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 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/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) = 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 27186.182 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79916 0 168.88381 12.5
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10 1288.6116 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.60722 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
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20 538.95827 -1942.7037 -1910.5731 -10725.675 -2803.7395 7.9078297 0.077926636 0 81.610054 0.22951925 -57.557099 0 30.331205 -10.178049 878.99014 -159.69256 0 89.316794 7
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30 463.09513 -1933.5765 -1905.9686 -33255.526 -2749.8591 -8.0154533 0.027628873 0 81.62739 0.11972403 -50.262284 0 20.820312 -9.6327039 851.88722 -149.49494 0 79.205672 8
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40 885.49116 -1958.9126 -1906.123 -4814.6959 -2795.6441 9.1506835 0.13747507 0 70.947963 0.24360514 -57.862673 0 19.076493 -11.141218 873.73898 -159.99394 0 92.434099 11
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50 861.1691 -1954.4598 -1903.1202 -1896.8779 -2784.8448 3.8270203 0.1579326 0 79.851903 3.3492208 -78.066129 0 32.629013 -7.9565355 872.81826 -190.98566 0 114.75994 10
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60 1167.7861 -1971.8427 -1902.2238 -3482.6559 -2705.8627 -17.121772 0.22749069 0 44.507644 7.8561147 -74.788923 0 16.256476 -4.6046327 835.83036 -188.33691 0 114.19412 10
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70 1440.0001 -1989.3024 -1903.4551 23845.322 -2890.7895 31.958913 0.26671723 0 85.758826 3.1803176 -71.002871 0 24.357078 -10.311326 905.8676 -175.38455 0 106.79634 10
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80 502.39424 -1930.7541 -1900.8033 -20356.365 -2703.8112 -18.662536 0.11285996 0 99.804396 2.032884 -76.171335 0 19.237003 -6.2786875 826.47433 -166.03121 0 92.539366 9
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90 749.08858 -1946.9836 -1902.3258 17798.514 -2863.7575 42.068829 0.24338073 0 96.181699 0.9618465 -69.955421 0 24.615236 -11.582776 903.6881 -190.13852 0 120.69151 11
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100 1109.7005 -1968.5871 -1902.431 -4490.1423 -2755.8949 -7.1235131 0.21757701 0 61.80622 7.0827961 -75.645322 0 20.114715 -6.2371564 863.56266 -198.56982 0 122.09964 10.5
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Loop time of 0.0666879 on 4 procs for 100 steps with 21 atoms
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Performance: 129.559 ns/day, 0.185 hours/ns, 1499.522 timesteps/s, 31.490 katom-step/s
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98.0% 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 | 0.023807 | 0.033573 | 0.04688 | 4.6 | 50.34
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Neigh | 0.0013829 | 0.001879 | 0.0024761 | 0.9 | 2.82
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Comm | 0.0015767 | 0.014898 | 0.024673 | 6.9 | 22.34
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Output | 0.00015887 | 0.00016828 | 0.00018839 | 0.0 | 0.25
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Modify | 0.015511 | 0.01612 | 0.016628 | 0.3 | 24.17
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Other | | 4.966e-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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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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