308 | 0.0 | 0.22 Other | | 0.03096 | | | 0.03 Nlocal: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12817 ave 12817 max 12817 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.51937e+06 ave 1.51937e+06 max 1.51937e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1519372 Ave neighs/atom = 189.9215 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T313.15.out" else "print 'not_converged' file output/vol_T313.15.out" print '${V}' file output/vol_T313.15.out 45783.9790039222 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0