update examples to standard lammps conventions
This commit is contained in:
Colin Denniston
@ -19,7 +19,7 @@ units micro
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dimension 3
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boundary p p f
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atom_style molecular
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read_data ../confinedcolloids.dat
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read_data confinedcolloids.dat
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mass * 0.00010287
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@ -102,4 +102,5 @@ fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
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thermo 50
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run 400
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#run 400
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run 100
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@ -0,0 +1,190 @@
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LAMMPS (17 Feb 2022)
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#===========================================================================#
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# System of colloidal particles under shear. #
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# #
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# Run consists of 10x12x4 particles, each composed of 3613 particle nodes #
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# (3612 particles forming a spherical shell, and 1 central particle). #
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# 280 x 280 x 101 lattice-Boltzmann grid sites. #
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# #
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# This simulation is used to illustrate the simulation time of a realistic #
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# implementation of the lb/fluid fix. #
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# The data file "confinedcolloids.dat" is quite large and so is not #
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# included here. It can be obtained from: #
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# http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz #
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# #
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# Sample output from this run can be found in the file: #
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# results64.out #
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#===========================================================================#
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units micro
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dimension 3
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boundary p p f
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atom_style molecular
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read_data confinedcolloids.dat
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Reading data file ...
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orthogonal box = (0 0 0) to (16.8 16.8 6)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1734240 atoms
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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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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.372 seconds
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read_data CPU = 34.950 seconds
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mass * 0.00010287
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#----------------------------------------------------------------------------
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# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
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# to ensure that the particles belonging to a given processor remain inside
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# that processors lattice-Boltzmann grid.
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# The arguments for neigh_modify have been set to "delay 0 every 1", again
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# to ensure that the particles belonging to a given processor remain inside
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# that processors lattice-Boltzmann grid. However, these values can likely
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# be somewhat increased without issue. If a problem does arise (a particle
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# is outside of its processors LB grid) an error message is printed and
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# the simulation is terminated.
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#----------------------------------------------------------------------------
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neighbor 0.03 bin
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neigh_modify delay 0 every 1
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neigh_modify exclude type 2 2
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neigh_modify exclude type 2 1
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#----------------------------------------------------------------------------
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# ForceAtoms are the particles at the center of each colloidal object which
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# do not interact with the fluid, but are used to implement the hard-sphere
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# interactions.
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#----------------------------------------------------------------------------
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group ForceAtoms type 1
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480 atoms in group ForceAtoms
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#----------------------------------------------------------------------------
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# FluidAtoms are the particles representing the surface of the colloidal
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# object which do interact with the fluid.
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#----------------------------------------------------------------------------
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group FluidAtoms type 2
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1733760 atoms in group FluidAtoms
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#----------------------------------------------------------------------------
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# Implement a hard-sphere interaction between the particles at the center of
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# each colloidal object (use a truncated and shifted Lennard-Jones
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# potential).
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#----------------------------------------------------------------------------
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pair_style lj/cut 1.572
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pair_coeff * * 0.0 0.0 1.572
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pair_coeff 1 1 10.0 1.400492785 1.572
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pair_modify shift yes
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timestep 0.001
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particles specified through FluidAtoms
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the lb/viscous fix).
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# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
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# lattice spacing dx=0.06.
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# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
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#----------------------------------------------------------------------------
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fix 1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
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Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (../fix_lb_fluid.cpp:486)
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Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
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#----------------------------------------------------------------------------
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# Apply the force due to the fluid onto the FluidAtoms particles (again,
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# these atoms represent the surface of the colloidal object, which should
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# interact with the fluid).
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#----------------------------------------------------------------------------
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fix 2 FluidAtoms lb/viscous
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#----------------------------------------------------------------------------
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# Each colloidal object (spherical shell of particles and central particle)
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# is specified as a separate molecule in the confinedcolloids.dat data
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# file. Integrate the motion of each of these sets of particles as rigid
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# objects which move and rotate together.
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#----------------------------------------------------------------------------
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fix 3 all rigid molecule
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480 rigid bodies with 1734240 atoms
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#----------------------------------------------------------------------------
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# Implement a repulsive interaction between the ForceAtoms particles, and the
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# upper and lower z-walls. (A truncated and shifted Lennard-Jones potential
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# is used).
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#----------------------------------------------------------------------------
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fix wallhi ForceAtoms wall/lj126 zhi 5.88 20.0 0.8071542386 0.906 units box
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fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
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#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
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thermo 50
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#run 400
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run 100
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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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- fix lb/fluid command:
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@Article{Denniston et al.,
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author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
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title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
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year = 2022,
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volume = 275,
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pages = {108318}
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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 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.602
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ghost atom cutoff = 1.602
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binsize = 0.801, bins = 21 21 8
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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/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 373.3 | 373.3 | 373.3 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 0 0 0 0
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50 4511970.8 0 0 89.610701 0.21526205
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100 16113793 0 0 320.0305 -0.54714356
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Loop time of 2168.87 on 4 procs for 100 steps with 1734240 atoms
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Performance: 3983.646 ns/day, 0.006 hours/ns, 0.046 timesteps/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 | 0.67377 | 0.70143 | 0.72779 | 2.5 | 0.03
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Bond | 4.19e-05 | 6.0825e-05 | 7.85e-05 | 0.0 | 0.00
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Neigh | 1978.7 | 1982.4 | 1985.9 | 6.3 | 91.40
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Comm | 9.4132 | 12.886 | 16.538 | 78.3 | 0.59
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Output | 0.0089264 | 0.016853 | 0.024638 | 4.3 | 0.00
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Modify | 171.19 | 171.23 | 171.27 | 0.3 | 7.89
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Other | | 1.598 | | | 0.07
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Nlocal: 433560 ave 433560 max 433560 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 397888 ave 397888 max 397888 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 60 ave 60 max 60 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 240
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Ave neighs/atom = 0.00013838915
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Ave special neighs/atom = 0
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Neighbor list builds = 16
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Dangerous builds = 0
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Total wall time: 0:39:00
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@ -1,83 +0,0 @@
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LAMMPS (29 Sep 2021 - Update 1)
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Reading data file ...
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.800000 16.800000 6.0000000)
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4 by 8 by 2 MPI processor grid
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reading atoms ...
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1734240 atoms
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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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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.018 seconds
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read_data CPU = 1.916 seconds
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480 atoms in group ForceAtoms
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1733760 atoms in group FluidAtoms
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Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (../fix_lb_fluid.cpp:477)
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Local Grid Geometry created. (../fix_lb_fluid.cpp:1023)
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First Run initialized
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480 rigid bodies with 1734240 atoms
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.602
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ghost atom cutoff = 1.602
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binsize = 0.801, bins = 21 21 8
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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/3d
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bin: standard
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Setting up Verlet run ...
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Unit style : micro
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Current step : 0
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Time step : 0.001
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Per MPI rank memory allocation (min/avg/max) = 97.31 | 97.33 | 97.36 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 0 0 0 0
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50 4511970.8 0 0 89.610701 0.21526205
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100 16113793 0 0 320.0305 -0.54714356
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150 31550748 67.191512 0 693.81006 1.2310415
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200 46439326 498.87168 0 1421.1872 4.0383841
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250 61684647 1043.9263 0 2269.0239 6.4736851
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300 80760268 1365.1861 0 2969.138 8.4186043
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350 1.0442842e+08 1296.934 0 3370.9509 8.9271065
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400 1.2759824e+08 817.33984 0 3351.5245 6.8724618
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Loop time of 528.696 on 64 procs for 400 steps with 1734240 atoms
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Performance: 65368.335 ns/day, 0.000 hours/ns, 0.757 timesteps/s
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99.2% CPU use with 64 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 | 0.053098 | 0.071612 | 0.096152 | 4.1 | 0.01
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Bond | 9.7577e-05 | 0.00012984 | 0.00017322 | 0.0 | 0.00
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Neigh | 301.06 | 394.1 | 493.41 | 450.6 | 74.54
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Comm | 7.8705 | 106.94 | 200.63 | 865.5 | 20.23
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Output | 0.0047098 | 0.0052866 | 0.0055549 | 0.3 | 0.00
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Modify | 25.511 | 26.848 | 28.764 | 17.8 | 5.08
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Other | | 0.736 | | | 0.14
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Nlocal: 27097.5 ave 28368 max 25504 min
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Histogram: 16 0 0 8 8 0 0 0 16 16
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Nghost: 166100.0 ave 167736 max 164146 min
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Histogram: 16 0 4 12 0 0 0 0 12 20
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Neighs: 14.0625 ave 21 max 6 min
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Histogram: 8 4 4 0 12 0 8 12 12 4
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Total # of neighbors = 900
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Ave neighs/atom = 0.00051895931
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Ave special neighs/atom = 0.0000000
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Neighbor list builds = 144
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Dangerous builds = 0
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LB equilibriumDist time: 3.490595
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LB update time: 8.100787
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LB PCalc time: 4.473729
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LB fluidForce time: 7.598387
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LB CorrectU time: 1.830964
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Total wall time: 0:08:54
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@ -2,13 +2,15 @@
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# Large colloidal sphere difusing around. #
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# #
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# In the first stage, the sphere is constructed by condensing atoms onto #
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# the surface of a spherica region. #
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# the surface of a spherical region. There are a flag you can change to #
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# either bond atoms into a spherical shell or integrate them as a rigid body#
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# #
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# To run this example, LAMMPS needs to be compiled with a the following #
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# packages: RIGID, LATBOTLZ #
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# #
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# Sample output from this run can be found in the file: #
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# 'dump.polymer.lammpstrj' #
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# If you uncomment the "dump..." line, sample output from this run #
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# can be found in the file: #
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# 'dump.trapnewsphere.lammpstrj' #
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# and viewed using, e.g., the VMD software. #
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# #
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#===========================================================================#
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@ -60,7 +62,7 @@ fix wall all wall/region mysphere lj93 15.0 1.5 5.28
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fix 2 all nve
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dump mydump all atom 10000 out.lammpstrj
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#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
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run 20000
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@ -191,7 +193,7 @@ if "${is_bonded} == 1" then &
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else &
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"variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
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fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
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#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
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run 10000
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#run 25000000
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@ -0,0 +1,388 @@
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LAMMPS (17 Feb 2022)
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#===========================================================================#
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# Large colloidal sphere difusing around. #
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# #
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# In the first stage, the sphere is constructed by condensing atoms onto #
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# the surface of a spherical region. There are a flag you can change to #
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# either bond atoms into a spherical shell or integrate them as a rigid body#
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# #
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# To run this example, LAMMPS needs to be compiled with a the following #
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# packages: RIGID, LATBOTLZ #
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# #
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# If you uncomment the "dump..." line, sample output from this run #
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# can be found in the file: #
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# 'dump.trapnewsphere.lammpstrj' #
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# and viewed using, e.g., the VMD software. #
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# #
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#===========================================================================#
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units nano
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dimension 3
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boundary p p p
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region mybox block -24 24 -24 24 -24 24
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# flag indicating whether sphere will be bonded or rigid, 0 or 1
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variable is_bonded equal 0
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# timestep for the LB run (setup uses different timesteps)
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variable tstep equal 0.00025
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# number of stencil points in any direction. could be 2, 3, or 4
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variable stpts equal 2
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if "${is_bonded} == 1" then "create_box 1 mybox bond/types 10 extra/bond/per/atom 12" else "create_box 1 mybox"
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create_box 1 mybox
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Created orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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#----------------------------------------------------------------------------
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# Create a spherical region and then fill it with atoms
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#----------------------------------------------------------------------------
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region mysphereinside sphere 0 0 0 4.0
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#variable n_nodes equal 216
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variable n_nodes equal 284
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create_atoms 1 random ${n_nodes} 1234 mysphereinside units box
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create_atoms 1 random 284 1234 mysphereinside units box
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Created 284 atoms
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using box units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.001 seconds
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pair_style soft 1.0
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pair_coeff * * 0.0
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variable prefactor equal ramp(0,30)
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fix 1 all adapt 1 pair soft a * * v_prefactor
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mass * 1.0
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#----------------------------------------------------------------------------
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# Set up and do an initial run to push the atoms apart as the random creation
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# could have them overlapping too much for stability.
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#----------------------------------------------------------------------------
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timestep 0.002
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# Define sphere where minimum of wall potential is at r=4 so
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# regions is 4 + (2/5)^(1/6) sigma
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region mysphere sphere 0 0 0 5.28756
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fix wall all wall/region mysphere lj93 15.0 1.5 5.28
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fix 2 all nve
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#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
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run 20000
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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 = 1.1
|
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ghost atom cutoff = 1.1
|
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binsize = 0.55, bins = 88 88 88
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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/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) = 3.944 | 3.944 | 3.944 Mbytes
|
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Step Temp E_pair E_mol TotEng Press
|
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0 0 0 0 0 0
|
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20000 317.05614 618.63581 0 2476.8578 0.030715
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Loop time of 0.573686 on 4 procs for 20000 steps with 284 atoms
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||||
|
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Performance: 6024197.192 ns/day, 0.000 hours/ns, 34862.252 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.062609 | 0.070036 | 0.076149 | 1.8 | 12.21
|
||||
Neigh | 0.21074 | 0.2209 | 0.2305 | 1.5 | 38.51
|
||||
Comm | 0.17847 | 0.19084 | 0.21153 | 3.0 | 33.26
|
||||
Output | 1.74e-05 | 2.58e-05 | 5.02e-05 | 0.0 | 0.00
|
||||
Modify | 0.079214 | 0.082596 | 0.085481 | 0.8 | 14.40
|
||||
Other | | 0.009288 | | | 1.62
|
||||
|
||||
Nlocal: 71 ave 73 max 69 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 54.75 ave 57 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 107.25 ave 127 max 85 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 429
|
||||
Ave neighs/atom = 1.5105634
|
||||
Neighbor list builds = 1996
|
||||
Dangerous builds = 1993
|
||||
|
||||
unfix wall
|
||||
fix wall all wall/region mysphere lj93 50.0 1.5 5.68
|
||||
|
||||
unfix 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Do a run to condense the atoms onto the spherical surface and anneal them
|
||||
# so they will be orderly aranged onto a semi-triangular mesh on the sphere
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 1.68359
|
||||
#pair_coeff * * 0.002 1.5 1.68369
|
||||
pair_coeff * * 0.0005 1.5 1.68369
|
||||
|
||||
fix 3 all langevin 1.5 0.01 100.0 5678
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
run 500000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.98369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 0.991845, bins = 49 49 49
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.277 | 3.277 | 3.277 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 317.05614 626.83186 0 2485.0538 0.034256287
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
Loop time of 12.8226 on 4 procs for 500000 steps with 284 atoms
|
||||
|
||||
Performance: 6738089.440 ns/day, 0.000 hours/ns, 38993.573 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6508 | 3.1904 | 3.6443 | 20.0 | 24.88
|
||||
Neigh | 0.68551 | 0.75012 | 0.80362 | 5.1 | 5.85
|
||||
Comm | 3.7915 | 4.3143 | 4.922 | 19.6 | 33.65
|
||||
Output | 2.26e-05 | 3.335e-05 | 6.29e-05 | 0.0 | 0.00
|
||||
Modify | 3.1825 | 3.2495 | 3.3155 | 2.6 | 25.34
|
||||
Other | | 1.318 | | | 10.28
|
||||
|
||||
Nlocal: 71 ave 74 max 69 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 109.75 ave 113 max 105 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 613.25 ave 718 max 495 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2453
|
||||
Ave neighs/atom = 8.6373239
|
||||
Neighbor list builds = 13515
|
||||
Dangerous builds = 0
|
||||
|
||||
minimize 0.0 1.0e-8 1000 100000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
520004 0.20789564 780.00993 0 781.22838 0.02889732
|
||||
Loop time of 0.00296133 on 4 procs for 4 steps with 284 atoms
|
||||
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
780.547473373201 780.009929329778 780.009929329778
|
||||
Force two-norm initial, final = 40.166574 13.723713
|
||||
Force max component initial, final = 4.2404394 1.5423956
|
||||
Final line search alpha, max atom move = 6.0381565e-11 9.3132257e-11
|
||||
Iterations, force evaluations = 4 69
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0009509 | 0.0010909 | 0.0014002 | 0.5 | 36.84
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0007064 | 0.0010256 | 0.0011795 | 0.6 | 34.63
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.000204 | 0.00024405 | 0.0002982 | 0.0 | 8.24
|
||||
Other | | 0.0006008 | | | 20.29
|
||||
|
||||
Nlocal: 71 ave 72 max 69 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 109.75 ave 113 max 107 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 612.75 ave 726 max 504 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2451
|
||||
Ave neighs/atom = 8.6302817
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix wall
|
||||
unfix 2
|
||||
unfix 3
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# If bonded, bond the atoms together at something close to their current
|
||||
# configuration
|
||||
#----------------------------------------------------------------------------
|
||||
|
||||
variable total_mass equal 0.002398
|
||||
variable node_mass equal "v_total_mass / v_n_nodes"
|
||||
mass * ${node_mass}
|
||||
mass * 8.44366197183099e-06
|
||||
|
||||
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 25.0 0.869333" "bond_coeff 2 25.0 0.948" "bond_coeff 3 25.0 1.026666" "bond_coeff 4 25.0 1.105333" "bond_coeff 5 25.0 1.184" "bond_coeff 6 25.0 1.262666" "bond_coeff 7 25.0 1.341333" "bond_coeff 8 25.0 1.42" "bond_coeff 9 25.0 1.498666" "bond_coeff 10 25.0 1.577333" "create_bonds many all all 1 0.83 0.908666" "create_bonds many all all 2 0.908667 0.987333" "create_bonds many all all 3 0.987334 1.066" "create_bonds many all all 4 1.066001 1.144666" "create_bonds many all all 5 1.144667 1.223333" "create_bonds many all all 6 1.223334 1.302" "create_bonds many all all 7 1.302001 1.380666" "create_bonds many all all 8 1.380667 1.459333" "create_bonds many all all 9 1.459334 1.538" "create_bonds many all all 10 1.538001 1.61667"
|
||||
|
||||
if "${is_bonded} == 1" then "pair_style lj/cut 5.05108" "pair_coeff * * 0.5 4.5" else "pair_style lj/cut 1.2" "pair_coeff * * 0.0 0.0"
|
||||
pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
|
||||
timestep ${tstep}
|
||||
timestep 0.00025
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# You could uncomment the following lines and then turn off the noise and
|
||||
# comment out the trap (following) to instead do a run that drags the
|
||||
# sphere through the fluid to measure the drag force.
|
||||
#----------------------------------------------------------------------------
|
||||
#variable total_force equal 8.0
|
||||
#variable node_force equal "v_total_force / v_n_nodes"
|
||||
#variable oscillateY equal cos(step*0.0005)/(-0.004+50*v_tstep)/v_n_nodes
|
||||
#variable oscillateZ equal cos(step*0.0003)/(-0.004+50*v_tstep)/v_n_nodes
|
||||
#fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Trap the sphere along x (could be done experimentally using optical
|
||||
# tweezers.
|
||||
#----------------------------------------------------------------------------
|
||||
variable fx atom -x*4.14195/284.0
|
||||
fix trap all addforce v_fx 0.0 0.0 # needs to go before fix lb/fluid and lb/viscous
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Set up the lb/fluid parameters for water and at a temperature of 300 K. If
|
||||
# the colloid is integrated with the rigid fix, the dof are not
|
||||
# automatically calculated correctly but as this would then be a rigid
|
||||
# sphere it is clear it should have 6 degrees of freedom.
|
||||
#----------------------------------------------------------------------------
|
||||
if "${is_bonded} == 1" then "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920" else "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6"
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 2 dx 1.2 noise 300.0 181920 dof 6
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
fix 2 all lb/viscous
|
||||
|
||||
if "${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
|
||||
fix 3 all rigid group 1 all
|
||||
1 rigid bodies with 284 atoms
|
||||
|
||||
#equilibration run
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520004 8.9102565e-07 0 0 1.8452924e-08 6.7761632e-05
|
||||
530004 3.474402 0 0 0.071954018 -0.00061159689
|
||||
Loop time of 238.57 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 905.396 ns/day, 0.027 hours/ns, 41.916 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.07901 | 0.086329 | 0.095378 | 2.0 | 0.04
|
||||
Neigh | 0.012928 | 0.013445 | 0.013795 | 0.3 | 0.01
|
||||
Comm | 0.18848 | 0.1969 | 0.20455 | 1.3 | 0.08
|
||||
Output | 4.07e-05 | 5.9575e-05 | 0.0001157 | 0.0 | 0.00
|
||||
Modify | 238.01 | 238.02 | 238.03 | 0.1 | 99.77
|
||||
Other | | 0.2536 | | | 0.11
|
||||
|
||||
Nlocal: 71 ave 84 max 59 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 110.75 ave 121 max 101 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 243.25 ave 285 max 209 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 52
|
||||
Dangerous builds = 0
|
||||
|
||||
# data gathering run
|
||||
reset_timestep 0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions/velocity of the colloids center
|
||||
# of mass.
|
||||
#----------------------------------------------------------------------------
|
||||
variable cmx equal xcm(all,x)
|
||||
variable cmy equal xcm(all,y)
|
||||
variable cmz equal xcm(all,z)
|
||||
|
||||
variable vcmx equal vcm(all,x)
|
||||
variable vcmy equal vcm(all,y)
|
||||
variable vcmz equal vcm(all,z)
|
||||
|
||||
if "${is_bonded} == 1" then "variable comdatafile string trap_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string trap_n284_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string trap_n284_st2_dt${tstep}.out
|
||||
variable comdatafile string trap_n284_st2_dt0.00025.out
|
||||
|
||||
#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.474402 0 0 0.071954018 0.00181615
|
||||
10000 2.6284662 0 0 0.054434894 0.00098091301
|
||||
Loop time of 237.772 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 908.435 ns/day, 0.026 hours/ns, 42.057 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.079283 | 0.087287 | 0.095198 | 2.6 | 0.04
|
||||
Neigh | 0.0133 | 0.013789 | 0.014439 | 0.3 | 0.01
|
||||
Comm | 0.18949 | 0.1975 | 0.20661 | 1.8 | 0.08
|
||||
Output | 2.88e-05 | 4.3675e-05 | 8.58e-05 | 0.0 | 0.00
|
||||
Modify | 237.21 | 237.22 | 237.22 | 0.0 | 99.77
|
||||
Other | | 0.253 | | | 0.11
|
||||
|
||||
Nlocal: 71 ave 87 max 54 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 110 ave 125 max 100 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 243.25 ave 264 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
#run 25000000
|
||||
Total wall time: 0:08:09
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,218 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 284 atoms
|
||||
using box units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.1
|
||||
ghost atom cutoff = 1.1
|
||||
binsize = 0.55, bins = 88 88 88
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.002
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.947 | 4.947 | 4.947 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
20000 317.05614 618.63581 0 2476.8578 0.030715
|
||||
Loop time of 1.04979 on 4 procs for 20000 steps with 284 atoms
|
||||
|
||||
Performance: 3292081.736 ns/day, 0.000 hours/ns, 19051.399 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.10763 | 0.11963 | 0.13214 | 2.9 | 11.40
|
||||
Neigh | 0.38332 | 0.41159 | 0.43122 | 2.8 | 39.21
|
||||
Comm | 0.31394 | 0.34969 | 0.3981 | 5.1 | 33.31
|
||||
Output | 0.0029418 | 0.0035883 | 0.0043197 | 0.8 | 0.34
|
||||
Modify | 0.13951 | 0.14727 | 0.15199 | 1.3 | 14.03
|
||||
Other | | 0.01802 | | | 1.72
|
||||
|
||||
Nlocal: 71.0000 ave 73 max 69 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 54.7500 ave 57 max 53 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 107.250 ave 127 max 85 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 429
|
||||
Ave neighs/atom = 1.5105634
|
||||
Neighbor list builds = 1996
|
||||
Dangerous builds = 1993
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.98369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 0.991845, bins = 49 49 49
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 20000
|
||||
Time step : 0.002
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.279 | 4.280 | 4.280 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 317.05614 626.83186 0 2485.0538 0.034256287
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
Loop time of 20.94 on 4 procs for 500000 steps with 284 atoms
|
||||
|
||||
Performance: 4126072.144 ns/day, 0.000 hours/ns, 23877.732 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.3543 | 5.0458 | 5.6845 | 21.6 | 24.10
|
||||
Neigh | 1.3816 | 1.444 | 1.5232 | 4.7 | 6.90
|
||||
Comm | 6.2693 | 7.0156 | 7.7783 | 21.0 | 33.50
|
||||
Output | 0.038337 | 0.072704 | 0.11121 | 10.0 | 0.35
|
||||
Modify | 4.9433 | 5.027 | 5.1022 | 2.9 | 24.01
|
||||
Other | | 2.335 | | | 11.15
|
||||
|
||||
Nlocal: 71.0000 ave 74 max 69 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 109.750 ave 113 max 105 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 613.250 ave 718 max 495 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2453
|
||||
Ave neighs/atom = 8.6373239
|
||||
Neighbor list builds = 13515
|
||||
Dangerous builds = 0
|
||||
Setting up cg style minimization ...
