forked from lijiext/lammps
124 lines
4.3 KiB
Groff
124 lines
4.3 KiB
Groff
LAMMPS (16 Mar 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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using 1 OpenMP thread(s) per MPI task
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# Rhodopsin model
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units real
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neighbor 2.0 bin
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neigh_modify delay 5 every 1
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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 charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.protein
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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 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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8 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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27723 bonds
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reading angles ...
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40467 angles
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reading dihedrals ...
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56829 dihedrals
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reading impropers ...
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1034 impropers
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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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24 = max # of 1-4 neighbors
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26 = max # of special neighbors
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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1617 = # of size 2 clusters
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3633 = # of size 3 clusters
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747 = # of size 4 clusters
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4233 = # of frozen angles
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fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo_style multi
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timestep 2.0
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.248835
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grid = 25 32 32
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0355478
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estimated relative force accuracy = 0.000107051
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using double precision FFTs
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3d grid and FFT values/proc = 13230 6400
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 10 13 13
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
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E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
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E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
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Volume = 307995.0335
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---------------- Step 100 ----- CPU = 6.3997 (sec) ----------------
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TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
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PotEng = -46882.6483 E_bond = 2567.9789 E_angle = 10781.9556
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E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
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E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
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Volume = 308133.9933
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Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
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Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
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98.8% 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 | 4.4434 | 4.5321 | 4.6846 | 4.3 | 70.82
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Bond | 0.17894 | 0.18568 | 0.19951 | 1.9 | 2.90
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Kspace | 0.4651 | 0.61064 | 0.69123 | 11.1 | 9.54
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Neigh | 0.7739 | 0.77394 | 0.774 | 0.0 | 12.09
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Comm | 0.057676 | 0.069183 | 0.07901 | 3.0 | 1.08
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Output | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 | 0.0 | 0.00
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Modify | 0.21444 | 0.21866 | 0.22524 | 0.9 | 3.42
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Other | | 0.009451 | | | 0.15
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Nlocal: 8000 ave 8143 max 7933 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 22733.5 ave 22769 max 22693 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 12028098
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Ave neighs/atom = 375.878
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 11
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Dangerous builds = 0
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Total wall time: 0:00:06
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