lammpstutorials-inputs/tutorial5/deform.log at 29Aug2024 · lammpstutorials/lammpstutorials-inputs

278 lines (266 loc) · 20.8 KB
  using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
Reading data file ...
  orthogonal box = (-3.5006045 2.3124413 1.3986991) to (24.086182 18.273136 19.186879)
  1 by 1 by 1 MPI processor grid
  reading atom labelmap ...
  reading atoms ...
  576 atoms
  reading velocities ...
  576 velocities
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.018 seconds
WARNING: Van der Waals parameters for element SI indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:249)
WARNING: Van der Waals parameters for element AL indicate inner wall+shielding, but earlier atoms indicate a different van der Waals method. This may cause division-by-zero errors. Keeping van der Waals setting for earlier atoms. (src/REAXFF/reaxff_ffield.cpp:249)
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
192 atoms in group grpSi
384 atoms in group grpO
WARNING: Detected non-ASCII characters in input. Will try to continue by replacing with ASCII equivalents where known. (src/input.cpp:478)
WARNING: Resetting reneighboring criteria to 'delay 0 every 5 check no' due to fix reaxff/species averaging of bond data (src/REAXFF/fix_reaxff_species.cpp:126)
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
- pair reaxff/omp and fix qeq/reaxff/omp command: doi:10.1177/1094342017746221
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Last active /omp style is pair_style reaxff/omp
Neighbor list info ...
  update: every = 5 steps, delay = 0 steps, check = no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 3 3
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair reaxff/omp, perpetual
      attributes: half, newton off, ghost, omp
      pair build: half/bin/newtoff/ghost/omp
      stencil: full/ghost/bin/3d
      bin: standard
  (2) fix qeq/reaxff/omp, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
Setting up Verlet run ...
  Unit style    : real
  Current step  : 0
  Time step     : 0.5
Per MPI rank memory allocation (min/avg/max) = 256.1 | 256.1 | 256.1 Mbytes
   Step          Temp          TotEng         Press          Volume         v_qSi           v_qO     
Loop time of 250.485 on 8 procs for 5000 steps with 576 atoms
Performance: 0.862 ns/day, 27.832 hours/ns, 19.961 timesteps/s, 11.498 katom-step/s
806.8% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 144.69     | 144.69     | 144.69     |   0.0 | 57.76
Bond    | 0.0014677  | 0.0014677  | 0.0014677  |   0.0 |  0.00
Neigh   | 35.626     | 35.626     | 35.626     |   0.0 | 14.22
Comm    | 0.6995     | 0.6995     | 0.6995     |   0.0 |  0.28
Output  | 4.9172     | 4.9172     | 4.9172     |   0.0 |  1.96
Modify  | 64.515     | 64.515     | 64.515     |   0.0 | 25.76
Nlocal:            576 ave         576 max         576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           5676 ave        5676 max        5676 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         240364 ave      240364 max      240364 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 240364
Ave neighs/atom = 417.29861
Ave special neighs/atom = 0
Neighbor list builds = 1000
Dangerous builds not checked
Last active /omp style is pair_style reaxff/omp
Setting up Verlet run ...
  Unit style    : real
  Current step  : 5000
  Time step     : 0.5
Per MPI rank memory allocation (min/avg/max) = 256.8 | 256.8 | 256.8 Mbytes
   Step          Temp          TotEng         Press          Volume         v_qSi           v_qO     
Loop time of 1008.96 on 8 procs for 25000 steps with 576 atoms
Performance: 1.070 ns/day, 22.421 hours/ns, 24.778 timesteps/s, 14.272 katom-step/s
805.8% CPU use with 1 MPI tasks x 8 OpenMP threads
MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 604.42     | 604.42     | 604.42     |   0.0 | 59.90
Bond    | 0.0072013  | 0.0072013  | 0.0072013  |   0.0 |  0.00
Neigh   | 125.16     | 125.16     | 125.16     |   0.0 | 12.40
Comm    | 2.9952     | 2.9952     | 2.9952     |   0.0 |  0.30
Output  | 25.323     | 25.323     | 25.323     |   0.0 |  2.51
Modify  | 250.79     | 250.79     | 250.79     |   0.0 | 24.86
Nlocal:            576 ave         576 max         576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4315 ave        4315 max        4315 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         191651 ave      191651 max      191651 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 191651
Ave neighs/atom = 332.72743
Ave special neighs/atom = 0
Neighbor list builds = 5000
Dangerous builds not checked
System init for write_data ...
Last active /omp style is pair_style reaxff/omp
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