272 lines
11 KiB
Groff
272 lines
11 KiB
Groff
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-345-g506bf886ee-modified)
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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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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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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 = 0.005 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) = 4.148 | 4.148 | 4.148 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 0.0365221 on 1 procs for 500 steps with 1200 atoms
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Performance: 5914221.123 tau/day, 13690.327 timesteps/s, 16.428 Matom-step/s
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89.2% CPU use with 1 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 | 0.022939 | 0.022939 | 0.022939 | 0.0 | 62.81
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Bond | 0.00073851 | 0.00073851 | 0.00073851 | 0.0 | 2.02
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Neigh | 0.0078339 | 0.0078339 | 0.0078339 | 0.0 | 21.45
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Comm | 0.00072134 | 0.00072134 | 0.00072134 | 0.0 | 1.98
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Output | 7.1419e-05 | 7.1419e-05 | 7.1419e-05 | 0.0 | 0.20
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Modify | 0.0034868 | 0.0034868 | 0.0034868 | 0.0 | 9.55
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Other | | 0.0007314 | | | 2.00
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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: 197 ave 197 max 197 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 3094 ave 3094 max 3094 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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) = 5.391 | 5.391 | 5.391 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 0.0650638 on 1 procs for 500 steps with 1200 atoms
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Performance: 3319817.322 tau/day, 7684.762 timesteps/s, 9.222 Matom-step/s
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100.0% CPU use with 1 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 | 0.027565 | 0.027565 | 0.027565 | 0.0 | 42.37
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Bond | 0.0007043 | 0.0007043 | 0.0007043 | 0.0 | 1.08
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Neigh | 0.012724 | 0.012724 | 0.012724 | 0.0 | 19.56
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Comm | 0.00091442 | 0.00091442 | 0.00091442 | 0.0 | 1.41
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Output | 6.004e-05 | 6.004e-05 | 6.004e-05 | 0.0 | 0.09
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Modify | 0.022329 | 0.022329 | 0.022329 | 0.0 | 34.32
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Other | | 0.0007666 | | | 1.18
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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: 411 ave 411 max 411 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 8759 ave 8759 max 8759 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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) = 9.306 | 9.306 | 9.306 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 2.1630988
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Loop time of 0.0592806 on 1 procs for 500 steps with 1200 atoms
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Performance: 3643690.276 tau/day, 8434.468 timesteps/s, 10.121 Matom-step/s
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100.0% CPU use with 1 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 | 0.026866 | 0.026866 | 0.026866 | 0.0 | 45.32
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Bond | 0.00071863 | 0.00071863 | 0.00071863 | 0.0 | 1.21
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Neigh | 0.010927 | 0.010927 | 0.010927 | 0.0 | 18.43
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Comm | 0.00084187 | 0.00084187 | 0.00084187 | 0.0 | 1.42
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Output | 6.8106e-05 | 6.8106e-05 | 6.8106e-05 | 0.0 | 0.11
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Modify | 0.019075 | 0.019075 | 0.019075 | 0.0 | 32.18
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Other | | 0.000783 | | | 1.32
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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: 417 ave 417 max 417 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 8654 ave 8654 max 8654 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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