LAMMPS (10 Feb 2021) # 3d Lennard-Jones melt # # This example requires that the KIM Simulator Model (PM) # `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000` # is installed. This can be done with the command # kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 # If this command does not work, you may need to setup your PATH to find the utility. # If you installed the kim-api using the LAMMPS CMake build, you can do the following # (where the current working directory is assumed to be the LAMMPS build directory) # source ./kim_build-prefix/bin/kim-api-activate # If you installed the kim-api using the LAMMPS Make build, you can do the following # (where the current working directory is assumed to be the LAMMPS src directory) # source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate # (where you should relplace X.Y.Z with the appropriate kim-api version number). # # See `https://openkim.org/doc/obtaining-models` for alternative options. # variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real #=== BEGIN kim init ========================================== # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 10 Feb 2021 # units real neighbor 2.0 bin # Angstroms timestep 1.0 # femtoseconds atom_style charge neigh_modify one 4000 #=== END kim init ============================================ lattice fcc 4.4300 Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 32000 atoms create_atoms CPU = 0.003 seconds kim interactions O #=== BEGIN kim interactions ================================== variable kim_periodic equal 1 pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/lmp_control safezone 2.0 mincap 100 pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx O Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx with DATE: 2010-02-19 fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/param.qeq #=== END kim interactions ==================================== mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 all nve #fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 run 100 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/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_107643900657_000#item-citation @Comment { \documentclass{article} \usepackage{url} \begin{document} This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}. \bibliographystyle{vancouver} \bibliography{kimcite-SM_107643900657_000.bib} \end{document} } @Misc{SM_107643900657_000, author = {Ellad Tadmor}, title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000}, doi = {10.25950/acd3fc89}, howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}}, keywords = {OpenKIM, Simulator Model, SM_107643900657_000}, publisher = {OpenKIM}, year = 2019, } @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{SM_107643900657_000a, author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.}, doi = {10.1103/PhysRevLett.91.098301}, issue = {9}, journal = {Physical Review Letters}, month = {Aug}, numpages = {4}, pages = {098301}, publisher = {American Physical Society}, title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}}, volume = {91}, year = {2003}, } - pair reax/c command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } - fix qeq/reax command: @Article{Aktulga12, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } 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: 4000, page size: 100000 master list distance cutoff = 10.3 ghost atom cutoff = 10.3 binsize = 5.15, bins = 18 18 18 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 1803.0 | 1803.0 | 1803.0 Mbytes Step Temp E_pair E_mol TotEng Press 0 200 -39091.147 0 -20014.559 19501.107 100 63.198252 -26042.062 0 -20014.027 21497.661 Loop time of 38.6526 on 1 procs for 100 steps with 32000 atoms Performance: 0.224 ns/day, 107.368 hours/ns, 2.587 timesteps/s 99.1% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.493 | 23.493 | 23.493 | 0.0 | 60.78 Neigh | 0.4498 | 0.4498 | 0.4498 | 0.0 | 1.16 Comm | 0.020568 | 0.020568 | 0.020568 | 0.0 | 0.05 Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00 Modify | 14.677 | 14.677 | 14.677 | 0.0 | 37.97 Other | | 0.01223 | | | 0.03 Nlocal: 32000.0 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 26825.0 ave 26825 max 26825 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.73924e+06 ave 3.73924e+06 max 3.73924e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3739236 Ave neighs/atom = 116.85112 Neighbor list builds = 3 Dangerous builds = 0 Total wall time: 0:00:39