forked from lijiext/lammps
reformat, simplify, add reference log files
This commit is contained in:
Axel Kohlmeyer
parent
b108da3e5c
commit
c49a533ad9
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@ -35,8 +35,8 @@ 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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fix 1 all nve
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timestep 0.01
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timestep 0.01
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restart 500 mid-run-*.restart
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#restart 500 mid-run-*.restart
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run 1000
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run 1000
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write_restart end-run.restart
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#write_restart end-run.restart
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@ -0,0 +1,156 @@
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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 1 by 1 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 = 0.013 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) = 21.70 | 21.70 | 21.70 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 60.690437 5700 3000 10 10 10
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50 0.99678169 31789.37 10.596457 61.967133 5700 3000 10 10 10
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100 1.016953 31770.946 10.590315 61.808425 5700 3000 10 10 10
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150 1.0151677 31737.965 10.579322 61.034423 5700 3000 10 10 10
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200 0.99241972 31766.458 10.588819 60.99902 5700 3000 10 10 10
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250 1.0101747 31816.098 10.605366 61.484391 5700 3000 10 10 10
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300 1.0058287 31824.98 10.608327 60.656545 5700 3000 10 10 10
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350 1.0093409 31839.963 10.613321 61.485931 5700 3000 10 10 10
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400 1.029692 31713.44 10.571147 61.442428 5700 3000 10 10 10
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450 1.0292264 31739.234 10.579745 61.026996 5700 3000 10 10 10
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500 1.0141131 31796.032 10.598677 61.099407 5700 3000 10 10 10
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550 0.99860738 31887.879 10.629293 61.412249 5700 3000 10 10 10
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600 1.0104436 31830.675 10.610225 60.725018 5700 3000 10 10 10
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650 1.0060939 31871.441 10.623814 61.12217 5700 3000 10 10 10
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700 1.0394405 31724.09 10.574697 60.652294 5700 3000 10 10 10
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750 1.0094386 31827.328 10.609109 61.274573 5700 3000 10 10 10
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800 0.99986353 31777.205 10.592402 60.652922 5700 3000 10 10 10
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850 0.9762615 31752.585 10.584195 61.448972 5700 3000 10 10 10
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900 0.99324534 31794.723 10.598241 61.191199 5700 3000 10 10 10
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950 1.0139717 31719.123 10.573041 61.876053 5700 3000 10 10 10
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1000 0.99850758 31774.801 10.5916 60.960607 5700 3000 10 10 10
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Deleted 2700 atoms, new total = 3000
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Loop time of 6.54135 on 1 procs for 1000 steps with 3000 atoms
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Performance: 132082.911 tau/day, 152.874 timesteps/s
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99.9% 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 | 4.5403 | 4.5403 | 4.5403 | 0.0 | 69.41
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Bond | 0.030682 | 0.030682 | 0.030682 | 0.0 | 0.47
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Neigh | 1.7065 | 1.7065 | 1.7065 | 0.0 | 26.09
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Comm | 0.20647 | 0.20647 | 0.20647 | 0.0 | 3.16
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Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01
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Modify | 0.034479 | 0.034479 | 0.034479 | 0.0 | 0.53
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Other | | 0.022 | | | 0.34
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Nlocal: 3000.00 ave 3000 max 3000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 12269.0 ave 12269 max 12269 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0.00000 ave 0 max 0 min
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Histogram: 1 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: 0:00:06
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@ -0,0 +1,156 @@
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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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||||||
