160 lines
7.7 KiB
Groff
160 lines
7.7 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
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using 1 OpenMP thread(s) per MPI task
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# ReaxFF potential for TATB system
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units real
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atom_style charge
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read_data data.tatb
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Reading data file ...
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triclinic box = (0 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
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WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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384 atoms
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read_data CPU = 0.001 seconds
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pair_style reaxff control.reax_c.tatb
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WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
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WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
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WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
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pair_coeff * * ffield.reax C H O N
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Reading potential file ffield.reax with DATE: 2010-02-19
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compute reax all pair reaxff
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variable eb equal c_reax[1]
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variable ea equal c_reax[2]
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variable elp equal c_reax[3]
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variable emol equal c_reax[4]
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variable ev equal c_reax[5]
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variable epen equal c_reax[6]
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variable ecoa equal c_reax[7]
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variable ehb equal c_reax[8]
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variable et equal c_reax[9]
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variable eco equal c_reax[10]
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variable ew equal c_reax[11]
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variable ep equal c_reax[12]
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variable efi equal c_reax[13]
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variable eqeq equal c_reax[14]
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neighbor 2.5 bin
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neigh_modify delay 0 every 5 check no
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fix 1 all nve
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fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
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fix 4 all reaxff/bonds 5 bonds.reaxff
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compute bonds all reaxff/atom bonds yes
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variable nqeq equal f_2
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# dumps out the local bond information
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dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
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# dumps out the peratom bond information
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dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
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thermo 5
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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
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timestep 0.0625
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#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
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#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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fix 3 all reaxff/species 1 5 5 species.tatb
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run 25
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- pair reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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number = {4--5},
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pages = {245--259}
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}
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- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
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@Article{Aktulga12,
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author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
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title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
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journal = {Parallel Computing},
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year = 2012,
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volume = 38,
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pages = {245--259}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update: every = 5 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25, bins = 5 4 3
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair reaxff, perpetual
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attributes: half, newton off, ghost
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pair build: half/bin/ghost/newtoff
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stencil: full/ghost/bin/3d
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bin: standard
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(2) fix qeq/reaxff, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 148.7 | 148.7 | 148.7 Mbytes
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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
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0 0 -44760.998 -44760.998 7827.7886 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6392 0 6391.0272 31.5
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5 0.61603945 -44761.698 -44760.994 8934.6263 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1931 0 6388.6691 10.5
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10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9689 0 6381.7066 8.5
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15 4.9013324 -44766.36 -44760.764 17716.909 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56848 -1566.3829 252.95174 -654.96611 18835.777 -8719.2637 0 6370.4299 9
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20 7.8294652 -44769.686 -44760.747 25205.631 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4897 0 6355.241 10
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25 10.697902 -44772.904 -44760.691 34232.78 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.364 0 6336.8448 10
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Loop time of 1.24712 on 1 procs for 25 steps with 384 atoms
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Performance: 0.108 ns/day, 221.710 hours/ns, 20.046 timesteps/s, 7.698 katom-step/s
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99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.87392 | 0.87392 | 0.87392 | 0.0 | 70.07
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Neigh | 0.1672 | 0.1672 | 0.1672 | 0.0 | 13.41
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Comm | 0.0010267 | 0.0010267 | 0.0010267 | 0.0 | 0.08
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Output | 0.0031358 | 0.0031358 | 0.0031358 | 0.0 | 0.25
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Modify | 0.20171 | 0.20171 | 0.20171 | 0.0 | 16.17
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Other | | 0.0001369 | | | 0.01
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Nlocal: 384 ave 384 max 384 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 7559 ave 7559 max 7559 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 286828 ave 286828 max 286828 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 286828
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Ave neighs/atom = 746.94792
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Neighbor list builds = 5
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Dangerous builds not checked
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Total wall time: 0:00:01
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