forked from lijiext/lammps
222 lines
9.3 KiB
Groff
222 lines
9.3 KiB
Groff
LAMMPS (27 Jun 2024)
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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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# charmmfsw example generated by https://charmm-gui.org/
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# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
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#
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# Dependencies: packages MOLECULE / KSPACE / RIGID
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# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
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units real
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boundary p p p
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newton off
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pair_style lj/charmmfsw/coul/long 10 12
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Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
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pair_modify mix arithmetic
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kspace_style pppm 1e-6
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmmfsw
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special_bonds charmm
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improper_style harmonic
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timestep 2
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fix cmap all cmap charmmff.cmap
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Reading CMAP parameters from: charmmff.cmap
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Read in CMAP data for 2 crossterm types
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fix_modify cmap energy yes
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read_data data.charmmfsw.gz fix cmap crossterm CMAP
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Reading data file ...
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orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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10245 atoms
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reading velocities ...
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10245 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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15 = max angles/atom
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scanning dihedrals ...
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48 = max dihedrals/atom
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scanning impropers ...
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4 = max impropers/atom
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orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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reading bonds ...
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6973 bonds
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reading angles ...
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4057 angles
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reading dihedrals ...
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1363 dihedrals
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reading impropers ...
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70 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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4 = max # of 1-2 neighbors
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9 = max # of 1-3 neighbors
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17 = max # of 1-4 neighbors
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21 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.068 seconds
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neighbor 2 bin
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neigh_modify delay 2 every 1
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fix 1 all shake 1e-6 100 100 m 1.008 a 142
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Finding SHAKE clusters ...
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75 = # of size 2 clusters
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47 = # of size 3 clusters
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9 = # of size 4 clusters
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3265 = # of frozen angles
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find clusters CPU = 0.001 seconds
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fix 2 all nvt temp 303.15 303.15 100.0
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thermo 10
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thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
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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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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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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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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.27938162
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grid = 54 54 54
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stencil order = 5
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estimated absolute RMS force accuracy = 0.00036407395
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estimated relative force accuracy = 1.0963718e-06
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using double precision FFTW3
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3d grid and FFT values/proc = 70516 40824
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Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 2 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmmfsw/coul/long, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: full/bin/3d
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bin: standard
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SHAKE stats (type/ave/delta/count) on step 0
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Bond: 16 1.09 1.38032e-07 6
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Bond: 18 1.09 1.00046e-07 3
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Bond: 34 1.111 1.11388e-06 10
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Bond: 39 1.111 4.83041e-08 5
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Bond: 43 1.111 1.97842e-07 10
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Bond: 44 1.111 1.71815e-06 10
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Bond: 59 1.111 8.42509e-08 2
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Bond: 62 1.111 2.84854e-08 2
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Bond: 63 1.111 2.14153e-07 46
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Bond: 64 1.111 1.59305e-07 18
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Bond: 65 1.08 5.67061e-07 16
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Bond: 66 1.08 1.43965e-06 4
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Bond: 67 1 1.81926e-07 10
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Bond: 68 1.01 0 1
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Bond: 69 1.08 1.34571e-07 5
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Bond: 70 1.09 0 1
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Bond: 71 1.083 0 1
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Bond: 72 0.9572 2.71955e-07 6530
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Bond: 75 1 1.46045e-07 10
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Bond: 79 0.997 5.24499e-07 17
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Bond: 81 1 1.32984e-07 4
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Bond: 84 1.04 7.65389e-07 9
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Bond: 87 1 0 1
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Bond: 95 0.96 5.75241e-07 2
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Bond: 97 1.325 4.3613e-08 3
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Angle: 142 104.52 2.67611e-05 3265
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Per MPI rank memory allocation (min/avg/max) = 76.88 | 77.06 | 77.25 Mbytes
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Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
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0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
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10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
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20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
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30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
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40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
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50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
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60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
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70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2032
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80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
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90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
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SHAKE stats (type/ave/delta/count) on step 100
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Bond: 16 1.09 3.78281e-07 6
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Bond: 18 1.09 1.12288e-07 3
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Bond: 34 1.111 7.60709e-07 10
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Bond: 39 1.111 2.37855e-07 5
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Bond: 43 1.111 6.00872e-07 10
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Bond: 44 1.111 3.75324e-07 10
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Bond: 59 1.111 1.12311e-07 2
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Bond: 62 1.111 2.99471e-07 2
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Bond: 63 1.111 6.10589e-07 46
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Bond: 64 1.111 4.50733e-07 18
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Bond: 65 1.08 2.90668e-07 16
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Bond: 66 1.08 1.61592e-07 4
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Bond: 67 1 5.4508e-07 10
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Bond: 68 1.01 0 1
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Bond: 69 1.08 4.1398e-07 5
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Bond: 70 1.09 0 1
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Bond: 71 1.083 0 1
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Bond: 72 0.9572 1.76706e-06 6530
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Bond: 75 1 3.96686e-07 10
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Bond: 79 0.997 7.72922e-07 17
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Bond: 81 1 1.30673e-07 4
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Bond: 84 1.04 1.44551e-07 9
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Bond: 87 1 0 1
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Bond: 95 0.96 1.03526e-07 2
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Bond: 97 1.325 3.64689e-08 3
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Angle: 142 104.52 0.000130126 3265
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100 -27913.241 3159.0676 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
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Loop time of 3.49837 on 4 procs for 100 steps with 10245 atoms
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Performance: 4.939 ns/day, 4.859 hours/ns, 28.585 timesteps/s, 292.851 katom-step/s
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99.4% 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 | 2.4572 | 2.5133 | 2.5634 | 2.6 | 71.84
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Bond | 0.0040264 | 0.0050718 | 0.0069286 | 1.6 | 0.14
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Kspace | 0.45979 | 0.50903 | 0.56364 | 5.6 | 14.55
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Neigh | 0.42029 | 0.42034 | 0.42036 | 0.0 | 12.02
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Comm | 0.013207 | 0.013292 | 0.013404 | 0.1 | 0.38
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Output | 0.00026525 | 0.00029549 | 0.00038249 | 0.0 | 0.01
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Modify | 0.035024 | 0.035546 | 0.03621 | 0.3 | 1.02
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Other | | 0.001504 | | | 0.04
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Nlocal: 2561.25 ave 2599 max 2520 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 16491.5 ave 16541 max 16442 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 1.99855e+06 ave 2.04035e+06 max 1.95468e+06 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 7994217
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Ave neighs/atom = 780.30425
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Ave special neighs/atom = 2.3664226
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Neighbor list builds = 10
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Dangerous builds = 0
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Total wall time: 0:00:03
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