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upgrade of lb/fluid fix

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This includes documentation files in the rst format in the doc/src directory, examples in the examples/PACKAGES/latboltz directory and source files in the src/LATBOLTZ directory.
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CDenniston
2021-12-01 14:31:57 -05:00
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doc/src/fix_lb_fluid.rst
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@ -12,54 +12,60 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* lb/fluid = style name of this fix command
* nevery = update the lattice-Boltzmann fluid every this many timesteps
* LBtype = 1 to use the standard finite difference LB integrator,
2 to use the LB integrator of :ref:`Ollila et al. <Ollila>`
* nevery = update the lattice-Boltzmann fluid every this many timesteps (should normally be 1)
* viscosity = the fluid viscosity (units of mass/(time\*length)).
* density = the fluid density.
* zero or more keyword/value pairs may be appended
* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read_restart* or *write_restart* or *zwall_velocity* or *bodyforce* or *printfluid*
* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *linearInit* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw*
.. parsed-literal::
*setArea* values = type node_area
type = atom type (1-N)
node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
*setGamma* values = gamma
gamma = user set value for the force coupling constant.
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*dx* values = dx_LB = the lattice spacing.
*dm* values = dm_LB = the lattice-Boltzmann mass unit.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*noise* values = Temperature seed
Temperature = fluid temperature.
seed = random number generator seed (positive integer)
*calcforce* values = N forcegroup-ID
N = output the force and torque every N timesteps
forcegroup-ID = ID of the particle group to calculate the force and torque of
*trilinear* values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*stencil* values = 2 (trilinear stencil, the default), 3 (3-point immersed boundary stencil), or 4 (4-point Keys' interpolation stencil)
*read_restart* values = restart file = name of the restart file to use to restart a fluid run.
*write_restart* values = N = write a restart file every N MD timesteps.
*zwall_velocity* values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
*pressurebcx* values = pgradav = imposes a pressure jump at the (periodic) x-boundary of pgradav*Lx*1000.
*bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
*printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps.
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*dumpxdmf* values = N file timeI
N = output the force and torque every N timesteps
file = output file name
timeI = 1 (use simulation time to index xdmf file), 0 (use output frame number to index xdmf file)
*linearInit* values = none use linear interpolation between boundary values for initialization (default is uniform density, 0 velocity)
*dof* values = dof = specify the number of degrees of freedom for temperature calculation
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*npits* values = npits h_p l_p l_pp l_e
npits = number of pit regions
h_p = z-height of pit regions (floor to bottom of slit)
l_p = x-length of pit regions
l_pp = x-length of slit regions between consecutive pits
l_e = x-length of slit regions at ends
*wp* values = w_p = y-width of slit regions (defaults to full width if not present or if sw active)
*sw* values = none (turns on y-sidewalls (in xz plane) if npits option active)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001 noise 300.0 2761
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 dm 10.0 dumpxdmf 500 fflow 0 pressurebcx 0.01 npits 2 20 40 5 0 wp 30
Description
"""""""""""
Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS
simulation domain. The MD particles described by *group-ID* apply a velocity
simulation domain. Note that this fix was updated in 2021 and is not backward compatible with the previous version. If you need the previous version, please download an older version of LAMMPS. The MD particles described by *group-ID* apply a velocity
dependent force to the fluid.
The lattice-Boltzmann algorithm solves for the fluid motion governed by
@ -85,7 +91,7 @@ respectively. Here, we have implemented
\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
with :math:`a_0` set to :math:`\frac{1}{3} \frac{dx}{dt}^2` by default.
with :math:`a_0` set to :math:`\frac{1}{3} \frac{dx}{dt}^2` by default. You should not normally need to change this default.
The algorithm involves tracking the time evolution of a set of partial
distribution functions which evolve according to a velocity
@ -100,13 +106,7 @@ relaxation towards the equilibrium distribution function, and :math:`\tau` is a
parameter physically related to the viscosity. On a technical note,
we have implemented a 15 velocity model (D3Q15) as default; however,
the user can switch to a 19 velocity model (D3Q19) through the use of
the *D3Q19* keyword. This fix provides the user with the choice of
two algorithms to solve this equation, through the specification of
the keyword *LBtype*\ . If *LBtype* is set equal to 1, the standard
finite difference LB integrator is used. If *LBtype* is set equal to
2, the algorithm of :ref:`Ollila et al. <Ollila>` is used.
Physical variables are then defined in terms of moments of the distribution
the *D3Q19* keyword. Physical variables are then defined in terms of moments of the distribution
functions,
.. math::
@ -129,78 +129,47 @@ calculated as:
where :math:`\mathbf{v}_n` is the velocity of the MD particle,
:math:`\mathbf{u}_f` is the fluid
velocity interpolated to the particle location, and :math:`\gamma` is the force
coupling constant. :math:`\zeta` is a weight assigned to the grid point,
coupling constant. This force, as with most forces in LAMMPS, and hence the velocities, are calculated at the half-time step. :math:`\zeta` is a weight assigned to the grid point,
obtained by distributing the particle to the nearest lattice sites.
For this, the user has the choice between a trilinear stencil, which
provides a support of 8 lattice sites, or the immersed boundary method
Peskin stencil, which provides a support of 64 lattice sites. While
the Peskin stencil is seen to provide more stable results, the
trilinear stencil may be better suited for simulation of objects close
to walls, due to its smaller support. Therefore, by default, the
Peskin stencil is used; however the user may switch to the trilinear
stencil by specifying the keyword, *trilinear*\ .
By default, the force coupling constant, :math:`\gamma`, is calculated
The force coupling constant, :math:`\gamma`, is calculated
according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t}\right)
Here, :math:`m_v` is the mass of the MD particle, :math:`m_u` is a
representative fluid mass at the particle location, and :math:`\Delta
t_{collision}` is a collision time, chosen such that
:math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and
Denniston <Mackay2>` for full details). In order to calculate :math:`m_u`,
the fluid density is interpolated to the MD particle location, and
multiplied by a volume, node_area * :math:`dx_{LB}`, where node_area
represents the portion of the surface area of the composite object
associated with a given MD particle. By default, node_area is set
equal to :math:`dx_{LB}^2`; however specific values for given atom types
can be set using the *setArea* keyword.
The user also has the option of specifying their own value for the
force coupling constant, for all the MD particles associated with the
fix, through the use of the *setGamma* keyword. This may be useful
when modelling porous particles. See :ref:`Mackay et al. <fluid-Mackay>` for a
detailed description of the method by which the user can choose an
appropriate :math:`\gamma` value.
t` is the time step. The fluid mass :math:`m_u` that the MD particle interacts with is calcuated internally.
This coupling is chosen to constrain the particle and associated fluid velocity to match at the end of the time step. As with other constraints, such as :doc:`shake <fix_shake>`, this constraint can remove degrees of freedom from the simulation which are accounted for internally in the algorithm.
.. note::
while this fix applies the force of the particles on the fluid,
it does not apply the force of the fluid to the particles. When the
force coupling constant is set using the default method, there is only
it does not apply the force of the fluid to the particles. There is only
one option to include this hydrodynamic force on the particles, and
that is through the use of the :doc:`lb/viscous <fix_lb_viscous>` fix.
This fix adds the hydrodynamic force to the total force acting on the
particles, after which any of the built-in LAMMPS integrators can be
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
:ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators
:doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and
:doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
cases. These integrators should not be used with the
:doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
to the particles directly. In addition, they can not be used if the
force coupling constant has been set the default way.
.. note::
if the force coupling constant is set using the default method,
and the :doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
hydrodynamic force to the total force acting on the particles, this
used to integrate the particle motion. If the :doc:`lb/viscous <fix_lb_viscous>`
fix is NOT used to add the hydrodynamic force to the total force acting on the particles, this
physically corresponds to a situation in which an infinitely massive
particle is moving through the fluid (since collisions between the
particle and the fluid do not act to change the particle's velocity).
Therefore, the user should set the mass of the particle to be
significantly larger than the mass of the fluid at the particle
location, in order to approximate an infinitely massive particle (see
the dragforce test run for an example).
particle and the fluid do not act to change the particle's velocity). In this case,
setting *scaleGamma* to -1 for the corresponding particle type will explicity take this
limit (of infinite particle mass) in computing the force coupling for the fluid force.
----------
Physical parameters describing the fluid are specified through
*viscosity* and *density*. These parameters should all be given in terms of
the mass, distance, and time units chosen for the main LAMMPS run, as
they are scaled by the LB timestep, lattice spacing, and mass unit,
inside the fix.
The *dx* keyword allows the user to specify a value for the LB grid
spacing and the *dm* keyword allows the user to specify the LB mass unit.
Inside the fix, parameters are scaled by the lattice-Boltzmann
timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
:math:`dm_{LB}`. :math:`dt_{LB}` is set equal to
@ -208,11 +177,8 @@ timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
By default,
:math:`dm_{LB}` is set equal to 1.0, and :math:`dx_{LB}` is chosen so that
:math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1.
However, the user has the option of specifying their own values for
:math:`dm_{LB}`, and :math:`dx_{LB}`, by using
the optional keywords *dm*, and *dx* respectively.
.. note::
.. note::
Care must be taken when choosing both a value for :math:`dx_{LB}`,
and a simulation domain size. This fix uses the same subdivision of
@ -223,68 +189,14 @@ the optional keywords *dm*, and *dx* respectively.
with equal lengths in all dimensions, and the default value for
:math:`dx_{LB}` is used, this will automatically be satisfied.
