141 lines
6.2 KiB
Groff
141 lines
6.2 KiB
Groff
LAMMPS (21 Nov 2023)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# REAX potential for high energy CHON systems
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# .....
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units real
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atom_style charge
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read_data data.RDX
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Reading data file ...
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orthogonal box = (0 0 0) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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105 atoms
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read_data CPU = 0.001 seconds
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pair_style reaxff lmp_control
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pair_coeff * * ffield.reax.rdx H C O N
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Reading potential file ffield.reax.rdx with DATE: 2010-02-19
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neighbor 2 bin
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neigh_modify every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
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fix 3 all temp/berendsen 500.0 500.0 100.0
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timestep 0.25
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thermo 100
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#dump 1 all atom 30 dump.reax.rdx
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run 3000
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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 = 10 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
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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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/newtoff/ghost
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stencil: full/ghost/bin/3d
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bin: standard
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(2) fix qeq/reax, 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) = 10.78 | 11.56 | 12.26 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -10197.932 0 -10197.932 38.347492
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100 47.47852 -10176.425 0 -10161.706 632.97359
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200 166.95287 -10181.513 0 -10129.757 -27.146803
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300 142.53582 -10148.039 0 -10103.852 5120.6397
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400 322.68523 -10178.868 0 -10078.834 2342.7187
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500 193.81484 -10117.984 0 -10057.901 8412.4559
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600 300.27165 -10134.473 0 -10041.388 -2801.9143
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700 272.63408 -10110.146 0 -10025.629 10749.2
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800 339.99669 -10114.123 0 -10008.723 5123.2489
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900 231.65632 -10068.587 0 -9996.7729 5306.0392
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1000 329.93324 -10088.777 0 -9986.4967 3190.4707
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1100 376.60924 -10092.398 0 -9975.6478 2920.8475
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1200 361.98231 -10076.598 0 -9964.3816 3612.0573
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1300 358.6599 -10069.366 0 -9958.1803 4341.9871
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1400 470.14856 -10098.552 0 -9952.8036 -146.9069
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1500 509.6454 -10106.577 0 -9948.5847 2355.4022
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1600 417.9276 -10075.284 0 -9945.7249 1749.565
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1700 453.25817 -10084.343 0 -9943.8306 -570.48011
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1800 472.9517 -10087.84 0 -9941.2226 1532.6424
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1900 507.14171 -10096.428 0 -9939.212 -404.84948
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2000 443.62843 -10076.86 0 -9939.3329 -132.17302
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2100 485.441 -10088.414 0 -9937.925 -609.75758
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2200 507.23914 -10095.067 0 -9937.8209 1288.5372
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2300 499.64956 -10090.665 0 -9935.7719 149.06622
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2400 457.97848 -10078.107 0 -9936.1317 2065.2075
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2500 510.58254 -10093.537 0 -9935.2543 -559.75965
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2600 440.97503 -10070.865 0 -9934.1605 1164.1078
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2700 500.4945 -10088.165 0 -9933.0096 1051.9016
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2800 485.77814 -10083.543 0 -9932.9498 294.64404
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2900 487.73983 -10082.939 0 -9931.7373 2208.263
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3000 504.69717 -10089.803 0 -9933.3447 1723.6386
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Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
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Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 katom-step/s
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99.3% CPU use with 4 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 | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
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Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
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Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
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Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
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Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
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Other | | 0.003062 | | | 0.11
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Nlocal: 26.25 ave 46 max 8 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 399.5 ave 512 max 288 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 1011.25 ave 1819 max 420 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 4045
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Ave neighs/atom = 38.52381
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Neighbor list builds = 300
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Dangerous builds not checked
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Total wall time: 0:00:02
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