|
||||
Unit style : nano
|
||||
Current step : 520000
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.404 | 5.405 | 5.405 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520000 0.20789564 780.54747 0 781.76592 0.028916791
|
||||
520004 0.20789564 780.00993 0 781.22838 0.02889732
|
||||
Loop time of 0.0052249 on 4 procs for 4 steps with 284 atoms
|
||||
|
||||
90.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
780.547473373201 780.009929329778 780.009929329778
|
||||
Force two-norm initial, final = 40.166574 13.723713
|
||||
Force max component initial, final = 4.2404394 1.5423956
|
||||
Final line search alpha, max atom move = 6.0381565e-11 9.3132257e-11
|
||||
Iterations, force evaluations = 4 69
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.000733 | 0.00099598 | 0.0013314 | 0.0 | 19.06
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0006855 | 0.0010138 | 0.0012766 | 0.7 | 19.40
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0.0002038 | 0.00023407 | 0.0003163 | 0.0 | 4.48
|
||||
Other | | 0.002981 | | | 57.05
|
||||
|
||||
Nlocal: 71.0000 ave 72 max 69 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 109.750 ave 113 max 107 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Neighs: 612.750 ave 726 max 504 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 2451
|
||||
Ave neighs/atom = 8.6302817
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 284 atoms
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 520004
|
||||
Time step : 0.00025
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
520004 8.9102565e-07 0 0 1.8452924e-08 6.7761632e-05
|
||||
530004 3.474402 0 0 0.071954018 -0.00061159689
|
||||
Loop time of 252.92 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 854.024 ns/day, 0.028 hours/ns, 39.538 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.083731 | 0.090623 | 0.098802 | 1.8 | 0.04
|
||||
Neigh | 0.016581 | 0.017116 | 0.018055 | 0.4 | 0.01
|
||||
Comm | 0.18954 | 0.19805 | 0.20528 | 1.3 | 0.08
|
||||
Output | 0.0011027 | 0.0018302 | 0.002624 | 1.3 | 0.00
|
||||
Modify | 252.35 | 252.37 | 252.39 | 0.1 | 99.78
|
||||
Other | | 0.2466 | | | 0.10
|
||||
|
||||
Nlocal: 71.0000 ave 84 max 59 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 110.750 ave 121 max 101 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 243.250 ave 285 max 209 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 52
|
||||
Dangerous builds = 0
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.00025
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.474402 0 0 0.071954018 0.00181615
|
||||
10000 2.6284662 0 0 0.054434894 0.00098091301
|
||||
Loop time of 296.345 on 4 procs for 10000 steps with 284 atoms
|
||||
|
||||
Performance: 728.880 ns/day, 0.033 hours/ns, 33.744 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.097394 | 0.10852 | 0.12099 | 3.3 | 0.04
|
||||
Neigh | 0.014447 | 0.015052 | 0.015762 | 0.4 | 0.01
|
||||
Comm | 0.23755 | 0.24986 | 0.26167 | 2.3 | 0.08
|
||||
Output | 0.0022544 | 0.0025083 | 0.0025944 | 0.3 | 0.00
|
||||
Modify | 295.67 | 295.69 | 295.72 | 0.1 | 99.78
|
||||
Other | | 0.28 | | | 0.09
|
||||
|
||||
Nlocal: 71.0000 ave 87 max 54 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 110.000 ave 125 max 100 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 243.250 ave 264 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 973
|
||||
Ave neighs/atom = 3.4260563
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 288.718806
|
||||
LB update time: 135.577114
|
||||
LB PCalc time: 76.637579
|
||||
LB fluidForce time: 25.590260
|
||||
LB CorrectU time: 19.713186
|
||||
Total wall time: 0:09:31
|
||||
@ -1,102 +0,0 @@
|
||||
# Fix print output for fix printCM
|
||||
0 0 0 -5.00000000070583e-08 0 0 0
|
||||
100 0.000862030487945766 0.0123054296765635 0.0122731465590126 0.0388471409686686 0.554171814767862 0.549353841801444
|
||||
200 0.00185887929142589 0.026504860571345 0.0263575026345381 0.0406164349263177 0.577485522778581 0.572358123657981
|
||||
300 0.00288609111410669 0.041071186430552 0.0407387949853162 0.0414733855376221 0.586334796005238 0.579029199408148
|
||||
400 0.00392999369142328 0.0557729852014459 0.0552309274319543 0.0420073620501712 0.589116414842769 0.579447580483091
|
||||
500 0.00498536275941171 0.070499164057003 0.0697415367523594 0.0424046217549586 0.588483528276922 0.579713082803989
|
||||
600 0.00604958471579167 0.0851758456067289 0.0842109166632151 0.0427225597696811 0.585256835192702 0.578675424528672
|
||||
700 0.00712105404933591 0.0997436526892664 0.0986256150648839 0.0429880258004064 0.579826819459789 0.574965309339321
|
||||
800 0.00819868650413988 0.114150894221279 0.112970143937093 0.0432171820009732 0.572436469824202 0.571379696846873
|
||||
900 0.00928167490285266 0.128350199155429 0.127214300017093 0.0434177041449832 0.563212233113465 0.568141900579381
|
||||
1000 0.0103693800467608 0.142297070506134 0.141346756412092 0.0435952275760965 0.552255756217314 0.563198941286352
|
||||
1100 0.0114612757740303 0.155949207303663 0.155363270006244 0.0437534628364653 0.539645345817638 0.557547826275249
|
||||
1200 0.0125569146112762 0.16926611615961 0.169243664446122 0.0438950800605928 0.525448494610828 0.552385484155222
|
||||
1300 0.0136559090539262 0.182208942626165 0.182971608380899 0.0440222186903751 0.509729009151129 0.546362371549647
|
||||
1400 0.0147579190343771 0.194740388291494 0.196542287352516 0.0441365813451693 0.49254820772961 0.53923843292572
|
||||
1500 0.0158626435855424 0.206824684659766 0.20994260685037 0.0442396069433182 0.473967311999804 0.532221947561911
|
||||
1600 0.016969815144629 0.218427601281069 0.223154967935698 0.0443325350264529 0.454048234578232 0.52490993166384
|
||||
1700 0.0180791952377331 0.229516470517873 0.23617097657798 0.0444164592397298 0.432854159986641 0.516564181615295
|
||||
1800 0.0191905712013339 0.240060223538286 0.248981532998294 0.044492359500651 0.41044987377188 0.507890446812699
|
||||
1900 0.0203037536403243 0.250029432395321 0.261570985506027 0.0445611192532371 0.386901867661691 0.499132572020635
|
||||
2000 0.0214185743448717 0.259396354393085 0.27392793783106 0.0446235485425134 0.36227844753556 0.489625430842279
|
||||
2100 0.0225348845239784 0.268134976647594 0.286044452302522 0.0446803959508529 0.33664970767355 0.479528537282853
|
||||
2200 0.0236525533438346 0.276221059771718 0.297907925422812 0.0447323522651497 0.310087425177735 0.469306149162182
|
||||
2300 0.0247714666787315 0.283632179279284 0.309505839706109 0.0447800603260404 0.282664970647061 0.458617441651712
|
||||
2400 0.0258915259587789 0.290347763502706 0.320829824034913 0.0448241232027665 0.254457178820598 0.44728722136532
|
||||
2500 0.0270126471290237 0.29634912772668 0.331869872099864 0.0448651027638521 0.225540156619441 0.435694872117013
|
||||
2600 0.0281347597089685 0.30161950408948 0.34261406670463 0.0449035206640385 0.195991101443378 0.423810112638771
|
||||
2700 0.0292578058434875 0.306144066595306 0.353053315437221 0.0449398633594251 0.165888127664992 0.41137110526867
|
||||
2800 0.030381739316435 0.309909951263501 0.363179201634917 0.0449745786568748 0.135310062250947 0.398557628586131
|
||||
2900 0.0315065245470535 0.312906271705092 0.372981337255243 0.0450080686588849 0.104336253816866 0.385510764564962
|
||||
3000 0.0326321354733442 0.315124130290068 0.38245041225465 0.0450406882166782 0.0730464235910661 0.372042169913947
|
||||
3100 0.0337585542236816 0.316556625622056 0.391578764333674 0.0450727382300617 0.0415205367630292 0.358160568106331
|
||||
3200 0.034885766256052 0.31719885875625 0.400357663441649 0.0451036547071826 0.00983907573551093 0.344030677469557
|
||||
3300 0.0360136872580489 0.317048008823491 0.408777748573793 0.045129040578256 -0.0219107556190337 0.32955676892105
|
||||
3400 0.0371421729145326 0.316103516604794 0.416830876205518 0.0451489780670191 -0.0536371623936908 0.314668838998143
|
||||
3500 0.0382710977786635 0.314367093900902 0.424509118504444 0.0451643056938233 -0.0852504239010061 0.299493529440764
|
||||
3600 0.039400355723286 0.311842668099774 0.431804221276515 0.0451757343394363 -0.116662994488708 0.284066192756869
|
||||
3700 0.0405298571235071 0.308536328771854 0.438709086698874 0.0451838769711716 -0.147789438945399 0.268314898256792
|
||||
3800 0.0416595266582488 0.304456275109671 0.445217419249879 0.0451892685671837 -0.178546427643007 0.252292051488811
|
||||
3900 0.0427893015653343 0.299612762874147 0.451322687530176 0.0451923807983904 -0.208852773056517 0.236070778082722
|
||||
4000 0.0439191302054448 0.294018050086672 0.457018894174797 0.0451936331558271 -0.238629493808845 0.219614191498541
|
||||
4100 0.0450489708508549 0.287686340949681 0.462300983177224 0.0451934002599296 -0.267799890966025 0.202923522400675
|
||||
4200 0.0461787906402368 0.280633727679951 0.46716400466032 0.0451920174774752 -0.296289636112744 0.186067111728447
|
||||
4300 0.0473085646518621 0.272878130115369 0.471603197062402 0.0451897853348954 -0.324026864816915 0.169048732639397
|
||||
4400 0.0484382750721604 0.264439232972262 0.475614593651548 0.0451869725702152 -0.350942268020778 0.151851130542203
|
||||
4500 0.049567910442748 0.255338420725821 0.479194641553675 0.045183819044704 -0.37696918707268 0.134518378555459
|
||||
4600 0.0506974649686312 0.245598710206154 0.482339905708537 0.0451805383879157 -0.402043707551555 0.117079995982193
|
||||
4700 0.0518269378826076 0.235244680971009 0.485047513161603 0.0451773197428711 -0.426104742058066 0.0995240797086898
|
||||
4800 0.052956332860714 0.224302403572179 0.487315158338437 0.0451743295087643 -0.449094108942282 0.0818709366680246
|
||||
4900 0.0540856574759206 0.212799365966729 0.489140744652625 0.0451717131537436 -0.470956607153122 0.0641572680070745
|
||||
5000 0.0552149226836002 0.200764398290593 0.490522557427433 0.0451695961979473 -0.491640075621893 0.04638589199498
|
||||
5100 0.0563441423344801 0.188227596194827 0.491459457220784 0.045168084821581 -0.511095441430305 0.0285636095658589
|
||||
5200 0.057473332702688 0.17522024305006 0.491950642641828 0.0451672665812737 -0.529276763383753 0.0107219134977892
|
||||
5300 0.0586025120187606 0.161774731300966 0.491995614110831 0.0451672105484937 -0.546141262620913 -0.00712340874154904
|
||||
5400 0.0597317000030321 0.147924483163387 0.491594377124997 0.0451679668568151 -0.561649340260399 -0.0249682994538472
|
||||
5500 0.0608609173904777 0.133703870891375 0.490747365943808 0.0451695662898269 -0.575764591653344 -0.0427904594790811
|
||||
5600 0.0619901854374394 0.119148136830319 0.489455318876335 0.045172019632285 -0.58845381491908 -0.0605675872373609
|
||||
5700 0.0631195254064262 0.104293313359254 0.487719399569343 0.0451753165168183 -0.599687010953726 -0.0782918862578729
|
||||
5800 0.0642489580246837 0.0891761427946867 0.48554123315084 0.0451794242166182 -0.609437382803975 -0.0959482954276833
|
||||
5900 0.0653785029101205 0.0738339973249388 0.482922791336815 0.0451842864271072 -0.617681336848454 -0.113513947143333
|
||||
6000 0.066508177961606 0.0583047989558168 0.479866421958322 0.0451898217427784 -0.624398482710512 -0.13097562667804
|
||||
6100 0.0676379987117821 0.0426269393910158 0.476374926355184 0.0451959219945778 -0.629571635891283 -0.148321352569801
|
||||
6200 0.0687679776380947 0.0268391997711945 0.472451499697091 0.0452024505874852 -0.633186826926119 -0.165530745880477
|
||||
6300 0.0698981234280855 0.010980670154477 0.468099704053854 0.0452092406152506 -0.635233314989177 -0.182586480506518
|
||||
6400 0.0710284401951811 -0.00490933141996686 0.463323535196445 0.0452160926978174 -0.6357036064805 -0.199476058698813
|
||||
6500 0.0721589266379823 -0.0207913404308021 0.45812741824118 0.0452227725683118 -0.634593480754686 -0.216181770202423
|
||||
6600 0.0732895751329617 -0.0366258280722564 0.4525161672434 0.0452290081924521 -0.631902021250181 -0.232684251091254
|
||||
6700 0.0744203707468311 -0.0523732842796794 0.446495021852624 0.0452344861625994 -0.627631650070581 -0.248968525167056
|
||||
6800 0.0755512901476198 -0.0679943016610313 0.440069676657587 0.0452388471144838 -0.621788164979803 -0.265018013055149
|
||||
6900 0.0766823003834517 -0.0834496603398142 0.433246256793092 0.0452416796548797 -0.614380775066988 -0.280812614225028
|
||||
7000 0.0778133574838834 -0.0987004136215648 0.426031330764786 0.0452425120772539 -0.605422129824962 -0.296334220434174
|
||||
7100 0.0789444048161975 -0.113707974241796 0.418431952538327 0.0452408008213928 -0.594928335060022 -0.311565205779314
|
||||
7200 0.0800753710948757 -0.128434200729008 0.410455666617559 0.0452359139442821 -0.582918944331306 -0.326484492981048
|
||||
7300 0.0812061678888613 -0.142841483083547 0.402110518367413 0.0452271068609726 -0.56941690886808 -0.34107027310023
|
||||
7400 0.0823366868879886 -0.156892832550369 0.393405100664375 0.0452137152253101 -0.554451229049732 -0.355302873244928
|
||||
7500 0.0834668517149059 -0.170552623647645 0.384348175871066 0.0451996568242026 -0.538109504133949 -0.3691955162588
|
||||
7600 0.0845966786525954 -0.183787343990598 0.374948167603608 0.0451866668285694 -0.520452068779317 -0.38274791022926
|
||||
7700 0.0857261928989984 -0.196564598620189 0.365213708220604 0.0451746173490727 -0.501519185936364 -0.395949104997471
|
||||
7800 0.0868554160875386 -0.208853033947754 0.355153722643092 0.0451633558994798 -0.481353961460688 -0.408788219630066
|
||||
7900 0.0879843659433281 -0.220622412047369 0.344777414582154 0.0451527246802332 -0.460002566524482 -0.421253498591182
|
||||
8000 0.0891130563099555 -0.23184368872928 0.334094257673578 0.0451425726521896 -0.437514339207557 -0.433334064382642
|
||||
8100 0.0902414974316455 -0.2424890932098 0.323113996077294 0.0451327640586105 -0.413941813252733 -0.445019966270824
|
||||
8200 0.0913696964100858 -0.252532207710901 0.311846632415356 0.0451231839591836 -0.389340685397376 -0.456300911536802
|
||||
8300 0.0924976577671853 -0.261948045581448 0.300302411401681 0.0451137412199365 -0.363769731247534 -0.467166979522632
|
||||
8400 0.0936253840550899 -0.270713126771119 0.288491813206727 0.0451043693754287 -0.337290679181815 -0.477609349083408
|
||||
8500 0.0947528764650488 -0.278805549717671 0.27642554360983 0.0450950257530967 -0.309968050973641 -0.487619421164766
|
||||
8600 0.0958801353970909 -0.286205058917463 0.264114517046721 0.0450856892760242 -0.281868977005235 -0.497188713267531
|
||||
8700 0.0970071609627085 -0.292893107630846 0.251569845366989 0.0450763573660472 -0.253062992836497 -0.506309612902325
|
||||
8800 0.0981339534030675 -0.298852915325574 0.238802829407755 0.0450670423558943 -0.223621822504895 -0.514975070718216
|
||||
8900 0.0992605134153133 -0.304069519580759 0.22582494504124 0.0450577677864475 -0.193619152641678 -0.523178137637988
|
||||
9000 0.100386842388707 -0.308529822260866 0.212647830382011 0.0450485649429167 -0.163130400331202 -0.530912414901356
|
||||
9100 0.101512942559987 -0.312222629827916 0.199283277442076 0.0450394698977844 -0.13223247655603 -0.538172167586218
|
||||
9200 0.102638817103052 -0.315138687696582 0.185743221236983 0.0450305212343208 -0.10100354632644 -0.544951888794609
|
||||
9300 0.103764470171021 -0.317270708558709 0.172039727157391 0.0450217585121602 -0.0695227861974757 -0.551246411933543
|
||||
9400 0.104889906908796 -0.318613394619428 0.158184981612494 0.0450132214234404 -0.0378701397929889 -0.557051185837414
|
||||
9500 0.106015133451531 -0.319163453704509 0.144191282694294 0.0450049494770458 -0.00612607214576512 -0.562362036167608
|
||||
9600 0.107140156919558 -0.318919609223059 0.130071028527096 0.0449969819880669 0.0256286759940099 -0.567175055659959
|
||||
9700 0.108264985414172 -0.317882604002936 0.115836707124747 0.0449893581153677 0.0573133323763313 -0.571486831413926
|
||||
9800 0.109389628012451 -0.316055198056751 0.101500887824999 0.0449821167122573 0.0888473342969765 -0.575294393321441
|
||||
9900 0.110514094754186 -0.313442160379143 0.0870762114315177 0.0449752958236126 0.120150564786057 -0.578595028443573
|
||||
10000 0.111638396610866 -0.310050254915132 0.0725753806410134 0.0449689317481374 0.151143582530835 -0.581386376944959
|
||||
@ -4,9 +4,10 @@
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with ".log" #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
@ -133,7 +134,7 @@ if "${is_bonded} == 1" then &
|
||||
else &
|
||||
"variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
|
||||
fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
#run 100000
|
||||
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.1
Normal file
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.1
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# single particle drag tests #
|
||||
# #
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style molecular
|
||||
|
||||
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Set up particles with n_nodes and decide if bonded or rigid
|
||||
#----------------------------------------------------------------------------
|
||||
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
|
||||
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
|
||||
# bond parameters set for n_node = 4 case)
|
||||
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
|
||||
|
||||
variable tstep equal 0.00025
|
||||
|
||||
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
|
||||
create_box 1 mydomain
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
|
||||
create_atoms 1 single 0.0 0.0 0.204124
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 -0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single 0.19245 0. -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interactions between particles & create bonds
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 5.88
|
||||
pair_coeff * * 0.0 0.0 5.88
|
||||
|
||||
variable total_mass equal 0.002398 # particle mass
|
||||
variable node_mass equal "v_total_mass / v_n_nodes"
|
||||
mass * ${node_mass}
|
||||
mass * 0.0005995
|
||||
|
||||
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
|
||||
|
||||
#velocity all set 0.02 0.0 0.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
|
||||
# to drag particles through the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
variable total_force equal 1.0 # total external force on the particle
|
||||
variable node_force equal "v_total_force / v_n_nodes"
|
||||
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
|
||||
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particle (group all here)
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
|
||||
# lattice spacing dx=1.2.
|
||||
# Different ".log" files in this directory show the output with the stencil
|
||||
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
|
||||
#----------------------------------------------------------------------------
|
||||
timestep ${tstep}
|
||||
timestep 0.00025
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
#dumpxdmf 1000 fflow
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object or an elastically bonded object
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
|
||||
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
|
||||
fix 3 all rigid group 1 all
|
||||
1 rigid bodies with 4 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions/velocity of the colloids center