Physical parameters describing the fluid are specified through
*viscosity*, *density*, and *a0*\ . If the force coupling constant is
set the default way, the surface area associated with the MD particles
is specified using the *setArea* keyword. If the user chooses to
specify a value for the force coupling constant, this is set using the
*setGamma* keyword. These parameters should all be given in terms of
the mass, distance, and time units chosen for the main LAMMPS run, as
they are scaled by the LB timestep, lattice spacing, and mass unit,
inside the fix.
----------
The *setArea* keyword allows the user to associate a surface area with
a given atom type. For example if a spherical composite object of
radius R is represented as a spherical shell of N evenly distributed
MD particles, all of the same type, the surface area per particle
associated with that atom type should be set equal to :math:`\frac{4\pi R^2}{N}`.
This keyword should only be used if the force coupling constant,
:math:`\gamma`, is set the default way.
The *setGamma* keyword allows the user to specify their own value for
the force coupling constant, :math:`\gamma`, instead of using the default
value.
The *scaleGamma* keyword should be used in conjunction with the
*setGamma* keyword, when the user wishes to specify different :math:`\gamma`
values for different atom types. This keyword allows the user to
scale the *setGamma* :math:`\gamma` value by a factor, gammaFactor,
for a given atom type.
The *dx* keyword allows the user to specify a value for the LB grid
spacing.
The *dm* keyword allows the user to specify the LB mass unit.
If the *a0* keyword is used, the value specified is used for the
square of the speed of sound in the fluid. If this keyword is not
present, the speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
as this may lead to instabilities.
If the *noise* keyword is used, followed by a positive temperature
value, and a positive integer random number seed, a thermal
lattice-Boltzmann algorithm is used. If *LBtype* is set equal to 1
(i.e. the standard LB integrator is chosen), the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used; however if *LBtype* is set
equal to 2 both the LB integrator, and thermal LB algorithm described
in :ref:`Ollila et al. <Ollila>` are used.
value, and a positive integer random number seed, the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used.
If the *calcforce* keyword is used, both the fluid force and torque
acting on the specified particle group are printed to the screen every
N timesteps.
If the keyword *trilinear* is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in :ref:`Mackay et al. <fluid-Mackay>`.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the keyword *stencil* is used, the value sets the number of interpolation points
used in each direction. For this, the user has the choice between a trilinear stencil (*stencil* 2), which
provides a support of 8 lattice sites, or the 3-point immersed boundary method
stencil (*stencil* 3), which provides a support of 27 lattice sites, or the 4-point Keys' interpolation stencil (stencil 4), which provides a support of 64 lattice sites. The trilinear stencil is the default as it is better suited for simulation of objects close to walls or other objects, due to its smaller support. The 3-point stencil provides smoother motion of the lattice and is suitable for particles not likely to be to close to walls or other objects.
If the keyword *write_restart* is used, followed by a positive
integer, N, a binary restart file is printed every N LB timesteps.
@ -308,12 +220,62 @@ conditions in the z-direction. If fixed boundary conditions are
present in the z-direction, and this keyword is not used, the walls
are assumed to be stationary.
If the *pressurebcx* keyword is used, a pressure jump (implemented by a step jump in density)
is imposed at the (periodic) x-boundary. The value set specifies what would be the resulting equilibrium average pressure gradient in the x-direction if the system had a constant cross-section (i.e. resistance to flow). It is converted to a pressure jump by multiplication by the system size in the x-direction. As this value should normally be quite small, it is also assumed to be scaled by 1000.
If the *bodyforce* keyword is used, a constant body force is added to
the fluid, defined by it's x, y and z components.
If the *printfluid* keyword is used, followed by a positive integer, N,
the fluid densities and velocities at each lattice site are printed to the
screen every N timesteps.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the *dumpxdmf* keyword is used, followed by a positive integer, N, and a file name, the fluid densities and velocities at each lattice site are output to an xdmf file every N timesteps. This is a binary file format that can be read by visualization packages such as `Paraview <https://www.paraview.org/>`_ . The xdmf file format contains a time index for each frame dump and the value timeI = 1 uses simulation time while 0 uses the output frame number to index xdmf file. The later can be useful if the :doc:`dump vtk <dump_vtk>` command is used to output the particle positions at the same timesteps and you want to visualize both the fluid and particle data together in `Paraview <https://www.paraview.org/>`_ .
The *scaleGamma* keyword allows the user to
scale the :math:`\gamma` value by a factor, gammaFactor,
for a given atom type. Setting *scaleGamma* to -1 for the corresponding particle type
will explicity take the limit of infinite particle mass in computing the force coupling for the fluid force (see note above).
If the *a0* keyword is used, the value specified is used for the
square of the speed of sound in the fluid. If this keyword is not
present, the speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
as this may lead to instabilities. As the speed of sound should usually be
much larger than any fluid velocity of interest, its value does not normally have
a significant impact on the results. As such, it is usually best to use the default
for this option.
The *npits* keyword (followed by integer arguments: npits, h_p, l_p, l_pp, l_e) sets the fluid domain to the pits geometry. These arguments should only be used if you actually want something more complex than a rectangular/cubic geometry. The npits value sets the number of pits regions (arranged along x). The remaining arguments are sizes measured in multiples of dx_lb: h_p is the z-height of the pit regions, l_p is the x-length of the pit regions, l_pp is the length of the region between consecutive pits (referred to as a "slit" region), and l_e is the x-length of the slit regions at each end of the channel. The pit geometry must fill the system in the x-direction but can be longer, in which case it is truncated (which enables asymmetric entrance/exit end sections). The additional *wp* keyword allows the width (in y-direction) of the pit to be specified (the default is full width) and the *sw* keyword indicates that there should be sidewalls in the y-direction (default is periodic in y-direction). These parameters are illustrated below::
Sideview (in xz plane) of pit geometry:
______________________________________________________________________
slit slit slit ^
|
<---le---><---------lp-------><---lpp---><-------lp--------><---le---> hs = (Nbz-1) - hp
|
__________ __________ __________ v
| | | | ^ z
| | | | | |
| pit | | pit | hp +-x
| | | | |
|__________________| |__________________| v
Endview (in yz plane) of pit geometry (no sw so wp is active):
_____________________
^
|
hs
|
_____________________ v
| | ^
| | | z
|<---wp--->| hp |
| | | +-y
|__________| v
----------
@ -333,9 +295,13 @@ binary restart files, if requested, independent of the main LAMMPS
is written to the main LAMMPS :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
fix.
The fix computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`. The scalar is the current temperature of the group of particles described by *group-ID* along with the fluid constrained to move with them. The temperature is computed via the kinetic energy of the group and fluid constrained to move with them and the total number of degrees of freedom (calculated internally). If the particles are not integrated independently (such as via :doc:`fix NVE <fix_nve>`) but have additional constraints imposed on them (such as via integration using :doc:`fix rigid <fix_rigid>`) the degrees of freedom removed from these additional constraints will not be properly accounted for. In this case, the user can specify the total degrees of freedom independently using the *dof* keyword.
The fix also computes a global array of values which can be accessed by various :doc:`output commands <Howto_output>`. There are 5 entries in the array. The first entry is the temperature of the fluid, the second entry is the total mass of the fluid plus particles, the third through fifth entries give the x, y, and z total momentum of the fluid plus particles.
No parameter of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
@ -346,45 +312,30 @@ was built with that package. See the :doc:`Build package <Build_package>` page
This fix can only be used with an orthogonal simulation domain.
Walls have only been implemented in the z-direction. Therefore, the
boundary conditions, as specified via the main LAMMPS boundary command
must be periodic for x and y, and either fixed or periodic for z.
The boundary conditions for the fluid are specified independently to the particles. However, these should normally be specified consistently via the main LAMMPS :doc:`boundary <boundary>` command (p p p, p p f, and p f f are the only consistent possibilities).
Shrink-wrapped boundary conditions are not permitted with this fix.
This fix must be used before any of :doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and/ or :doc:`fix lb/pc <fix_lb_pc>` , as the fluid needs to be initialized before
This fix must be used before any of :doc:`fix lb/viscous <fix_lb_viscous>` and :doc:`fix lb/momentum <fix_lb_momentum>` as the fluid needs to be initialized before
any of these routines try to access its properties. In addition, in
order for the hydrodynamic forces to be added to the particles, this
fix must be used in conjunction with the
:doc:`lb/viscous <fix_lb_viscous>` fix if the force coupling constant is
set by default, or either the :doc:`lb/viscous <fix_lb_viscous>` fix or
one of the :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` or
:doc:`lb/pc <fix_lb_pc>` integrators, if the user chooses to specify
their own value for the force coupling constant.
:doc:`lb/viscous <fix_lb_viscous>` fix.
This fix needs to be used in conjuntion with a standard LAMMPS integrator such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid <fix_rigid>`.
Related commands
""""""""""""""""
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, :doc:`fix lb/pc <fix_lb_pc>`
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`
Default
"""""""
By default, the force coupling constant is set according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at
the particle node location, is assumed.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} =
\frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} = \frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dm* is set equal to 1.0.
*a0* is set equal to :math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
The Peskin stencil is used as the default interpolation method.
The trilinear stencil is used as the default interpolation method.
The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
If walls are present, they are assumed to be stationary.
----------
@ -403,3 +354,5 @@ If walls are present, they are assumed to be stationary.
.. _Adhikari:
**(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.

