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 4 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) = 4.182 | 4.794 | 5.472 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 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
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400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
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600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
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800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
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1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
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1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
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1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
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1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
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1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
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2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
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2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
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2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
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2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
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2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
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3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
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Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
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Performance: 553164.568 tau/day, 640.237 timesteps/s
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95.6% 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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---------------------------------------------------------------
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Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
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Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
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Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
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Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
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Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
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Other | | 2.338 | | | 49.90
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Nlocal: 480 ave 1011 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Nghost: 860 ave 1771 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 11697.8 ave 30095 max 0 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Total # of neighbors = 46791
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Ave neighs/atom = 24.370313
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Neighbor list builds = 99
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Dangerous builds = 0
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Total wall time: 0:00:04
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