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 harmonic
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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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1 by 1 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) = 47.18 | 47.18 | 47.18 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000
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PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642
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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 = 105.8245
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---------------- Step 200 ----- CPU = 11.2074 (sec) ----------------
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TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441
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PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608
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E_coul = 0.0000 E_long = 0.0000 Press = 29.3660
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---------------- Step 400 ----- CPU = 22.6113 (sec) ----------------
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TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316
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PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067
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E_coul = 0.0000 E_long = 0.0000 Press = 16.4419
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---------------- Step 600 ----- CPU = 34.0551 (sec) ----------------
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TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478
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PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435
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E_coul = 0.0000 E_long = 0.0000 Press = 14.0304
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---------------- Step 800 ----- CPU = 45.5316 (sec) ----------------
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TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372
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PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910
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E_coul = 0.0000 E_long = 0.0000 Press = -6.8312
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---------------- Step 1000 ----- CPU = 56.9111 (sec) ----------------
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TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800
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PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925
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E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639
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E_coul = 0.0000 E_long = 0.0000 Press = 0.0980
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Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms
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Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s
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99.8% CPU use with 1 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 | 50.775 | 50.775 | 50.775 | 0.0 | 89.22
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Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55
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Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94
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Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26
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Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00
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Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83
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Other | | 0.1127 | | | 0.20
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Nlocal: 40140 ave 40140 max 40140 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 25968 ave 25968 max 25968 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5691680
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Ave neighs/atom = 141.796
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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: 0:00:57
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