mirror of https://github.com/lammps/lammps.git
add example input and logfiles for using fix qeq/shielded with pair style reax/c
This commit is contained in:
Axel Kohlmeyer
parent
327ca344ff
commit
a93d8dda3c
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# ReaxFF potential for RDX system
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# this run is equivalent to reax/in.reax.rdx
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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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pair_style reax/c control.reax_c.rdx
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pair_coeff * * ffield.reax C H O N
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compute reax all pair reax/c
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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 reax/c
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thermo 10
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thermo_style custom step temp epair etotal press &
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v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
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v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
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timestep 1.0
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#dump 1 all atom 10 dump.reaxc.rdx
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#dump 2 all image 25 image.*.jpg type type &
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# 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 &
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# 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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@ -0,0 +1,55 @@
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# ReaxFF potential for TATB system
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# this run is equivalent to reax/in.reax.tatb,
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units real
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atom_style charge
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read_data data.tatb
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pair_style reax/c control.reax_c.tatb
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pair_coeff * * ffield.reax C H O N
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compute reax all pair reax/c
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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 delay 0 every 5 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 reax/c
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fix 4 all reax/c/bonds 5 bonds.reaxc
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thermo 5
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thermo_style custom step temp epair etotal press &
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v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
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v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
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timestep 0.0625
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#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
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#dump 2 all image 5 image.*.jpg type type &
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# 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 5 movie.mpg type type &
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# axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3
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fix 3 all reax/c/species 1 5 5 species.tatb
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run 25
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@ -0,0 +1,116 @@
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LAMMPS (4 Jan 2019)
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# ReaxFF potential for RDX system
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# this run is equivalent to reax/in.reax.rdx
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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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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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pair_style reax/c control.reax_c.rdx
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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 reax/c
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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 reax/c
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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
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timestep 1.0
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#dump 1 all atom 10 dump.reaxc.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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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 reax/c, 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: half/ghost/bin/3d/newtoff
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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) = 15.54 | 15.54 | 15.54 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
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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 -244.79939 0 168.88404
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10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
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20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512
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30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749
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40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085
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50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995
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60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414
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70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648
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80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464
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90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914
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100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951
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Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms
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Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s
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99.3% CPU use with 1 MPI tasks x no 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 | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21
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Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14
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Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24
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Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06
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Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32
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Other | | 0.000154 | | | 0.02
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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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FullNghs: 1306 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 = 62.1905
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Neighbor list builds = 10
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Dangerous builds not checked
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:00
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@ -0,0 +1,116 @@
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LAMMPS (4 Jan 2019)
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# ReaxFF potential for RDX system
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# this run is equivalent to reax/in.reax.rdx
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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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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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pair_style reax/c control.reax_c.rdx
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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 reax/c
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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 reax/c
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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
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timestep 1.0
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#dump 1 all atom 10 dump.reaxc.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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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 reax/c, 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: half/ghost/bin/3d/newtoff
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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) = 10.62 | 12.08 | 13.84 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
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0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452
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10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934
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20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929
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30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706
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40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076
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50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999
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60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412
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||||||
|
70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967
|
||||||
|
80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525
|
||||||
|
90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126
|
||||||
|
100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944
|
||||||
|
Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms
|
||||||
|
|
||||||
|
Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s
|
||||||
|
93.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37
|
||||||
|
Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90
|
||||||
|
Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28
|
||||||
|
Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09
|
||||||
|
Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34
|
||||||
|
Other | | 0.0001715 | | | 0.03
|
||||||
|
|
||||||
|
Nlocal: 5.25 ave 15 max 0 min
|
||||||
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||||
|
Nghost: 355.5 ave 432 max 282 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Neighs: 298.75 ave 822 max 0 min
|
||||||
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||||
|
FullNghs: 326.5 ave 927 max 0 min
|
||||||
|
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1306
|
||||||
|
Ave neighs/atom = 62.1905
|
||||||
|
Neighbor list builds = 10
|
||||||
|
Dangerous builds not checked
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
|
@ -0,0 +1,114 @@
|
||||||
|
LAMMPS (4 Jan 2019)
|
||||||
|
# ReaxFF potential for TATB system
|
||||||
|
# this run is equivalent to reax/in.reax.tatb,
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.tatb
|
||||||
|
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
384 atoms
|
||||||
|
|
||||||
|
pair_style reax/c control.reax_c.tatb
|
||||||
|
pair_coeff * * ffield.reax C H O N
|
||||||
|
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||||
|
|
||||||
|
compute reax all pair reax/c
|
||||||
|
|
||||||
|
variable eb equal c_reax[1]
|
||||||
|
variable ea equal c_reax[2]
|
||||||
|
variable elp equal c_reax[3]
|
||||||
|
variable emol equal c_reax[4]
|
||||||
|
variable ev equal c_reax[5]
|
||||||
|
variable epen equal c_reax[6]
|
||||||
|
variable ecoa equal c_reax[7]
|
||||||
|
variable ehb equal c_reax[8]
|
||||||
|
variable et equal c_reax[9]
|
||||||
|
variable eco equal c_reax[10]
|
||||||
|
variable ew equal c_reax[11]
|
||||||
|
variable ep equal c_reax[12]
|
||||||
|
variable efi equal c_reax[13]
|
||||||
|
variable eqeq equal c_reax[14]
|
||||||
|
|
||||||
|
neighbor 2.5 bin
|
||||||
|
neigh_modify delay 0 every 5 check no
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
|
||||||
|
fix 4 all reax/c/bonds 5 bonds.reaxc
|
||||||
|
|
||||||
|
thermo 5
|
||||||
|
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
|
||||||
|
|
||||||
|
timestep 0.0625
|
||||||
|
|
||||||
|
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
|
||||||
|
|
||||||
|
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 3
|
||||||
|
|
||||||
|
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 3
|
||||||
|
|
||||||
|