2
doc/src/fix_lb_momentum.rst
View File

@ -38,7 +38,7 @@ lattice-Boltzmann fluid is present.
Zero the total linear momentum of the system, including both the atoms
specified by group-ID and the lattice-Boltzmann fluid every nevery
timesteps. This is accomplished by adjusting the particle velocities
timesteps. If there are no atoms specified by group-ID only the fluid momentum is affected. This is accomplished by adjusting the particle velocities
and the fluid velocities at each lattice site.
.. note::

41
doc/src/fix_lb_pc.rst
View File

@ -23,43 +23,4 @@ Examples
Description
"""""""""""
Update the positions and velocities of the individual particles
described by *group-ID*, experiencing velocity-dependent hydrodynamic
forces, using the integration algorithm described in :ref:`Mackay et al. <Mackay1>`. This integration algorithm should only be used if a
user-specified value for the force-coupling constant used in :doc:`fix lb/fluid <fix_lb_fluid>` has been set; do not use this integration
algorithm if the force coupling constant has been set by default.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>` :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
Default
"""""""
none.
----------
.. _Mackay1:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
This fix was part of the old LATBOLTZ package and is now defunct. LAMMPS standard integrator :doc:`fix NVE <fix_nve>` can be used in its place.

118
doc/src/fix_lb_rigid_pc_sphere.rst
View File

@ -46,122 +46,6 @@ Examples
Description
"""""""""""
This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
created to be used in place of that fix, to integrate the equations of
motion of spherical rigid bodies when a lattice-Boltzmann fluid is
present with a user-specified value of the force-coupling constant.
The fix uses the integration algorithm described in :ref:`Mackay et
al. <Mackay>` to update the positions, velocities, and orientations of
a set of spherical rigid bodies experiencing velocity dependent
hydrodynamic forces. The spherical bodies are assumed to rotate as
solid, uniform density spheres, with moments of inertia calculated
using the combined sum of the masses of all the constituent particles
(which are assumed to be point particles).
This fix was part of the old LATBOLTZ package and is now defunct. LAMMPS standard :doc:`fix rigid <fix_rigid>` can be used in its place.
----------
By default, all of the atoms that this fix acts on experience a
hydrodynamic force due to the presence of the lattice-Boltzmann fluid.
However, the *innerNodes* keyword allows the user to specify atoms
belonging to a rigid object which do not interact with the
lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic
force from the lattice-Boltzmann fluid). This can be used to
distinguish between atoms on the surface of a non-porous object, and
those on the inside.
This feature can be used, for example, when implementing a hard sphere
interaction between two spherical objects. Instead of interactions
occurring between the particles on the surfaces of the two spheres, it
is desirable simply to place an atom at the center of each sphere,
which does not contribute to the hydrodynamic force, and have these
central atoms interact with one another.
----------
Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see
:doc:`fix rigid <fix_rigid>` for a complete documentation.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about the *rigid* and *rigid/nve* fixes are written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
computes a global scalar which can be accessed by various :doc:`output
commands <Howto_output>`. The scalar value calculated by these fixes
is "intensive". The scalar is the current temperature of the
collection of rigid bodies. This is averaged over all rigid bodies
and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v\^2, where m = total
mass of the body and v = the velocity of its center of mass. The
rotational energy of a rigid body is 1/2 I w\^2, where I = the moment
of inertia tensor of the body and w = its angular velocity. Degrees
of freedom constrained by the *force* and *torque* keywords are
removed from this calculation.
All of these fixes compute a global array of values which can be
accessed by various :doc:`output commands <Howto_output>`. The number
of rows in the array is equal to the number of rigid bodies. The
number of columns is 15. Thus for each rigid body, 15 values are
stored: the xyz coords of the center of mass (COM), the xyz components
of the COM velocity, the xyz components of the force acting on the
COM, the xyz components of the torque acting on the COM, and the xyz
image flags of the COM, which have the same meaning as image flags for
atom positions (see the "dump" command). The force and torque values
in the array are not affected by the *force* and *torque* keywords in
the fix rigid command; they reflect values before any changes are made
by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the *single* keyword there is just one rigid body. For the
*molecule* keyword, the bodies are ordered by ascending molecule ID.
For the *group* keyword, the list of group IDs determines the ordering
of bodies.
The array values calculated by these fixes are "intensive", meaning
they are independent of the number of atoms in the simulation.
No parameter of these fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command. Should only be used if the force coupling constant used in
:doc:`fix lb/fluid <fix_lb_fluid>` has been set by the user; this
integration fix cannot be used if the force coupling constant is set
by default.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`
Default
"""""""
The defaults are force \* on on on, and torque \* on on on.
----------
.. _Mackay:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

24
doc/src/fix_lb_viscous.rst
View File

@ -25,26 +25,13 @@ Description
This fix is similar to the :doc:`fix viscous <fix_viscous>` command, and
is to be used in place of that command when a lattice-Boltzmann fluid
is present, and the user wishes to integrate the particle motion using
one of the built in LAMMPS integrators.
is present using the :doc:`fix lb/fluid <fix_lb_fluid>`. This should be used in conjunction with one of the built-in LAMMPS integrators, such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid <fix_rigid>`.
This fix adds a force, F = - Gamma\*(velocity-fluid_velocity), to each
atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid <fix_lb_fluid>` command (which applies an equal and
opposite force to the fluid).
.. note::
This fix should only be used in conjunction with one of the
built in LAMMPS integrators; it should not be used with the :doc:`fix lb/pc <fix_lb_pc>` or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrators, which
already include the hydrodynamic forces. These latter fixes should
only be used if the force coupling constant has been set by the user
(instead of using the default value); if the default force coupling
value is used, then this fix provides the only method for adding the
hydrodynamic forces to the particles.
This fix adds a viscous force to each atom to cause it move with the same velocity as the fluid (an equal and opposite force is applied to the fluid via :doc:`fix lb/fluid <fix_lb_fluid>`). When :doc:`fix lb/fluid <fix_lb_fluid>` is called with the noise option, the atoms will also experience random forces which will thermalize them to the same temperature as the fluid. In this way, the combination of this fix with :doc:`fix lb/fluid <fix_lb_fluid>` and a LAMMPS integrator like :doc:`fix NVE <fix_nve>` is analogous to :doc:`fix langevin <fix_langevin>` except here the fluid is explicit. The temperature of the particles can be monitored via the scalar output of :doc:`fix lb/fluid <fix_lb_fluid>`.
----------
For further details, as well as descriptions and results of several
For details of an earlier implementation of this fix, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <Mackay3>`. Please include a citation to
this paper if this fix is used in work contributing to published
research.
@ -78,14 +65,11 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
This fix should not be used if either the :doc:`fix lb/pc <fix_lb_pc>`
or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrator is
used.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
:doc:`fix lb/fluid <fix_lb_fluid>`
Default
"""""""

