Merge pull request #4069 from vladgl/fix_wall_flow
New fix implementing flow boundary conditions
This commit is contained in:
Axel Kohlmeyer
@ -877,6 +877,9 @@ Bibliography
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**(PLUMED)**
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G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
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**(Pavlov)**
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D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
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**(Paquay)**
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Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
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@ -263,6 +263,7 @@ OPT.
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* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
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* :doc:`wall/colloid <fix_wall>`
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* :doc:`wall/ees <fix_wall_ees>`
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* :doc:`wall/flow (k) <fix_wall_flow>`
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* :doc:`wall/gran (k) <fix_wall_gran>`
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* :doc:`wall/gran/region <fix_wall_gran_region>`
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* :doc:`wall/harmonic <fix_wall>`
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@ -428,6 +428,7 @@ accelerated styles exist.
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* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>` - time integration for body particles of style :doc:`rounded/polyhedron <Howto_body>`
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* :doc:`wall/colloid <fix_wall>` - Lennard-Jones wall interacting with finite-size particles
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* :doc:`wall/ees <fix_wall_ees>` - wall for ellipsoidal particles
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* :doc:`wall/flow <fix_wall_flow>` - flow boundary conditions
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* :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
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* :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
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* :doc:`wall/harmonic <fix_wall>` - harmonic spring wall
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175
doc/src/fix_wall_flow.rst
Normal file
175
doc/src/fix_wall_flow.rst
Normal file
@ -0,0 +1,175 @@
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.. index:: fix wall/flow
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.. index:: fix wall/flow/kk
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fix wall/flow command
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=====================
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Accelerator Variants: *wall/flow/kk*
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID wall/flow axis vflow T seed N coords ... keyword value
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* wall/flow = style name of this fix command
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* axis = flow axis (*x*, *y*, or *z*)
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* vflow = generated flow velocity in *axis* direction (velocity units)
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* T = flow temperature (temperature units)
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* seed = random seed for stochasticity (positive integer)
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* N = number of walls
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* coords = list of N wall positions along the *axis* direction in ascending order (distance units)
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* zero or more keyword/value pairs may be appended
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* keyword = *units*
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.. parsed-literal::
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*units* value = *lattice* or *box*
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*lattice* = wall positions are defined in lattice units
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*box* = the wall positions are defined in simulation box units
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all wall/flow x 0.4 1.5 593894 4 2.0 4.0 6.0 8.0
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Description
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"""""""""""
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.. versionadded:: TBD
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This fix implements flow boundary conditions (FBC) introduced in
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:ref:`(Pavlov1) <fbc-Pavlov1>` and :ref:`(Pavlov2) <fbc-Pavlov2>`.
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The goal is to generate a stationary flow with a shifted Maxwell
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velocity distribution:
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.. math::
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f_a(v_a) \propto \exp{\left(-\frac{m (v_a-v_{\text{flow}})^2}{2 kB T}\right)}
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where :math:`v_a` is the component of velocity along the specified
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*axis* argument (a = x,y,z), :math:`v_{\text{flow}}` is the flow
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velocity specified as the *vflow* argument, *T* is the specified flow
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temperature, *m* is the particle mass, and *kB* is the Boltzmann
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constant.
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This is achieved by defining a series of *N* transparent walls along
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the flow *axis* direction. Each wall is at the specified position
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listed in the *coords* argument. Note that an additional transparent
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wall is defined by the code at the boundary of the (periodic)
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simulation domain in the *axis* direction. So there are effectively
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N+1 walls.
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Each time a particle in the specified group passes through one of the
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transparent walls, its velocity is re-assigned. Particles not in the
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group do not interact with the wall. This can be used, for example, to
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add obstacles composed of atoms, or to simulate a solution of complex
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molecules in a one-atom liquid (note that the fix has been tested for
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one-atom systems only).
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Conceptually, the velocity re-assignment represents creation of a new
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particle within the system with simultaneous removal of the particle
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which passed through the wall. The velocity components in directions
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parallel to the wall are re-assigned according to the standard Maxwell
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velocity distribution for the specified temperature *T*. The velocity
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component perpendicular to the wall is re-assigned according to the
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shifted Maxwell distribution defined above:
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.. math::
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f_{\text{a generated}}(v_a) \propto v_a f_a(v_a)
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It can be shown that for an ideal-gas scenario this procedure makes
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the velocity distribution of particles between walls exactly as
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desired.
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Since in most cases simulated systems are not an ideal gas, multiple
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walls can be defined, since a single wall may not be sufficient for
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maintaining a stationary flow without "congestion" which can manifest
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itself as regions in the flow with increased particle density located
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upstream from static obstacles.
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For the same reason, the actual temperature and velocity of the
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generated flow may differ from what is requested. The degree of
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discrepancy is determined by how different from an ideal gas the
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simulated system is. Therefore, a calibration procedure may be
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required for such a system as described in :ref:`(Pavlov)
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<fbc-Pavlov2>`.
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Note that the interactions between particles on different sides of a
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transparent wall are not disabled or neglected. Likewise particle
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positions are not altered by the velocity reassignment. This removes
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the need to modify the force field to work correctly in cases when a
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particle is close to a wall.
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For example, if particle positions were uniformly redistributed across
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the surface of a wall, two particles could end up too close to each
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other, potentially causing the simulation to explode. However due to
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this compromise, some collective phenomena such as regions with
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increased/decreased density or collective movements are not fully
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removed when particles cross a wall. This unwanted consequence can
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also be potentially mitigated by using more multiple walls.
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.. note::
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When the specified flow has a high velocity, a lost atoms error can
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occur (see :doc:`error messages <Errors_messages>`). If this
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happens, you should ensure the checks for neighbor list rebuilds,
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set via the :doc:`neigh_modify <neigh_modify>` command, are as
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conservative as possible (every timestep if needed). Those are the
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default settings.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files
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<restart>`.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to
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this fix.
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No global or per-atom quantities are stored by this fix for access by
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various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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Fix *wall_flow* is part of the EXTRA-FIX package. It is only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Flow boundary conditions should not be used with rigid bodies such as
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those defined by a "fix rigid" command.
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This fix can only be used with periodic boundary conditions along the
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flow axis. The size of the box in this direction must not change. Also,
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the fix is designed to work only in an orthogonal simulation box.
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Related commands
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""""""""""""""""
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:doc:`fix wall/reflect <fix_wall>` command
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Default
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"""""""
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The default for the units keyword is lattice.
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----------
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.. _fbc-Pavlov1:
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**(Pavlov1)** Pavlov, Kolotinskii, Stegailov, "GPU-Based Molecular Dynamics of Turbulent Liquid Flows with OpenMM", Proceedings of PPAM-2022, LNCS (Springer), vol. 13826, pp. 346-358 (2023)
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.. _fbc-Pavlov2:
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**(Pavlov2)** Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
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