128 lines
5.1 KiB
Groff
128 lines
5.1 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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dimension 3
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atom_style angle
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# enforce that in z-direction there is only one
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# processor (could be two) for optimal performance
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processors * * 1
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# read topology and force field
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pair_style lj/sdk 15.0
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bond_style harmonic
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angle_style sdk
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special_bonds lj/coul 0.0 0.0 1.0
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read_data data.pegc12e8.gz
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orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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40140 atoms
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reading velocities ...
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40140 velocities
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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13284 bonds
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reading angles ...
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12177 angles
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of special neighbors
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neighbor 3.0 bin
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neigh_modify delay 5
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timestep 5.0
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#dump 1 all xtc 200 pegc12e8-1.xtc
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#dump_modify 1 unwrap yes
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#dump 2 all dcd 200 pegc12e8-1.dcd unwrap
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#dump_modify 2 unwrap yes
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velocity all create 303.0 46659 mom yes rot yes dist gaussian
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fix 1 all nvt temp 303.0 303.0 100.0
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thermo_style multi
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thermo 200
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run 1000
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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 = 18
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ghost atom cutoff = 18
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binsize = 9, bins = 15 15 45
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/sdk, 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) = 15.87 | 15.87 | 15.87 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000
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PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151
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E_coul = 0.0000 E_long = 0.0000 Press = 114.4952
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---------------- Step 200 ----- CPU = 3.0597 (sec) ----------------
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TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634
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PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887
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E_coul = 0.0000 E_long = 0.0000 Press = 39.4030
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---------------- Step 400 ----- CPU = 6.2514 (sec) ----------------
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TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848
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PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627
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E_coul = 0.0000 E_long = 0.0000 Press = 9.8923
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---------------- Step 600 ----- CPU = 9.4073 (sec) ----------------
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TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770
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PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301
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E_coul = 0.0000 E_long = 0.0000 Press = 25.6392
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---------------- Step 800 ----- CPU = 12.6096 (sec) ----------------
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TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854
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PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043
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E_coul = 0.0000 E_long = 0.0000 Press = -1.6281
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---------------- Step 1000 ----- CPU = 15.9134 (sec) ----------------
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TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541
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PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949
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E_coul = 0.0000 E_long = 0.0000 Press = -7.3081
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Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms
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Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 timesteps/s
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99.0% 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 | 13.325 | 13.6 | 13.755 | 4.7 | 85.46
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Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57
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Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79
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Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61
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Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00
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Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09
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Other | | 0.0768 | | | 0.48
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Nlocal: 10035 ave 10084 max 9971 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 14548.8 ave 14610 max 14509 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Total # of neighbors = 5686756
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Ave neighs/atom = 141.673
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Ave special neighs/atom = 1.26861
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Neighbor list builds = 38
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Dangerous builds = 0
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#write_restart pegc12e8-1.restart
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Total wall time: 0:00:16
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