25
examples/PACKAGES/latboltz/confined_colloid/in.confined_colloids → examples/PACKAGES/latboltz/confined_colloid/confined_colloids.in
View File

@ -6,10 +6,10 @@
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb_fluid fix. #
# implementation of the lb/fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://www.apmaths.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
@ -19,7 +19,7 @@ units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
read_data ../confinedcolloids.dat
mass * 0.00010287
@ -62,23 +62,18 @@ pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.0006
timestep 0.001
#---------------------------------------------------------------------------
# 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 viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation makes use of the surface area
# of the composite object represented by each particle node. Since this is
# not equal to dx*dx, it is input through the setArea keyword (i.e.
# particles of type 2 correspond to a surface area of 0.0018337299).
# Implement walls moving at speeds of 20.0 in opposite directions.
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
# lattice spacing dx=0.06.
# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 1.0 dx 0.06 dm 0.00003 setArea 2 0.0018337299 zwall_velocity -20.0 20.0
fix 1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
@ -105,4 +100,6 @@ fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
thermo 50
run 400

100
examples/PACKAGES/latboltz/confined_colloid/results64.out
View File

@ -1,41 +1,83 @@
LAMMPS (22 Feb 2013)
Scanning data file ...
LAMMPS (29 Sep 2021 - Update 1)
Reading data file ...
orthogonal box = (0 0 0) to (16.8 16.8 6)
orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.800000 16.800000 6.0000000)
4 by 8 by 2 MPI processor grid
reading atoms ...
1734240 atoms
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special 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 = 0.018 seconds
read_data CPU = 1.916 seconds
480 atoms in group ForceAtoms
1733760 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (fix_lb_fluid.cpp:341)
480 rigid bodies with 1734240 atoms
Setting up run ...
Memory usage per processor = 79.5765 Mbytes
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (../fix_lb_fluid.cpp:477)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1023)
First Run initialized
480 rigid bodies with 1734240 atoms
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.602
ghost atom cutoff = 1.602
binsize = 0.801, bins = 21 21 8
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 : micro
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 97.31 | 97.33 | 97.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
400 65143387 608.21941 0 1902.0097 4.5858406
Loop time of 503.932 on 64 procs for 400 steps with 1734240 atoms
50 4511970.8 0 0 89.610701 0.21526205
100 16113793 0 0 320.0305 -0.54714356
150 31550748 67.191512 0 693.81006 1.2310415
200 46439326 498.87168 0 1421.1872 4.0383841
250 61684647 1043.9263 0 2269.0239 6.4736851
300 80760268 1365.1861 0 2969.138 8.4186043
350 1.0442842e+08 1296.934 0 3370.9509 8.9271065
400 1.2759824e+08 817.33984 0 3351.5245 6.8724618
Loop time of 528.696 on 64 procs for 400 steps with 1734240 atoms
Pair time (%) = 0.151149 (0.0299939)
Bond time (%) = 0.000111468 (2.21197e-05)
Neigh time (%) = 308.546 (61.2278)
Comm time (%) = 88.6413 (17.5899)
Outpt time (%) = 0.00124746 (0.000247546)
Other time (%) = 106.592 (21.152)
Performance: 65368.335 ns/day, 0.000 hours/ns, 0.757 timesteps/s
99.2% CPU use with 64 MPI tasks x no OpenMP threads
Nlocal: 27097.5 ave 27415 max 26825 min
Histogram: 8 0 12 12 8 0 8 4 8 4
Nghost: 159582 ave 161567 max 158145 min
Histogram: 32 0 0 0 0 4 12 0 0 16
Neighs: 3.75 ave 6 max 2 min
Histogram: 16 0 16 0 0 16 0 0 0 16
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.053098 | 0.071612 | 0.096152 | 4.1 | 0.01
Bond | 9.7577e-05 | 0.00012984 | 0.00017322 | 0.0 | 0.00
Neigh | 301.06 | 394.1 | 493.41 | 450.6 | 74.54
Comm | 7.8705 | 106.94 | 200.63 | 865.5 | 20.23
Output | 0.0047098 | 0.0052866 | 0.0055549 | 0.3 | 0.00
Modify | 25.511 | 26.848 | 28.764 | 17.8 | 5.08
Other | | 0.736 | | | 0.14
Total # of neighbors = 240
Ave neighs/atom = 0.000138389
Ave special neighs/atom = 0
Neighbor list builds = 68
Nlocal: 27097.5 ave 28368 max 25504 min
Histogram: 16 0 0 8 8 0 0 0 16 16
Nghost: 166100.0 ave 167736 max 164146 min
Histogram: 16 0 4 12 0 0 0 0 12 20
Neighs: 14.0625 ave 21 max 6 min
Histogram: 8 4 4 0 12 0 8 12 12 4
Total # of neighbors = 900
Ave neighs/atom = 0.00051895931
Ave special neighs/atom = 0.0000000
Neighbor list builds = 144
Dangerous builds = 0
LB equilibriumDist time: 3.490595
LB update time: 8.100787
LB PCalc time: 4.473729
LB fluidForce time: 7.598387
LB CorrectU time: 1.830964
Total wall time: 0:08:54

16701
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examples/PACKAGES/latboltz/diffusingsphere/trap_n284_st2_dt0.00025.out Normal file
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197
examples/PACKAGES/latboltz/diffusingsphere/trapnewsphere.in Normal file
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@ -0,0 +1,197 @@
#===========================================================================#
# Large colloidal sphere difusing around. #
# #
# In the first stage, the sphere is constructed by condensing atoms onto #
# the surface of a spherica region. #
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: RIGID, LATBOTLZ #
# #
# 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 p
region mybox block -24 24 -24 24 -24 24
# flag indicating whether sphere will be bonded or rigid, 0 or 1
variable is_bonded equal 0
# timestep for the LB run (setup uses different timesteps)
variable tstep equal 0.00025
# number of stencil points in any direction. could be 2, 3, or 4
variable stpts equal 2
if "${is_bonded} == 1" then &
"create_box 1 mybox bond/types 10 extra/bond/per/atom 12" &
else &
"create_box 1 mybox"
#----------------------------------------------------------------------------
# Create a spherical region and then fill it with atoms
#----------------------------------------------------------------------------
region mysphereinside sphere 0 0 0 4.0
#variable n_nodes equal 216
variable n_nodes equal 284
create_atoms 1 random ${n_nodes} 1234 mysphereinside units box
pair_style soft 1.0
pair_coeff * * 0.0
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
mass * 1.0
#----------------------------------------------------------------------------
# Set up and do an initial run to push the atoms apart as the random creation
# could have them overlapping too much for stability.
#----------------------------------------------------------------------------
timestep 0.002
# Define sphere where minimum of wall potential is at r=4 so
# regions is 4 + (2/5)^(1/6) sigma
region mysphere sphere 0 0 0 5.28756
fix wall all wall/region mysphere lj93 15.0 1.5 5.28
fix 2 all nve
dump mydump all atom 10000 out.lammpstrj
run 20000
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
minimize 0.0 1.0e-8 1000 100000
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 * ${node_mass}
if "${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"
timestep ${tstep}
#----------------------------------------------------------------------------
# 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 ${stpts} dx 1.2 noise 300.0 181920 dof 6"
fix 2 all lb/viscous
if "${is_bonded} == 1" then &
"fix 3 all nve" &
else &
"fix 3 all rigid group 1 all"
#equilibration run
run 10000
# 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${tstep}.out"
fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
#run 25000000

218
examples/PACKAGES/latboltz/diffusingsphere/trapnewsphere.out Normal file
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@ -0,0 +1,218 @@
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

10035
examples/PACKAGES/latboltz/dragforce/defaultgamma_drag.out
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examples/PACKAGES/latboltz/dragforce/drag_n4_st3_dt0.00025.out Normal file
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@ -0,0 +1,102 @@
# 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

140
examples/PACKAGES/latboltz/dragforce/dragtest.in Normal file
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#===========================================================================#
# 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. #
# #
# 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 "${is_bonded} == 1" then &
"create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" &
else &
"create_box 1 mydomain"
if "${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"
#----------------------------------------------------------------------------
# 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 * ${node_mass}
if "${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
#---------------------------------------------------------------------------
# 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}
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
#dumpxdmf 1000 fflow
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object or an elastically bonded object
#----------------------------------------------------------------------------
fix 2 all lb/viscous
if "${n_nodes} == 1 || ${is_bonded} == 1" then &
"fix 3 all nve" &
else &
"fix 3 all rigid group 1 all"
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${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"
fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
#run 100000

