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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2 by 2 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 = 0.000175714 secs
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read_data CPU = 0.00145626 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 = 7.22408e-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) = 3.758 | 3.85 | 4.126 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 0.0389124 on 4 procs for 1000 steps with 1200 atoms
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Performance: 11101855.138 tau/day, 25698.739 timesteps/s
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95.7% 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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Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73
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Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08
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Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59
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Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12
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Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71
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Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34
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Other | | 0.002501 | | | 6.43
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Nlocal: 300 ave 305 max 292 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 100.25 ave 108 max 93 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 784 ave 815 max 739 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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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) = 5.251 | 5.282 | 5.374 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 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869
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2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671
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3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553
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4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215
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5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897
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6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512
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7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309
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8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852
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9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071
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10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464
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11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699
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12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823
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13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171
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14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645
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15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206
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16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281
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17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975
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18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943
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19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417
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20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952
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Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
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Performance: 5025468.853 tau/day, 11633.030 timesteps/s
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98.2% 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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Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77
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Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27
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Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16
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Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92
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Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03
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Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76
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Other | | 0.05327 | | | 3.10
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Nlocal: 300 ave 303 max 298 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Nghost: 218.5 ave 226 max 215 min
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Histogram: 2 1 0 0 0 0 0 0 0 1
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Neighs: 2258.75 ave 2283 max 2216 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Total # of neighbors = 9035
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Ave neighs/atom = 7.52917
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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 = 5.43594e-05 secs
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150 rigid bodies with 450 atoms
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0.916597 = 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) = 8.568 | 8.6 | 8.691 Mbytes
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Step Temp E_pair E_mol TotEng Press
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20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643
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21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285
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22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965
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23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871
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24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675
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25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122
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26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501
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27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661
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28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448
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29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989
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30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951
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31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891
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32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966
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33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641
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34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091
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35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508
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36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696
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37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854
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38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763
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39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345
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40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727
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Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
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Performance: 6885775.862 tau/day, 15939.296 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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Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30
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Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72
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Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51
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Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27
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Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04
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Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52
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Other | | 0.03321 | | | 2.65
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Nlocal: 300 ave 304 max 293 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 215.25 ave 217 max 213 min
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Histogram: 1 0 0 0 0 1 0 1 0 1
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Neighs: 2340 ave 2378 max 2290 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 9360
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Ave neighs/atom = 7.8
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Ave special neighs/atom = 0.5
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Neighbor list builds = 1579
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Dangerous builds = 0
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Total wall time: 0:00:03
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