# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 3.521391734480858*${_u_distance} variable latticeconst_converted equal 3.521391734480858*1 lattice fcc ${latticeconst_converted} lattice fcc 3.52139173448086 Lattice spacing in x,y,z = 3.5213917 3.5213917 3.5213917 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (35.213917 35.213917 35.213917) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (35.213917 35.213917 35.213917) create_atoms CPU = 0.001 seconds variable mass_converted equal 58.6934*${_u_mass} variable mass_converted equal 58.6934*1 kim interactions Ni #=== BEGIN kim interactions ================================== variable kim_update equal 0 variable kim_periodic equal 1 pair_style meam/c pair_coeff * * /tmp/kim-shared-library-parameter-file-directory-XXXXXXq6W8Ds/library.VNiTi_maisel.meam V Ni Ti /tmp/kim-shared-library-parameter-file-directory-XXXXXXq6W8Ds/VNiTi_maisel.meam Ni #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 58.6934 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 43665.9608973572 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9608973572/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9608973572/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 43665.9608973572/(1*1*${_u_distance}) variable V0_metal equal 43665.9608973572/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 43665.9608973572*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 43665.9608973572 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_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/SM_971529344487_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 11 11 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair meam/c, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair meam/c, perpetual, half/full from (1) attributes: half, newton on pair build: halffull/newton stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 18.72 | 18.72 | 18.72 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -17638.129 -17638.129 -17800 -17800 313.15 313.15 43665.961 43665.961 3959.549 3959.549 1000 -17474.998 -17474.998 -17634.706 -17634.706 308.9657 308.9657 44201.257 44201.257 -1919.4524 -1919.4524 Loop time of 56.1496 on 1 procs for 1000 steps with 4000 atoms Performance: 1.539 ns/day, 15.597 hours/ns, 17.810 timesteps/s, 71.238 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 | 55.979 | 55.979 | 55.979 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023747 | 0.023747 | 0.023747 | 0.0 | 0.04 Output | 0.00016043 | 0.00016043 | 0.00016043 | 0.0 | 0.00 Modify | 0.13253 | 0.13253 | 0.13253 | 0.0 | 0.24 Other | | 0.01453 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 268000 ave 268000 max 268000 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 536000 ave 536000 max 536000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 536000 Ave neighs/atom = 134 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 = ${P}" flag: Temp = 311.493327307397, Press = -23.2724975956745 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 18.78 | 18.78 | 18.78 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -17474.998 -17474.998 -17634.706 -17634.706 308.9657 308.9657 44201.257 44201.257 -1919.4524 -1919.4524 2000 -17476.249 -17476.249 -17636.29 -17636.29 309.60956 309.60956 44138.047 44138.047 661.66291 661.66291 Loop time of 70.95 on 1 procs for 1000 steps with 4000 atoms Performance: 1.218 ns/day, 19.708 hours/ns, 14.094 timesteps/s, 56.378 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.762 | 70.762 | 70.762 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026163 | 0.026163 | 0.026163 | 0.0 | 0.04 Output | 8.7144e-05 | 8.7144e-05 | 8.7144e-05 | 0.0 | 0.00 Modify | 0.14472 | 0.14472 | 0.14472 | 0.0 | 0.20 Other | | 0.01679 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6193 ave 6193 max 6193 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 270639 ave 270639 max 270639 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 541278 ave 541278 max 541278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541278 Ave neighs/atom = 135.3195 Neighbor list builds = 0 Dangerous builds = 0 if "${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 = ${P}" flag: Temp = 312.952093796299, Press = 7.55202020893608 next a jump SELF top variable a loop 2000 run 1000 Per MPI rank memory allocation (min/avg/max) = 18.78 | 18.78 | 18.78 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 2000 -17476.249 -17476.249 -17636.29 -17636.29 309.60956 309.60956 44138.047 44138.047 661.66291 661.66291 3000 -17473.823 -17473.823 -17634.418 -17634.418 310.6818 310.6818 44174.07 44174.07 -583.03026 -583.03026 Loop time of 68.4919 on 1 procs for 1000 steps with 4000 atoms Performance: 1.261 ns/day, 19.026 hours/ns, 14.600 timesteps/s, 58.401 katom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 68.318 | 68.318 | 68.318 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.024216 | 0.024216 | 0.024216 | 0.0 | 0.04 Output | 8.499e-05 | 8.499e-05 | 8.499e-05 | 0.0 | 0.00 Modify | 0.13471 | 0.13471 | 0.13471 | 0.0 | 0.20 Other | | 0.01478 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6208 ave 6208 max 6208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 270625 ave 270625 max 270625 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 541250 ave 541250 max 541250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541250 Ave neighs/atom = 135.3125 Neighbor list builds = 0 Dangerous builds = 0 if "${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 44155.2208398115 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0