80
examples/PACKAGES/latboltz/dragforce/in.defaultgamma_drag
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@ -1,80 +0,0 @@
#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. The resulting equilibrium drag force #
# should correspond to the Stokes drag force on a sphere with a slightly #
# larger "hydrodynamic" radius, than that given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'defaultgamma_drag.out' #
#===========================================================================#
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
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
velocity all set 0.0 0.0001 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.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

68
examples/PACKAGES/latboltz/dragforce/in.setgamma_drag
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@ -1,68 +0,0 @@
#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.0 for this simulation.) This #
# type of simulation is used to calibrate the value for gamma which will #
# give the desired Stokes drag force. #
# #
# Sample output from this run can be found in the file: #
# 'setgamma13d0_drag.out' #
#===========================================================================#
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
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# 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
velocity all set 0.0 0.0001 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.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

75
examples/PACKAGES/latboltz/dragforce/screen.out Normal file
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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

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examples/PACKAGES/latboltz/dragforce/setgamma13d0_drag.out
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1290
examples/PACKAGES/latboltz/fourspheres/data.four
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15039
examples/PACKAGES/latboltz/fourspheres/fourspheres_velocity0d0001_defaultgamma.out
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15039
examples/PACKAGES/latboltz/fourspheres/fourspheres_velocity0d0001_setgamma.out
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84
examples/PACKAGES/latboltz/fourspheres/in.fourspheres_default_gamma
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@ -1,84 +0,0 @@
#===========================================================================#
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# slightly larger "hydrodynamic" radii than given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_defaultgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
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 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 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.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 2.640508625).
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 2.640508625 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

76
examples/PACKAGES/latboltz/fourspheres/in.fourspheres_set_gamma
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@ -1,76 +0,0 @@
#===========================================================================#
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 3.303 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_setgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
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 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 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.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=3.303, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 3.303 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

113
examples/PACKAGES/latboltz/microrheology/in.microrheology_set_gamma
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@ -1,113 +0,0 @@
#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 1.4692 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
#----------------------------------------------------------------------------
# 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
#----------------------------------------------------------------------------
# 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 0.00045
#----------------------------------------------------------------------------
# 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
group FluidAtoms type 2
#---------------------------------------------------------------------------
# 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 rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 1.0, fluid density= 0.0009982071,
# value for gamma=1.4692, lattice spacing dx=1.2, and mass unit, dm=0.003.
# 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 2 1.0 0.0009982071 setGamma 1.4692 dx 1.2 dm 0.003 noise 300.0 2762
#----------------------------------------------------------------------------
# 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.
# 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. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 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]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
run 2000000000

33
examples/PACKAGES/latboltz/microrheology/in.microrheology_default_gamma → examples/PACKAGES/latboltz/microrheology/microrheology.in
View File

@ -4,11 +4,6 @@
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
@ -35,6 +30,8 @@ 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
@ -62,22 +59,16 @@ group FluidAtoms type 2
# 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 viscous_lb fix).
# Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid
# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.3015928947).
# 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 1.0 0.0009982071 setArea 2 0.3015928947 dx 1.2 dm 0.003 trilinear noise 300.0 2762
fix 1 FluidAtoms lb/fluid 1 1.0 0.0009982071 dx 1.2 stencil 2 noise 300.0 2762
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
@ -96,10 +87,10 @@ fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out 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 10000 linear 1 1 1
fix 4 all lb/momentum 50000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
@ -113,7 +104,9 @@ variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.data screen no
thermo_style custom step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 100
run 2000000000
run 2000
#run 2000000000

96
examples/PACKAGES/latboltz/microrheology/microrheology.out Normal file
View File

@ -0,0 +1,96 @@
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

50000
examples/PACKAGES/latboltz/microrheology/microrheology_defaultgamma.out
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File diff suppressed because it is too large Load Diff

50000
examples/PACKAGES/latboltz/microrheology/microrheology_setgamma.out
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File diff suppressed because it is too large Load Diff

22
examples/PACKAGES/latboltz/microrheology/twocolloid.data Normal file
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@ -0,0 +1,22 @@
# 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

307
examples/PACKAGES/latboltz/pit_geometry/dumpatoms0.vtp Normal file
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@ -0,0 +1,307 @@
<?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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76.121864319 5.5458760262 18.992940903 78.447967529 6.5581660271 19.68305397
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</Lines>
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</Strips>
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22
examples/PACKAGES/latboltz/pit_geometry/dumpatoms2500_boundingBox.vtr Normal file
View File

@ -0,0 +1,22 @@
<?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>

BIN
examples/PACKAGES/latboltz/pit_geometry/fflow.raw Normal file
View File

Binary file not shown.

71
examples/PACKAGES/latboltz/pit_geometry/fflow.xdmf Normal file
View File

@ -0,0 +1,71 @@
<?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>

6
examples/PACKAGES/latboltz/planewall/data.one_radius16d2 → examples/PACKAGES/latboltz/pit_geometry/one_radius16d2.data
View File

@ -2,9 +2,9 @@
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-40.0 280.0 zlo zhi
-120.0 120.0 xlo xhi
-100.0 100.0 ylo yhi
-120.0 120.0 zlo zhi
Atoms

85
examples/PACKAGES/latboltz/planewall/in.planewall_set_gamma → examples/PACKAGES/latboltz/pit_geometry/pits.in
View File

@ -1,16 +1,17 @@
#===========================================================================#
# 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. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.655 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Rigid sphere freely moving in a system with pressure driven flow through #
# a pit geometry. #
# #
# Sample output from this run can be found in the file: #
# 'wall_setgamma.out' #
# 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. #
# 'screen.out' ... terminal output from the run. #
#===========================================================================#
units micro
@ -32,7 +33,7 @@ atom_style atomic
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
read_data one_radius16d2.data
#----------------------------------------------------------------------------
# None of the particles interact with one another.
@ -42,7 +43,7 @@ pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 4.0
timestep 2.0
group sphere1 id <> 1 320
@ -54,26 +55,48 @@ 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 rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.655, lattice spacing dx=4.0, and mass unit, dm=10.0.
# 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.
# (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 2 1.0 1.0 setGamma 13.655 dx 4.0 dm 10.0 zwall_velocity 0.0 0.0001
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
#-----------------------------------------------------------------------------
# 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.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere group 1 sphere1
#----------------------------------------------------------------------------
fix 2 all lb/viscous
fix 3 all rigid group 1 sphere1
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
@ -86,7 +109,9 @@ variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 10
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 500
run 200000
dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
run 2500

70
examples/PACKAGES/latboltz/pit_geometry/pits.out Normal file
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@ -0,0 +1,70 @@
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
examples/PACKAGES/latboltz/dragforce/data.one_radius16d2 → examples/PACKAGES/latboltz/planewall/one_radius16d2.data
View File

@ -2,9 +2,9 @@
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-160.0 160.0 zlo zhi
-120.0 120.0 xlo xhi
-120.0 120.0 ylo yhi
-120.0 120.0 zlo zhi
Atoms

66
examples/PACKAGES/latboltz/planewall/in.planewall_default_gamma → examples/PACKAGES/latboltz/planewall/planewall.in
View File

@ -1,16 +1,13 @@
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# the sphere are printed to the screen. #
# 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: #
# 'wall_defaultgamma.out' #
# 'planewall.out' #
#===========================================================================#
units micro
@ -28,11 +25,14 @@ atom_style atomic
# 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
read_data one_radius16d2.data
#----------------------------------------------------------------------------
# None of the particles interact with one another.
@ -41,8 +41,9 @@ pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 3.0
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
@ -55,21 +56,15 @@ 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 viscous_lb fix.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# 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 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear zwall_velocity 0.0 0.0001
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 zwall_velocity 0.0 0.0001
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the particles.
@ -78,13 +73,18 @@ fix 2 all lb/viscous
#----------------------------------------------------------------------------
# Integrate the motion of the particles, constraining them to move and
# rotate together as a single rigid spherical object.
# 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
fix 3 all rigid group 1 sphere1
#fix 3 all rigid group 1 sphere1 force * off off off torque * off off off
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
# 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)
@ -92,8 +92,14 @@ 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
thermo 10
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 200000
run 7500