|
||||
# of mass.
|
||||
#----------------------------------------------------------------------------
|
||||
variable cmx equal xcm(all,x)
|
||||
variable cmy equal xcm(all,y)
|
||||
variable cmz equal xcm(all,z)
|
||||
|
||||
variable vcmx equal vcm(all,x)
|
||||
variable vcmy equal vcm(all,y)
|
||||
variable vcmz equal vcm(all,z)
|
||||
|
||||
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt0.00025.out
|
||||
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 185.434 on 1 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1164.837 ns/day, 0.021 hours/ns, 53.928 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.02024 | 0.02024 | 0.02024 | 0.0 | 0.01
|
||||
Bond | 0.0011585 | 0.0011585 | 0.0011585 | 0.0 | 0.00
|
||||
Neigh | 8.88e-05 | 8.88e-05 | 8.88e-05 | 0.0 | 0.00
|
||||
Comm | 0.011615 | 0.011615 | 0.011615 | 0.0 | 0.01
|
||||
Output | 8.32e-05 | 8.32e-05 | 8.32e-05 | 0.0 | 0.00
|
||||
Modify | 185.36 | 185.36 | 185.36 | 0.0 | 99.96
|
||||
Other | | 0.04469 | | | 0.02
|
||||
|
||||
Nlocal: 4 ave 4 max 4 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
#run 100000
|
||||
|
||||
Total wall time: 0:03:05
|
||||
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.4
Normal file
212
examples/PACKAGES/latboltz/dragforce/log.09Mar22.dragtest.g++.4
Normal file
@ -0,0 +1,212 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# single particle drag tests #
|
||||
# #
|
||||
# Run consists of a colloidal particle being dragged with a constant force #
|
||||
# through an LB-fluid. The colloidal particle could be single atom or #
|
||||
# be a composite particle. Composite particles could be bonded or just #
|
||||
# rigidly constrained to stay together. You can set flags in the script to #
|
||||
# change these. #
|
||||
# #
|
||||
# Sample output from this run can be found in the files with "log." #
|
||||
# located in the same directory. #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style molecular
|
||||
|
||||
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Set up particles with n_nodes and decide if bonded or rigid
|
||||
#----------------------------------------------------------------------------
|
||||
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
|
||||
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
|
||||
# bond parameters set for n_node = 4 case)
|
||||
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
|
||||
|
||||
variable tstep equal 0.00025
|
||||
|
||||
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
|
||||
create_box 1 mydomain
|
||||
Created orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
|
||||
create_atoms 1 single 0.0 0.0 0.204124
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 1 single -0.096225 -0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single -0.096225 0.166667 -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
create_atoms 1 single 0.19245 0. -0.0680414
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interactions between particles & create bonds
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 5.88
|
||||
pair_coeff * * 0.0 0.0 5.88
|
||||
|
||||
variable total_mass equal 0.002398 # particle mass
|
||||
variable node_mass equal "v_total_mass / v_n_nodes"
|
||||
mass * ${node_mass}
|
||||
mass * 0.0005995
|
||||
|
||||
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
|
||||
|
||||
#velocity all set 0.02 0.0 0.0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
|
||||
# to drag particles through the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
variable total_force equal 1.0 # total external force on the particle
|
||||
variable node_force equal "v_total_force / v_n_nodes"
|
||||
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
|
||||
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
|
||||
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particle (group all here)
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
|
||||
# lattice spacing dx=1.2.
|
||||
# Different ".log" files in this directory show the output with the stencil
|
||||
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
|
||||
#----------------------------------------------------------------------------
|
||||
timestep ${tstep}
|
||||
timestep 0.00025
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
|
||||
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
#dumpxdmf 1000 fflow
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object or an elastically bonded object
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
|
||||
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
|
||||
fix 3 all rigid group 1 all
|
||||
1 rigid bodies with 4 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions/velocity of the colloids center
|
||||
# of mass.
|
||||
#----------------------------------------------------------------------------
|
||||
variable cmx equal xcm(all,x)
|
||||
variable cmy equal xcm(all,y)
|
||||
variable cmz equal xcm(all,z)
|
||||
|
||||
variable vcmx equal vcm(all,x)
|
||||
variable vcmy equal vcm(all,y)
|
||||
variable vcmz equal vcm(all,z)
|
||||
|
||||
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
|
||||
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt${tstep}.out
|
||||
variable comdatafile string drag_n4_st3_dt0.00025.out
|
||||
|
||||
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
|
||||
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.857 | 7.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 154.466 on 4 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1398.367 ns/day, 0.017 hours/ns, 64.739 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.013169 | 0.01792 | 0.021577 | 2.3 | 0.01
|
||||
Bond | 0.0019565 | 0.0021447 | 0.0023408 | 0.4 | 0.00
|
||||
Neigh | 7.55e-05 | 9.69e-05 | 0.0001173 | 0.0 | 0.00
|
||||
Comm | 0.07056 | 0.076818 | 0.084499 | 2.1 | 0.05
|
||||
Output | 2.85e-05 | 4.4925e-05 | 9.24e-05 | 0.0 | 0.00
|
||||
Modify | 154.16 | 154.17 | 154.18 | 0.1 | 99.81
|
||||
Other | | 0.1998 | | | 0.13
|
||||
|
||||
Nlocal: 1 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 3 ave 4 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 1.5 ave 6 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
#run 100000
|
||||
|
||||
Total wall time: 0:02:34
|
||||
@ -1,75 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
Created 1 atoms
|
||||
using lattice units in orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
create_atoms CPU = 0.008 seconds
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 4 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 16 16 16
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.00025
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:739)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.857 | 7.138 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 2.1529156e-12
|
||||
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
|
||||
Loop time of 146.77 on 4 procs for 10000 steps with 4 atoms
|
||||
|
||||
Performance: 1471.691 ns/day, 0.016 hours/ns, 68.134 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.013542 | 0.017622 | 0.022577 | 2.8 | 0.01
|
||||
Bond | 0.001794 | 0.0018995 | 0.0021441 | 0.3 | 0.00
|
||||
Neigh | 6.97e-05 | 0.00011273 | 0.0001386 | 0.0 | 0.00
|
||||
Comm | 0.10125 | 0.13954 | 0.17353 | 7.3 | 0.10
|
||||
Output | 6.19e-05 | 0.00030725 | 0.0003896 | 0.0 | 0.00
|
||||
Modify | 146.37 | 146.4 | 146.45 | 0.2 | 99.75
|
||||
Other | | 0.2122 | | | 0.14
|
||||
|
||||
Nlocal: 1.00000 ave 4 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 3.00000 ave 4 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 1.50000 ave 6 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6
|
||||
Ave neighs/atom = 1.5000000
|
||||
Ave special neighs/atom = 0.0000000
|
||||
Neighbor list builds = 9
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 25.615363
|
||||
LB update time: 62.136116
|
||||
LB PCalc time: 36.863810
|
||||
LB fluidForce time: 11.645698
|
||||
LB CorrectU time: 9.399909
|
||||
Total wall time: 0:02:26
|
||||
@ -4,8 +4,9 @@
|
||||
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
|
||||
# thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# 'microrheology_setgamma.out' #
|
||||
# If you uncomment the "fix printCM..." line, sample output from this run #
|
||||
# can be found in the file: #
|
||||
# 'twocolloid.out' #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
@ -104,7 +105,7 @@ variable x2 equal x[242]
|
||||
variable y2 equal y[242]
|
||||
variable z2 equal z[242]
|
||||
|
||||
fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.data screen no
|
||||
#fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.out screen no
|
||||
thermo_style custom step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
|
||||
thermo 100
|
||||
|
||||
@ -0,0 +1,216 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# 2 particle microrheology test #
|
||||
# #
|
||||
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
|
||||
# thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# If you uncomment the "fix printCM..." line, sample output from this run #
|
||||
# can be found in the file: #
|
||||
# 'twocolloid.out' #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style molecular
|
||||
read_data data.two
|
||||
Reading data file ...
|
||||
orthogonal box = (-48 -48 -48) to (48 48 48)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
482 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.033 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
|
||||
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each colloidal object (use a truncated and shifted Lennard-Jones
|
||||
# potential).
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 5.88
|
||||
pair_coeff * * 0.0 0.0 5.88
|
||||
pair_coeff 1 1 100.0 5.238484463 5.88
|
||||
pair_modify shift yes
|
||||
|
||||
mass * 0.0002398
|
||||
timestep 0.00025
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each colloidal object which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the colloidal
|
||||
# object which do interact with the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
2 atoms in group ForceAtoms
|
||||
group FluidAtoms type 2
|
||||
480 atoms in group FluidAtoms
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicitly apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071 (water), and a
|
||||
# lattice spacing dx=1.2.
|
||||
# Use the trilinear interpolation stencil to distribute the force from
|
||||
# a given particle onto the fluid mesh.
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=2762). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 1 1.0 0.0009982071 dx 1.2 stencil 2 noise 300.0 2762
|
||||
Using a lattice-Boltzmann grid of 80 by 80 by 80 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force due to the fluid onto the FluidAtoms particles (again,
|
||||
# these atoms represent the surface of the colloidal object, which should
|
||||
# interact with the fluid).
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 FluidAtoms lb/viscous
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Each colloidal object (spherical shell of particles and central particle)
|
||||
# is specified as a separate molecule in the confinedcolloids.dat data
|
||||
# file. Integrate the motion of these sets of particles as rigid objects
|
||||
# which each move and rotate together.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 3 all rigid molecule
|
||||
2 rigid bodies with 482 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# To ensure that numerical errors do not lead to a buildup of momentum in the
|
||||
# system, the momentum_lb fix is used every 50000 timesteps to zero out the
|
||||
# total (particle plus fluid) momentum in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 4 all lb/momentum 50000 linear 1 1 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables containing the positions of the central atoms (these
|
||||
# values should correspond to the center of mass of each composite
|
||||
# colloidal particle), and output these quantities to the screen.
|
||||
#----------------------------------------------------------------------------
|
||||
variable x1 equal x[1]
|
||||
variable y1 equal y[1]
|
||||
variable z1 equal z[1]
|
||||
variable x2 equal x[242]
|
||||
variable y2 equal y[242]
|
||||
variable z2 equal z[242]
|
||||
|
||||
#fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.out screen no
|
||||
thermo_style custom step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
|
||||
thermo 100
|
||||
|
||||
run 2000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 32 32 32
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.071 | 7.133 | 7.196 Mbytes
|
||||
Step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
|
||||
0 -6 -6 -6 6 6 6
|
||||
100 -5.9728258 -6.0005827 -5.9442685 5.9742978 6.0301171 5.9331116
|
||||
200 -5.9160265 -5.9832234 -5.9485519 6.0258914 6.0954103 5.8748455
|
||||
300 -5.859605 -5.9503512 -5.9827305 6.0472442 6.0610438 5.8531801
|
||||
400 -5.8495832 -5.923183 -6.0205706 6.1502952 5.9975714 5.8964144
|
||||
500 -5.8229958 -5.9256007 -5.963852 6.1738854 5.8961268 5.8723276
|
||||
600 -5.7813718 -5.9423848 -5.9309537 6.2083705 5.866578 5.9308017
|
||||
700 -5.7652512 -5.8737534 -5.9083059 6.2502919 5.757157 5.9690204
|
||||
800 -5.7586139 -5.8559089 -5.8863028 6.2708214 5.7307727 5.9443721
|
||||
900 -5.7200104 -5.8603762 -5.8944329 6.28719 5.7723113 5.9660136
|
||||
1000 -5.7224239 -5.8487095 -5.9013071 6.3156272 5.8026721 5.9558441
|
||||
1100 -5.576187 -5.8604571 -5.9254376 6.3778561 5.7655467 5.9702619
|
||||
1200 -5.5348377 -5.8086817 -5.9982829 6.3979309 5.8028207 5.930579
|
||||
1300 -5.5937473 -5.7733457 -6.0596682 6.3630776 5.937045 5.9662317
|
||||
1400 -5.6207137 -5.7027974 -6.0641922 6.3079248 5.9631009 5.9707377
|
||||
1500 -5.6648138 -5.6229854 -6.0989624 6.2784552 5.9448163 5.9254903
|
||||
1600 -5.6905161 -5.5479418 -6.0704567 6.3133179 5.941372 5.8933924
|
||||
1700 -5.6878847 -5.5415566 -6.0222328 6.3633902 5.9957476 5.7994115
|
||||
1800 -5.6500526 -5.5204331 -5.9767389 6.4081067 5.9651289 5.7297962
|
||||
1900 -5.7221835 -5.4972898 -5.9670446 6.4470403 5.9161644 5.6902098
|
||||
2000 -5.7427378 -5.4637388 -6.0196569 6.3668465 5.9127502 5.6931183
|
||||
Loop time of 358.9 on 4 procs for 2000 steps with 482 atoms
|
||||
|
||||
Performance: 120.368 ns/day, 0.199 hours/ns, 5.573 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0026566 | 0.0054654 | 0.0084461 | 3.6 | 0.00
|
||||
Bond | 0.0003946 | 0.000476 | 0.0005288 | 0.0 | 0.00
|
||||
Neigh | 0.0011268 | 0.0045933 | 0.0080717 | 5.0 | 0.00
|
||||
Comm | 0.053156 | 0.057764 | 0.062919 | 1.9 | 0.02
|
||||
Output | 0.0009824 | 0.0018621 | 0.0043906 | 3.4 | 0.00
|
||||
Modify | 358.62 | 358.63 | 358.64 | 0.0 | 99.93
|
||||
Other | | 0.1963 | | | 0.05
|
||||
|
||||
Nlocal: 120.5 ave 241 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 181 ave 297 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 20
|
||||
Dangerous builds = 0
|
||||
#run 2000000000
|
||||
Total wall time: 0:05:59
|
||||
@ -1,96 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Reading data file ...
|
||||
orthogonal box = (-48.000000 -48.000000 -48.000000) to (48.000000 48.000000 48.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
482 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.014 seconds
|
||||
2 atoms in group ForceAtoms
|
||||
480 atoms in group FluidAtoms
|
||||
Using a lattice-Boltzmann grid of 80 by 80 by 80 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
2 rigid bodies with 482 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.18
|
||||
ghost atom cutoff = 6.18
|
||||
binsize = 3.09, bins = 32 32 32
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.00025
|
||||
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:739)
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.071 | 7.133 | 7.196 Mbytes
|
||||
Step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
|
||||
0 -6 -6 -6 6 6 6
|
||||
100 -5.9728258 -6.0005827 -5.9442685 5.9742978 6.0301171 5.9331116
|
||||
200 -5.9160265 -5.9832234 -5.9485519 6.0258914 6.0954103 5.8748455
|
||||
300 -5.859605 -5.9503512 -5.9827305 6.0472442 6.0610438 5.8531801
|
||||
400 -5.8495832 -5.923183 -6.0205706 6.1502952 5.9975714 5.8964144
|
||||
500 -5.8229958 -5.9256007 -5.963852 6.1738854 5.8961268 5.8723276
|
||||
600 -5.7813718 -5.9423848 -5.9309537 6.2083705 5.866578 5.9308017
|
||||
700 -5.7652512 -5.8737534 -5.9083059 6.2502919 5.757157 5.9690204
|
||||
800 -5.7586139 -5.8559089 -5.8863028 6.2708214 5.7307727 5.9443721
|
||||
900 -5.7200104 -5.8603762 -5.8944329 6.28719 5.7723113 5.9660136
|
||||
1000 -5.7224239 -5.8487095 -5.9013071 6.3156272 5.8026721 5.9558441
|
||||
1100 -5.576187 -5.8604571 -5.9254376 6.3778561 5.7655467 5.9702619
|
||||
1200 -5.5348377 -5.8086817 -5.9982829 6.3979309 5.8028207 5.930579
|
||||
1300 -5.5937473 -5.7733457 -6.0596682 6.3630776 5.937045 5.9662317
|
||||
1400 -5.6207137 -5.7027974 -6.0641922 6.3079248 5.9631009 5.9707377
|
||||
1500 -5.6648138 -5.6229854 -6.0989624 6.2784552 5.9448163 5.9254903
|
||||
1600 -5.6905161 -5.5479418 -6.0704567 6.3133179 5.941372 5.8933924
|
||||
1700 -5.6878847 -5.5415566 -6.0222328 6.3633902 5.9957476 5.7994115
|
||||
1800 -5.6500526 -5.5204331 -5.9767389 6.4081067 5.9651289 5.7297962
|
||||
1900 -5.7221835 -5.4972898 -5.9670446 6.4470403 5.9161644 5.6902098
|
||||
2000 -5.7427378 -5.4637388 -6.0196569 6.3668465 5.9127502 5.6931183
|
||||
Loop time of 337.139 on 4 procs for 2000 steps with 482 atoms
|
||||
|
||||
Performance: 128.137 ns/day, 0.187 hours/ns, 5.932 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0025147 | 0.0050251 | 0.0075003 | 3.5 | 0.00
|
||||
Bond | 0.0004674 | 0.00047853 | 0.0004909 | 0.0 | 0.00
|
||||
Neigh | 0.0005738 | 0.0036401 | 0.0068179 | 5.0 | 0.00
|
||||
Comm | 0.056088 | 0.063835 | 0.071507 | 2.3 | 0.02
|
||||
Output | 0.0026851 | 0.0074911 | 0.0090938 | 3.2 | 0.00
|
||||
Modify | 336.86 | 336.88 | 336.9 | 0.1 | 99.92
|
||||
Other | | 0.1791 | | | 0.05
|
||||
|
||||
Nlocal: 120.500 ave 241 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 181.000 ave 297 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Ave special neighs/atom = 0.0000000
|
||||
Neighbor list builds = 20
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 185.672949
|
||||
LB update time: 78.463559
|
||||
LB PCalc time: 43.293723
|
||||
LB fluidForce time: 16.211223
|
||||
LB CorrectU time: 13.017318
|
||||
Total wall time: 0:05:37
|
||||
@ -1,22 +0,0 @@
|
||||
# Fix print output for fix printCM
|
||||
0 -6 -6 -6 6 6 6
|
||||
100 -5.9728258390363 -6.00058270846511 -5.94426846143197 5.97429784670672 6.03011708896542 5.93311158594508
|
||||
200 -5.91602646162167 -5.9832233858717 -5.94855193796953 6.02589142858035 6.09541031873856 5.87484550008362
|
||||
300 -5.85960503513375 -5.95035117058311 -5.98273054879889 6.04724424485127 6.06104384188688 5.85318010531015
|
||||
400 -5.84958318427899 -5.92318300778995 -6.0205706276695 6.15029520354417 5.99757137700149 5.8964143570282
|
||||
500 -5.8229957990533 -5.92560068752847 -5.96385200914485 6.17388543466333 5.89612680507036 5.87232755414486
|
||||
600 -5.78137178827873 -5.94238476653933 -5.93095367414376 6.20837053568049 5.86657804207129 5.93080172251295
|
||||
700 -5.76525119778907 -5.87375336226389 -5.9083058512149 6.25029186802515 5.75715699239055 5.9690203907764
|
||||
800 -5.75861389468995 -5.85590887490732 -5.88630276459582 6.2708213544238 5.73077273842208 5.94437207297023
|
||||
900 -5.72001041550187 -5.86037621773229 -5.89443290411243 6.28718998830012 5.77231130470684 5.96601364415703
|
||||
1000 -5.72242391722508 -5.84870945302511 -5.90130708799915 6.31562723862135 5.802672067251 5.95584407951942
|
||||
1100 -5.57618701057034 -5.8604571230511 -5.92543761678951 6.37785612529918 5.7655466995849 5.97026185233192
|
||||
1200 -5.53483774079645 -5.80868168559119 -5.9982829389625 6.39793085074462 5.80282069928233 5.93057895371063
|
||||
1300 -5.59374730222166 -5.77334569741735 -6.05966819406177 6.36307756870586 5.93704500047883 5.9662317452964
|
||||
1400 -5.62071369379104 -5.70279744043298 -6.06419223778362 6.30792475952201 5.96310087566106 5.97073771117513
|
||||
1500 -5.66481383664855 -5.62298536173757 -6.0989623809087 6.2784552368717 5.94481631143006 5.92549033887773
|
||||
1600 -5.69051607540066 -5.54794180980933 -6.07045673682844 6.31331787941986 5.94137200838204 5.89339244198547
|
||||
1700 -5.68788472257104 -5.54155660268121 -6.0222328152897 6.36339021564644 5.9957476424637 5.79941151400367
|
||||
1800 -5.65005256416692 -5.52043305892636 -5.97673894263548 6.4081066664191 5.96512894011256 5.72979619115097
|
||||
1900 -5.72218349101654 -5.49728980937974 -5.96704455955022 6.44704025453208 5.91616438703042 5.69020975592141
|
||||
2000 -5.74273781133623 -5.46373877287724 -6.0196569280068 6.36684647495879 5.91275021020995 5.6931183094732
|
||||
@ -1,307 +0,0 @@
|
||||
<?xml version="1.0"?>
|
||||
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<PolyData>
|
||||
<Piece NumberOfPoints="320" NumberOfVerts="320" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
|
||||
<PointData>
|
||||
</PointData>
|
||||
<CellData>
|
||||
</CellData>
|
||||
<Points>
|
||||
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|
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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205 206 207 208 209 210
|
||||
211 212 213 214 215 216
|
||||
217 218 219 220 221 222
|
||||
223 224 225 226 227 228
|
||||
229 230 231 232 233 234
|
||||
235 236 237 238 239 240
|
||||
241 242 243 244 245 246
|
||||
247 248 249 250 251 252
|
||||
253 254 255 256 257 258
|
||||
259 260 261 262 263 264
|
||||
265 266 267 268 269 270
|
||||
271 272 273 274 275 276
|
||||
277 278 279 280 281 282
|
||||
283 284 285 286 287 288
|
||||
289 290 291 292 293 294
|
||||
295 296 297 298 299 300
|
||||
301 302 303 304 305 306
|
||||
307 308 309 310 311 312
|
||||
313 314 315 316 317 318
|
||||
319 320
|
||||
</DataArray>
|
||||
</Verts>
|
||||
<Lines>
|
||||
<DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="0" RangeMax="319">
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1" RangeMax="320">
|
||||
</DataArray>
|
||||
</Lines>
|
||||
<Strips>
|
||||
<DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="0" RangeMax="319">
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1" RangeMax="320">
|
||||
</DataArray>
|
||||
</Strips>
|
||||
<Polys>
|
||||
<DataArray type="Int64" Name="connectivity" format="ascii" RangeMin="0" RangeMax="319">
|
||||
</DataArray>
|
||||
<DataArray type="Int64" Name="offsets" format="ascii" RangeMin="1" RangeMax="320">
|
||||
</DataArray>
|
||||
</Polys>
|
||||
</Piece>
|
||||
</PolyData>
|
||||
</VTKFile>
|
||||
@ -1,22 +0,0 @@
|
||||
<?xml version="1.0"?>
|
||||
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
|
||||
<RectilinearGrid WholeExtent="0 1 0 1 0 1">
|
||||
<Piece Extent="0 1 0 1 0 1">
|
||||
<PointData>
|
||||
</PointData>
|
||||
<CellData>
|
||||
</CellData>
|
||||
<Coordinates>
|
||||
<DataArray type="Float64" Name="Array 0x555d54977d40" format="ascii" RangeMin="-120" RangeMax="120">
|
||||
-120 120
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="Array 0x555d54977eb0" format="ascii" RangeMin="-100" RangeMax="100">
|
||||
-100 100
|
||||
</DataArray>
|
||||
<DataArray type="Float64" Name="Array 0x555d54978020" format="ascii" RangeMin="-120" RangeMax="120">
|
||||
-120 120
|
||||
</DataArray>
|
||||
</Coordinates>
|
||||
</Piece>
|
||||
</RectilinearGrid>
|
||||
</VTKFile>
|
||||
Binary file not shown.
