LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified) using 1 OpenMP thread(s) per MPI task # ReaxFF potential for TATB system units real atom_style charge read_data data.tatb Reading data file ... triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288) WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221) 1 by 2 by 2 MPI processor grid reading atoms ... 384 atoms read_data CPU = 0.001 seconds pair_style reaxff control.reax_c.tatb WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99) WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99) pair_coeff * * ffield.reax C H O N Reading potential file ffield.reax with DATE: 2010-02-19 compute reax all pair reaxff variable eb equal c_reax[1] variable ea equal c_reax[2] variable elp equal c_reax[3] variable emol equal c_reax[4] variable ev equal c_reax[5] variable epen equal c_reax[6] variable ecoa equal c_reax[7] variable ehb equal c_reax[8] variable et equal c_reax[9] variable eco equal c_reax[10] variable ew equal c_reax[11] variable ep equal c_reax[12] variable efi equal c_reax[13] variable eqeq equal c_reax[14] neighbor 2.5 bin neigh_modify delay 0 every 5 check no fix 1 all nve fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff fix 4 all reaxff/bonds 5 bonds.reaxff compute bonds all reaxff/atom bonds yes variable nqeq equal f_2 # dumps out the local bond information dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3] # dumps out the peratom bond information dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*] thermo 5 thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq timestep 0.0625 #dump 1 all custom 100 dump.reaxff.tatb id type q x y z #dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 #dump_modify 2 pad 3 #dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 fix 3 all reaxff/species 1 5 5 species.tatb run 25 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, number = {4--5}, pages = {245--259} } - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical 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 = 5 steps, delay = 0 steps, check = no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 binsize = 6.25, bins = 5 4 3 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reaxff, perpetual attributes: half, newton off, ghost pair build: half/bin/ghost/newtoff stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 99.8 | 99.8 | 99.8 Mbytes Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 31 5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 8.5 10 2.352554 -44763.227 -44760.541 12288.582 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10 15 4.9013231 -44766.36 -44760.764 17716.979 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2473 0 6370.4136 7 20 7.8294566 -44769.686 -44760.747 25205.638 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4803 0 6355.2315 8.5 25 10.6979 -44772.904 -44760.691 34232.844 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3433 0 6336.8241 9.5 Loop time of 0.771261 on 4 procs for 25 steps with 384 atoms Performance: 0.175 ns/day, 137.113 hours/ns, 32.414 timesteps/s, 12.447 katom-step/s 99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56965 | 0.57597 | 0.58104 | 0.5 | 74.68 Neigh | 0.097254 | 0.097483 | 0.097832 | 0.1 | 12.64 Comm | 0.003347 | 0.0083916 | 0.014749 | 4.5 | 1.09 Output | 0.00131 | 0.0022935 | 0.0026708 | 1.2 | 0.30 Modify | 0.086284 | 0.086988 | 0.088382 | 0.3 | 11.28 Other | | 0.0001324 | | | 0.02 Nlocal: 96 ave 96 max 96 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 5118 ave 5118 max 5118 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 79754 ave 79754 max 79754 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319016 Ave neighs/atom = 830.77083 Neighbor list builds = 5 Dangerous builds not checked Total wall time: 0:00:00