fix 3 all reax/c/species 1 5 5 species.tatb
|
||||||
|
|
||||||
|
run 25
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 5 steps, delay 0 steps, check no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12.5
|
||||||
|
ghost atom cutoff = 12.5
|
||||||
|
binsize = 6.25, bins = 5 4 3
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair reax/c, perpetual
|
||||||
|
attributes: half, newton off, ghost
|
||||||
|
pair build: half/bin/newtoff/ghost
|
||||||
|
stencil: half/ghost/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) fix qeq/shielded, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 169.6 | 169.6 | 169.6 Mbytes
|
||||||
|
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
|
||||||
|
0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
|
||||||
|
5 0.61603942 -44761.698 -44760.994 8934.628 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
|
||||||
|
10 2.3525549 -44763.227 -44760.541 12288.614 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9684 0 6381.7061
|
||||||
|
15 4.9013311 -44766.36 -44760.764 17716.982 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2449 0 6370.4111
|
||||||
|
20 7.8294673 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5142 0 6355.2654
|
||||||
|
25 10.697904 -44772.904 -44760.691 34232.821 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3541 0 6336.8349
|
||||||
|
Loop time of 7.80985 on 1 procs for 25 steps with 384 atoms
|
||||||
|
|
||||||
|
Performance: 0.017 ns/day, 1388.418 hours/ns, 3.201 timesteps/s
|
||||||
|
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 5.003 | 5.003 | 5.003 | 0.0 | 64.06
|
||||||
|
Neigh | 1.1164 | 1.1164 | 1.1164 | 0.0 | 14.29
|
||||||
|
Comm | 0.0065806 | 0.0065806 | 0.0065806 | 0.0 | 0.08
|
||||||
|
Output | 0.00029969 | 0.00029969 | 0.00029969 | 0.0 | 0.00
|
||||||
|
Modify | 1.6831 | 1.6831 | 1.6831 | 0.0 | 21.55
|
||||||
|
Other | | 0.0004976 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 384 ave 384 max 384 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 7559 ave 7559 max 7559 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 286828 ave 286828 max 286828 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 336304 ave 336304 max 336304 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 336304
|
||||||
|
Ave neighs/atom = 875.792
|
||||||
|
Neighbor list builds = 5
|
||||||
|
Dangerous builds not checked
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:08
|
||||||
|
|
@ -0,0 +1,114 @@
|
||||||
|
LAMMPS (4 Jan 2019)
|
||||||
|
# ReaxFF potential for TATB system
|
||||||
|
# this run is equivalent to reax/in.reax.tatb,
|
||||||
|
|
||||||
|
units real
|
||||||
|
|
||||||
|
atom_style charge
|
||||||
|
read_data data.tatb
|
||||||
|
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
384 atoms
|
||||||
|
|
||||||
|
pair_style reax/c control.reax_c.tatb
|
||||||
|
pair_coeff * * ffield.reax C H O N
|
||||||
|
Reading potential file ffield.reax with DATE: 2010-02-19
|
||||||
|
|
||||||
|
compute reax all pair reax/c
|
||||||
|
|
||||||
|
variable eb equal c_reax[1]
|
||||||
|
variable ea equal c_reax[2]
|
||||||
|
variable elp equal c_reax[3]
|
||||||
|
variable emol equal c_reax[4]
|
||||||
|
variable ev equal c_reax[5]
|
||||||
|
variable epen equal c_reax[6]
|
||||||
|
variable ecoa equal c_reax[7]
|
||||||
|
variable ehb equal c_reax[8]
|
||||||
|
variable et equal c_reax[9]
|
||||||
|
variable eco equal c_reax[10]
|
||||||
|
variable ew equal c_reax[11]
|
||||||
|
variable ep equal c_reax[12]
|
||||||
|
variable efi equal c_reax[13]
|
||||||
|
variable eqeq equal c_reax[14]
|
||||||
|
|
||||||
|
neighbor 2.5 bin
|
||||||
|
neigh_modify delay 0 every 5 check no
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c
|
||||||
|
fix 4 all reax/c/bonds 5 bonds.reaxc
|
||||||
|
|
||||||
|
thermo 5
|
||||||
|
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
|
||||||
|
|
||||||
|
timestep 0.0625
|
||||||
|
|
||||||
|
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
|
||||||
|
|
||||||
|
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 2 pad 3
|
||||||
|
|
||||||
|
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||||
|
#dump_modify 3 pad 3
|
||||||
|
|
||||||
|
fix 3 all reax/c/species 1 5 5 species.tatb
|
||||||
|
|
||||||
|
run 25
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 5 steps, delay 0 steps, check no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 12.5
|
||||||
|
ghost atom cutoff = 12.5
|
||||||
|
binsize = 6.25, bins = 5 4 3
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||||
|
(1) pair reax/c, perpetual
|
||||||
|
attributes: half, newton off, ghost
|
||||||
|
pair build: half/bin/newtoff/ghost
|
||||||
|
stencil: half/ghost/bin/3d/newtoff
|
||||||
|
bin: standard
|
||||||
|
(2) fix qeq/shielded, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes
|
||||||
|
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
|
||||||
|
0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277
|
||||||
|
5 0.61603968 -44761.698 -44760.994 8934.6336 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666
|
||||||
|
10 2.3525543 -44763.227 -44760.541 12288.588 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9756 0 6381.7133
|
||||||
|
15 4.9013233 -44766.36 -44760.764 17716.934 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2627 0 6370.4289
|
||||||
|
20 7.8294615 -44769.686 -44760.747 25205.586 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4958 0 6355.2471
|
||||||
|
25 10.697919 -44772.904 -44760.691 34232.898 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3285 0 6336.8093
|
||||||
|
Loop time of 4.34178 on 4 procs for 25 steps with 384 atoms
|
||||||
|
|
||||||
|
Performance: 0.031 ns/day, 771.872 hours/ns, 5.758 timesteps/s
|
||||||
|
96.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.1756 | 3.1763 | 3.1771 | 0.0 | 73.16
|
||||||
|
Neigh | 0.58917 | 0.59661 | 0.6035 | 0.9 | 13.74
|
||||||
|
Comm | 0.0088837 | 0.010178 | 0.011116 | 0.8 | 0.23
|
||||||
|
Output | 0.00036407 | 0.0019013 | 0.003552 | 2.7 | 0.04
|
||||||
|
Modify | 0.54882 | 0.55637 | 0.56413 | 0.8 | 12.81
|
||||||
|
Other | | 0.0004123 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 96 ave 96 max 96 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 5118 ave 5118 max 5118 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 79754 ave 79754 max 79754 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 84076 ave 84076 max 84076 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 336304
|
||||||
|
Ave neighs/atom = 875.792
|
||||||
|
Neighbor list builds = 5
|
||||||
|
Dangerous builds not checked
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:04
|
||||||
Loading…
Reference in New Issue