139
examples/PACKAGES/latboltz/planewall/planewall.out Normal file
View File

@ -0,0 +1,139 @@
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 = 0.008 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
-2.3202888e-15 6.0709101e-09 -2.4412623e-13 -3.320168e-10 -1.1339769e-14 3.4045799e-14 -4.5990491e-16 3.6944668e-08 -1.4797148e-12 -3.3087894e-07 -3.2319943e-12 4.0825356e-11
2.2614166e-13 3.5465948e-07 -9.9990351e-12 -1.2716738e-08 -5.1515303e-13 1.1802563e-12 4.4099503e-13 6.2398067e-07 -1.4010079e-11 -3.2779726e-06 -5.5610241e-11 3.8420418e-10
9.9446526e-13 1.6203654e-06 -2.9965809e-11 -4.2770461e-08 -1.8551769e-12 3.935908e-12 7.0873308e-13 1.3654678e-06 -1.6036096e-11 -4.7351845e-06 -9.5164548e-11 5.5370816e-10
1.8577304e-12 3.6408926e-06 -4.7867194e-11 -7.6340276e-08 -3.4227185e-12 7.0027746e-12 6.4525598e-13 1.8162442e-06 -1.2450308e-11 -4.49885e-06 -9.721214e-11 5.2404154e-10
2.5784818e-12 6.0541618e-06 -6.1511675e-11 -1.0586215e-07 -4.8340636e-12 9.6842864e-12 5.0954806e-13 2.0115015e-06 -9.6836459e-12 -3.7358552e-06 -8.3756951e-11 4.3294805e-10
3.1388911e-12 8.606157e-06 -7.2849939e-11 -1.2968814e-07 -5.9880947e-12 1.18341e-11 3.9602348e-13 2.0531243e-06 -8.7301633e-12 -2.9477e-06 -6.7497759e-11 3.3979481e-10
3.5088487e-12 1.1153105e-05 -8.4778552e-11 -1.4827121e-07 -6.9042127e-12 1.3490413e-11 1.4926704e-13 2.012457e-06 -1.1121284e-11 -2.2774279e-06 -5.6689366e-11 2.5766138e-10
3.6203369e-12 1.3620493e-05 -1.0074918e-10 -1.6255823e-07 -7.6327828e-12 1.4733197e-11 2.8190134e-14 1.9308502e-06 -1.3951766e-11 -1.743828e-06 -4.5410719e-11 1.9387811e-10
3.5893239e-12 1.5972746e-05 -1.1992769e-10 -1.7347444e-07 -8.2060683e-12 1.5658564e-11 -7.5902354e-14 1.8309433e-06 -1.6655785e-11 -1.3300214e-06 -3.6956327e-11 1.4453207e-10
3.4369216e-12 1.8195336e-05 -1.4242882e-10 -1.8179239e-07 -8.6609693e-12 1.6339062e-11 -1.5582523e-13 1.7248165e-06 -1.9125572e-11 -1.0126439e-06 -3.0479042e-11 1.0521684e-10
3.1272907e-12 2.0284863e-05 -1.6693014e-10 -1.8812271e-07 -9.0539095e-12 1.6840547e-11 -3.2806998e-13 1.6187734e-06 -1.7338933e-11 -7.7034531e-07 -4.18956e-11 7.893297e-11
2.6336268e-12 2.2243653e-05 -1.8945116e-10 -1.9293745e-07 -9.4581385e-12 1.720649e-11 -4.4473581e-13 1.5159979e-06 -1.8187251e-11 -5.858335e-07 -3.9427386e-11 5.7483932e-11
2.0046303e-12 2.4076859e-05 -2.0991971e-10 -1.9659836e-07 -9.7540611e-12 1.7464607e-11 -5.3232938e-13 1.417998e-06 -1.33357e-11 -4.4535934e-07 -2.2183067e-11 4.087927e-11
1.8043659e-12 2.57909e-05 -2.251392e-10 -1.9938137e-07 -9.9135163e-12 1.7702226e-11 -8.1829532e-14 1.3253893e-06 -1.1758285e-11 -3.3855787e-07 -1.1111144e-11 3.6790045e-11
1.6716765e-12 2.7392642e-05 -2.3970723e-10 -2.0149677e-07 -1.0039419e-11 1.7837499e-11 -9.9475985e-14 1.2383189e-06 -1.1662512e-11 -2.5732441e-07 -9.4988118e-12 2.1805637e-11
1.4587868e-12 2.8888967e-05 -2.5363201e-10 -2.0310437e-07 -1.0169348e-11 1.7892616e-11 -5.6898373e-14 1.1566938e-06 -9.8557007e-12 -1.9551474e-07 -1.9984471e-11 4.8846772e-12
1.4100591e-12 3.0286556e-05 -2.6363101e-10 -2.0432561e-07 -1.0375492e-11 1.7885827e-11 -2.116508e-13 1.0803004e-06 -7.2760242e-12 -1.484988e-07 -1.9669998e-11 -3.7541543e-12
5.0115337e-13 3.1591785e-05 -2.7207072e-10 -2.0525299e-07 -1.040677e-11 1.7783826e-11 -8.2321665e-13 1.0088701e-06 -4.5772437e-12 -1.1272217e-07 4.4307683e-12 -3.0620406e-12
-5.8233e-13 3.2810682e-05 -2.7706702e-10 -2.0595685e-07 -1.0331077e-11 1.7711421e-11 -9.0024161e-13 9.4212051e-07 -1.7450813e-12 -8.552747e-08 1.6465807e-11 -1.1919394e-11
-1.2278986e-12 3.3948917e-05 -2.7737567e-10 -2.0649056e-07 -1.0269686e-11 1.7690544e-11 -2.7606089e-13 8.7976413e-07 1.1137199e-12 -6.4828506e-08 5.969611e-12 6.1895863e-12
-1.5406065e-12 3.5011807e-05 -2.7530664e-10 -2.0689506e-07 -1.0230405e-11 1.7713982e-11 -2.4182843e-13 8.2152268e-07 2.0572801e-12 -4.9118994e-08 6.9332841e-12 4.3109123e-12
-1.8436988e-12 3.6004328e-05 -2.7268697e-10 -2.0720139e-07 -1.0182673e-11 1.7730423e-11 -2.4623511e-13 7.6712961e-07 2.060507e-12 -3.7177338e-08 8.304141e-12 2.8568851e-12
-2.1592812e-12 3.693113e-05 -2.7044735e-10 -2.074331e-07 -1.0124124e-11 1.7740913e-11 -2.6133386e-13 7.1633405e-07 1.4428527e-12 -2.8098731e-08 9.7066289e-12 1.8079946e-12
-2.1007619e-12 3.7796564e-05 -2.6680968e-10 -2.0760821e-07 -9.9957059e-12 1.7730904e-11 3.5315241e-13 6.689009e-07 3.8443622e-12 -2.1224576e-08 2.4710992e-11 -1.7986278e-12
-1.9557805e-12 3.860469e-05 -2.5957119e-10 -2.0774047e-07 -9.8753834e-12 1.7718848e-11 -2.9478921e-14 6.2460647e-07 6.106131e-12 -1.6021507e-08 1.1023998e-11 4.1076291e-12
-2.032736e-12 3.9359303e-05 -2.5158305e-10 -2.0784005e-07 -9.7873438e-12 1.7712473e-11 -5.9512464e-14 5.8324585e-07 6.1916716e-12 -1.2039909e-08 1.2585113e-11 -1.3834171e-12
-2.1127776e-12 4.0063946e-05 -2.440354e-10 -2.0791478e-07 -9.6912281e-12 1.7690577e-11 -6.3724538e-14 5.4462318e-07 5.7542824e-12 -9.0191552e-09 1.4276089e-11 -2.3574292e-12
-2.3902344e-12 4.0721927e-05 -2.3654619e-10 -2.0797067e-07 -9.6167465e-12 1.7704683e-11 -4.4176097e-13 5.0855857e-07 6.2479839e-12 -6.7282157e-09 6.7015199e-12 9.6977453e-12
-2.9449998e-12 4.1336337e-05 -2.2904024e-10 -2.0801226e-07 -9.5792815e-12 1.7759253e-11 -4.1120238e-13 4.7488125e-07 5.6719561e-12 -4.9923338e-09 5.5881453e-12 9.0637113e-12
-3.4106994e-12 4.191006e-05 -2.2244742e-10 -2.0804302e-07 -9.5439345e-12 1.7819348e-11 -3.2449553e-13 4.4343429e-07 4.8497242e-12 -3.6777395e-09 5.1150823e-12 9.0947463e-12
-3.5852249e-12 4.2445791e-05 -2.1618947e-10 -2.080656e-07 -9.4749377e-12 1.7845812e-11 1.0655839e-13 4.1407045e-07 5.2707815e-12 -2.6881271e-09 1.5541392e-11 -1.5116726e-12
-3.4019698e-12 4.2946045e-05 -2.1010849e-10 -2.0808201e-07 -9.3573737e-12 1.7835452e-11 1.6858729e-13 3.8665059e-07 4.4152799e-12 -1.938804e-09 1.7265863e-11 -1.6678153e-12
-3.1820565e-12 4.3413174e-05 -2.0519131e-10 -2.0809376e-07 -9.2323294e-12 1.782123e-11 2.7307342e-13 3.6104485e-07 4.5405606e-12 -1.381731e-09 7.844705e-12 -2.1593177e-11
-1.9265518e-12 4.3849368e-05 -1.9974093e-10 -2.081021e-07 -9.2365556e-12 1.7734315e-11 9.3143689e-13 3.3713551e-07 4.5961813e-12 -9.3911384e-10 -1.0492532e-11 -3.4710604e-11
-7.5558483e-13 4.4256676e-05 -1.9451038e-10 -2.0810757e-07 -9.2981772e-12 1.7593311e-11 8.8290403e-13 3.1481065e-07 3.7293121e-12 -5.9201041e-10 -1.920229e-12 -4.5261347e-12