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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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@ -449,10 +449,10 @@ int FixSRP::unpack_border(int n, int first, double *buf)
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int m = 0;
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int m = 0;
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last = first + n;
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last = first + n;
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for (i = first; i < last; i++) {
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for (i = first; i < last; i++) {
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array[i][0] = buf[m++];
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array[i][0] = buf[m++];
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array[i][1] = buf[m++];
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array[i][1] = buf[m++];
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}
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}
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return m;
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return m;
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}
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}
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@ -68,7 +68,7 @@ static int srp_instance = 0;
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set size of pair comms in constructor
|
set size of pair comms in constructor
|
||||||
---------------------------------------------------------------------- */
|
---------------------------------------------------------------------- */
|
||||||
|
|
||||||
PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp)
|
PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp), fix_id(nullptr)
|
||||||
{
|
{
|
||||||
writedata = 1;
|
writedata = 1;
|
||||||
single_enable = 0;
|
single_enable = 0;
|
||||||
|
|
@ -118,18 +118,16 @@ void PairSRP::allocate()
|
||||||
|
|
||||||
PairSRP::~PairSRP()
|
PairSRP::~PairSRP()
|
||||||
{
|
{
|
||||||
if (allocated)
|
if (allocated) {
|
||||||
{
|
memory->destroy(setflag);
|
||||||
memory->destroy(setflag);
|
memory->destroy(cutsq);
|
||||||
memory->destroy(cutsq);
|
memory->destroy(cut);
|
||||||
memory->destroy(cut);
|
memory->destroy(a0);
|
||||||
memory->destroy(a0);
|
memory->destroy(segment);
|
||||||
memory->destroy(segment);
|
}
|
||||||
}
|
|
||||||
|
|
||||||
// check nfix in case all fixes have already been deleted
|
// check nfix in case all fixes have already been deleted
|
||||||
if (modify->nfix) modify->delete_fix(fix_id);
|
if (modify->nfix) modify->delete_fix(f_srp->id);
|
||||||
free(fix_id);
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|
@ -412,33 +410,31 @@ void PairSRP::settings(int narg, char **arg)
|
||||||
|
|
||||||
void PairSRP::coeff(int narg, char **arg)
|
void PairSRP::coeff(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg < 3 || narg > 4)
|
if (narg < 3 || narg > 4)
|
||||||
error->all(FLERR,"PairSRP: Incorrect args for pair coeff");
|
error->all(FLERR,"PairSRP: Incorrect args for pair coeff");
|
||||||
if (!allocated) allocate();
|
if (!allocated) allocate();
|
||||||
|
|
||||||
// set ij bond-bond cutoffs
|
// set ij bond-bond cutoffs
|
||||||
int ilo, ihi, jlo, jhi;
|
int ilo, ihi, jlo, jhi;
|
||||||
utils::bounds(FLERR,arg[0], 1, bptype, ilo, ihi, error);
|
utils::bounds(FLERR,arg[0], 1, bptype, ilo, ihi, error);
|
||||||
utils::bounds(FLERR,arg[1], 1, bptype, jlo, jhi, error);
|
utils::bounds(FLERR,arg[1], 1, bptype, jlo, jhi, error);
|
||||||
|
|
||||||
double a0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
double a0_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||||
double cut_one = cut_global;
|
double cut_one = cut_global;
|
||||||
if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp);
|
if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||||
|
|
||||||
int count = 0;
|
int count = 0;
|
||||||
for (int i = ilo; i <= ihi; i++)
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
{
|
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||||
for (int j = MAX(jlo,i); j <= jhi; j++)
|
a0[i][j] = a0_one;
|
||||||
{
|
cut[i][j] = cut_one;
|
||||||
a0[i][j] = a0_one;
|
cutsq[i][j] = cut_one * cut_one;
|
||||||
cut[i][j] = cut_one;
|
setflag[i][j] = 1;
|
||||||
cutsq[i][j] = cut_one * cut_one;
|
count++;
|
||||||
setflag[i][j] = 1;
|
|
||||||
count++;
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
}
|
||||||
|
|
||||||
if (count == 0) error->warning(FLERR,"PairSRP: No pair coefficients were set");
|
if (count == 0) error->warning(FLERR,"PairSRP: No pair coefficients were set");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|
@ -452,8 +448,7 @@ void PairSRP::init_style()
|
||||||
|
|
||||||
// verify that fix SRP is still defined and has not been changed.
|
// verify that fix SRP is still defined and has not been changed.
|
||||||
|
|
||||||
int ifix = modify->find_fix(fix_id);
|
if (strcmp(f_srp->style,"SRP") != 0)
|
||||||
if (f_srp != (FixSRP *)modify->fix[ifix])
|
|
||||||
error->all(FLERR,"Fix SRP has been changed unexpectedly");
|
error->all(FLERR,"Fix SRP has been changed unexpectedly");
|
||||||
|
|
||||||
if (comm->me == 0)
|
if (comm->me == 0)
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue