# 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 ${neigh_skin} bin neighbor 2 bin # create a supercell with cubic lattice (fcc, bcc, sc, or diamond) # using 10*10*10 conventional (orthogonal) unit cells variable latticeconst_converted equal 4.032082714140415*${_u_distance} variable latticeconst_converted equal 4.032082714140415*1 lattice fcc ${latticeconst_converted} lattice fcc 4.03208271414042 Lattice spacing in x,y,z = 4.0320827 4.0320827 4.0320827 region simbox block 0 10 0 10 0 10 units lattice create_box 1 simbox Created orthogonal box = (0 0 0) to (40.320827 40.320827 40.320827) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (40.320827 40.320827 40.320827) create_atoms CPU = 0.001 seconds variable mass_converted equal 26.981538*${_u_mass} variable mass_converted equal 26.981538*1 kim interactions Al #=== BEGIN kim interactions ================================== pair_style kim EAM_ErcolessiAdams_1994_Al__MO_324507536345_003 WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1127) pair_coeff * * Al #=== END kim interactions ==================================== mass 1 ${mass_converted} mass 1 26.981538 # initial volume variable v equal vol # assign formula variable V0 equal ${v} # evaluate initial value variable V0 equal 65552.3549080547 variable V0_metal equal ${V0}/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 65552.3549080547/(${_u_distance}*${_u_distance}*${_u_distance}) variable V0_metal equal 65552.3549080547/(1*${_u_distance}*${_u_distance}) variable V0_metal equal 65552.3549080547/(1*1*${_u_distance}) variable V0_metal equal 65552.3549080547/(1*1*1) variable V0_metal_times1000 equal ${V0_metal}*1000 variable V0_metal_times1000 equal 65552.3549080547*1000 print "Initial system volume: ${V0_metal} Angstroms^3" Initial system volume: 65552.3549080547 Angstroms^3 # set the time step to 0.001 picoseconds variable timestep_converted equal 0.001*${_u_time} variable timestep_converted equal 0.001*1 timestep ${timestep_converted} timestep 0.001 variable temp_converted equal 253.15*${_u_temperature} variable temp_converted equal 253.15*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 253.15 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 253.15 ${temp_converted} ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 ${Tdamp_converted} iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso ${press_converted} ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 ${press_converted} ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 ${Pdamp_converted} fix ensemble all npt temp 253.15 253.15 0.01 iso 0 0 0.1 # compute the time averages of pressure, temperature, and volume, respectively # ignore the first 5000 timesteps variable etotal_metal equal etotal/${_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 "253.15 - 1.0" variable T_up equal "253.15 + 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_324507536345_003#item-citation @Comment { \documentclass{article} \usepackage{url} \begin{document} This Model originally published in \cite{MO_324507536345_002a} is archived in OpenKIM~\cite{MO_324507536345_002, tadmor:elliott:2011, elliott:tadmor:2011}. \bibliographystyle{vancouver} \bibliography{kimcite-MO_324507536345_002.bib} \end{document} } @Misc{MO_324507536345_002, author = {Ellad Tadmor}, title = {{G}lue potential ({EAM}-style) ({LAMMPS} cubic hermite tabulation) for {A}l developed by {E}rcolessi and {A}dams (1994) v002}, doi = {10.25950/58328955}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/58328955}}, keywords = {OpenKIM, Model, MO_324507536345_002}, publisher = {OpenKIM}, year = 2018, } @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 = {7}, pages = {17}, doi = {10.1007/s11837-011-0102-6}, } @Misc{elliott:tadmor:2011, author = {Ryan S. Elliott and Ellad B. Tadmor}, title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})}, howpublished = {\url{https://openkim.org/kim-api}}, publisher = {OpenKIM}, year = 2011, doi = {10.25950/ff8f563a}, } @Article{MO_324507536345_002a, author = {F. Ercolessi and J. B. Adams}, doi = {10.1209/0295-5075/26/8/005}, journal = {Europhysics Letters}, number = {8}, pages = {583}, title = {Interatomic Potentials from First-Principles Calculations: {T}he Force-Matching Method}, volume = {26}, year = {1994}, } 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, 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) = 5.37 | 5.37 | 5.37 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 0 -13309.144 -13309.144 -13440 -13440 253.15 253.15 65552.355 65552.355 2132.1713 2132.1713 1000 -13175.679 -13175.679 -13307.333 -13307.333 254.69523 254.69523 66484.417 66484.417 -1329.9495 -1329.9495 Loop time of 11.7253 on 1 procs for 1000 steps with 4000 atoms Performance: 7.369 ns/day, 3.257 hours/ns, 85.286 timesteps/s, 341.144 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 | 11.563 | 11.563 | 11.563 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.023271 | 0.023271 | 0.023271 | 0.0 | 0.20 Output | 0.00030776 | 0.00030776 | 0.00030776 | 0.0 | 0.00 Modify | 0.12656 | 0.12656 | 0.12656 | 0.0 | 1.08 Other | | 0.01244 | | | 0.11 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: 0 ave 0 max 0 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 = ${P}" flag: Temp = 253.124197313845, Press = -58.3578599262634 next a jump SELF top variable a loop 2000 run 1000 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 11 11 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step TotEng v_etotal_metal PotEng v_pe_metal Temp v_T_metal Volume v_V_metal Press v_P_metal 1000 -13175.679 -13175.679 -13307.333 -13307.333 254.69523 254.69523 66484.417 66484.417 -1329.9495 -1329.9495 2000 -13175.209 -13175.209 -13307.719 -13307.719 256.35034 256.35034 66301.949 66301.949 817.37812 817.37812 Loop time of 13.3182 on 1 procs for 1000 steps with 4000 atoms Performance: 6.487 ns/day, 3.699 hours/ns, 75.085 timesteps/s, 300.342 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.162 | 13.162 | 13.162 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020992 | 0.020992 | 0.020992 | 0.0 | 0.16 Output | 5.0053e-05 | 5.0053e-05 | 5.0053e-05 | 0.0 | 0.00 Modify | 0.12393 | 0.12393 | 0.12393 | 0.0 | 0.93 Other | | 0.01135 | | | 0.09 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5841 ave 5841 max 5841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 426986 ave 426986 max 426986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 426986 Ave neighs/atom = 106.7465 Neighbor list builds = 0 Dangerous builds = 0 if "${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_T253.15.out" else "print 'not_converged' file output/vol_T253.15.out" print '${V}' file output/vol_T253.15.out 66352.6341322581 print "LAMMPS calculation completed" LAMMPS calculation completed quit 0