-6.8078423e-14 4.4637011e-05 -1.9017e-10 -2.0811091e-07 -9.2985302e-12 1.7560504e-11 2.3613824e-13 2.9396314e-07 2.8306791e-12 -3.6072498e-10 1.919591e-12 5.7324777e-14
-2.6872645e-13 4.4992159e-05 -1.8489448e-10 -2.081129e-07 -9.1988109e-12 1.7585096e-11 -3.7386314e-13 2.7449607e-07 4.3641203e-12 -2.0179873e-10 1.7903185e-11 9.4883417e-12
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-1.0073144e-12 4.5633459e-05 -1.7567167e-10 -2.0811405e-07 -8.9461618e-12 1.7602722e-11 -8.8146729e-14 2.3934617e-07 2.900483e-12 1.3609831e-11 1.8144897e-11 -1.0950951e-12
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-1.2336249e-12 4.6192637e-05 -1.7082009e-10 -2.0811304e-07 -8.6931853e-12 1.7534253e-11 -1.0358975e-13 2.0869604e-07 9.8971584e-13 1.1034572e-10 1.8570854e-11 -4.1945968e-12
-1.395039e-12 4.644477e-05 -1.7090836e-10 -2.0811204e-07 -8.5394724e-12 1.7470422e-11 -2.2192138e-13 1.9487513e-07 -1.0653437e-12 1.5048013e-10 2.2960595e-11 -7.9254026e-12
-1.5887239e-12 4.6680205e-05 -1.726235e-10 -2.0811078e-07 -8.3735722e-12 1.7394789e-11 5.3191009e-14 1.8196634e-07 -1.4136613e-12 2.2963534e-10 2.654505e-11 -1.8261053e-12
-1.4689452e-12 4.6900047e-05 -1.7480066e-10 -2.081091e-07 -8.2058094e-12 1.7351678e-11 1.2094829e-13 1.6991911e-07 -2.6013388e-12 2.4677201e-10 1.76692e-11 -7.1825235e-12
-1.3595687e-12 4.7105333e-05 -1.7899795e-10 -2.081074e-07 -8.0435813e-12 1.7311436e-11 -2.3058185e-13 1.586669e-07 -5.9352116e-12 2.143538e-10 3.2425344e-11 -1.0330713e-11
-1.6431943e-12 4.7297025e-05 -1.8929524e-10 -2.0810597e-07 -7.7996954e-12 1.7199148e-11 -2.3195078e-13 1.4815965e-07 -9.1089087e-12 2.0069043e-10 2.7268474e-11 -1.5424889e-11
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-2.5677362e-12 4.7799238e-05 -2.3224794e-10 -2.0810274e-07 -7.733652e-12 1.6817843e-11 4.7024153e-15 1.2062891e-07 -1.6977112e-11 1.0067875e-10 -5.9706483e-12 -6.6309632e-12
-2.5737947e-12 4.7944975e-05 -2.542538e-10 -2.0810213e-07 -7.6510888e-12 1.676216e-11 -3.154599e-14 1.1264034e-07 -1.7155189e-11 8.6731774e-11 1.320634e-11 -5.9239428e-12
-3.3012431e-12 4.808106e-05 -2.7606974e-10 -2.0810154e-07 -7.5285751e-12 1.6730121e-11 -5.5195274e-13 1.051819e-07 -1.8102675e-11 7.9086408e-11 2.549833e-11 3.8248179e-12
-4.0407963e-12 4.8208133e-05 -2.9913872e-10 -2.0810087e-07 -7.3675841e-12 1.6729661e-11 -1.056947e-13 9.8215693e-08 -2.0564122e-11 8.9889186e-11 9.0969559e-12 -5.0411456e-12
-4.0017866e-12 4.8326792e-05 -3.2578824e-10 -2.0810019e-07 -7.3309734e-12 1.6685377e-11 3.9903591e-14 9.1714102e-08 -2.2544733e-11 9.4144708e-11 -9.2931714e-12 5.3254879e-12
-3.7606866e-12 4.8437596e-05 -3.5569049e-10 -2.080996e-07 -7.4780802e-12 1.6680934e-11 2.7466593e-13 8.5641003e-08 -2.425075e-11 7.7669196e-11 -2.2631547e-11 5.8077979e-13
-3.4574887e-12 4.8541063e-05 -3.8545474e-10 -2.0809901e-07 -7.6093713e-12 1.6646067e-11 2.5876746e-14 7.997313e-08 -2.317586e-11 1.0544046e-10 -1.5314944e-11 6.8357155e-12
-2.9114149e-12 4.8637681e-05 -4.1425452e-10 -2.0809838e-07 -7.7070087e-12 1.6659672e-11 6.2786281e-13 7.4677646e-08 -2.2436087e-11 8.9235324e-11 -1.3645085e-11 1.4694507e-11
-2.2825362e-12 4.8727902e-05 -4.4462584e-10 -2.0809808e-07 -7.7463431e-12 1.6727387e-11 4.986996e-13 6.973271e-08 -2.3823592e-11 4.8349103e-11 -4.917953e-12 1.0180248e-11
-1.6721448e-12 4.881215e-05 -4.7395477e-10 -2.080978e-07 -7.798864e-12 1.6781065e-11 5.8461703e-13 6.5116697e-08 -2.2923269e-11 3.3917578e-11 -1.4512356e-11 3.0753823e-12
-1.0108835e-12 4.889082e-05 -5.0054848e-10 -2.0809742e-07 -7.8734886e-12 1.6821117e-11 5.5262937e-13 6.0804995e-08 -2.0048603e-11 6.7540691e-11 -9.5748309e-12 5.1419531e-12
-5.2913704e-13 4.8964281e-05 -5.2361079e-10 -2.0809688e-07 -7.9342525e-12 1.6809498e-11 1.7857863e-13 5.6779412e-08 -1.7008275e-11 8.4873628e-11 -8.0821684e-12 -1.3432203e-11
-6.0869323e-13 4.9032877e-05 -5.4391464e-10 -2.0809612e-07 -7.9700834e-12 1.6669189e-11 -2.2181063e-13 5.3018043e-08 -1.6188875e-11 1.2254388e-10 -3.4719243e-12 -2.5582696e-11
5.3160987e-14 4.909693e-05 -5.685844e-10 -2.0809534e-07 -7.8445232e-12 1.6543112e-11 3.7931128e-13 4.9508006e-08 -2.3478774e-11 1.0539577e-10 3.8278786e-11 -1.7435743e-11
6.9879599e-13 4.9156741e-05 -6.0029127e-10 -2.0809434e-07 -7.4710339e-12 1.6485438e-11 5.2135936e-13 4.6228138e-08 -2.7953013e-11 1.1306415e-10 3.9827585e-11 -4.0676347e-12
1.3291032e-12 4.921259e-05 -6.3478917e-10 -2.0809343e-07 -7.1919325e-12 1.6475734e-11 8.0744289e-13 4.3164468e-08 -2.9352787e-11 1.9393928e-10 2.1395748e-11 -1.3540015e-11
1.9099631e-12 4.9264739e-05 -6.713946e-10 -2.0809198e-07 -7.14109e-12 1.6362552e-11 5.0399245e-13 4.0306735e-08 -3.0085714e-11 2.4238628e-10 -1.2562062e-11 -3.1127285e-11
2.5888559e-12 4.9313435e-05 -7.0699965e-10 -2.0809031e-07 -7.149238e-12 1.6227991e-11 5.2667785e-13 3.7637786e-08 -2.8432993e-11 2.6235217e-10 -2.232043e-12 -2.2764185e-11
3.2694582e-12 4.9358908e-05 -7.414765e-10 -2.0808825e-07 -7.1300019e-12 1.6100817e-11 5.4583215e-13 3.5147252e-08 -2.5050106e-11 3.5891383e-10 3.6724193e-12 -1.8864321e-11
3.3319364e-12 4.9401369e-05 -7.717209e-10 -2.0808576e-07 -7.1044853e-12 1.6070581e-11 -1.2307553e-12 3.2817485e-08 -1.9476032e-11 3.1425065e-10 2.5407039e-13 2.4318892e-12
1.3098859e-12 4.9441018e-05 -7.9443484e-10 -2.0808358e-07 -7.0912957e-12 1.6079833e-11 -1.9382883e-12 3.0644803e-08 -1.7818422e-11 3.1668434e-10 -1.5502234e-12 -3.3879027e-12
-9.4132416e-13 4.9478041e-05 -8.1438431e-10 -2.0808148e-07 -7.0899773e-12 1.6074809e-11 -1.1537277e-12 2.8614527e-08 -1.2295571e-11 2.623115e-10 -1.1222739e-12 6.3245613e-12
-1.6613373e-12 4.9512612e-05 -8.2794953e-10 -2.0807969e-07 -7.0886692e-12 1.6035491e-11 -3.2150631e-13 2.6719935e-08 -1.0632544e-11 2.5483461e-10 -7.889241e-13 -4.5931115e-12
-2.0923849e-12 4.9544894e-05 -8.4103126e-10 -2.080779e-07 -7.0787296e-12 1.598084e-11 -3.6458701e-13 2.4950759e-08 -1.0668225e-11 2.5363261e-10 2.557409e-12 -7.4330019e-12
-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
Performance: 7320228141.222 ns/day, 0.000 hours/ns, 21.181 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
Nlocal: 80.0000 ave 86 max 74 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 122.750 ave 126 max 120 min
Histogram: 1 0 0 1 0 1 0 0 0 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
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