@ -1,71 +0,0 @@
|
||||
<?xml version="1.0" ?>
|
||||
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
|
||||
<Xdmf Version="2.0">
|
||||
<Domain>
|
||||
<Grid Name="fluid" GridType="Collection" CollectionType="Temporal">
|
||||
|
||||
<Grid Name="0">
|
||||
<Time Value="0.000000"/>
|
||||
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="61 51 61"/>
|
||||
<Geometry GeometryType="ORIGIN_DXDYDZ">
|
||||
<DataItem Dimensions="3">
|
||||
-120.000000 -100.000000 -120.000000
|
||||
</DataItem>
|
||||
<DataItem Dimensions="3">
|
||||
4.000000 4.000000 4.000000
|
||||
</DataItem>
|
||||
</Geometry>
|
||||
|
||||
<Attribute Name="density">
|
||||
<DataItem ItemType="Function" Function="$0 * 1.000000" Dimensions="61 51 61">
|
||||
<DataItem Precision="8" Format="Binary" Seek="0" Dimensions="61 51 61">
|
||||
fflow.raw
|
||||
</DataItem>
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
|
||||
<Attribute Name="velocity" AttributeType="Vector">
|
||||
<DataItem ItemType="Function" Function="$0 * 2.000000" Dimensions="61 51 61 3">
|
||||
<DataItem Precision="8" Format="Binary" Seek="1518168" Dimensions="61 51 61 3">
|
||||
fflow.raw
|
||||
</DataItem>
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
|
||||
</Grid>
|
||||
|
||||
<Grid Name="2500">
|
||||
<Time Value="1.000000"/>
|
||||
|
||||
<Topology TopologyType="3DCoRectMesh" Dimensions="61 51 61"/>
|
||||
<Geometry GeometryType="ORIGIN_DXDYDZ">
|
||||
<DataItem Dimensions="3">
|
||||
-120.000000 -100.000000 -120.000000
|
||||
</DataItem>
|
||||
<DataItem Dimensions="3">
|
||||
4.000000 4.000000 4.000000
|
||||
</DataItem>
|
||||
</Geometry>
|
||||
|
||||
<Attribute Name="density">
|
||||
<DataItem ItemType="Function" Function="$0 * 1.000000" Dimensions="61 51 61">
|
||||
<DataItem Precision="8" Format="Binary" Seek="6072672" Dimensions="61 51 61">
|
||||
fflow.raw
|
||||
</DataItem>
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
|
||||
<Attribute Name="velocity" AttributeType="Vector">
|
||||
<DataItem ItemType="Function" Function="$0 * 2.000000" Dimensions="61 51 61 3">
|
||||
<DataItem Precision="8" Format="Binary" Seek="7590840" Dimensions="61 51 61 3">
|
||||
fflow.raw
|
||||
</DataItem>
|
||||
</DataItem>
|
||||
</Attribute>
|
||||
|
||||
</Grid>
|
||||
|
||||
</Grid>
|
||||
</Domain>
|
||||
</Xdmf>
|
||||
@ -2,7 +2,7 @@
|
||||
# Rigid sphere freely moving in a system with pressure driven flow through #
|
||||
# a pit geometry. #
|
||||
# #
|
||||
# The example produces several output files: #
|
||||
# If uncommented, the example produces several output files: #
|
||||
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
|
||||
# fluid density and velocity which can be read#
|
||||
# and plotted using Paraview. #
|
||||
@ -11,7 +11,6 @@
|
||||
# compiled with the vtk package). These filed#
|
||||
# can also be read and plotted using Paraview.#
|
||||
# XX is the timestep of the dump output. #
|
||||
# 'screen.out' ... terminal output from the run. #
|
||||
#===========================================================================#
|
||||
|
||||
units micro
|
||||
@ -33,7 +32,7 @@ atom_style atomic
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
read_data one_radius16d2.data
|
||||
read_data data.one_radius16d2
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# None of the particles interact with one another.
|
||||
@ -66,7 +65,7 @@ velocity all set 0.0 0.0 0.0 units box
|
||||
# The initial conditions are set as linear interpolation between boundary
|
||||
# values using the linearInit option.
|
||||
#-----------------------------------------------------------------------------
|
||||
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 dumpxdmf 2500 fflow 0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30
|
||||
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# You can get some other interesting geometries by replacing the npits options
|
||||
@ -112,6 +111,6 @@ variable omegaz equal omega(all,z)
|
||||
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
thermo 500
|
||||
|
||||
dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
|
||||
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
|
||||
|
||||
run 2500
|
||||
193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.1
Normal file
193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.1
Normal file
@ -0,0 +1,193 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# Rigid sphere freely moving in a system with pressure driven flow through #
|
||||
# a pit geometry. #
|
||||
# #
|
||||
# If uncommented, the example produces several output files: #
|
||||
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
|
||||
# fluid density and velocity which can be read#
|
||||
# and plotted using Paraview. #
|
||||
# 'dumpatomsXX.vtp', 'dumpatomsXX_boundingBox.vtr' ... produces by the #
|
||||
# dumpvtk routine (requires that lammps be #
|
||||
# compiled with the vtk package). These filed#
|
||||
# can also be read and plotted using Paraview.#
|
||||
# XX is the timestep of the dump output. #
|
||||
#===========================================================================#
|
||||
|
||||
units micro
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
read_data data.one_radius16d2
|
||||
Reading data file ...
|
||||
orthogonal box = (-120 -100 -120) to (120 100 120)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
320 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# None of the particles interact with one another.
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 2.45
|
||||
pair_coeff * * 0.0 0.0 2.45
|
||||
neigh_modify exclude type 1 1
|
||||
|
||||
mass * 100.0
|
||||
timestep 2.0
|
||||
|
||||
group sphere1 id <> 1 320
|
||||
320 atoms in group sphere1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Colloidal particle is initially stationary.
|
||||
#----------------------------------------------------------------------------
|
||||
velocity all set 0.0 0.0 0.0 units box
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# All of the particles in the simulation apply a force to the fluid.
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Set the fluid density = 1.0, fluid viscosity = 1.0 (water), and lattice
|
||||
# spacing dx=4.0.
|
||||
# dumpxdmf is set to output to the xdmf file (fflow.xdmf and fflow.raw) every
|
||||
# 2500 steps, indexed by the frame number (rather than timestep).
|
||||
# The flow is generated via a pressure jump at the otherwise periodic x-
|
||||
# boundary using the pressurebcx option.
|
||||
# The initial conditions are set as linear interpolation between boundary
|
||||
# values using the linearInit option.
|
||||
#-----------------------------------------------------------------------------
|
||||
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
|
||||
Using a lattice-Boltzmann grid of 60 by 50 by 61 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
length of pits and end segments larger than system size in x-direction: truncation will occur (../fix_lb_fluid.cpp:505)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# You can get some other interesting geometries by replacing the npits options
|
||||
# at the end of the above lb/fluid fix with one of the following:
|
||||
#-----------------------------------------------------------------------------
|
||||
# Channel with 2 pits placed symmetrically about center in x:
|
||||
#npits 2 20 20 10 5 sw
|
||||
|
||||
# Channel with 1 pit placed at center:
|
||||
#npits 1 20 20 20 sw
|
||||
|
||||
# Full channel with 1 "speedbump" placed in right end of the channel:
|
||||
#npits 2 20 40 5 0 sw
|
||||
|
||||
# Channel with 2 "potholes" placed symmetrically about center in x:
|
||||
#npits 2 20 15 10 10 wp 30
|
||||
|
||||
# Channel with T-shaped cross-section with a "speedbump" in right end:
|
||||
#npits 2 20 40 5 0 wp 30
|
||||
|
||||
# Long rectangular channel (all pit, no slit):
|
||||
#npits 1 20 65 5 0 sw
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
fix 3 all rigid group 1 sphere1
|
||||
1 rigid bodies with 320 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables for the center-of-mass and angular velocities, and output
|
||||
# these quantities to the screen.
|
||||
#----------------------------------------------------------------------------
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
variable vz equal vcm(all,z)
|
||||
variable omegax equal omega(all,x)
|
||||
variable omegay equal omega(all,y)
|
||||
variable omegaz equal omega(all,z)
|
||||
|
||||
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
thermo 500
|
||||
|
||||
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
|
||||
|
||||
run 2500
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.45
|
||||
ghost atom cutoff = 3.45
|
||||
binsize = 1.725, bins = 140 116 140
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.01 | 14.01 | 14.01 Mbytes
|
||||
Step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
0 10054461 0 0 0 0 0 0
|
||||
500 10055203 0.008268321 2.9442616e-05 0.0019660229 -5.0307394e-07 2.1873981e-05 2.2701522e-07
|
||||
1000 10055487 0.015301314 4.219514e-05 0.0029217734 -6.9936017e-07 6.8198965e-05 5.2031048e-07
|
||||
1500 10055663 0.02117119 2.9194379e-05 0.002365636 -7.5401298e-07 0.00011557032 4.0311183e-07
|
||||
2000 10055781 0.02523262 -9.149834e-06 -0.0001724854 -2.5872732e-07 0.00014864932 3.7644295e-07
|
||||
2500 10055866 0.02651785 -5.2469712e-05 -0.0030476651 2.9151609e-07 0.00014663544 7.8650891e-07
|
||||
Loop time of 111.461 on 1 procs for 2500 steps with 320 atoms
|
||||
|
||||
Performance: 3875808849.457 ns/day, 0.000 hours/ns, 22.429 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0072314 | 0.0072314 | 0.0072314 | 0.0 | 0.01
|
||||
Neigh | 0.26791 | 0.26791 | 0.26791 | 0.0 | 0.24
|
||||
Comm | 0.0092553 | 0.0092553 | 0.0092553 | 0.0 | 0.01
|
||||
Output | 0.0054858 | 0.0054858 | 0.0054858 | 0.0 | 0.00
|
||||
Modify | 111.15 | 111.15 | 111.15 | 0.0 | 99.72
|
||||
Other | | 0.01779 | | | 0.02
|
||||
|
||||
Nlocal: 320 ave 320 max 320 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:51
|
||||
193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.4
Normal file
193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.4
Normal file
@ -0,0 +1,193 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# Rigid sphere freely moving in a system with pressure driven flow through #
|
||||
# a pit geometry. #
|
||||
# #
|
||||
# If uncommented, the example produces several output files: #
|
||||
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
|
||||
# fluid density and velocity which can be read#
|
||||
# and plotted using Paraview. #
|
||||
# 'dumpatomsXX.vtp', 'dumpatomsXX_boundingBox.vtr' ... produces by the #
|
||||
# dumpvtk routine (requires that lammps be #
|
||||
# compiled with the vtk package). These filed#
|
||||
# can also be read and plotted using Paraview.#
|
||||
# XX is the timestep of the dump output. #
|
||||
#===========================================================================#
|
||||
|
||||
units micro
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
read_data data.one_radius16d2
|
||||
Reading data file ...
|
||||
orthogonal box = (-120 -100 -120) to (120 100 120)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
320 atoms
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# None of the particles interact with one another.
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 2.45
|
||||
pair_coeff * * 0.0 0.0 2.45
|
||||
neigh_modify exclude type 1 1
|
||||
|
||||
mass * 100.0
|
||||
timestep 2.0
|
||||
|
||||
group sphere1 id <> 1 320
|
||||
320 atoms in group sphere1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Colloidal particle is initially stationary.
|
||||
#----------------------------------------------------------------------------
|
||||
velocity all set 0.0 0.0 0.0 units box
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# All of the particles in the simulation apply a force to the fluid.
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix).
|
||||
# Set the fluid density = 1.0, fluid viscosity = 1.0 (water), and lattice
|
||||
# spacing dx=4.0.
|
||||
# dumpxdmf is set to output to the xdmf file (fflow.xdmf and fflow.raw) every
|
||||
# 2500 steps, indexed by the frame number (rather than timestep).
|
||||
# The flow is generated via a pressure jump at the otherwise periodic x-
|
||||
# boundary using the pressurebcx option.
|
||||
# The initial conditions are set as linear interpolation between boundary
|
||||
# values using the linearInit option.
|
||||
#-----------------------------------------------------------------------------
|
||||
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
|
||||
Using a lattice-Boltzmann grid of 60 by 50 by 61 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
length of pits and end segments larger than system size in x-direction: truncation will occur (../fix_lb_fluid.cpp:505)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# You can get some other interesting geometries by replacing the npits options
|
||||
# at the end of the above lb/fluid fix with one of the following:
|
||||
#-----------------------------------------------------------------------------
|
||||
# Channel with 2 pits placed symmetrically about center in x:
|
||||
#npits 2 20 20 10 5 sw
|
||||
|
||||
# Channel with 1 pit placed at center:
|
||||
#npits 1 20 20 20 sw
|
||||
|
||||
# Full channel with 1 "speedbump" placed in right end of the channel:
|
||||
#npits 2 20 40 5 0 sw
|
||||
|
||||
# Channel with 2 "potholes" placed symmetrically about center in x:
|
||||
#npits 2 20 15 10 10 wp 30
|
||||
|
||||
# Channel with T-shaped cross-section with a "speedbump" in right end:
|
||||
#npits 2 20 40 5 0 wp 30
|
||||
|
||||
# Long rectangular channel (all pit, no slit):
|
||||
#npits 1 20 65 5 0 sw
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
fix 3 all rigid group 1 sphere1
|
||||
1 rigid bodies with 320 atoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables for the center-of-mass and angular velocities, and output
|
||||
# these quantities to the screen.
|
||||
#----------------------------------------------------------------------------
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
variable vz equal vcm(all,z)
|
||||
variable omegax equal omega(all,x)
|
||||
variable omegay equal omega(all,y)
|
||||
variable omegaz equal omega(all,z)
|
||||
|
||||
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
thermo 500
|
||||
|
||||
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
|
||||
|
||||
run 2500
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.45
|
||||
ghost atom cutoff = 3.45
|
||||
binsize = 1.725, bins = 140 116 140
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.973 | 6.973 | 6.973 Mbytes
|
||||
Step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
0 10054461 0 0 0 0 0 0
|
||||
500 10055203 0.008268321 2.9442616e-05 0.0019660229 -5.0307394e-07 2.1873981e-05 2.2701522e-07
|
||||
1000 10055487 0.015301314 4.219514e-05 0.0029217734 -6.9936017e-07 6.8198965e-05 5.2031048e-07
|
||||
1500 10055663 0.02117119 2.9194379e-05 0.002365636 -7.5401298e-07 0.00011557032 4.0311183e-07
|
||||
2000 10055781 0.02523262 -9.149834e-06 -0.0001724854 -2.5872732e-07 0.00014864932 3.7644295e-07
|
||||
2500 10055866 0.02651785 -5.2469712e-05 -0.0030476651 2.9151609e-07 0.00014663544 7.8650891e-07
|
||||
Loop time of 86.7379 on 4 procs for 2500 steps with 320 atoms
|
||||
|
||||
Performance: 4980523049.256 ns/day, 0.000 hours/ns, 28.822 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.005625 | 0.0081021 | 0.011663 | 2.9 | 0.01
|
||||
Neigh | 0.25946 | 0.26966 | 0.28604 | 2.0 | 0.31
|
||||
Comm | 0.032947 | 0.047576 | 0.069872 | 7.0 | 0.05
|
||||
Output | 0.0038996 | 0.0041104 | 0.0047328 | 0.6 | 0.00
|
||||
Modify | 86.297 | 86.325 | 86.351 | 0.3 | 99.52
|
||||
Other | | 0.08361 | | | 0.10
|
||||
|
||||
Nlocal: 80 ave 219 max 0 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Nghost: 17.75 ave 36 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:26
|
||||
@ -1,70 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Reading data file ...
|
||||
orthogonal box = (-120.00000 -100.00000 -120.00000) to (120.00000 100.00000 120.00000)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
320 atoms
|
||||
read_data CPU = 0.008 seconds
|
||||
320 atoms in group sphere1
|
||||
Using a lattice-Boltzmann grid of 60 by 50 by 61 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
length of pits and end segments larger than system size in x-direction: truncation will occur (../fix_lb_fluid.cpp:494)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 320 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.45
|
||||
ghost atom cutoff = 3.45
|
||||
binsize = 1.725, bins = 140 116 140
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : micro
|
||||
Current step : 0
|
||||
Time step : 2
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.225 | 7.225 | 7.225 Mbytes
|
||||
Step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
|
||||
0 10054461 0 0 0 0 0 0
|
||||
500 10055203 0.008268321 2.9442616e-05 0.0019660229 -5.0307394e-07 2.1873981e-05 2.2701522e-07
|
||||
1000 10055487 0.015301314 4.219514e-05 0.0029217734 -6.9936017e-07 6.8198965e-05 5.2031048e-07
|
||||
1500 10055663 0.02117119 2.9194379e-05 0.002365636 -7.5401298e-07 0.00011557032 4.0311183e-07
|
||||
2000 10055781 0.02523262 -9.149834e-06 -0.0001724854 -2.5872732e-07 0.00014864932 3.7644295e-07
|
||||
2500 10055866 0.02651785 -5.2469712e-05 -0.0030476651 2.9151609e-07 0.00014663544 7.8650891e-07
|
||||
Loop time of 88.7186 on 4 procs for 2500 steps with 320 atoms
|
||||
|
||||
Performance: 4869327934.296 ns/day, 0.000 hours/ns, 28.179 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0049214 | 0.0074319 | 0.01069 | 2.9 | 0.01
|
||||
Neigh | 0.25996 | 0.26957 | 0.28281 | 1.9 | 0.30
|
||||
Comm | 0.034344 | 0.047966 | 0.066438 | 6.3 | 0.05
|
||||
Output | 0.027428 | 0.039502 | 0.04364 | 3.5 | 0.04
|
||||
Modify | 88.227 | 88.258 | 88.292 | 0.3 | 99.48
|
||||
Other | | 0.09591 | | | 0.11
|
||||
|
||||
Nlocal: 80.0000 ave 219 max 0 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Nghost: 17.7500 ave 36 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 16.184525
|
||||
LB update time: 35.882755
|
||||
LB PCalc time: 22.914380
|
||||
LB fluidForce time: 8.049794
|
||||
LB CorrectU time: 5.031811
|
||||
Total wall time: 0:01:28
|
||||
@ -6,8 +6,6 @@
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: RIGID, LATBOLTZ #
|
||||
# #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# 'planewall.out' #
|
||||
#===========================================================================#
|
||||
|
||||
units micro
|
||||
@ -32,7 +30,7 @@ neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1
|
||||
comm_modify cutoff 10.0
|
||||
|
||||
read_data one_radius16d2.data
|
||||
read_data data.one_radius16d2
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# None of the particles interact with one another.
|
||||
@ -1,15 +1,135 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# Rigid sphere freely moving near a stationary plane wall in a system #
|
||||
# undergoing shear flow. #
|
||||
# Every 10 time steps the center of mass velocity and angular velocity of #
|
||||
# the sphere are printed to the screen. #
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: RIGID, LATBOLTZ #
|
||||
# #
|
||||
#===========================================================================#
|
||||
|
||||
units micro
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The arguments for neigh_modify have been set to "delay 0 every 1", again
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid. However, these values can likely
|
||||
# be somewhat increased without issue. If a problem does arise (a particle
|
||||
# is outside of its processors LB grid) an error message is printed and
|
||||
# the simulation is terminated.
|
||||
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
|
||||
# processor ghost fluid region (of width 2dx) are known to local processor.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1
|
||||
comm_modify cutoff 10.0
|
||||
|
||||
read_data data.one_radius16d2
|
||||
Reading data file ...
|
||||
orthogonal box = (-120.00000 -120.00000 -120.00000) to (120.00000 120.00000 120.00000)
|
||||
orthogonal box = (-120 -120 -120) to (120 120 120)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
320 atoms
|
||||
read_data CPU = 0.008 seconds
|
||||
read_data CPU = 0.015 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# None of the particles interact with one another.
|
||||
#----------------------------------------------------------------------------
|
||||
pair_style lj/cut 2.45
|
||||
pair_coeff * * 0.0 0.0 2.45
|
||||
neigh_modify exclude type 1 1
|
||||
|
||||
mass * 1.0
|
||||
|
||||
timestep 4.0
|
||||
|
||||
group sphere1 id <> 1 320
|
||||
320 atoms in group sphere1
|
||||
Using a lattice-Boltzmann grid of 60 by 60 by 61 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Colloidal particle is initially stationary.
|
||||
#----------------------------------------------------------------------------
|
||||
velocity all set 0.0 0.0 0.0 units box
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# All of the particles in the simulation apply a force to the fluid.
|
||||
# (however, this fix does not explicitly apply a force back on to these
|
||||
# particles...this is accomplished through the use of the lb/viscous fix.
|
||||
# Use a fluid density = 1.0, fluid viscosity = 1.0 (water), and a lattice
|
||||
# spacing dx=4.0.
|
||||
# Use the trilinear interpolation stencil (default) to distribute the force
|
||||
# from a given particle onto the fluid mesh.
|
||||
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
|
||||
# along the y-direction, while keeping the lower z-wall stationary.
|
||||
#-----------------------------------------------------------------------------
|
||||
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 zwall_velocity 0.0 0.0001
|
||||
Using a lattice-Boltzmann grid of 60 by 60 by 61 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force due to the fluid onto the particles.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Integrate the motion of the particles, constraining them to move and
|
||||
# rotate together as a single rigid spherical object. Use the first
|
||||
# version to allow the sphere to freely rotate and move with the fluid
|
||||
# and the 2nd version to measure the force and torque on a fixed sphere
|
||||
# in the shear flow which will allow you to measure the Stokes drag and
|
||||
# torque on the sphere.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 3 all rigid group 1 sphere1
|
||||
1 rigid bodies with 320 atoms
|
||||
#fix 3 all rigid group 1 sphere1 force * off off off torque * off off off
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Create variables for the center-of-mass velocities, angular velocities, and
|
||||
# force and torque on the CM. Then output these quantities to the screen.
|
||||
#----------------------------------------------------------------------------
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
variable vz equal vcm(all,z)
|
||||
variable omegax equal omega(all,x)
|
||||
variable omegay equal omega(all,y)
|
||||
variable omegaz equal omega(all,z)
|
||||
variable fx equal fcm(all,x)
|
||||
variable fy equal fcm(all,y)
|
||||
variable fz equal fcm(all,z)
|
||||
variable tx equal torque(all,x)
|
||||
variable ty equal torque(all,y)
|
||||
variable tz equal torque(all,z)
|
||||
|
||||
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
|
||||
thermo 100
|
||||
|
||||
run 7500
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -22,10 +142,6 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : micro
|
||||
Current step : 0
|
||||
Time step : 4
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.426 | 8.426 | 8.426 Mbytes
|
||||
v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
|
||||
0 0 0 0 0 0 0 0 0 0 0 0
|
||||
@ -104,36 +220,30 @@ v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
|
||||
-2.6074079e-12 4.9575038e-05 -8.5484831e-10 -2.0807608e-07 -7.0458889e-12 1.5917995e-11 -4.6370161e-13 2.3298683e-08 -1.1706817e-11 2.5798545e-10 6.4493257e-12 -9.0570787e-12
|
||||
-3.1912867e-12 4.9603187e-05 -8.7103016e-10 -2.0807419e-07 -6.9729658e-12 1.5869196e-11 -5.4662034e-13 2.1756065e-08 -1.4183469e-11 2.6950321e-10 1.2401403e-11 -9.1121813e-12
|
||||
-2.6896504e-12 4.9629471e-05 -8.8354072e-10 -2.0807269e-07 -6.9518789e-12 1.5862597e-11 7.7697632e-13 2.0315473e-08 -9.1356461e-12 1.9455164e-10 -5.2929772e-13 -4.0871645e-12
|
||||
Loop time of 354.087 on 4 procs for 7500 steps with 320 atoms
|
||||
Loop time of 348.592 on 4 procs for 7500 steps with 320 atoms
|
||||
|
||||
Performance: 7320228141.222 ns/day, 0.000 hours/ns, 21.181 timesteps/s
|
||||
Performance: 7435633235.428 ns/day, 0.000 hours/ns, 21.515 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.02245 | 0.024017 | 0.025793 | 0.9 | 0.01
|
||||
Neigh | 0.0043829 | 0.0046506 | 0.0049014 | 0.4 | 0.00
|
||||
Comm | 0.16337 | 0.1673 | 0.17244 | 0.9 | 0.05
|
||||
Output | 0.011278 | 0.016279 | 0.031255 | 6.8 | 0.00
|
||||
Modify | 353.57 | 353.58 | 353.6 | 0.1 | 99.86
|
||||
Other | | 0.2924 | | | 0.08
|
||||
Pair | 0.024506 | 0.025477 | 0.026424 | 0.6 | 0.01
|
||||
Neigh | 0.030494 | 0.03257 | 0.034614 | 1.0 | 0.01
|
||||
Comm | 0.2132 | 0.21532 | 0.22048 | 0.6 | 0.06
|
||||
Output | 0.011234 | 0.016341 | 0.031613 | 6.9 | 0.00
|
||||
Modify | 347.96 | 347.98 | 348 | 0.1 | 99.83
|
||||
Other | | 0.3181 | | | 0.09
|
||||
|
||||
Nlocal: 80.0000 ave 86 max 74 min
|
||||
Nlocal: 80 ave 86 max 74 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 122.750 ave 126 max 120 min
|
||||
Nghost: 122.75 ave 126 max 120 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 74.234376
|
||||
LB update time: 137.610462
|
||||
LB PCalc time: 90.368082
|
||||
LB fluidForce time: 30.518506
|
||||
LB CorrectU time: 20.319747
|
||||
Total wall time: 0:05:54
|
||||
Total wall time: 0:05:48
|
||||
@ -1,139 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Reading data file ...
