forked from lijiext/lammps
197 lines
7.2 KiB
Groff
197 lines
7.2 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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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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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style multi
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thermo 50
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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group peptide type <= 12
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84 atoms in group peptide
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#dump 1 peptide atom 10 dump.peptide
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#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 2 pad 3
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#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 3 pad 3
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#compute bnd all property/local btype batom1 batom2
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#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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run 300
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 4312 960
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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 = 5 5 5
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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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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
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PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
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E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
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E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
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---------------- Step 50 ----- CPU = 0.2858 (sec) ----------------
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TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745
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PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785
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E_coul = 26804.4441 E_long = -33907.7003 Press = -1331.7946
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80613e-07
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6 0.997 1.06181e-06
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8 1.08 6.20292e-07
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10 1.111 6.23284e-07
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12 1.08 2.67996e-07
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14 0.96 0
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18 0.957201 5.3796e-06
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31 104.52 0.000502278
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---------------- Step 100 ----- CPU = 0.5744 (sec) ----------------
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TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663
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PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273
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E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820
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---------------- Step 150 ----- CPU = 0.8756 (sec) ----------------
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TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737
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PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594
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E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675
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E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18699e-07
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6 0.997 1.50563e-07
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8 1.08 6.575e-08
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10 1.111 5.54187e-07
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12 1.08 1.9884e-07
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14 0.96 0
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18 0.957201 3.59627e-06
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31 104.52 0.000388335
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---------------- Step 200 ----- CPU = 1.1602 (sec) ----------------
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TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421
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PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040
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E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221
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E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400
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---------------- Step 250 ----- CPU = 1.4629 (sec) ----------------
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TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359
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PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996
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E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589
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E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.79043e-06
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6 0.997001 3.6052e-06
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8 1.08 2.09369e-06
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10 1.111 5.6484e-06
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12 1.08 2.10677e-06
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14 0.96 0
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18 0.957202 7.72579e-06
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31 104.52 0.000806203
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---------------- Step 300 ----- CPU = 1.7662 (sec) ----------------
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TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297
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PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274
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E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474
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E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904
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Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms
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Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 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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Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92
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Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19
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Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00
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Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05
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Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61
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Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02
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Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92
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Other | | 0.004988 | | | 0.28
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Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6587.75 ave 6632 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177005 ave 180556 max 170207 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708020
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Ave neighs/atom = 353.303
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 26
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Dangerous builds = 0
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Total wall time: 0:00:01
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