145 lines
8.4 KiB
Groff
145 lines
8.4 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 RDX system
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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 = (35 35 35) to (48 48 48)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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21 atoms
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read_data CPU = 0.001 seconds
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pair_style reaxff control.reax_c.rdx
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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 every 10 delay 0 check no
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fix 1 all nve
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fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
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variable nqeq equal f_2
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thermo 10
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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 1.0
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#dump 1 all atom 10 dump.reaxff.rdx
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#dump 2 all image 25 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 25 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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run 100
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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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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 = 12.5
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ghost atom cutoff = 12.5
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binsize = 6.25, bins = 3 3 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/shielded, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 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 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
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10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
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20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
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30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
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40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
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50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
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60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
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70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
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80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
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90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
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100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
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Loop time of 0.0643048 on 4 procs for 100 steps with 21 atoms
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Performance: 134.360 ns/day, 0.179 hours/ns, 1555.095 timesteps/s, 32.657 katom-step/s
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96.7% 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 | 0.023311 | 0.03235 | 0.044316 | 4.2 | 50.31
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Neigh | 0.0013612 | 0.0019412 | 0.002633 | 1.0 | 3.02
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Comm | 0.0010934 | 0.013057 | 0.022095 | 6.7 | 20.31
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Output | 0.00014529 | 0.00015387 | 0.00016787 | 0.0 | 0.24
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Modify | 0.016042 | 0.016754 | 0.017353 | 0.4 | 26.05
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Other | | 4.816e-05 | | | 0.07
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Nlocal: 5.25 ave 15 max 0 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Nghost: 355.5 ave 432 max 282 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Neighs: 298.75 ave 822 max 0 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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FullNghs: 326.5 ave 927 max 0 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 1306
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Ave neighs/atom = 62.190476
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Neighbor list builds = 10
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Dangerous builds not checked
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Total wall time: 0:00:00
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