155 lines
8.0 KiB
Groff
155 lines
8.0 KiB
Groff
LAMMPS (2 Jul 2021)
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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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# 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 = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
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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:97)
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WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
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WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
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WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
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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/reaxff 1 0.0 10.0 1.0e-6 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:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical 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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- fix qeq/reaxff command:
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@Article{Aktulga12,
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author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
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title = {Parallel reactive molecular dynamics: Numerical 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 = 12.5
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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/newtoff/ghost
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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, ghost
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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) = 9.353 | 10.52 | 11.73 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 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 12
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10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252292 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
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20 538.95847 -1942.7037 -1910.5731 -10725.668 -2803.7395 7.9078328 0.077926688 0 81.610045 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69262 0 89.316856 7
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30 463.09521 -1933.5765 -1905.9685 -33255.503 -2749.8591 -8.0154614 0.027628708 0 81.627408 0.11972393 -50.262275 0 20.820319 -9.6327031 851.88721 -149.49497 0 79.205707 8
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40 885.49559 -1958.9126 -1906.1227 -4814.661 -2795.644 9.1506103 0.13747486 0 70.948058 0.24360549 -57.862693 0 19.076514 -11.141211 873.73894 -159.9939 0 92.434063 11
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50 861.16222 -1954.4601 -1903.1209 -1896.7328 -2784.8449 3.8269573 0.15793301 0 79.851661 3.3492101 -78.066131 0 32.628939 -7.9565311 872.81847 -190.9857 0 114.75999 10
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60 1167.7838 -1971.8434 -1902.2246 -3482.8253 -2705.8639 -17.121553 0.22749078 0 44.507707 7.8560156 -74.789002 0 16.256509 -4.6046674 835.83076 -188.33689 0 114.19413 10
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70 1439.9922 -1989.3024 -1903.4556 23845.682 -2890.7894 31.958742 0.26671722 0 85.758402 3.1803955 -71.002937 0 24.357176 -10.311293 905.86805 -175.38494 0 106.79668 10
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80 502.39847 -1930.7549 -1900.8038 -20356.357 -2703.8111 -18.662668 0.11286141 0 99.803668 2.0329484 -76.17132 0 19.236866 -6.2786536 826.47435 -166.03145 0 92.539587 9
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90 749.0857 -1946.984 -1902.3263 17798.657 -2863.7584 42.068704 0.24338054 0 96.181666 0.96183837 -69.955527 0 24.615445 -11.58275 903.68864 -190.13828 0 120.69127 11
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100 1109.695 -1968.5879 -1902.4321 -4490.3441 -2755.8984 -7.1226574 0.21757683 0 61.806014 7.0826278 -75.645456 0 20.115306 -6.2372466 863.56451 -198.56953 0 122.09941 10.5
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Loop time of 0.371707 on 4 procs for 100 steps with 21 atoms
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Performance: 23.244 ns/day, 1.033 hours/ns, 269.029 timesteps/s
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91.8% 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 | 0.13518 | 0.19123 | 0.24947 | 9.7 | 51.45
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Neigh | 0.0073075 | 0.0096968 | 0.012228 | 1.8 | 2.61
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Comm | 0.034511 | 0.093329 | 0.14912 | 14.0 | 25.11
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Output | 0.00081416 | 0.0011345 | 0.0019655 | 1.4 | 0.31
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Modify | 0.073177 | 0.075449 | 0.078618 | 0.7 | 20.30
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Other | | 0.0008711 | | | 0.23
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Nlocal: 5.25000 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: 355.500 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: 298.750 ave 822 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 = 1195
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Ave neighs/atom = 56.904762
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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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