|
||||
orthogonal box = (-120.00000 -120.00000 -120.00000) to (120.00000 120.00000 120.00000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
320 atoms
|
||||
read_data CPU = 0.010 seconds
|
||||
320 atoms in group sphere1
|
||||
Using a lattice-Boltzmann grid of 60 by 60 by 61 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
1 rigid bodies with 320 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.45
|
||||
ghost atom cutoff = 10
|
||||
binsize = 1.725, bins = 140 140 140
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : micro
|
||||
Current step : 0
|
||||
Time step : 4
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.426 | 8.426 | 8.426 Mbytes
|
||||
v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
|
||||
0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0 0 0 0 0 0 4.239889e-13 8.8817291e-07 -2.8255287e-11 -8.3760967e-06 -3.4292821e-11 1.4413627e-09
|
||||
0 0 0 0 0 0 1.4315002e-10 4.8664591e-05 -3.7829664e-10 -0.00030396599 -1.5178649e-09 5.8286332e-08
|
||||
0 0 0 0 0 0 7.4346125e-10 0.00021263259 1.4837899e-09 -0.00099915016 -5.4814944e-09 2.0970524e-07
|
||||
0 0 0 0 0 0 1.6937683e-09 0.00046298302 6.9867552e-09 -0.0017633394 -1.0234552e-08 3.9564168e-07
|
||||
0 0 0 0 0 0 2.7893371e-09 0.00075233887 1.512364e-08 -0.002430003 -1.4664452e-08 5.7543419e-07
|
||||
0 0 0 0 0 0 3.9059765e-09 0.0010508836 2.473915e-08 -0.0029656977 -1.843702e-08 7.3546258e-07
|
||||
0 0 0 0 0 0 4.9837024e-09 0.0013431931 3.5023862e-08 -0.0033824332 -2.154284e-08 8.7378862e-07
|
||||
0 0 0 0 0 0 5.9972036e-09 0.0016220459 4.5458108e-08 -0.0037022957 -2.4071195e-08 9.9238011e-07
|
||||
0 0 0 0 0 0 6.9382202e-09 0.0018845001 5.571997e-08 -0.0039464067 -2.6127149e-08 1.0941409e-06
|
||||
0 0 0 0 0 0 7.8064955e-09 0.0021297688 6.5611103e-08 -0.0041322536 -2.7805365e-08 1.1818894e-06
|
||||
0 0 0 0 0 0 8.6053202e-09 0.0023581155 7.5022305e-08 -0.0042735978 -2.9184146e-08 1.2580602e-06
|
||||
0 0 0 0 0 0 9.3393725e-09 0.0025702889 8.3893991e-08 -0.0043810513 -3.0326009e-08 1.3246619e-06
|
||||
0 0 0 0 0 0 1.001368e-08 0.0027672363 9.2208859e-08 -0.0044627274 -3.128007e-08 1.3833192e-06
|
||||
0 0 0 0 0 0 1.0633157e-08 0.0029499614 9.9966263e-08 -0.0045248072 -3.2084685e-08 1.4353358e-06
|
||||
0 0 0 0 0 0 1.1202408e-08 0.003119455 1.0718596e-07 -0.0045719925 -3.2769709e-08 1.4817567e-06
|
||||
0 0 0 0 0 0 1.1725673e-08 0.0032766636 1.1388989e-07 -0.0046078577 -3.335838e-08 1.5234208e-06
|
||||
0 0 0 0 0 0 1.2206811e-08 0.0034224769 1.2010982e-07 -0.0046351195 -3.3868829e-08 1.5610047e-06
|
||||
0 0 0 0 0 0 1.2649333e-08 0.0035577241 1.2587419e-07 -0.0046558425 -3.4315213e-08 1.5950578e-06
|
||||
0 0 0 0 0 0 1.3056425e-08 0.0036831753 1.31216e-07 -0.0046715955 -3.4708664e-08 1.6260295e-06
|
||||
0 0 0 0 0 0 1.3430996e-08 0.0037995442 1.3616361e-07 -0.0046835712 -3.505795e-08 1.6542904e-06
|
||||
0 0 0 0 0 0 1.3775686e-08 0.0039074918 1.407471e-07 -0.0046926757 -3.5370035e-08 1.6801491e-06
|
||||
0 0 0 0 0 0 1.4092912e-08 0.0040076304 1.4499244e-07 -0.0046995979 -3.5650478e-08 1.7038651e-06
|
||||
0 0 0 0 0 0 1.4384883e-08 0.0041005268 1.4892558e-07 -0.0047048612 -3.5903729e-08 1.7256585e-06
|
||||
0 0 0 0 0 0 1.4653619e-08 0.0041867065 1.5256951e-07 -0.0047088634 -3.6133445e-08 1.745718e-06
|
||||
0 0 0 0 0 0 1.490098e-08 0.0042666563 1.5594609e-07 -0.0047119071 -3.6342564e-08 1.7642066e-06
|
||||
0 0 0 0 0 0 1.5128662e-08 0.0043408273 1.5907544e-07 -0.0047142221 -3.6533538e-08 1.7812667e-06
|
||||
0 0 0 0 0 0 1.5338233e-08 0.0044096378 1.6197577e-07 -0.0047159831 -3.670842e-08 1.7970233e-06
|
||||
0 0 0 0 0 0 1.5531126e-08 0.0044734757 1.646646e-07 -0.0047173229 -3.6868911e-08 1.8115874e-06
|
||||
0 0 0 0 0 0 1.5708666e-08 0.0045327006 1.6715708e-07 -0.0047183425 -3.7016486e-08 1.8250577e-06
|
||||
0 0 0 0 0 0 1.5872071e-08 0.0045876461 1.6946841e-07 -0.0047191186 -3.7152397e-08 1.8375231e-06
|
||||
0 0 0 0 0 0 1.6022457e-08 0.0046386215 1.7161128e-07 -0.0047197095 -3.7277723e-08 1.8490635e-06
|
||||
0 0 0 0 0 0 1.6160856e-08 0.0046859138 1.7359882e-07 -0.0047201596 -3.7393419e-08 1.8597512e-06
|
||||
0 0 0 0 0 0 1.6288218e-08 0.0047297892 1.7544172e-07 -0.0047205027 -3.7500311e-08 1.8696524e-06
|
||||
0 0 0 0 0 0 1.6405415e-08 0.0047704946 1.7715127e-07 -0.0047207642 -3.7599158e-08 1.8788269e-06
|
||||
0 0 0 0 0 0 1.6513252e-08 0.0048082591 1.7873657e-07 -0.0047209638 -3.7690613e-08 1.8873299e-06
|
||||
0 0 0 0 0 0 1.6612471e-08 0.0048432952 1.802073e-07 -0.0047211162 -3.7775283e-08 1.8952118e-06
|
||||
0 0 0 0 0 0 1.6703756e-08 0.0048758 1.8157127e-07 -0.0047212327 -3.7853677e-08 1.9025188e-06
|
||||
0 0 0 0 0 0 1.6787736e-08 0.0049059565 1.8283671e-07 -0.0047213218 -3.7926309e-08 1.9092938e-06
|
||||
0 0 0 0 0 0 1.6864987e-08 0.0049339342 1.8401041e-07 -0.0047213902 -3.7993601e-08 1.9155759e-06
|
||||
0 0 0 0 0 0 1.6936047e-08 0.0049598906 1.8509932e-07 -0.0047214426 -3.8055984e-08 1.9214015e-06
|
||||
0 0 0 0 0 0 1.7001408e-08 0.0049839718 1.8610939e-07 -0.004721483 -3.8113818e-08 1.926804e-06
|
||||
0 0 0 0 0 0 1.706152e-08 0.0050063132 1.8704646e-07 -0.0047215141 -3.8167432e-08 1.9318145e-06
|
||||
0 0 0 0 0 0 1.7116801e-08 0.0050270405 1.8791576e-07 -0.0047215382 -3.8217147e-08 1.9364615e-06
|
||||
0 0 0 0 0 0 1.7167636e-08 0.0050462704 1.8872221e-07 -0.0047215569 -3.8263258e-08 1.9407716e-06
|
||||
0 0 0 0 0 0 1.7214381e-08 0.005064111 1.8947039e-07 -0.0047215715 -3.8306026e-08 1.9447693e-06
|
||||
0 0 0 0 0 0 1.7257357e-08 0.0050806626 1.9016445e-07 -0.0047215829 -3.8345683e-08 1.9484773e-06
|
||||
0 0 0 0 0 0 1.7296867e-08 0.0050960185 1.9080841e-07 -0.0047215918 -3.8382478e-08 1.9519167e-06
|
||||
0 0 0 0 0 0 1.7333189e-08 0.005110265 1.9140576e-07 -0.0047215989 -3.8416608e-08 1.955107e-06
|
||||
0 0 0 0 0 0 1.7366574e-08 0.0051234822 1.9196003e-07 -0.0047216046 -3.8448262e-08 1.9580663e-06
|
||||
0 0 0 0 0 0 1.7397262e-08 0.0051357445 1.9247416e-07 -0.0047216092 -3.8477636e-08 1.9608112e-06
|
||||
0 0 0 0 0 0 1.7425463e-08 0.005147121 1.9295122e-07 -0.0047216128 -3.8504879e-08 1.9633575e-06
|
||||
0 0 0 0 0 0 1.745138e-08 0.0051576755 1.9339373e-07 -0.0047216159 -3.8530161e-08 1.9657193e-06
|
||||
0 0 0 0 0 0 1.7475194e-08 0.0051674675 1.9380435e-07 -0.0047216184 -3.8553607e-08 1.9679102e-06
|
||||
0 0 0 0 0 0 1.7497073e-08 0.0051765521 1.9418523e-07 -0.0047216204 -3.8575366e-08 1.9699425e-06
|
||||
0 0 0 0 0 0 1.7517174e-08 0.0051849803 1.9453865e-07 -0.0047216222 -3.8595551e-08 1.9718277e-06
|
||||
0 0 0 0 0 0 1.753564e-08 0.0051927997 1.9486648e-07 -0.0047216237 -3.8614279e-08 1.9735764e-06
|
||||
0 0 0 0 0 0 1.7552601e-08 0.0052000541 1.9517068e-07 -0.0047216249 -3.8631647e-08 1.9751986e-06
|
||||
0 0 0 0 0 0 1.7568178e-08 0.0052067844 1.9545286e-07 -0.004721626 -3.864777e-08 1.9767033e-06
|
||||
0 0 0 0 0 0 1.7582482e-08 0.0052130285 1.9571468e-07 -0.004721627 -3.8662724e-08 1.9780991e-06
|
||||
0 0 0 0 0 0 1.7595618e-08 0.0052188215 1.9595756e-07 -0.0047216278 -3.8676592e-08 1.9793939e-06
|
||||
0 0 0 0 0 0 1.7607679e-08 0.005224196 1.9618291e-07 -0.0047216286 -3.8689479e-08 1.980595e-06
|
||||
0 0 0 0 0 0 1.761875e-08 0.0052291822 1.9639198e-07 -0.0047216293 -3.8701417e-08 1.9817091e-06
|
||||
0 0 0 0 0 0 1.7628913e-08 0.0052338081 1.9658594e-07 -0.0047216299 -3.87125e-08 1.9827426e-06
|
||||
0 0 0 0 0 0 1.7638241e-08 0.0052380998 1.9676589e-07 -0.0047216304 -3.8722782e-08 1.9837013e-06
|
||||
0 0 0 0 0 0 1.7646803e-08 0.0052420815 1.9693283e-07 -0.0047216309 -3.8732329e-08 1.9845906e-06
|
||||
0 0 0 0 0 0 1.7654657e-08 0.0052457755 1.9708773e-07 -0.0047216313 -3.8741169e-08 1.9854156e-06
|
||||
0 0 0 0 0 0 1.7661865e-08 0.0052492027 1.9723142e-07 -0.0047216317 -3.8749387e-08 1.9861808e-06
|
||||
0 0 0 0 0 0 1.7668477e-08 0.0052523822 1.9736474e-07 -0.0047216321 -3.8756997e-08 1.9868906e-06
|
||||
0 0 0 0 0 0 1.7674543e-08 0.0052553321 1.9748842e-07 -0.0047216325 -3.8764064e-08 1.9875491e-06
|
||||
0 0 0 0 0 0 1.7680105e-08 0.0052580688 1.9760317e-07 -0.0047216328 -3.8770626e-08 1.9881599e-06
|
||||
0 0 0 0 0 0 1.7685205e-08 0.0052606078 1.9770962e-07 -0.0047216331 -3.877671e-08 1.9887264e-06
|
||||
0 0 0 0 0 0 1.7689882e-08 0.0052629634 1.978084e-07 -0.0047216333 -3.8782352e-08 1.989252e-06
|
||||
0 0 0 0 0 0 1.769417e-08 0.0052651488 1.9790002e-07 -0.0047216336 -3.8787592e-08 1.9897395e-06
|
||||
0 0 0 0 0 0 1.7698101e-08 0.0052671763 1.9798504e-07 -0.0047216338 -3.8792458e-08 1.9901918e-06
|
||||
0 0 0 0 0 0 1.7701702e-08 0.0052690573 1.9806391e-07 -0.004721634 -3.8796971e-08 1.9906113e-06
|
||||
Loop time of 348.316 on 4 procs for 7500 steps with 320 atoms
|
||||
|
||||
Performance: 7441508527.485 ns/day, 0.000 hours/ns, 21.532 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022385 | 0.02409 | 0.026109 | 0.9 | 0.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.14613 | 0.14777 | 0.14918 | 0.3 | 0.04
|
||||
Output | 0.010513 | 0.015329 | 0.02974 | 6.7 | 0.00
|
||||
Modify | 347.82 | 347.85 | 347.86 | 0.1 | 99.87
|
||||
Other | | 0.2818 | | | 0.08
|
||||
|
||||
Nlocal: 80.0000 ave 82 max 78 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 122.500 ave 124 max 121 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0.00000 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0.0000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 72.754071
|
||||
LB update time: 135.699228
|
||||
LB PCalc time: 88.586456
|
||||
LB fluidForce time: 30.088636
|
||||
LB CorrectU time: 20.191920
|
||||
Total wall time: 0:05:48
|
||||
@ -7,7 +7,7 @@
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: MOLECULE, RIGID, LATBOTLZ #
|
||||
# #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# If uncommented, sample output from this run can be found in the file: #
|
||||
# 'dump.polymer.lammpstrj' #
|
||||
# and viewed using, e.g., the VMD software. #
|
||||
# #
|
||||
@ -18,7 +18,7 @@ dimension 3
|
||||
boundary p p f
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data polymer.data
|
||||
read_data data.polymer
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
@ -105,7 +105,7 @@ fix 3 all rigid/small molecule
|
||||
fix 4 all lb/momentum 100000 linear 1 1 1
|
||||
|
||||
|
||||
dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
|
||||
#dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
|
||||
|
||||
#run 2000001
|
||||
run 10000
|
||||
199
examples/PACKAGES/latboltz/polymer/log.09Mar22.polymer.g++.4
Normal file
199
examples/PACKAGES/latboltz/polymer/log.09Mar22.polymer.g++.4
Normal file
@ -0,0 +1,199 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# polymer test #
|
||||
# #
|
||||
# Run consists of a lone 32-bead coarse-grained polymer #
|
||||
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: MOLECULE, RIGID, LATBOTLZ #
|
||||
# #
|
||||
# If uncommented, sample output from this run can be found in the file: #
|
||||
# 'dump.polymer.lammpstrj' #
|
||||
# and viewed using, e.g., the VMD software. #
|
||||
# #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data data.polymer
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (40 40 40)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
992 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.037 seconds
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
|
||||
# processor ghost fluid region (of width 2dx) are known to local processor.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each monomer (use a truncated and shifted Lennard-Jones potential).
|
||||
#----------------------------------------------------------------------------
|
||||
bond_style fene
|
||||
bond_coeff 1 60.0 2.25 4.14195 1.5
|
||||
pair_style lj/cut 1.68369
|
||||
pair_coeff 1 1 4.14195 1.5 1.68369
|
||||
pair_coeff 1 2 4.14195 1.5 1.68369
|
||||
pair_coeff 2 2 0 1.0
|
||||
|
||||
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
|
||||
# nodes in a single monomer
|
||||
mass * 0.00000318
|
||||
timestep 0.0001
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each monomer which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the monomer
|
||||
# which do interact with the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
32 atoms in group ForceAtoms
|
||||
group FluidAtoms type 2
|
||||
960 atoms in group FluidAtoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Placement of a trap (similar to an 1D optical trap) for the polymer
|
||||
# Note that the addforce fix needs to go before the lb/fluid and lb/viscous
|
||||
# fix as these fixes rescale the forces to account for the added mass of the
|
||||
# fluid that gets dragged around with the particle so need prior knowledge of
|
||||
# all forces applied to the particles involved in these fixes before they are
|
||||
# called.
|
||||
#----------------------------------------------------------------------------
|
||||
variable fx atom -(x-20.0)*20.0/31.0
|
||||
fix trap all addforce v_fx 0.0 0.0 # call before fix lb/fluid and lb/viscous
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles. This is accomplished through the use of the lb/viscous fix).
|
||||
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
|
||||
# means the kinematic viscosity is idential to that of water but the
|
||||
# dynamic viscosity is a factor of 10 less than that of water which
|
||||
# increases the diffusive dynamics by a corresponding factor of 10.
|
||||
# lattice spacing dx=1.0.
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=15003). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 all lb/fluid 1 0.1 0.00009982071 dx 1.0 noise 300.0 15003
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining each monomerto move and rotate as a single rigid
|
||||
# spherical object.
|
||||
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
|
||||
# shell) should move and rotate together, this fix is applied to all of
|
||||
# the atoms in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/viscous
|
||||
fix 3 all rigid/small molecule
|
||||
create bodies CPU = 0.000 seconds
|
||||
32 rigid bodies with 992 atoms
|
||||
0.70010803 = max distance from body owner to body atom
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# To ensure that numerical errors do not lead to a buildup of momentum in the
|
||||
# system, the momentum_lb fix is used every 100000 timesteps to zero out the
|
||||
# total (particle plus fluid) momentum in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 4 all lb/momentum 100000 linear 1 1 1
|
||||
|
||||
|
||||
#dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
|
||||
|
||||
#run 2000001
|
||||
run 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.18369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.091845, bins = 37 37 37
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:723)
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.861 | 9.842 | 11.95 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8.2758489 2790.7741 2782.4982 0.85835765
|
||||
10000 15.559756 -10.240592 2817.6714 2827.7319 -0.0015697449
|
||||
Loop time of 269.705 on 4 procs for 10000 steps with 992 atoms
|
||||
|
||||
Performance: 320.351 ns/day, 0.075 hours/ns, 37.078 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.01457 | 0.047368 | 0.1221 | 20.3 | 0.02
|
||||
Bond | 0.010081 | 0.022047 | 0.043793 | 9.3 | 0.01
|
||||
Neigh | 0.61943 | 0.62713 | 0.63223 | 0.7 | 0.23
|
||||
Comm | 0.10937 | 0.33658 | 0.61517 | 39.3 | 0.12
|
||||
Output | 3.44e-05 | 7.7575e-05 | 0.0001653 | 0.0 | 0.00
|
||||
Modify | 268.04 | 268.34 | 268.53 | 1.2 | 99.49
|
||||
Other | | 0.3359 | | | 0.12
|
||||
|
||||
Nlocal: 248 ave 802 max 0 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 113.25 ave 190 max 42 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4.25 ave 15 max 0 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 17
|
||||
Ave neighs/atom = 0.017137097
|
||||
Ave special neighs/atom = 0.0625
|
||||
Neighbor list builds = 495
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:04:29
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,81 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (40.000000 40.000000 40.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
992 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.027 seconds
|
||||
32 atoms in group ForceAtoms
|
||||
960 atoms in group FluidAtoms
|
||||
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:475)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1021)
|
||||
First Run initialized
|
||||
create bodies CPU = 0.000 seconds
|
||||
32 rigid bodies with 992 atoms
|
||||
0.70010803 = max distance from body owner to body atom
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.18369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.091845, bins = 37 37 37
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 0.0001
|
||||
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:730)
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.114 | 10.07 | 12.65 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8.2758489 2790.7741 2782.4982 0.85835765
|
||||
10000 15.559756 -10.240592 2817.6714 2827.7319 -0.0015697449
|
||||
Loop time of 217.363 on 4 procs for 10000 steps with 992 atoms
|
||||
|
||||
Performance: 397.491 ns/day, 0.060 hours/ns, 46.006 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.013036 | 0.048243 | 0.13073 | 22.1 | 0.02
|
||||
Bond | 0.0098736 | 0.02098 | 0.040036 | 8.4 | 0.01
|
||||
Neigh | 0.4698 | 0.4764 | 0.48073 | 0.7 | 0.22
|
||||
Comm | 0.085369 | 0.27273 | 0.51085 | 36.0 | 0.13
|
||||
Output | 0.13148 | 0.36286 | 1.0297 | 63.9 | 0.17
|
||||
Modify | 215.41 | 215.91 | 216.3 | 2.2 | 99.33
|
||||
Other | | 0.2725 | | | 0.13
|
||||
|
||||
Nlocal: 248.000 ave 802 max 0 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 113.250 ave 190 max 42 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4.25000 ave 15 max 0 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 17
|
||||
Ave neighs/atom = 0.017137097
|
||||
Ave special neighs/atom = 0.062500000
|
||||
Neighbor list builds = 495
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 94.576600
|
||||
LB update time: 66.882962
|
||||
LB PCalc time: 33.159861
|
||||
LB fluidForce time: 11.576858
|
||||
LB CorrectU time: 8.640308
|
||||
Total wall time: 0:03:37
|
||||
@ -1,3 +1,12 @@
|
||||
#===========================================================================#
|
||||
# Toy car driving down a system with a floor and ceiling. #
|
||||
# #
|
||||
# The car is first constructed by condensing particles onto various regions#
|
||||
# that make up the car's parts. Then the car moves in a lattice Boltzmann #
|
||||
# fluid. This requires compilation with the RIGID and LATBOLTZ packages #
|
||||
# You will need to uncomment the dump options to get useful output. #
|
||||
#===========================================================================#
|
||||
|
||||
units cgs
|
||||
dimension 3
|
||||
boundary p p f
|
||||
@ -375,7 +384,7 @@ neigh_modify delay 0 every 1 check yes
|
||||
#variable commcutoff equal "v_dx*2"
|
||||
#comm_modify cutoff ${commcutoff}
|
||||
|
||||
dump mydump all atom 10000 out.lammpstrj
|
||||
#dump mydump all atom 10000 out.lammpstrj
|
||||
thermo 5000
|
||||
|
||||
#------------------------------------------------------------------------#
|
||||
@ -390,7 +399,7 @@ fix 3 all langevin 31000000.0 50000.0 100.0 5678
|
||||
|
||||
fix 2 all nve
|
||||
|
||||
restart 100000 ParticleRestart
|
||||
#restart 100000 ParticleRestart
|
||||
|
||||
run 100000
|
||||
|
||||
@ -466,13 +475,13 @@ velocity all set 0.0 -7.5.0 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 dumpxdmf 1000 sflow 0
|
||||
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 # dumpxdmf 1000 sflow 0
|
||||
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
variable vz equal vcm(all,z)
|
||||
|
||||
dump mydumpvtk all vtk 1000 out*.vtp vx vy vz
|
||||
#dump mydumpvtk all vtk 1000 out*.vtp vx vy vz
|
||||
|
||||
fix 2 all lb/viscous
|
||||
|
||||
1034
examples/PACKAGES/latboltz/toycar/log.09Mar22.toycar.g++.4
Normal file
1034
examples/PACKAGES/latboltz/toycar/log.09Mar22.toycar.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -1,346 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Created orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
1 by 8 by 2 MPI processor grid
|
||||
Created 618 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
618 atoms in group gcylinder1
|
||||
Created 618 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
618 atoms in group gcylinder2
|
||||
Created 618 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
618 atoms in group gcylinder3
|
||||
Created 618 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
618 atoms in group gcylinder4
|
||||
Created 1876 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
1876 atoms in group gprism1
|
||||
Created 251 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
251 atoms in group gprism2
|
||||
Created 64 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
64 atoms in group gprism3
|
||||
Created 130 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
130 atoms in group gprism4
|
||||
Created 107 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
107 atoms in group gprism5
|
||||
Created 12 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
12 atoms in group gball2
|
||||
Created 50 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
50 atoms in group gprism6
|
||||
Created 50 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
50 atoms in group gprism7
|
||||
Created 40 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
40 atoms in group gprism8
|
||||
Created 40 atoms
|
||||
using box units in orthogonal box = (-48.000000 -90.000000 -9.0000000) to (48.000000 630.00000 87.000000)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
40 atoms in group gprism9
|
||||
2472 atoms in group wheels
|
||||
2620 atoms in group not_wheels
|
||||
744 atoms in group aero_group
|
||||
4348 atoms in group chassis_group
|
||||
5092 atoms in group surge_group
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5255396
|
||||
ghost atom cutoff = 2.5255396
|
||||
binsize = 1.2627698, bins = 77 571 77
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : cgs
|
||||
Current step : 0
|
||||
Time step : 0.2
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.689 | 2.134 | 5.251 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29653357 4.7734395e-06 0 3.6037973e-05 3.9588004e-12
|
||||
10000 27574618 7.2702735e-06 0 3.6343122e-05 4.3745405e-12
|
||||
15000 26623925 8.3820954e-06 0 3.6452596e-05 4.8194698e-12
|
||||
20000 25215034 8.4921576e-06 0 3.5077217e-05 5.063101e-12
|
||||
25000 23697715 8.1953844e-06 0 3.3180683e-05 5.2366712e-12
|
||||
30000 21932332 7.7249763e-06 0 3.0848972e-05 5.2459369e-12
|
||||
35000 20053097 7.4020494e-06 0 2.8544705e-05 5.3033614e-12
|
||||
40000 18850984 6.6058004e-06 0 2.6481028e-05 5.2482481e-12
|
||||
45000 16878277 5.732186e-06 0 2.3527521e-05 5.0022257e-12
|
||||
50000 15969329 5.4014349e-06 0 2.2238436e-05 4.9694943e-12
|
||||
55000 14332838 4.6078293e-06 0 1.9719423e-05 4.7358656e-12
|
||||
60000 12797460 3.8856372e-06 0 1.737843e-05 4.4893714e-12
|
||||
65000 11185599 3.3207593e-06 0 1.5114113e-05 4.1387741e-12
|
||||
70000 9354337.4 2.6757523e-06 0 1.2538345e-05 3.7235349e-12
|
||||
75000 7853652.1 2.1282565e-06 0 1.0408626e-05 3.3014585e-12
|
||||
80000 6406387 1.6177406e-06 0 8.3722101e-06 2.8929882e-12
|
||||
85000 4908480.7 1.0936224e-06 0 6.2687989e-06 2.3307841e-12
|
||||
90000 3240017.2 7.1493728e-07 0 4.1309966e-06 1.8051168e-12
|
||||
95000 1767252.1 3.3323177e-07 0 2.1965051e-06 1.1574583e-12
|
||||
100000 214990.95 4.3210787e-08 0 2.6988298e-07 3.7669124e-13
|
||||
Loop time of 224.453 on 16 procs for 100000 steps with 5092 atoms
|
||||
|
||||
99.5% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0041508 | 3.2305 | 26.286 | 475.0 | 1.44
|
||||
Neigh | 0.48891 | 1.7037 | 10.24 | 245.1 | 0.76
|
||||
Comm | 0.14989 | 0.36541 | 2.0492 | 80.6 | 0.16
|
||||
Output | 0.029068 | 0.071852 | 0.077982 | 5.9 | 0.03
|
||||
Modify | 0.19877 | 22.782 | 185.72 |1252.2 | 10.15
|
||||
Other | | 196.3 | | | 87.46
|
||||
|
||||
Nlocal: 318.250 ave 2599 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 19.6250 ave 160 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4980.25 ave 40336 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 79684
|
||||
Ave neighs/atom = 15.648861
|
||||
Neighbor list builds = 4955
|
||||
Dangerous builds = 0
|
||||
Setting up Verlet run ...
|
||||
Unit style : cgs
|
||||
Current step : 100000
|
||||
Time step : 0.2
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.741 | 2.195 | 5.326 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 214990.95 0 0 2.266722e-07 2.2773618e-14
|
||||
105000 103970.88 6.6908938e-08 0 1.7652894e-07 7.0362091e-13
|
||||
110000 97146.949 6.4681094e-08 0 1.6710639e-07 7.0498855e-13
|
||||
115000 93498.926 6.6281932e-08 0 1.64861e-07 7.159638e-13
|
||||
120000 90495.811 6.4208007e-08 0 1.5962079e-07 7.1712077e-13
|
||||
125000 87959.045 6.5517546e-08 0 1.5825573e-07 7.2366609e-13
|
||||
130000 86381.625 6.1168787e-08 0 1.5224384e-07 6.9916073e-13
|
||||
135000 83153.956 6.2250238e-08 0 1.4992225e-07 7.04846e-13
|
||||
140000 80984.294 6.3000049e-08 0 1.4838452e-07 7.1539396e-13
|
||||
145000 79533.597 5.9676346e-08 0 1.435313e-07 6.9841788e-13
|
||||
150000 77000.73 6.1523884e-08 0 1.4270835e-07 7.120063e-13
|
||||
155000 73683.759 5.9946159e-08 0 1.3763343e-07 7.0660837e-13
|
||||
160000 72974.826 6.0724099e-08 0 1.3766392e-07 7.1071605e-13
|
||||
165000 69691.128 6.0460845e-08 0 1.3393855e-07 7.180638e-13
|
||||
170000 67189.78 5.9914539e-08 0 1.3075499e-07 7.2033578e-13
|
||||
175000 65055.667 5.6825296e-08 0 1.2541568e-07 6.9616887e-13
|
||||
180000 61592.611 5.5166561e-08 0 1.2010573e-07 6.8759774e-13
|
||||
185000 60089.16 5.308612e-08 0 1.1644015e-07 6.8210284e-13
|
||||
190000 56806.407 5.2255502e-08 0 1.1214841e-07 6.7415401e-13
|
||||
195000 55413.919 5.2741451e-08 0 1.1116621e-07 6.7996563e-13
|
||||
200000 52455.282 5.1001789e-08 0 1.0630716e-07 6.7516294e-13
|
||||
205000 49276.345 5.0081869e-08 0 1.0203558e-07 6.7176307e-13
|
||||
210000 47382.758 4.9770319e-08 0 9.9727556e-08 6.6796671e-13
|
||||
215000 45468.582 4.8494832e-08 0 9.6433889e-08 6.640538e-13
|
||||
220000 43747.344 4.9228162e-08 0 9.5352459e-08 6.7748697e-13
|
||||
225000 39986.728 4.6849936e-08 0 8.9009291e-08 6.6080957e-13
|
||||
230000 38695.786 4.7036406e-08 0 8.7834676e-08 6.704184e-13
|
||||
235000 35860.086 4.5515831e-08 0 8.3324328e-08 6.6254084e-13
|
||||
240000 33134.143 4.3643806e-08 0 7.8578249e-08 6.4337478e-13
|
||||
245000 31499.136 4.3700119e-08 0 7.691072e-08 6.5695058e-13
|
||||
250000 29235.08 4.1903104e-08 0 7.2726633e-08 6.4670433e-13
|
||||
255000 26534.656 3.990631e-08 0 6.7882692e-08 6.2974614e-13
|
||||
260000 24003.589 4.0601032e-08 0 6.5908824e-08 6.4499768e-13
|
||||
265000 21943.577 3.8935897e-08 0 6.2071749e-08 6.3562405e-13
|
||||
270000 19653.579 3.7402165e-08 0 5.8123595e-08 6.3432146e-13
|
||||
275000 17275.037 3.6209636e-08 0 5.442329e-08 6.2936445e-13
|
||||
280000 14732.579 3.5846593e-08 0 5.1379647e-08 6.2971704e-13
|
||||
285000 12342.93 3.4985594e-08 0 4.7999161e-08 6.3361065e-13
|
||||
290000 9958.5787 3.3757377e-08 0 4.4257042e-08 6.3251877e-13
|
||||
295000 7752.6563 3.2166604e-08 0 4.0340491e-08 6.2435198e-13
|
||||
300000 5153.3153 3.1185774e-08 0 3.6619088e-08 6.2358439e-13
|
||||
Loop time of 428.577 on 16 procs for 200000 steps with 5092 atoms
|
||||
|
||||
99.5% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0078672 | 7.2993 | 59.383 | 714.2 | 1.70
|
||||
Neigh | 0.013027 | 0.032544 | 0.16934 | 27.9 | 0.01
|
||||
Comm | 0.054276 | 0.37785 | 3.5462 | 147.8 | 0.09
|
||||
Output | 0.06532 | 0.14529 | 0.1567 | 7.7 | 0.03
|
||||
Modify | 0.025902 | 44.512 | 365.8 |1764.9 | 10.39
|
||||
Other | | 376.2 | | | 87.78
|
||||
|
||||
Nlocal: 318.250 ave 2602 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 17.5625 ave 143 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4789.38 ave 38883 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76630
|
||||
Ave neighs/atom = 15.049097
|
||||
Neighbor list builds = 118
|
||||
Dangerous builds = 0
|
||||
Setting up cg style minimization ...
|
||||
Unit style : cgs
|
||||
Current step : 300000
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.741 | 2.335 | 6.451 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5153.3153 3.1185774e-08 0 3.6619088e-08 6.2358439e-13
|
||||
301000 5153.3153 3.1178966e-08 0 3.661228e-08 6.2353588e-13
|
||||
Loop time of 2.19014 on 16 procs for 1000 steps with 5092 atoms
|
||||
|
||||
99.5% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.11857740502293e-08 3.11789729919519e-08 3.11789661924564e-08
|
||||
Force two-norm initial, final = 8.1990455e-08 8.1892870e-08
|
||||
Force max component initial, final = 3.0741586e-09 3.0685608e-09
|
||||
Final line search alpha, max atom move = 1.0000000 3.0685608e-09
|
||||
Iterations, force evaluations = 1000 1000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1437e-05 | 0.056621 | 0.4634 | 62.9 | 2.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0001289 | 0.0024177 | 0.028614 | 14.3 | 0.11
|
||||
Output | 3.6288e-05 | 3.7468e-05 | 3.8983e-05 | 0.0 | 0.00
|
||||
Modify | 4.4937e-05 | 0.20167 | 1.6571 | 118.8 | 9.21
|
||||
Other | | 1.929 | | | 88.09
|
||||
|
||||
Nlocal: 318.250 ave 2602 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 17.5625 ave 143 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 4789.38 ave 38883 max 0 min
|
||||
Histogram: 14 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76630
|
||||
Ave neighs/atom = 15.049097
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 total grid points. (../fix_lb_fluid.cpp:477)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1023)
|
||||
First Run initialized
|
||||
4 rigid bodies with 2472 atoms
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7
|
||||
ghost atom cutoff = 3
|
||||
binsize = 0.85, bins = 113 848 113
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : cgs
|
||||
Current step : 0
|
||||
Time step : 0.025
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.238 | 4.872 | 9.308 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 0.21831855 10.819389 -2.3665527
|
||||
200 5092 98.193244 265447.33 0.081352555 13.33314 0.24750908
|
||||
300 5092 98.193244 265447.33 -0.13723109 12.179202 0.35802438
|
||||
400 5092 98.193244 265447.33 -0.057588432 14.508288 3.3901771
|
||||
500 5092 98.193244 265447.33 -0.05026018 11.590396 3.3204264
|
||||
600 5092 98.193244 265447.33 0.0092174774 10.829799 0.55313683
|
||||
700 5092 98.193244 265447.33 -0.20861033 10.801467 1.5288445
|
||||
800 5092 98.193244 265447.33 -0.17761042 12.668514 1.8746262
|
||||
900 5092 98.193244 265447.33 -0.046957187 10.410009 2.5061791
|
||||
1000 5092 98.193244 265447.33 0.017637786 10.502295 1.4603753
|
||||
1100 5092 98.193244 265447.33 -0.1992929 9.5275081 1.926958
|
||||
1200 5092 98.193244 265447.33 -0.10276752 12.112636 2.6301022
|
||||
1300 5092 98.193244 265447.33 0.055577062 10.390509 2.8449094
|
||||
1400 5092 98.193244 265447.33 0.13383948 10.283919 3.2933858
|
||||
1500 5092 98.193244 265447.33 -0.10521833 9.9952804 3.0181533
|
||||
1600 5092 98.193244 265447.33 -0.045015836 12.123929 3.0026447
|
||||
1700 5092 98.193244 265447.33 0.035497645 10.360672 1.0635496
|
||||
1800 5092 98.193244 265447.33 0.08147355 9.3665483 3.0104928
|
||||
1900 5092 98.193244 265447.33 -0.14473824 8.5432989 2.9728625
|
||||
2000 5092 98.193244 265447.33 -0.041564059 11.63113 1.5867575
|
||||
2100 5092 98.193244 265447.33 0.0045129003 9.9456671 1.436601
|
||||
2200 5092 98.193244 265447.33 -0.0096402369 9.8767813 1.6785458
|
||||
2300 5092 98.193244 265447.33 -0.10765247 10.631171 3.1290797
|
||||
2400 5092 98.193244 265447.33 -0.12241137 9.8917039 3.56271
|
||||
2500 5092 98.193244 265447.33 0.017303567 10.134216 2.5224533
|
||||
2600 5092 98.193244 265447.33 -0.093777044 10.200634 1.3519144
|
||||
2700 5092 98.193244 265447.33 -0.15578186 9.6684009 2.5384049
|
||||
2800 5092 98.193244 265447.33 -0.094570471 11.481058 2.5282483
|
||||
2900 5092 98.193244 265447.33 0.089970872 10.289575 1.3841899
|
||||
3000 5092 98.193244 265447.33 0.041066985 10.330879 1.6643933
|
||||
3100 5092 98.193244 265447.33 -0.088145926 9.8790269 1.9878739
|
||||
3200 5092 98.193244 265447.33 -0.021810579 10.686768 3.0303691
|
||||
3300 5092 98.193244 265447.33 0.015098791 10.043207 1.6937351
|
||||
3400 5092 98.193244 265447.33 0.031969826 11.142544 0.63633496
|
||||
3500 5092 98.193244 265447.33 -0.10691176 9.6246461 0.81948178
|
||||
3600 5092 98.193244 265447.33 -0.082628312 10.739668 2.3316856
|
||||
3700 5092 98.193244 265447.33 0.062856304 9.2410456 2.8655012
|
||||
3800 5092 98.193244 265447.33 0.035815853 9.5050341 2.073665
|
||||
3900 5092 98.193244 265447.33 -0.11890515 8.9851356 2.3096977
|
||||
4000 5092 98.193244 265447.33 -0.088669613 11.336617 2.2657778
|
||||
4100 5092 98.193244 265447.33 0.22672389 9.4970608 1.8177659
|
||||
4200 5092 98.193244 265447.33 0.12883496 9.1661101 1.8263211
|
||||
4300 5092 98.193244 265447.33 0.058908552 10.145263 2.904343
|
||||
4400 5092 98.193244 265447.33 -0.14535243 11.420664 1.3192619
|
||||
4500 5092 98.193244 265447.33 0.16208072 10.039004 0.83706642
|
||||
4600 5092 98.193244 265447.33 0.29778162 9.8285181 1.1165466
|
||||
4700 5092 98.193244 265447.33 0.20330429 9.7335442 1.6344298
|
||||
4800 5092 98.193244 265447.33 0.035461857 10.651313 1.7290641
|
||||
4900 5092 98.193244 265447.33 0.079871784 8.9574124 1.5475086
|
||||
5000 5092 98.193244 265447.33 -0.34561831 9.7951232 2.004021
|
||||
Loop time of 593.648 on 16 procs for 5000 steps with 5092 atoms
|
||||
|
||||
98.8% CPU use with 16 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0028639 | 0.15264 | 0.46504 | 41.8 | 0.03
|
||||
Neigh | 1.5874 | 2.0111 | 2.8263 | 25.2 | 0.34
|
||||
Comm | 0.13471 | 0.27155 | 0.52658 | 25.6 | 0.05
|
||||
Output | 0.25503 | 0.25532 | 0.25559 | 0.0 | 0.04
|
||||
Modify | 571.75 | 581.55 | 590.84 | 26.3 | 97.96
|
||||
Other | | 9.407 | | | 1.58
|
||||
|
||||
Nlocal: 318.250 ave 5092 max 0 min
|
||||
Histogram: 15 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0.00000 ave 0 max 0 min
|
||||
Histogram: 16 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2221.19 ave 35539 max 0 min
|
||||
Histogram: 15 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 35539
|
||||
Ave neighs/atom = 6.9793794
|
||||
Neighbor list builds = 2500
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 95.366086
|
||||
LB update time: 209.233008
|
||||
LB PCalc time: 163.998163
|
||||
LB fluidForce time: 60.986279
|
||||
LB CorrectU time: 45.025690
|
||||
Total wall time: 0:20:49
|
||||
@ -6,11 +6,12 @@
|
||||
# under pressure-driven lattice-Boltzmann fluid flow #
|
||||
# #
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: MOLECULE, RIGID, USER-LB, USER-VTK #
|
||||
# packages: MOLECULE, RIGID, LATBOLTZ, USER-VTK #
|
||||
# #
|
||||
#To run this example on N cores, use command: #
|
||||
# mpirun -n N /LAMMPS/EXE/FILE -in polymer.in > output.out #
|
||||
# mpirun -n N /LAMMPS/EXE/FILE -in in.polymer > output.out #
|
||||
# #
|
||||
# If uncommented: #
|
||||
# Sample output for polymer from this run can be found in the file: #
|
||||
# 'translocationdump.lammpstrj' #
|
||||
# and viewed using, the VMD software. #
|
||||
@ -28,7 +29,7 @@ dimension 3
|
||||
boundary p p p
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data translocation.data
|
||||
read_data data.translocation
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
#Creating a atomistic wall on an FCC lattice and removing the block from the
|
||||
@ -104,7 +105,7 @@ group WallAtoms type 3
|
||||
# increases the diffusive dynamics by a corresponding factor of 10.
|
||||
# lattice spacing dx=1.0, and mass unit, dm=0.00009982071 (makes density 1)
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=15003). This enables the particles to undergo Brownian motion in
|
||||
# seed=5252). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
# In this case we use the scaleGamma argument to set the mass of the WallAtoms
|
||||
# to infinity.
|
||||
@ -112,7 +113,7 @@ group WallAtoms type 3
|
||||
# which should be similar to the average flow field in the case with noise.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 noise 300.0 5252
|
||||
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow5252
|
||||
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow 0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
@ -172,9 +173,9 @@ thermo 1000
|
||||
# trajectory and vtk format (commented out here). Write xyz dump file
|
||||
#--------------------------------------------------------------------------------
|
||||
variable numofsteps equal 400001
|
||||
dump 1 ForceAtoms custom 500 translocationdump.lammpstrj id xu yu zu vx vy vz
|
||||
#dump 1 ForceAtoms custom 500 translocationdump.lammpstrj id xu yu zu vx vy vz
|
||||
#dump 2 ForceAtoms vtk 1000 dump*.translocation.vtk id xu yu zu vx vy vz
|
||||
dump 4 WallAtoms xyz $(v_numofsteps-1) walldump.xyz
|
||||
#dump 4 WallAtoms xyz $(v_numofsteps-1) walldump.xyz
|
||||
|
||||
#restart 50000 4nmrestart.*
|
||||
|
||||
@ -0,0 +1,678 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
#===========================================================================#
|
||||
# Immersed Boundary Wall #
|
||||
# #
|
||||
# Run consists of a 32-bead coarse-grained polymer #
|
||||
# translocating through a solid-state atomistic wall #
|
||||
# under pressure-driven lattice-Boltzmann fluid flow #
|
||||
# #
|
||||
# To run this example, LAMMPS needs to be compiled with a the following #
|
||||
# packages: MOLECULE, RIGID, LATBOLTZ, USER-VTK #
|
||||
# #
|
||||
#To run this example on N cores, use command: #
|
||||
# mpirun -n N /LAMMPS/EXE/FILE -in in.polymer > output.out #
|
||||
# #
|
||||
# If uncommented: #
|
||||
# Sample output for polymer from this run can be found in the file: #
|
||||
# 'translocationdump.lammpstrj' #
|
||||
# and viewed using, the VMD software. #
|
||||
# OR #
|
||||
# 'dump.translocation.vtk' #
|
||||
# and viewed using the Paraview software. #
|
||||
# #
|
||||
# Sample output for the wall from this run can be found in the file: #
|
||||
# 'walldump.xyz' #
|
||||
# and can be viewed using the VMD or Paraview Software. #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data data.translocation
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (48 32 32)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
992 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.044 seconds
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
#Creating a atomistic wall on an FCC lattice and removing the block from the
|
||||
#middle to create the nanopore
|
||||
#---------------------------------------------------------------------------
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
region wall block 28 38 0 32 0 32
|
||||
create_atoms 3 region wall
|
||||
Created 43008 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (48 32 32)
|
||||
create_atoms CPU = 0.011 seconds
|
||||
|
||||
region hole block 28 38 14 18 14 18
|
||||
delete_atoms region hole compress no
|
||||
Deleted 851 atoms, new total = 43149
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
|
||||
# processor ghost fluid region (of width 2dx) are known to local processor.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
neigh_modify exclude type 2 3
|
||||
neigh_modify exclude type 3 3
|
||||
comm_modify cutoff 2.5
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each monomer with each other and the wall atoms
|
||||
# (use a truncated and shifted Lennard-Jones potential).
|
||||
#----------------------------------------------------------------------------
|
||||
bond_style fene
|
||||
bond_coeff 1 60.0 2.25 4.14195 1.5
|
||||
pair_style lj/cut 1.68369
|
||||
pair_coeff * * 0 1.5
|
||||
pair_coeff 1 1 4.14195 1.5 1.68369
|
||||
pair_coeff 1 3 4.14195 1.5 1.68369
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
|
||||
# nodes in a single monomer. The mass of wall atoms is chosen heavy as they
|
||||
# are fixed.
|
||||
# ----------------------------------------------------------------------------
|
||||
mass * 0.00000318
|
||||
|
||||
#-----------------------------------------------------------------------------
|
||||
timestep 0.00005
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each monomer which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the monomer
|
||||
# which do interact with the fluid. The nanopore particles are also included
|
||||
# in this group as they interact with the fluid.
|
||||
# Polymer is the entire set of monomers of the composite polymer chain.
|
||||
# WallAtoms are the particles of the nanopore.
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
32 atoms in group ForceAtoms
|
||||
group FluidAtoms type 2 3
|
||||
43117 atoms in group FluidAtoms
|
||||
group Polymer type 1 2
|
||||
992 atoms in group Polymer
|
||||
group WallAtoms type 3
|
||||
42157 atoms in group WallAtoms
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles. This is accomplished through the use of the lb/viscous fix).
