273 lines
11 KiB
Groff
273 lines
11 KiB
Groff
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551)
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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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Reading data file ...
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orthogonal box = (0 0 -0.1) to (35.85686 35.85686 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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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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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 = 0.000 seconds
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read_data CPU = 0.004 seconds
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special_bonds fene
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 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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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 500
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
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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
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bin: standard
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WARNING: Communication cutoff 1.42246 is shorter than a bond length based estimate of 1.425. This may lead to errors. (../comm.cpp:730)
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Per MPI rank memory allocation (min/avg/max) = 4.126 | 4.126 | 4.127 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 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
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100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
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150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
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200 0.45 1.01454 0.10663502 1.5708 4.7598476
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250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
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300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
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350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
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400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
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450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
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500 0.45 0.66669513 0.13695201 1.2532721 6.807146
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Loop time of 0.0138659 on 4 procs for 500 steps with 1200 atoms
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Performance: 15577811.312 tau/day, 36059.748 timesteps/s, 43.272 Matom-step/s
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99.9% CPU use with 4 MPI tasks x no 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 | 0.0053896 | 0.0057144 | 0.0060899 | 0.4 | 41.21
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Bond | 0.00020074 | 0.00021422 | 0.00022291 | 0.0 | 1.54
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Neigh | 0.0025301 | 0.0025401 | 0.0025501 | 0.0 | 18.32
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Comm | 0.0031194 | 0.0035074 | 0.0038196 | 0.4 | 25.30
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Output | 6.4137e-05 | 6.7743e-05 | 7.7909e-05 | 0.0 | 0.49
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Modify | 0.0013391 | 0.0013582 | 0.0013972 | 0.1 | 9.80
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Other | | 0.0004638 | | | 3.34
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Nlocal: 300 ave 304 max 292 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Nghost: 103.5 ave 108 max 98 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 773.5 ave 792 max 735 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Total # of neighbors = 3094
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Ave neighs/atom = 2.5783333
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Ave special neighs/atom = 0.5
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Neighbor list builds = 52
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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 50
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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 500
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.375 | 5.375 | 5.375 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
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50 0.77344732 -1.6944083 0.13695201 -0.92967487 0.58657109
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100 0.53530681 -1.7006195 0.13695201 -1.1291768 0.11219772
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150 0.60820175 -1.8071581 0.13695201 -1.176549 1.5161796
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200 0.49410558 -1.7945459 0.13695201 -1.2565449 4.0469262
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250 0.52460847 -1.8528672 0.13695201 -1.290108 2.9929445
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300 0.46596803 -1.8680499 0.13695201 -1.3528872 2.7958851
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350 0.48831812 -1.8723486 0.13695201 -1.3390451 -4.5106818
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400 0.46798432 -1.9008529 0.13695201 -1.3840536 -4.3096566
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450 0.46000658 -1.9081144 0.13695201 -1.3977904 3.3360611
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500 0.45822409 -1.9077531 0.13695201 -1.3988759 0.45428738
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Loop time of 0.0381773 on 4 procs for 500 steps with 1200 atoms
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Performance: 5657810.772 tau/day, 13096.784 timesteps/s, 15.716 Matom-step/s
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99.6% CPU use with 4 MPI tasks x no 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 | 0.0059651 | 0.0062314 | 0.0066404 | 0.3 | 16.32
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Bond | 0.00021057 | 0.00022477 | 0.0002333 | 0.0 | 0.59
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Neigh | 0.0041424 | 0.0041487 | 0.0041512 | 0.0 | 10.87
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Comm | 0.004264 | 0.0047244 | 0.0050297 | 0.4 | 12.37
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Output | 8.2396e-05 | 8.6559e-05 | 9.6749e-05 | 0.0 | 0.23
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Modify | 0.021833 | 0.021946 | 0.022094 | 0.1 | 57.48
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Other | | 0.0008157 | | | 2.14
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Nlocal: 300 ave 303 max 296 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Nghost: 216.25 ave 219 max 214 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 2189.75 ave 2205 max 2173 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 8759
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Ave neighs/atom = 7.2991667
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Ave special neighs/atom = 0.5
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Neighbor list builds = 46
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Dangerous builds = 2
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unfix 2
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unfix 4
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unfix 5
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fix 5 solute rigid/small molecule
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create bodies CPU = 0.000 seconds
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150 rigid bodies with 450 atoms
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1.3043524 = max distance from body owner to body atom
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fix 4 all enforce2d
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run 500
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 9.233 | 9.233 | 9.234 Mbytes
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Step Temp E_pair E_mol TotEng Press
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500 0.45822409 -1.9077531 0.13695201 -1.3988759 2.4509752
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550 0.46736204 -1.9141964 0.13695201 -1.3979022 2.1695662
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600 0.47872194 -1.9232781 0.13695201 -1.3977635 2.0058379
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650 0.47491575 -1.9224109 0.13695201 -1.3999857 2.0637789
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700 0.44714331 -1.8990682 0.13695201 -1.3991848 2.4863082
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750 0.49089274 -1.9231004 0.13695201 -1.3877071 2.123147
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800 0.4753839 -1.8959698 0.13695201 -1.3731645 2.3030481
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850 0.46870816 -1.8972225 0.13695201 -1.3798357 2.2464703
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900 0.49610454 -1.9070748 0.13695201 -1.3674513 2.2196388
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950 0.4773035 -1.8925765 0.13695201 -1.3682132 2.3534786
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1000 0.50413702 -1.9292393 0.13695201 -1.383096 2.1630987
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Loop time of 0.0236819 on 4 procs for 500 steps with 1200 atoms
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Performance: 9120883.727 tau/day, 21113.157 timesteps/s, 25.336 Matom-step/s
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99.9% CPU use with 4 MPI tasks x no 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 | 0.0058656 | 0.0059718 | 0.0061355 | 0.1 | 25.22
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Bond | 0.0002083 | 0.00022447 | 0.00023485 | 0.0 | 0.95
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Neigh | 0.0035477 | 0.0035644 | 0.0035824 | 0.0 | 15.05
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Comm | 0.0041037 | 0.0042227 | 0.0043024 | 0.1 | 17.83
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Output | 7.4355e-05 | 7.8273e-05 | 8.7777e-05 | 0.0 | 0.33
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Modify | 0.008976 | 0.0090549 | 0.0091663 | 0.1 | 38.24
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Other | | 0.0005654 | | | 2.39
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Nlocal: 300 ave 306 max 295 min
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Histogram: 1 0 1 0 0 1 0 0 0 1
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Nghost: 221 ave 226 max 217 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 2163.5 ave 2271 max 2100 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 8654
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Ave neighs/atom = 7.2116667
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Ave special neighs/atom = 0.5
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Neighbor list builds = 39
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Dangerous builds = 0
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Total wall time: 0:00:00
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