291 lines
12 KiB
Groff
291 lines
12 KiB
Groff
LAMMPS (28 Feb 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
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using 1 OpenMP thread(s) per MPI task
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# 2d micelle simulation
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dimension 2
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_style bond
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# Soft potential push-off
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read_data data.micelle
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orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1200 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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300 bonds
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000271559 secs
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read_data CPU = 0.00115585 secs
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special_bonds fene
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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 = 8.39233e-05 secs
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pair_style soft 1.12246
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pair_coeff * * 0.0 1.12246
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bond_style harmonic
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bond_coeff 1 50.0 0.75
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velocity all create 0.45 2349852
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variable prefactor equal ramp(1.0,20.0)
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fix 1 all nve
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fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
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fix 3 all adapt 1 pair soft a * * v_prefactor
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fix 4 all enforce2d
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thermo 50
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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 = 1.42246
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ghost atom cutoff = 1.42246
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binsize = 0.71123, bins = 51 51 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair soft, 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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
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50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
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100 0.45 0.73046745 0.054836584 1.234929 2.3196516
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150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
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200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
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250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
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300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
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350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
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400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
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450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
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500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
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550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
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600 0.45 0.58193041 0.088386617 1.119942 5.131481
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650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
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700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
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750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
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800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
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850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
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900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
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950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
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1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
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Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms
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Performance: 4029800.456 tau/day, 9328.242 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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Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20
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Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72
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Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00
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Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71
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Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15
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Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95
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Other | | 0.002429 | | | 2.27
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Nlocal: 1200 ave 1200 max 1200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 195 ave 195 max 195 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3136 ave 3136 max 3136 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 3136
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Ave neighs/atom = 2.61333
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Ave special neighs/atom = 0.5
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Neighbor list builds = 92
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Dangerous builds = 0
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unfix 3
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# Main run
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pair_style lj/cut 2.5
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# solvent/head - full-size and long-range
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 2 2 1.0 1.0 2.5
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pair_coeff 1 2 1.0 1.0 2.5
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# tail/tail - size-averaged and long-range
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pair_coeff 3 3 1.0 0.75 2.5
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pair_coeff 4 4 1.0 0.50 2.5
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pair_coeff 3 4 1.0 0.67 2.5
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# solvent/tail - full-size and repulsive
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pair_coeff 1 3 1.0 1.0 1.12246
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pair_coeff 1 4 1.0 1.0 1.12246
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# head/tail - size-averaged and repulsive
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pair_coeff 2 3 1.0 0.88 1.12246
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pair_coeff 2 4 1.0 0.75 1.12246
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thermo 1000
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#dump 1 all atom 2000 dump.micelle
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#dump 2 all image 2000 image.*.jpg type type zoom 1.6
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#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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#dump 3 all movie 2000 movie.mpg type type zoom 1.6
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#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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reset_timestep 0
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group solvent molecule 0
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750 atoms in group solvent
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group solute subtract all solvent
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450 atoms in group solute
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unfix 1
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unfix 2
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unfix 4
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fix 1 solvent nve
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fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
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fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
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150 rigid bodies with 450 atoms
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fix 4 all enforce2d
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run 20000
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 26 26 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
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1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
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2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
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3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
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4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
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5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
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6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
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7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
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8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
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9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
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10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
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11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
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12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
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13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
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14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
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15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
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16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
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17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
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18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
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19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
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20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
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Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
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Performance: 2347175.802 tau/day, 5433.277 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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Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13
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Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16
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Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33
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Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33
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Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01
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Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58
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Other | | 0.05369 | | | 1.46
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Nlocal: 1200 ave 1200 max 1200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 395 ave 395 max 395 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 8915 ave 8915 max 8915 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 8915
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Ave neighs/atom = 7.42917
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Ave special neighs/atom = 0.5
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Neighbor list builds = 1580
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Dangerous builds = 0
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unfix 5
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unfix 4
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fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
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create bodies CPU = 0.00012517 secs
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150 rigid bodies with 450 atoms
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1.04536 = max distance from body owner to body atom
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fix 4 all enforce2d
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run 20000
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Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
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Step Temp E_pair E_mol TotEng Press
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20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
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21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
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22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
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23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
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24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
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25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
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26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
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27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
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28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
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29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
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30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
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31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
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32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
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33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
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34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
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35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
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36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
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37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
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38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
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39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
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40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
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Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
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Performance: 2341388.948 tau/day, 5419.882 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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Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59
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Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15
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Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30
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Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31
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Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01
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Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19
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Other | | 0.05386 | | | 1.46
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Nlocal: 1200 ave 1200 max 1200 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 393 ave 393 max 393 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9091 ave 9091 max 9091 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9091
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Ave neighs/atom = 7.57583
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Ave special neighs/atom = 0.5
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Neighbor list builds = 1582
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Dangerous builds = 0
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Total wall time: 0:00:07
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