|
||||
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
|
||||
# means the kinematic viscosity is idential to that of water but the
|
||||
# dynamic viscosity is a factor of 10 less than that of water which
|
||||
# increases the diffusive dynamics by a corresponding factor of 10.
|
||||
# lattice spacing dx=1.0, and mass unit, dm=0.00009982071 (makes density 1)
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=5252). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
# In this case we use the scaleGamma argument to set the mass of the WallAtoms
|
||||
# to infinity.
|
||||
# The commented out line can be substituted to look at the flow without noise
|
||||
# which should be similar to the average flow field in the case with noise.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 noise 300.0 5252
|
||||
Using a lattice-Boltzmann grid of 48 by 32 by 32 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow 0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining each monomer to move and rotate as a single rigid
|
||||
# spherical object.
|
||||
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
|
||||
# shell) should move and rotate together, this fix is applied to all Polymer
|
||||
# of atoms in the system.
|
||||
# The wall atoms are frozen in space and all the calculated forces on the atoms
|
||||
# are set to zero at each timestep.
|
||||
#----------------------------------------------------------------------------#
|
||||
fix 2 FluidAtoms lb/viscous
|
||||
fix 3 Polymer rigid/small molecule
|
||||
create bodies CPU = 0.001 seconds
|
||||
32 rigid bodies with 992 atoms
|
||||
0.70019686 = max distance from body owner to body atom
|
||||
fix freeze WallAtoms setforce 0 0 0
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Write position and velocity coordinates into a file every 2000 time steps.
|
||||
#----------------------------------------------------------------------------
|
||||
#variable x1 equal x[1]
|
||||
#variable y1 equal y[1]
|
||||
#variable z1 equal z[1]
|
||||
#variable vx1 equal vx[1]
|
||||
#variable vy1 equal vy[1]
|
||||
#variable vz1 equal vz[1]
|
||||
#variable x2 equal x[249]
|
||||
#variable y2 equal y[249]
|
||||
#variable z2 equal z[249]
|
||||
#variable vx2 equal vx[249]
|
||||
#variable vy2 equal vy[249]
|
||||
#variable vz2 equal vz[249]
|
||||
#variable x3 equal x[497]
|
||||
#variable y3 equal y[497]
|
||||
#variable z3 equal z[497]
|
||||
#variable vx3 equal vx[497]
|
||||
#variable vy3 equal vy[497]
|
||||
#variable vz3 equal vz[497]
|
||||
#variable x4 equal x[745]
|
||||
#variable y4 equal y[745]
|
||||
#variable z4 equal z[745]
|
||||
#variable vx4 equal vx[745]
|
||||
#variable vy4 equal vy[745]
|
||||
#variable vz4 equal vz[745]
|
||||
|
||||
#thermo_style custom v_x1 v_y1 v_z1 v_vx1 v_vy1 v_vz1 v_x2 v_y2 v_z2 v_vx2 v_vy2 v_vz2 v_x3 v_y3 v_z3 v_vx3 v_vy3 v_vz3 v_x4 v_y4 v_z4 v_x4 v_y4 v_z4
|
||||
#thermo 10
|
||||
|
||||
#---------------------------------------------------------------------------------
|
||||
# Write coordinates of the centre of mass and radius of gyration tensor components
|
||||
#---------------------------------------------------------------------------------
|
||||
compute centre ForceAtoms com
|
||||
compute rg ForceAtoms gyration
|
||||
thermo_style custom c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
|
||||
thermo 1000
|
||||
|
||||
#--------------------------------------------------------------------------------
|
||||
# Define number of steps variable. Write dump files for the polymer in both LAMMPS
|
||||
# trajectory and vtk format (commented out here). Write xyz dump file
|
||||
#--------------------------------------------------------------------------------
|
||||
variable numofsteps equal 400001
|
||||
#dump 1 ForceAtoms custom 500 translocationdump.lammpstrj id xu yu zu vx vy vz
|
||||
#dump 2 ForceAtoms vtk 1000 dump*.translocation.vtk id xu yu zu vx vy vz
|
||||
#dump 4 WallAtoms xyz $(v_numofsteps-1) walldump.xyz
|
||||
|
||||
#restart 50000 4nmrestart.*
|
||||
|
||||
run ${numofsteps} # For 250001 steps without noise, 16 minutes on AMD Ryzen Threadripper 1950X 16-Core, 41 mintues on Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz 4-core
|
||||
run 400001
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.18369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.091845, bins = 44 30 30
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:723)
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.44 | 20.02 | 30.41 Mbytes
|
||||
c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
|
||||
5.6791248 22.61273 5.110682 4.5290465 6.700106 3.8164024 3.4765595 12.000543 11.573384 10.635513
|
||||
5.5867637 21.257084 5.1321825 4.822662 5.634175 3.7281301 3.6276614 11.962266 11.452708 10.387815
|
||||
5.668832 21.596665 5.6165458 4.9224455 5.647044 4.0344015 4.0048875 11.821122 11.451665 10.569963
|
||||
5.6598062 20.600614 6.0567785 5.3760133 6.6053545 4.0554069 4.415185 11.9427 11.557594 10.571476
|
||||
5.8889045 23.387471 6.0242487 5.2674768 7.6894041 4.652066 4.2066414 11.8858 11.664507 10.642731
|
||||
6.1002855 26.57562 5.2572121 5.3806503 7.2669892 5.4963641 3.9022322 12.020013 11.658221 10.555459
|
||||
6.3802913 30.250297 4.3928513 6.0649685 7.4030928 6.8471704 3.7581107 11.942494 11.656142 10.62799
|
||||
6.4211512 30.052916 4.0869264 7.0913409 6.4493764 7.3015592 4.274762 11.983282 11.552276 10.499697
|
||||
6.4029294 29.889365 4.0196733 7.0884671 6.5903461 6.8110154 4.0382413 11.9905 11.501962 10.425593
|
||||
6.3161388 28.57849 3.8057293 7.5093902 5.7575295 6.6646378 4.1567522 12.113646 11.531039 10.529351
|
||||
6.4338248 29.706116 3.4974686 8.1905167 5.5124312 7.9019084 4.5042964 12.426431 11.340065 10.399931
|
||||
6.5364361 30.677501 3.6562753 8.3912202 5.1990078 7.3140488 4.8107991 12.472307 11.438123 10.425278
|
||||
6.6943364 31.785713 3.6152177 9.4132091 5.6058833 7.7153622 5.1164739 12.583773 11.540381 10.504743
|
||||
6.7208928 32.711587 3.7061318 8.7526817 6.8070192 6.7581599 4.5471865 12.517937 11.50458 10.470699
|
||||
6.6375209 30.970999 3.6881577 9.3975267 7.3010233 5.4926275 4.1912585 12.684547 11.592933 10.675434
|
||||
6.8324705 33.049694 4.0146629 9.6182957 8.7999601 7.2978407 4.3307267 12.660956 11.750078 10.71392
|
||||
6.779281 33.083238 3.9016444 8.9737675 8.7458049 7.7168786 4.3419836 12.501914 11.814334 10.76077
|
||||
6.6792036 32.828561 3.2387228 8.5444765 7.7842222 8.5969674 3.4661156 12.790705 11.968511 10.642253
|
||||
6.5389782 31.772538 3.0722036 7.9134935 6.9299213 8.9153301 3.3680216 12.861509 11.85712 10.51657
|
||||
6.4748361 31.540469 3.0212413 7.3617912 6.3057097 8.4191336 3.2625709 12.657649 11.704529 10.392716
|
||||
6.3985321 29.710818 2.6283214 8.6020734 5.8853082 9.3362301 3.397929 12.688643 11.780723 10.424565
|
||||
6.5059208 31.090823 2.6100712 8.6261116 6.5141681 10.225958 3.6286489 12.725294 12.0647 10.108992
|
||||
6.4892221 30.985335 2.4997331 8.6249351 6.4886837 10.018904 3.3600422 12.855965 12.036702 9.9287436
|
||||
6.4795231 30.758266 2.8637784 8.3621758 7.1748369 10.562754 3.5302178 12.896069 12.260403 10.11639
|
||||
6.4439652 28.968436 2.3431114 10.21314 6.6140604 10.553576 3.2945616 12.721326 12.375786 10.216421
|
||||
6.4585206 28.635315 2.1556643 10.921509 6.5660708 11.04493 3.0441915 12.688395 12.432736 10.446406
|
||||
6.4828021 29.600008 2.0553059 10.371409 6.1193108 11.704064 2.6435946 12.670355 12.450579 10.754392
|
||||
6.562285 30.709961 1.9685065 10.385117 5.9437889 12.632018 2.3117868 12.914159 12.707126 10.756693
|
||||
6.6264405 31.273462 2.410996 10.225256 7.2739788 12.4541 2.9699821 12.81881 12.66146 10.672797
|
||||
6.7415185 32.457723 2.3242798 10.666069 7.2496003 13.12296 2.9964595 12.784276 12.647643 10.60663
|
||||
6.9008565 33.656929 2.7042837 11.260607 8.5449163 14.476583 3.8202075 12.710092 12.579311 10.58884
|
||||
7.061302 35.296351 3.5107103 11.054924 10.064083 15.035769 4.4216887 13.175009 12.627831 10.482424
|
||||
7.1032842 36.482445 3.6799052 10.294296 10.673901 14.749052 4.3151465 13.200713 12.621232 10.584217
|
||||
7.1414828 36.185373 4.297132 10.518271 11.586979 15.307501 5.1527843 13.234596 12.688071 10.498004
|
||||
6.9448583 33.990665 2.8733935 11.366998 8.6757703 15.425795 3.8675398 13.552629 12.904762 10.360584
|
||||
7.0012016 32.933829 3.6133714 12.469623 9.9078147 16.084749 4.8325968 13.711685 12.775596 10.565942
|
||||
7.0165074 33.824117 3.4135972 11.993662 9.4449537 15.727888 4.3550075 13.648024 12.818681 10.403745
|
||||
7.0456647 33.8123 3.8273095 12.001781 9.9901691 15.354572 4.7262984 13.704142 12.865313 10.379126
|
||||
7.0704851 35.593578 4.4753601 9.922821 10.815193 14.191266 4.3671704 13.568897 12.968225 10.27463
|
||||
7.2622103 36.997176 5.0189577 10.723566 11.931013 15.173822 5.1502453 13.704027 12.992135 10.023658
|
||||
7.3237142 36.361814 5.4045676 11.870409 12.36988 16.523084 5.9090879 13.732808 12.986696 9.6059086
|
||||
7.4085072 37.338445 4.6635913 12.883943 11.559431 18.221441 5.9749906 13.822776 13.056276 9.4491435
|
||||
7.5435451 38.642986 4.8108253 13.451262 11.762286 19.25048 6.2716652 13.76389 13.028638 9.3396345
|
||||
7.5041212 37.242572 4.2407367 14.828527 10.397401 20.55556 6.0212974 13.656341 13.093764 9.1329939
|
||||
7.4871925 37.814264 4.2622814 13.981507 10.161983 20.447606 5.7021938 13.637928 13.132284 8.9440227
|
||||
7.3541675 36.518431 4.6241377 12.941211 10.094391 18.64877 5.616799 13.607907 13.208134 8.8058927
|
||||
7.3886114 36.915543 4.9408074 12.735228 10.630813 18.896827 5.7094032 13.752166 13.333961 8.6671299
|
||||
7.2634179 32.71655 5.167184 14.873507 10.523039 19.079411 6.3878762 13.935234 13.303392 8.6048102
|
||||
7.3106746 33.990367 5.5659367 13.88966 11.693262 18.632011 6.5331934 13.883039 13.479355 8.6248803
|
||||
7.2557189 35.200297 4.4884764 12.956683 10.303503 17.915053 5.6282044 13.728328 13.609539 8.6112695
|
||||
7.3353193 37.845973 3.3837009 12.577235 8.6243964 18.581563 3.7985161 13.536049 13.443702 8.4039237
|
||||
7.6187173 41.73183 4.4262573 11.886765 10.443613 18.59631 3.7033134 13.201011 13.445133 8.1443418
|
||||
7.6874247 44.184475 4.0611444 10.850879 10.846122 17.980387 3.5984272 12.76067 13.517519 8.0974318
|
||||
7.5889076 42.515998 3.8244222 11.251099 9.9966093 17.458176 3.1726154 12.592342 13.578402 8.0274103
|
||||
7.7744651 44.148982 4.2129835 12.080342 11.586008 18.953803 4.6881973 12.781052 13.744522 8.1609444
|
||||
7.8762095 46.571962 4.2336595 11.229055 11.956938 18.998552 4.4303527 12.78768 13.885168 8.5476521
|
||||
7.5991537 41.910661 4.1811631 11.655312 11.231672 18.166889 4.3773455 12.90303 13.93913 8.622434
|
||||
7.5180184 41.555253 4.1818325 10.783516 11.789934 16.439025 4.5300192 12.834806 13.889747 8.7422201
|
||||
7.3943137 38.451129 3.5281391 12.696607 10.233182 17.033555 4.7102974 13.063809 13.856187 8.8178674
|
||||
7.4384703 37.718734 2.9933066 14.6188 8.9987509 18.607817 4.5600437 13.330138 13.653329 8.830152
|
||||
7.3814288 36.318864 2.9682884 15.198339 8.1447589 18.551238 4.1590099 13.403412 13.460209 8.9327916
|
||||
7.5394784 38.362656 3.0647462 15.416333 8.1640602 19.326608 4.2298797 13.537652 13.374601 8.977215
|
||||
7.7262621 40.829884 2.5614313 16.30381 7.5956765 20.560929 3.8808909 13.585574 13.235011 8.8738183
|
||||
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|
||||
5.6255541 12.164987 11.206002 8.2758691 -8.025322 -5.3792409 1.1986695 51.611135 8.5875627 13.566069
|
||||
5.5133857 11.606727 10.723956 8.0667388 -7.7006341 -5.2202906 1.9875435 51.388763 8.7848101 13.507427
|
||||
5.4265893 10.157731 10.818492 8.4716483 -7.2474454 -5.5265731 2.3854803 51.641035 9.0938068 13.599211
|
||||
5.3182965 8.9651318 10.943437 8.3757082 -6.2007545 -5.056881 1.1368514 51.610352 8.8929902 13.581376
|
||||
5.3652496 8.7911989 10.665272 9.3294322 -6.021771 -5.8424869 1.5414913 51.493178 8.8854513 13.589163
|
||||
5.3805842 9.6022799 10.412131 8.9362757 -6.4477204 -6.2779449 1.5157437 51.327589 9.1502737 13.533597
|
||||
5.2813743 9.1701671 10.023078 8.6996694 -6.0616833 -6.4098214 1.8031144 51.511357 9.2882162 13.650399
|
||||
5.3364358 9.231983 11.525441 7.7201223 -6.9372423 -6.0456921 2.1560811 51.415333 9.3789596 13.489693
|
||||
5.2216315 9.0360698 10.74146 7.4879054 -6.7659877 -5.938263 2.4099896 51.579168 9.3391723 13.574691
|
||||
5.2693755 8.8173745 11.502891 7.4460527 -6.5889143 -5.7866818 2.2888995 52.060607 9.3152636 13.482747
|
||||
5.4527243 8.5751661 11.995218 9.1618189 -6.9426365 -5.9167953 2.7288445 52.217794 9.3216261 13.5881
|
||||
5.5407737 9.0460762 12.020147 9.6339496 -7.3040599 -6.139166 2.6263873 52.032689 8.9970713 13.417335
|
||||
5.4925322 8.3617555 12.50312 9.3030345 -6.6442559 -6.1599685 2.4847009 51.93956 9.095662 13.106108
|
||||
5.4926197 8.7073708 11.787574 9.6739262 -6.5363865 -6.1921413 2.0929306 51.793926 9.2630432 13.163065
|
||||
5.4150044 9.0159527 11.803322 8.5029979 -6.7351289 -5.7640713 1.6928394 51.827107 9.4306778 13.249457
|
||||
5.548641 8.5050176 13.749623 8.5327765 -7.6118043 -5.0191659 2.2519682 52.060941 9.5239621 13.306295
|
||||
5.5564204 9.1514243 14.595798 7.1265851 -8.5613345 -4.1757282 2.0741589 52.01808 9.6698309 13.145877
|
||||
5.5699457 9.7851734 14.35299 6.8861324 -9.1237528 -4.9959942 2.8960143 52.052156 9.5620341 13.337446
|
||||
5.5749693 10.703974 13.128121 7.2481879 -8.9798879 -5.7134968 2.3496775 51.721725 9.7689869 13.356096
|
||||
5.638834 11.099617 12.820822 7.8760101 -9.506886 -6.1070228 2.6709612 51.794599 9.6156719 13.48407
|
||||
5.6598728 10.885534 12.78006 8.368566 -9.4902335 -5.5729542 2.3342113 52.174765 9.8576644 13.478152
|
||||
5.5904285 10.369004 11.992327 8.8915605 -8.76821 -6.5618387 3.193141 52.02322 9.81365 13.359337
|
||||
5.3741317 9.2405221 11.282499 8.3582708 -8.3727501 -5.8355484 3.3370204 51.866988 9.6388128 13.149419
|
||||
5.2958639 7.1886261 12.977706 7.8798428 -8.1460083 -4.3881982 3.1812473 51.731285 9.4481046 13.141767
|
||||
5.402274 7.7470987 12.805009 8.6324567 -8.2179556 -5.2078319 3.1582169 51.804468 9.3848268 13.29982
|
||||
5.6483697 9.1018115 13.787511 9.0147582 -9.5567762 -5.2509413 3.01344 51.996155 9.1895779 13.300818
|
||||
5.601747 9.3576298 13.664124 8.3578152 -9.1305397 -5.6217469 3.1180397 52.111675 9.0877198 13.152291
|
||||
5.5124655 8.9590865 13.684809 7.7433812 -8.7096272 -4.9754549 2.3270945 52.254841 8.8351679 13.21258
|
||||
5.3988525 8.3910773 12.905567 7.8509638 -7.5245856 -5.0395065 2.3481322 52.263451 8.6620437 13.36041
|
||||
5.3040294 7.1552401 13.671387 7.3061011 -6.4221018 -4.6709838 2.4084256 52.472518 8.5802722 13.163192
|
||||
5.3191867 8.2855513 13.241158 6.7670382 -6.7383913 -5.0033962 2.180615 52.183195 8.4360708 13.155001
|
||||
5.3566829 9.1699753 12.113433 7.410643 -6.9922004 -5.2635118 2.1340211 52.182193 8.6892458 12.963203
|
||||
5.2008701 8.5170789 12.263922 6.2680487 -6.167442 -4.7136418 1.8542571 52.273008 8.793237 12.860908
|
||||
4.9919839 7.5835928 11.100441 6.2358693 -5.5481586 -4.3678074 2.2821251 52.335558 8.6666578 12.845611
|
||||
5.1501062 7.7815697 13.038317 5.7037072 -6.8790721 -3.6697847 2.040492 52.205555 8.4930645 12.655618
|
||||
5.1693291 8.0359508 12.95638 5.7296317 -7.0564916 -3.8355504 1.9139954 51.959464 8.6423307 12.53081
|
||||
5.2077361 8.8897921 12.530741 5.6999822 -7.3764196 -3.4364468 0.90215052 51.838638 8.8383661 12.569833
|
||||
5.1502621 9.0122487 11.77156 5.741391 -7.5423335 -3.5938885 0.88296798 51.822123 8.8415423 12.937326
|
||||
5.1896461 9.2854716 11.585603 6.0613521 -7.9119183 -3.6359858 0.5268641 51.860261 8.8721682 12.909944
|
||||
5.2091113 9.6776461 11.157445 6.2997493 -8.1731907 -3.4404707 0.52470693 51.955093 9.1847066 12.772563
|
||||
5.1487426 9.9171868 11.039362 5.5530018 -8.1346651 -2.7100655 -0.081164579 51.895699 8.999741 12.652846
|
||||
5.1505237 9.8208447 11.636584 5.0704661 -8.0048156 -2.9229925 -0.38313937 51.846388 9.0258296 12.575848
|
||||
5.0498117 9.2192048 11.698429 4.582964 -8.0200334 -2.3752653 -0.36708212 51.782671 9.3279563 12.544301
|
||||
5.0573261 9.5294354 11.88401 4.1631027 -7.5144401 -2.4806001 -0.65999869 51.913647 9.3854399 12.401641
|
||||
5.0811302 9.3959886 11.808889 4.6130067 -7.0405242 -2.5037582 -1.2769295 52.005268 9.6317929 12.370306
|
||||
5.1166203 9.3288823 12.45974 4.3911809 -7.2243887 -2.5156447 -1.0041202 52.088074 9.6003874 12.346141
|
||||
5.2045026 10.450174 12.394069 4.2426047 -7.9173751 -2.3028313 -1.1127183 52.287028 9.4892589 12.53898
|
||||
4.9696787 9.062347 11.35845 4.2769086 -5.9385609 -2.12694 -1.6437193 52.757473 9.3837415 12.690198
|
||||
4.9877386 9.1392669 11.48237 4.2558994 -5.5388281 -2.4000297 -1.4755205 52.764043 9.6175641 12.662539
|
||||
4.8284868 7.8848934 11.225247 4.2041439 -5.3018102 -1.8375233 -1.5376081 53.041399 9.451146 12.688581
|
||||
4.8237993 7.3389077 11.55467 4.3754617 -5.6106066 -1.4157198 -1.5132442 53.279168 9.5338443 12.633672
|
||||
4.8314395 7.3896489 11.215416 4.7377428 -6.0145077 -1.7225945 -0.69655935 53.818846 9.5420479 12.368433
|
||||
4.8765154 8.0784101 10.572769 5.1292237 -6.3322936 -1.8164643 -0.64830774 53.966255 9.5234973 12.344916
|
||||
4.9186704 8.6712371 10.378472 5.1436092 -6.5208107 -2.2558782 -0.71144157 53.70529 9.6007242 12.232148
|
||||
4.9251997 7.5655071 11.081228 5.610857 -6.3320091 -2.1481047 -1.5093486 53.793445 9.7713313 12.221771
|
||||
4.8304168 7.0698238 10.038672 6.2244307 -5.0756276 -2.9001352 -1.4313228 53.859149 9.7696343 12.172882
|
||||
4.7501946 7.6420634 8.8240346 6.0982512 -4.983994 -2.7043286 -1.3804654 53.836157 10.006061 12.283256
