145 lines
7.8 KiB
Groff
145 lines
7.8 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 1 by 1 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/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:
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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/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) = 13.86 | 13.86 | 13.86 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 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
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10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
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20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
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30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
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40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
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50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
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60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
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70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
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80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
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90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
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100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
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Loop time of 0.23792 on 1 procs for 100 steps with 21 atoms
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Performance: 36.315 ns/day, 0.661 hours/ns, 420.310 timesteps/s
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99.3% 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 | 0.21046 | 0.21046 | 0.21046 | 0.0 | 88.46
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Neigh | 0.010947 | 0.010947 | 0.010947 | 0.0 | 4.60
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Comm | 0.00060345 | 0.00060345 | 0.00060345 | 0.0 | 0.25
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Output | 0.00071705 | 0.00071705 | 0.00071705 | 0.0 | 0.30
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Modify | 0.014873 | 0.014873 | 0.014873 | 0.0 | 6.25
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Other | | 0.0003213 | | | 0.14
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Nlocal: 21.0000 ave 21 max 21 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 546.000 ave 546 max 546 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1096.00 ave 1096 max 1096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 1306.00 ave 1306 max 1306 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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