125 lines
4.4 KiB
Plaintext
125 lines
4.4 KiB
Plaintext
LAMMPS (29 Sep 2021 - Update 3)
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variable T equal 0.2
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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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read_data read_data.vesicle1026
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Reading data file ...
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orthogonal box = (-35.000000 -35.000000 -35.000000) to (35.000000 35.000000 35.000000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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2938 atoms
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2938 ellipsoids
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read_data CPU = 0.008 seconds
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compute ali all temp/com
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compute rott all temp/asphere bias ali
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velocity all create ${T} 87287 loop geom
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velocity all create 0.2 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 0.001
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dump 1 all atom 10 onlymembrane2.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.2 ${T} ${LD} 48279
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fix 1 all langevin 0.2 0.2 ${LD} 48279
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fix 1 all langevin 0.2 0.2 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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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 = 39 39 39
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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) = 6.203 | 6.203 | 6.203 Mbytes
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Step Temp Press Pxx Pyy
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0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
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200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
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400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
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600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
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800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
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1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
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1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
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1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
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1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
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1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
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2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
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2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
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2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
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2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
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2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
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3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
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Loop time of 7.2222 on 1 procs for 3000 steps with 2938 atoms
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Performance: 35889.329 tau/day, 415.386 timesteps/s
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99.9% 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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---------------------------------------------------------------
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Pair | 6.0158 | 6.0158 | 6.0158 | 0.0 | 83.30
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Neigh | 0.034308 | 0.034308 | 0.034308 | 0.0 | 0.48
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Comm | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.02
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Output | 0.31567 | 0.31567 | 0.31567 | 0.0 | 4.37
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Modify | 0.83787 | 0.83787 | 0.83787 | 0.0 | 11.60
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Other | | 0.01702 | | | 0.24
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Nlocal: 2938.00 ave 2938 max 2938 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0.00000 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 73242.0 ave 73242 max 73242 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 73242
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Ave neighs/atom = 24.929204
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Neighbor list builds = 26
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Dangerous builds = 0
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# notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem.
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# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
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# notes-3: pressure reach equilibrium much quicker than temperature
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Total wall time: 0:00:07
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