160 lines
6.0 KiB
Groff
160 lines
6.0 KiB
Groff
LAMMPS (15 Sep 2022)
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using 1 OpenMP thread(s) per MPI task
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# flat membrane demo
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variable r0 equal 0.97
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variable d1 equal ${r0}
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variable d1 equal 0.97
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variable d2 equal sqrt(3.0)*${r0}
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variable d2 equal sqrt(3.0)*0.97
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variable d3 equal 3.0*${r0}
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variable d3 equal 3.0*0.97
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variable ro equal 2./${d1}/${d2}/${d3}
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variable ro equal 2./0.97/${d2}/${d3}
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variable ro equal 2./0.97/1.68008928334181/${d3}
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variable ro equal 2./0.97/1.68008928334181/2.91
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variable T equal 0.23
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variable LD equal 1.0
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units lj
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atom_style ellipsoid
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boundary p p p
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lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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Lattice spacing in x,y,z = 0.97 1.6800893 2.91
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region box block 0 40 0 24 -20 20
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create_box 1 box
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Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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1 by 1 by 1 MPI processor grid
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region membrane block 0 40 0 24 -0.5 0.5
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create_atoms 1 region membrane
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Created 1920 atoms
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using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
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create_atoms CPU = 0.001 seconds
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group membrane region membrane
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1920 atoms in group membrane
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set type 1 mass 1.0
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Setting atom values ...
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1920 settings made for mass
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set type 1 shape 1 1 1
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Setting atom values ...
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1920 settings made for shape
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set group all quat 0 -1 0 90
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Setting atom values ...
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1920 settings made for quat
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#compute memb all temp/com
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#compute rot all temp/asphere bias memb
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velocity all create ${T} 87287 loop geom
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velocity all create 0.23 87287 loop geom
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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neighbor 1.0 bin
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thermo_style custom step temp press pxx pyy
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thermo 200
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timestep 0.01
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#dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.23 ${T} ${LD} 48279
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fix 1 all langevin 0.23 0.23 ${LD} 48279
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fix 1 all langevin 0.23 0.23 1 48279
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fix 2 all nve/asphere
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run 3000
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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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- pair ylz command:
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@Article{Yuan10,
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author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
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title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
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journal = {Phys. Rev. E},
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year = 2010,
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volume = 82,
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pages = {011905}
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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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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 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 = 3.6
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ghost atom cutoff = 3.6
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binsize = 1.8, bins = 22 23 65
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair ylz, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
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Step Temp Press Pxx Pyy
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
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200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
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400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
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600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
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800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
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1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
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1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
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1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
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1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
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1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
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2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
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2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
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2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
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2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
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2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
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3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
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Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
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Performance: 383058.431 tau/day, 443.355 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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---------------------------------------------------------------
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Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
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Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
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Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
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Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
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Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
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Other | | 0.02181 | | | 0.32
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Nlocal: 1920 ave 1920 max 1920 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 772 ave 772 max 772 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46804 ave 46804 max 46804 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46804
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Ave neighs/atom = 24.377083
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Neighbor list builds = 99
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Dangerous builds = 0
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Total wall time: 0:00:06
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