155 lines
8.7 KiB
Groff
155 lines
8.7 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 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 = 0.000 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/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: 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 = 12.5
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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/reaxff, 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) = 13.36 | 13.36 | 13.36 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 -244.79947 0 168.88412 12
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10 1288.6115 -1989.6644 -1912.8422 -19456.35 -2734.6769 -15.607219 0.20177961 0 54.629555 3.1252295 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43321 0 107.75934 8
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20 538.95838 -1942.7037 -1910.5731 -10725.629 -2803.7395 7.9078326 0.07792674 0 81.610044 0.22951951 -57.557111 0 30.331206 -10.178049 878.99011 -159.6897 0 89.31394 6.5
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30 463.09527 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.0154824 0.027628758 0 81.627415 0.11972401 -50.262282 0 20.82031 -9.6327011 851.88713 -149.49499 0 79.205722 8
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40 885.49524 -1958.9125 -1906.1227 -4814.6579 -2795.6439 9.1505958 0.13747478 0 70.948066 0.24360531 -57.862686 0 19.076518 -11.141211 873.73887 -159.9939 0 92.434064 11
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50 861.1608 -1954.4602 -1903.121 -1896.6931 -2784.8449 3.8269759 0.15793298 0 79.851634 3.349206 -78.06613 0 32.628956 -7.9565349 872.81845 -190.98568 0 114.75998 10
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60 1167.7834 -1971.8435 -1902.2247 -3482.8529 -2705.8639 -17.121541 0.2274908 0 44.507704 7.8559998 -74.789016 0 16.256511 -4.60467 835.83072 -188.33689 0 114.19413 10
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70 1439.9911 -1989.3024 -1903.4556 23845.704 -2890.7894 31.958692 0.2667172 0 85.758357 3.1804062 -71.002958 0 24.3572 -10.311286 905.86808 -175.385 0 106.79674 10
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80 502.3988 -1930.755 -1900.8039 -20356.389 -2703.8108 -18.662751 0.11286169 0 99.803574 2.032954 -76.171326 0 19.236814 -6.2786428 826.47419 -166.03149 0 92.539626 9
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90 749.08532 -1946.9839 -1902.3263 17798.667 -2863.7584 42.06871 0.24338047 0 96.181692 0.96182992 -69.955524 0 24.615455 -11.582756 903.68873 -190.13825 0 120.69125 11
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100 1109.6964 -1968.5879 -1902.432 -4490.4599 -2755.8982 -7.1227208 0.21757669 0 61.806042 7.082597 -75.645484 0 20.115271 -6.2372452 863.56435 -198.56945 0 122.09933 10.5
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Loop time of 0.0666662 on 1 procs for 100 steps with 21 atoms
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Performance: 129.601 ns/day, 0.185 hours/ns, 1500.011 timesteps/s, 31.500 katom-step/s
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99.4% 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 | 0.060081 | 0.060081 | 0.060081 | 0.0 | 90.12
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Neigh | 0.0029204 | 0.0029204 | 0.0029204 | 0.0 | 4.38
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Comm | 0.000161 | 0.000161 | 0.000161 | 0.0 | 0.24
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Output | 0.00014497 | 0.00014497 | 0.00014497 | 0.0 | 0.22
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Modify | 0.0033107 | 0.0033107 | 0.0033107 | 0.0 | 4.97
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Other | | 4.861e-05 | | | 0.07
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Nlocal: 21 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 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 ave 1096 max 1096 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1096
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Ave neighs/atom = 52.190476
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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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