|
||||
4.7494587 8.0630304 8.6152981 5.879029 -5.1608283 -2.6103501 -1.0780193 53.72011 10.254128 12.239037
|
||||
4.7488472 8.0743919 8.6038151 5.8733427 -5.1682417 -2.6109895 -1.0859021 53.721404 10.254774 12.239811
|
||||
Loop time of 13125.6 on 4 procs for 400001 steps with 43149 atoms
|
||||
|
||||
Performance: 131.651 ns/day, 0.182 hours/ns, 30.475 timesteps/s
|
||||
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.1325 | 53.155 | 102.87 | 679.4 | 0.40
|
||||
Bond | 1.1958 | 1.5762 | 2.4077 | 38.6 | 0.01
|
||||
Neigh | 546.84 | 548 | 549.18 | 4.6 | 4.18
|
||||
Comm | 186.71 | 228.91 | 309.92 | 321.6 | 1.74
|
||||
Output | 0.13475 | 0.18939 | 0.30625 | 16.1 | 0.00
|
||||
Modify | 12088 | 12129 | 12174 | 27.8 | 92.41
|
||||
Other | | 164.7 | | | 1.25
|
||||
|
||||
Nlocal: 10787.2 ave 21162 max 24 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 6082.25 ave 11981 max 60 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 3 ave 12 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 12
|
||||
Ave neighs/atom = 0.0002781061
|
||||
Ave special neighs/atom = 0.0014368815
|
||||
Neighbor list builds = 7486
|
||||
Dangerous builds = 0
|
||||
Total wall time: 3:38:45
|
||||
@ -1,488 +0,0 @@
|
||||
LAMMPS (29 Sep 2021 - Update 1)
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (48.000000 32.000000 32.000000)
|
||||
4 by 4 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
992 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
31 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.007 seconds
|
||||
read_data CPU = 0.053 seconds
|
||||
Lattice spacing in x,y,z = 1.0000000 1.0000000 1.0000000
|
||||
Created 43008 atoms
|
||||
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (48.000000 32.000000 32.000000)
|
||||
create_atoms CPU = 0.004 seconds
|
||||
Deleted 851 atoms, new total = 43149
|
||||
32 atoms in group ForceAtoms
|
||||
43117 atoms in group FluidAtoms
|
||||
992 atoms in group Polymer
|
||||
42157 atoms in group WallAtoms
|
||||
Using a lattice-Boltzmann grid of 48 by 32 by 32 total grid points. (../fix_lb_fluid.cpp:477)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1023)
|
||||
First Run initialized
|
||||
create bodies CPU = 0.002 seconds
|
||||
32 rigid bodies with 992 atoms
|
||||
0.70019686 = max distance from body owner to body atom
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.18369
|
||||
ghost atom cutoff = 2.5
|
||||
binsize = 1.091845, bins = 44 30 30
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : nano
|
||||
Current step : 0
|
||||
Time step : 5e-05
|
||||
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:730)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.696 | 13.21 | 19.34 Mbytes
|
||||
c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
|
||||
5.6791248 22.61273 5.110682 4.5290465 6.700106 3.8164024 3.4765595 12.000543 11.573384 10.635513
|
||||
5.5296724 22.405009 4.4498228 3.7224454 5.5008707 3.032453 3.0465034 11.827904 11.74858 10.838698
|
||||
5.5203014 23.097359 3.8320444 3.5443241 4.0898642 3.6212497 2.5439412 11.733889 11.623028 10.74456
|
||||
5.5743173 23.418282 3.5662245 4.0885075 2.5599966 3.831838 2.6389438 11.802165 11.600249 10.548378
|
||||
5.4710145 22.69495 3.2918761 3.9451736 2.4523656 3.8066778 2.2693201 11.9393 11.855376 10.432584
|
||||
5.7249197 25.10717 3.3525382 4.3149979 3.2367275 5.3139646 2.5816744 12.062877 11.866058 10.517373
|
||||
5.6029865 23.932976 3.1579223 4.3025592 3.6696865 5.2925377 2.4574798 11.702614 11.719522 10.694965
|
||||
5.8584265 25.726803 3.591555 5.0028025 4.3743183 6.3872181 3.0561159 11.952428 11.484249 10.689449
|
||||
5.9031743 26.839358 3.4117665 4.5963428 4.7974775 5.8755164 2.8253733 12.10545 11.305079 10.99087
|
||||
5.871274 25.566645 3.9526358 4.9525777 4.5955534 6.0483781 3.4112111 12.411365 11.160128 11.127671
|
||||
5.971686 26.102288 3.6365256 5.9222201 4.2634774 6.5495138 3.6764429 12.391364 11.066566 11.116462
|
||||
5.8409377 26.194249 3.0926214 4.8296833 3.7115072 6.099581 2.8849802 12.313864 11.045442 11.115979
|
||||
5.7364744 25.925302 2.6150435 4.366793 2.82037 5.4514289 2.2321838 12.289131 11.219661 11.147242
|
||||
5.7564899 25.275185 3.3789897 4.483002 2.7279122 5.2027203 2.3538567 12.684248 11.16195 11.369676
|
||||
5.8534787 27.157326 3.5165098 3.5893769 2.3556605 5.3231652 1.7070055 12.565231 11.069269 11.337457
|
||||
5.9408552 27.966349 3.3982116 3.9291994 1.8322283 6.180127 1.8538634 12.278692 11.177211 11.039221
|
||||
5.9991641 28.500275 3.4480936 4.0416007 1.4369922 6.2844053 2.1097089 12.235666 11.132757 10.904201
|
||||
5.9827547 28.122241 3.6720826 3.99903 1.6442854 6.5053103 2.1950703 12.375314 10.984735 11.141669
|
||||
5.7242437 24.434905 3.648822 4.6832392 1.821415 6.4501646 2.4028702 12.670431 10.977806 11.410258
|
||||
5.9013116 26.357569 3.0063195 5.4615893 2.0091238 7.228626 2.3442628 12.493765 11.119713 11.390818
|
||||
5.9102199 26.680495 3.3358499 4.9143549 1.9055918 6.4412945 2.276014 12.436401 11.018703 11.296939
|
||||
5.7574386 25.75443 3.5724979 3.8211712 1.1599229 5.4240531 1.9894834 12.410879 10.842471 11.538406
|
||||
5.7962483 26.429288 3.5017822 3.6654244 1.351938 5.3252517 2.0282575 12.612201 10.893438 11.631667
|
||||
5.8025098 26.466059 3.5624898 3.6405708 1.133526 5.0789389 1.9460322 12.544642 10.689038 11.643796
|
||||
5.7641125 25.654408 3.5345151 4.0360697 -0.83109583 5.2108762 1.6905126 12.397222 10.493385 11.696253
|
||||
5.8072019 25.679442 3.7582386 4.2859131 -1.1772031 4.1938521 2.2160298 12.296673 10.42008 11.579109
|
||||
5.7001985 24.189016 3.4982895 4.8049581 -0.79453271 5.1362216 2.1827354 12.429957 10.390496 11.673153
|
||||
5.6941506 24.093688 3.7459033 4.5837599 0.3856992 4.4633959 2.3263501 12.627162 10.503343 11.82833
|
||||
5.7372955 23.890143 4.118775 4.9076412 0.38805722 5.2566643 2.4772406 12.606965 10.572847 11.676506
|
||||
5.7428616 23.766824 3.8880982 5.3255366 -0.33675724 5.3218988 2.2539972 12.572964 10.534064 11.764667
|
||||
5.6499731 23.349011 3.8192146 4.7539703 -0.53788179 5.0455279 2.0044363 12.757771 10.584261 11.688338
|
||||
5.561088 22.635914 3.2874113 5.0023747 -0.95881516 4.9526458 1.9768975 12.886108 10.648817 11.470577
|
||||
5.5065659 22.592866 2.7699655 4.9594365 -1.0429502 4.9746672 1.8842364 12.735278 10.699875 11.654034
|
||||
5.5460253 23.096944 3.142451 4.5190012 -1.1377029 4.83551 1.9918703 12.593307 10.943414 11.675934
|
||||
5.6481034 23.145496 3.9046837 4.8508926 -0.91586514 5.3258558 2.0990811 12.351415 11.054151 11.919751
|
||||
5.5866973 22.272242 4.165557 4.7733879 0.18094082 5.5362212 2.2702355 12.209321 11.022481 12.234607
|
||||
5.6750688 22.935992 4.2668031 5.0036106 0.72144434 6.2570228 2.2604028 12.463617 11.080389 12.412865
|
||||
5.534307 22.260525 3.8054072 4.5626216 1.2420249 5.5967501 2.1125147 12.276273 10.798486 12.715741
|
||||
5.4350673 21.62159 3.3869298 4.5314364 0.28258213 5.392389 1.4911895 12.089432 10.737925 12.813536
|
||||
5.4001425 20.624748 3.7570393 4.7797519 -0.34050458 5.0506345 1.5269124 12.371365 10.573888 13.11618
|
||||
5.2688943 20.156887 3.1510052 4.4533547 -0.24239841 3.7818288 1.6612474 12.609371 10.459128 13.266976
|
||||
5.2982505 20.253797 2.7325109 5.0851506 0.97176123 4.4929627 1.8231597 12.327457 10.618473 13.130165
|
||||
5.4414697 21.984831 2.4606178 5.1641442 1.5740444 3.9075737 1.8170722 12.373628 10.567596 13.222471
|
||||
5.5707319 23.29693 2.6131294 5.1229945 2.0993935 4.6052431 1.8168365 12.240404 10.428094 13.196731
|
||||
5.5618536 23.293232 2.6635368 4.9774466 2.0107618 4.729051 2.1105567 11.893503 10.441165 13.520945
|
||||
5.3824015 21.722018 2.1221208 5.1261065 0.086745541 5.2274385 1.4581085 11.959975 10.242092 13.763089
|
||||
5.3110156 21.58712 2.1313837 4.4883826 -0.069494245 4.791078 1.0062878 11.779291 10.464336 13.80227
|
||||
5.3948376 22.671798 1.9091101 4.5233651 -0.11280005 5.0086281 0.89597813 11.614655 10.656549 13.820591
|
||||
5.5809034 24.867625 1.3844025 4.8944556 0.21411272 5.3612716 0.72590718 11.282652 10.763637 14.08913
|
||||
5.4622685 23.739255 1.24356 4.8535622 0.13581426 5.7501671 0.53683532 11.3626 10.542723 14.066682
|
||||
5.6094798 24.636207 1.6172433 5.2128136 -0.097584809 6.1198559 0.69895129 11.287109 10.558667 14.044154
|
||||
5.4165614 22.021973 1.4818718 5.8352917 0.89764161 6.0173972 1.1757975 11.480403 10.533196 14.164959
|
||||
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|
||||
7.1941395 44.987299 1.8067519 4.9615922 -6.3356156 9.7180954 -1.1612817 20.28777 17.125718 16.108976
|
||||
7.2887783 46.379714 1.5557102 5.1908645 -6.4322837 10.690947 -1.4689741 20.722572 16.994585 15.851479
|
||||
7.3717223 48.09482 1.3874085 4.8600604 -6.3212069 10.637209 -1.4412978 21.145149 17.10172 15.626257
|
||||
7.3103292 47.259496 1.3153081 4.8661097 -6.1167747 10.684898 -1.4517047 21.428737 17.11633 15.522888
|
||||
7.3474083 48.062136 1.2368688 4.6854041 -5.6025782 11.183963 -1.4659443 21.751501 17.021464 15.227136
|
||||
7.3974278 49.792552 0.91072848 4.018657 -4.0765455 11.022114 -1.0871425 22.192155 16.813026 15.026038
|
||||
7.517569 52.091339 0.84745921 3.5750462 -4.2468388 10.727176 -1.0474924 22.730902 16.677036 14.980871
|
||||
7.6892478 54.263113 1.0592439 3.8021738 -5.1057643 11.818169 -1.4872384 23.316002 16.603974 14.850614
|
||||
7.7872283 56.561426 0.84791834 3.2315808 -4.2529665 10.696077 -1.1478533 23.634655 16.489411 14.936932
|
||||
7.7547771 56.201611 0.87067007 3.0642868 -4.2366377 10.131149 -0.95264498 24.163744 16.54509 14.977185
|
||||
8.0531769 61.107193 0.8690226 2.8774426 -4.644315 10.929799 -0.94163247 24.68465 16.571341 14.924763
|
||||
8.3310719 65.787139 0.74155575 2.8780643 -4.5926971 11.449945 -0.98674983 25.293252 16.500118 14.981323
|
||||
8.642708 71.198421 0.5590228 2.9389584 -4.1285672 12.599427 -0.92098043 25.76361 16.40755 14.923297
|
||||
8.8281194 74.787989 0.57383779 2.5738649 -4.6176409 12.215755 -0.92509188 26.434103 16.447768 14.965872
|
||||
9.0576712 78.737429 0.69514572 2.6088322 -5.6897098 12.978088 -1.1362365 27.012606 16.536097 14.88788
|
||||
9.2009546 81.167026 0.82443581 2.6661034 -6.6858174 13.205957 -1.3008143 27.626219 16.536581 14.96208
|
||||
9.2666904 82.050263 0.7734027 3.047885 -6.1976828 14.376645 -1.2400628 28.324969 16.488721 14.813316
|
||||
9.148695 80.122762 0.87475577 2.701102 -6.3325063 13.21717 -1.2745178 29.145946 16.473304 14.98538
|
||||
9.001243 77.397716 0.94205086 2.6826087 -6.5634383 12.728307 -1.3523873 29.819452 16.552882 15.018783
|
||||
9.0777055 78.466989 1.0113835 2.9263656 -6.8428264 13.079194 -1.4744992 30.300781 16.494792 15.048552
|
||||
9.1009918 79.260722 0.9807463 2.5865839 -6.9312724 12.560048 -1.3522864 30.999146 16.471303 15.124403
|
||||
9.0922708 79.831399 0.87867232 1.9593164 -5.683661 10.699977 -1.0353506 31.615948 16.294124 15.18771
|
||||
8.9936285 78.360142 0.78531808 1.7398937 -5.6675013 9.909593 -0.91667657 32.113631 16.251319 15.191646
|
||||
8.9309778 76.82727 0.73333331 2.2017606 -5.1030576 11.366822 -0.97500449 32.507368 16.223113 15.275399
|
||||
8.8207322 75.200264 0.62545687 1.9795954 -3.5875432 10.549107 -0.67108507 33.167808 16.17782 15.14988
|
||||
8.6517106 71.668227 0.74290008 2.4409698 -3.9392699 11.85099 -0.82153294 33.605742 16.23708 15.409707
|
||||
8.6365567 71.615778 0.6557002 2.318633 -2.5495576 11.358758 -0.63414526 34.331039 16.120944 15.587085
|
||||
8.4130814 67.865585 0.754676 2.1596775 -1.4350363 10.614042 -0.3239519 35.000501 16.175439 15.699587
|
||||
8.25002 64.653951 0.759895 2.6489843 -0.047026072 11.681153 -0.13402085 35.45585 16.237441 15.745117
|
||||
8.075486 62.03899 0.84399975 2.3304839 -1.559837 10.460056 -0.25112144 36.185943 16.115537 16.064387
|
||||
7.8366364 58.016635 0.96063734 2.4355976 -2.4951475 10.236931 -0.45638427 36.580625 15.876486 16.081116
|
||||
7.6720504 54.91855 1.2311355 2.7106709 -3.5013889 9.7007273 -0.66989632 37.007795 15.653434 16.295477
|
||||
7.5459026 51.853751 1.7389758 3.3479194 -5.6826188 10.993022 -1.2532598 37.378257 15.3961 16.447817
|
||||
7.2539465 47.14327 2.2098583 3.2666111 -5.2847693 10.216356 -1.1334835 37.700742 15.603925 16.685365
|
||||
6.9312041 42.558067 2.0941643 3.389359 -5.1200095 9.2432158 -1.1926306 37.97708 15.532295 16.728937
|
||||
6.6532233 38.946916 1.7705815 3.5478824 -4.0065169 7.8359509 -0.83714023 38.405624 15.528978 16.743439
|
||||
6.4133222 35.120916 1.8588526 4.1509331 -3.0514447 8.3796131 -0.92728331 38.703448 15.549252 17.02516
|
||||
6.194238 32.712424 1.9939435 3.6622163 -2.9701683 7.2047379 -0.83562437 39.394386 15.666429 17.049729
|
||||
5.8186585 27.776333 2.3363751 3.744079 -2.9891432 5.6379939 -0.70461591 39.752658 15.579909 16.96213
|
||||
5.5897628 24.780413 2.8056262 3.6594096 -3.5134633 4.8264986 -0.83946107 40.102769 15.377182 16.947572
|
||||
5.3769903 22.280115 2.7709055 3.8610039 -3.2364022 5.1813564 -0.89638947 40.62343 15.506131 17.106031
|
||||
5.1063868 19.312622 2.7094113 4.0531534 -2.8471083 5.2213352 -0.75324965 40.782169 15.678787 17.244642
|
||||
4.8077716 16.355397 2.5693106 4.1899599 -2.9764819 4.4411865 -0.37353275 41.153908 15.362181 17.131944
|
||||
4.6501775 13.736158 2.7819846 5.1060086 -2.6188497 4.2731016 -0.30895652 41.43999 15.550215 17.143943
|
||||
4.4679179 11.9096 3.1313145 4.9213756 -2.2525965 3.2760982 0.024244645 41.952085 15.610097 16.767273
|
||||
4.3970823 10.284487 3.4378841 5.6119617 -2.8529271 3.0105925 -0.28501613 42.27667 15.387805 16.667092
|
||||
4.1183382 7.7103211 3.1939304 6.0564583 -2.8656845 1.4859707 -0.61456694 42.340765 15.229562 16.314725
|
||||
4.0619303 6.9788743 3.1868475 6.3335563 -2.7990968 0.75885865 -0.44694743 42.645174 15.308083 15.966746
|
||||
3.966833 5.7341201 3.6149267 6.386717 -2.6076681 0.23182741 -0.55240201 42.803996 15.001363 15.941201
|
||||
3.856119 4.9814639 4.2483123 5.6398778 -2.2386782 -0.13547369 -0.89035526 43.126699 15.153933 15.89549
|
||||
3.7114748 4.0042689 4.3938101 5.3769663 -1.8867009 -0.58098164 -0.73115634 43.078128 15.143311 16.029522
|
||||
3.6867902 4.1618237 4.0102813 5.420317 -1.3839677 -0.94227417 -0.42855978 43.320812 15.246681 15.979576
|
||||
3.8247407 3.7506299 3.8415311 7.0364804 -1.1968819 -1.2946647 0.0095104673 43.246474 15.254632 15.896513
|
||||
3.7969091 3.6706948 3.7264602 7.0193638 -1.410513 -1.6211384 0.065695724 43.437836 15.168521 15.595894
|
||||
3.9389477 3.6358719 4.0877764 7.7916611 -1.3246694 -2.3413686 -0.094860157 43.279214 15.353806 15.465847
|
||||
4.1666861 3.7657753 3.9029422 9.6925552 -1.7091472 -2.6645858 0.34650579 43.360362 15.336299 15.42574
|
||||
4.2623587 4.4445738 3.4732435 10.249884 -1.3299476 -3.19818 0.30614208 43.755796 15.269714 15.56183
|
||||
4.4120457 3.8158033 3.6700357 11.980309 -1.5546486 -2.757901 0.51296075 43.639154 15.641714 15.748073
|
||||
4.4239787 3.2243265 4.0831065 12.264154 -1.5893887 -2.0627321 0.25747441 43.691108 15.342315 15.898168
|
||||
4.3056135 2.6280527 4.4356932 11.474562 -1.2707147 -1.8263383 0.028806485 43.63839 15.318566 15.950982
|
||||
4.349789 2.8919037 4.3719925 11.656769 -1.5097124 -1.9948391 0.06144347 43.634788 15.022389 15.690407
|
||||
4.3584229 2.5260376 4.7064974 11.763315 -1.4326427 -2.1258969 0.58036467 43.669703 15.051132 15.460037
|
||||
4.4931654 3.070312 4.8135505 12.304673 -1.5549189 -2.1245695 -0.56145055 43.885773 14.796557 15.347812
|
||||
4.506235 3.6553777 4.612885 12.037891 -1.7868374 -2.1271702 -0.55704196 44.308855 14.646028 15.434641
|
||||
4.76806 3.5190536 5.3464268 13.868916 -2.4421853 -1.5912198 -0.2360655 44.315508 14.457266 15.563807
|
||||
4.8223857 3.6610784 5.4198637 14.174462 -2.8064522 -1.3051469 -0.42653793 44.222252 14.398241 15.500107
|
||||
4.8602836 3.5383663 6.011611 14.07238 -3.1390617 -1.2231969 -0.33733589 44.041646 13.941675 15.540578
|
||||
4.8402613 3.561673 5.4778139 14.388642 -3.153822 -0.31270493 0.085236932 44.131733 13.924553 15.515988
|
||||
4.8827383 3.6880053 4.8661009 15.287027 -2.9776139 -0.75910995 0.38846204 44.443177 13.900337 15.349413
|
||||
5.0135514 3.6606405 5.7817724 15.693285 -3.0567538 -0.36222976 0.52025814 44.435911 13.698528 15.337839
|
||||
5.0124579 3.6521656 5.7745828 15.697985 -3.0461172 -0.36613542 0.52093553 44.434268 13.698785 15.336717
|
||||
Loop time of 734.556 on 64 procs for 400001 steps with 43149 atoms
|
||||
|
||||
Performance: 2352.449 ns/day, 0.010 hours/ns, 544.548 timesteps/s
|
||||
99.6% CPU use with 64 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.023708 | 0.79185 | 2.8291 | 113.7 | 0.11
|
||||
Bond | 0.022931 | 0.049119 | 0.10765 | 10.6 | 0.01
|
||||
Neigh | 18.159 | 20.016 | 22.121 | 39.2 | 2.72
|
||||
Comm | 0.48376 | 85.357 | 168.32 | 840.8 | 11.62
|
||||
Output | 0.20377 | 0.23043 | 0.2857 | 2.8 | 0.03
|
||||
Modify | 536.61 | 611.99 | 690.61 | 296.2 | 83.31
|
||||
Other | | 16.12 | | | 2.19
|
||||
|
||||
Nlocal: 674.203 ave 2048 max 0 min
|
||||
Histogram: 32 0 1 13 1 1 0 0 0 16
|
||||
Nghost: 2113.72 ave 5607 max 0 min
|
||||
Histogram: 32 0 0 0 2 14 0 0 4 12
|
||||
Neighs: 0.218750 ave 10 max 0 min
|
||||
Histogram: 61 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14
|
||||
Ave neighs/atom = 0.00032445711
|
||||
Ave special neighs/atom = 0.0014368815
|
||||
Neighbor list builds = 7140
|
||||
Dangerous builds = 0
|
||||
|
||||
LB equilibriumDist time: 137.365442
|
||||
LB update time: 54.652305
|
||||
LB PCalc time: 105.068066
|
||||
LB fluidForce time: 237.915672
|
||||
LB CorrectU time: 50.912956
|
||||
Total wall time: 0:12:14
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user