157 lines
6.7 KiB
Groff
157 lines
6.7 KiB
Groff
LAMMPS (28 Jul 2021)
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using 1 OpenMP thread(s) per MPI task
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units lj
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atom_style full
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boundary p p p
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special_bonds lj/coul 1 1 1
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newton on on
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# save an extra atom type for bond particles
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read_data data.chain
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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3000 atoms
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reading velocities ...
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3000 velocities
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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2700 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.011 seconds
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neighbor 2.0 bin
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neigh_modify every 10 check yes
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bond_style harmonic
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bond_coeff * 225.0 0.85
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comm_modify vel yes
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comm_modify cutoff 3.6
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# must use pair hybrid, since srp bond particles
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# do not interact with other atoms types
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pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid
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pair_coeff 1 1 dpd 60.0 4.5 1.0
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pair_coeff 1 2 none
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pair_coeff 2 2 srp 100.0
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# auto normalization of thermo quantities is turned off by pair srp
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# just divide by natoms
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variable natoms equal count(all)
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variable nPotEng equal c_thermo_pe/v_natoms
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thermo 50
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thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz
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fix 1 all nve
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timestep 0.01
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#restart 500 mid-run-*.restart
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run 1000
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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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- @Article{Sirk2012
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author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm},
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title = {An enhanced entangled polymer model for dissipative particle dynamics},
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journal = {J.~Chem.~Phys.},
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year = 2012,
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volume = 136,
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pages = {134903}
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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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Using type 2 for bond particles
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Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486)
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Neighbor list info ...
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update every 10 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3
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ghost atom cutoff = 3.6
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binsize = 1.5, bins = 7 7 7
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair dpd, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair srp, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, 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
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bin: standard
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Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250)
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Per MPI rank memory allocation (min/avg/max) = 10.35 | 10.35 | 10.35 Mbytes
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Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz
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0 0.98262092 31772.336 10.590779 60.908146 5700 3000 10 10 10
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50 1.0094645 31632.293 10.544098 61.107394 5700 3000 10 10 10
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100 1.0067657 31633.525 10.544508 61.721089 5700 3000 10 10 10
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150 0.99163624 31751.06 10.583687 60.437789 5700 3000 10 10 10
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200 0.98701756 31674.754 10.558251 60.897782 5700 3000 10 10 10
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250 0.99422545 31689.944 10.563315 61.748317 5700 3000 10 10 10
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300 0.98351268 31756.124 10.585375 61.164735 5700 3000 10 10 10
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350 0.99570183 31840.098 10.613366 61.210337 5700 3000 10 10 10
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400 1.0025719 31832.008 10.610669 61.270633 5700 3000 10 10 10
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450 0.99464256 31812.213 10.604071 60.625168 5700 3000 10 10 10
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500 0.98753036 31822.577 10.607526 61.007786 5700 3000 10 10 10
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550 0.98085348 31779.406 10.593135 61.268608 5700 3000 10 10 10
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600 1.0031999 31849.695 10.616565 61.938464 5700 3000 10 10 10
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650 1.0102644 31912.564 10.637521 61.298438 5700 3000 10 10 10
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700 1.0238545 31799.622 10.599874 61.424427 5700 3000 10 10 10
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750 1.0186874 31781.261 10.593754 60.706143 5700 3000 10 10 10
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800 1.0245821 31738.473 10.579491 61.550865 5700 3000 10 10 10
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850 1.0179726 31720.521 10.573507 61.881576 5700 3000 10 10 10
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900 1.0154591 31760.887 10.586962 61.673156 5700 3000 10 10 10
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950 0.99349056 31834.644 10.611548 61.624864 5700 3000 10 10 10
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1000 1.0033121 31820.089 10.606696 60.698277 5700 3000 10 10 10
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Deleted 2700 atoms, new total = 3000
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Loop time of 2.18923 on 4 procs for 1000 steps with 3000 atoms
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Performance: 394659.660 tau/day, 456.782 timesteps/s
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98.1% 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 | 1.2744 | 1.2921 | 1.3222 | 1.6 | 59.02
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Bond | 0.0092027 | 0.0093722 | 0.009696 | 0.2 | 0.43
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Neigh | 0.47767 | 0.47768 | 0.47769 | 0.0 | 21.82
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Comm | 0.34932 | 0.37877 | 0.39403 | 2.9 | 17.30
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Output | 0.001045 | 0.0015711 | 0.003145 | 2.3 | 0.07
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Modify | 0.015498 | 0.016073 | 0.017271 | 0.6 | 0.73
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Other | | 0.01362 | | | 0.62
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Nlocal: 750.000 ave 754 max 743 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 6941.25 ave 6967 max 6911 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0.0000000
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Ave special neighs/atom = 1.8000000
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Neighbor list builds = 21
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Dangerous builds = 0
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#write_restart end-run.restart
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Total wall time: 0:00:02
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