139
examples/PACKAGES/latboltz/planewall/planewall_fixed.out Normal file
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@ -0,0 +1,139 @@
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

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examples/PACKAGES/latboltz/planewall/wall_defaultgamma.out
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105
examples/PACKAGES/latboltz/polymer/in.polymer_setgamma
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@ -1,105 +0,0 @@
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
# Santtu Ollila #
# santtu.ollila@aalto.fi #
# Aalto University #
# August 14, 2013 #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# 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.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# 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
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# 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
group FluidAtoms type 2
#---------------------------------------------------------------------------
# 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 rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 0.023333333,
# fluid density= 0.0000166368,
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# 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 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# 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.
# 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. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run 2000001

83
examples/PACKAGES/latboltz/polymer/out.polymer_default_gamma
View File

@ -1,83 +0,0 @@
LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 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
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.111926 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 1.9081958e-20
2000001 4.3017148 0 2792.6037 2798.2163 -0.00077006865
Loop time of 51900 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.33729 (0.00835701)
Bond time (%) = 3.33134 (0.00641876)
Neigh time (%) = 35.1247 (0.0676777)
Comm time (%) = 61.528 (0.118551)
Outpt time (%) = 0.361813 (0.000697135)
Other time (%) = 51795.3 (99.7983)
Nlocal: 62 ave 465 max 0 min
Histogram: 11 0 3 1 0 0 0 0 0 1
Nghost: 94.8125 ave 340 max 0 min
Histogram: 9 0 0 0 4 0 0 1 0 2
Neighs: 0.25 ave 2 max 0 min
Histogram: 13 0 0 0 0 2 0 0 0 1
Total # of neighbors = 4
Ave neighs/atom = 0.00403226
Ave special neighs/atom = 0.0625
Neighbor list builds = 23853
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883849: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer_default> was used as the working directory.
Started at Mon Aug 24 11:13:12 2015
Results reported at Tue Aug 25 01:38:50 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 829343.88 sec.
Max Memory : 43 MB
Max Swap : 805 MB
The output (if any) is above this job summary.

83
examples/PACKAGES/latboltz/polymer/out.polymer_setgamma
View File

@ -1,83 +0,0 @@
LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 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
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.108554 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 -0.00085093693
2000001 0.5548925 0 2792.3403 2803.7286 -0.0037777326
Loop time of 50862.3 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.10128 (0.0080635)
Bond time (%) = 3.29621 (0.00648066)
Neigh time (%) = 40.0195 (0.0786822)
Comm time (%) = 89.3201 (0.175612)
Outpt time (%) = 1.05399 (0.00207224)
Other time (%) = 50724.5 (99.7291)
Nlocal: 62 ave 501 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Nghost: 29 ave 259 max 0 min
Histogram: 14 0 0 0 0 0 0 1 0 1
Neighs: 0.375 ave 3 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Total # of neighbors = 6
Ave neighs/atom = 0.00604839
Ave special neighs/atom = 0.0625
Neighbor list builds = 30671
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883848: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer> was used as the working directory.
Started at Mon Aug 24 11:12:37 2015
Results reported at Tue Aug 25 01:20:46 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 812767.44 sec.
Max Memory : 44 MB
Max Swap : 812 MB
The output (if any) is above this job summary.

0
examples/PACKAGES/latboltz/polymer/data.polymer → examples/PACKAGES/latboltz/polymer/polymer.data
View File

106
examples/PACKAGES/latboltz/polymer/in.polymer_default_gamma → examples/PACKAGES/latboltz/polymer/polymer.in
View File

@ -4,11 +4,10 @@
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 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: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
@ -16,23 +15,26 @@
units nano
dimension 3
boundary p p p
boundary p p f
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
read_data polymer.data
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# 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.
#----------------------------------------------------------------------------
# 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
# 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
@ -42,66 +44,68 @@ 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
mass * 0.000000771064
timestep 0.00003
# 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
# 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.
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. Monomer surface is shell of radius 0.7
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#----------------------------------------------------------------------------
# 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 explicitly apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous
# fix).
# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
# dm=0.0000166368.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.2025=4 Pi R^2/N ).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# 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 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
fix 1 all lb/fluid 1 0.1 0.00009982071 dx 1.0 noise 300.0 15003
#----------------------------------------------------------------------------
# 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.
# 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. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation.
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system.
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
fix 3 all rigid molecule
fix 2 all lb/viscous
fix 3 all rigid/small molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out 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 10000 linear 1 1 1
fix 4 all lb/momentum 100000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
run 2000001
dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
#run 2000001
run 10000

41041
examples/PACKAGES/latboltz/polymer/trapped_polymer.lammpstrj Normal file
View File

File diff suppressed because it is too large Load Diff

81
examples/PACKAGES/latboltz/polymer/trapped_polymer.out Normal file
View File

@ -0,0 +1,81 @@
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

491
examples/PACKAGES/latboltz/toycar/toycar.in Normal file
View File

@ -0,0 +1,491 @@
units cgs
dimension 3
boundary p p f
atom_style atomic
#-------------------------------------------------------------------------#
# Set up the simulation box
#-------------------------------------------------------------------------#
variable dx equal 1.5
variable more equal 6.5
variable xl equal "-32*v_dx"
variable xh equal "32*v_dx"
variable yl equal "-60*v_dx"
variable yh equal "420*v_dx"
variable zl equal "-6*v_dx"
variable zh equal "58*v_dx"
region mybox block ${xl} ${xh} ${yl} ${yh} ${zl} ${zh}
create_box 14 mybox
#-------------------------------------------------------------------------#
# Creating the regions and filling them with atoms assigned to surge_group
#-------------------------------------------------------------------------#
variable density equal 0.001184
variable sigma equal "1.2*v_dx" #"1.2*v_dx"
variable rcutlj equal "v_sigma*2^(1/6)"
variable rcutlj93 equal "v_sigma*(2/5)^(1/6)"
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal 12.5
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal 9.5
variable hi equal 12.5
region mycylinderinside1 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_1 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 1 random ${n_nodes_Cy_1} 1234 mycylinderinside1 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + 2*v_rcutlj93"
variable lo_2 equal "v_lo - v_rcutlj93"
region mycylinder1 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder1 region mycylinder1
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal -9.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal 9.5
variable hi equal 12.5
region mycylinderinside2 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_2 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 2 random ${n_nodes_Cy_2} 1234 mycylinderinside2 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + 2*v_rcutlj93"
variable lo_2 equal "v_lo - v_rcutlj93"
region mycylinder2 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder2 region mycylinder2
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal -9.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal -12.5
variable hi equal -9.5
region mycylinderinside3 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_3 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 3 random ${n_nodes_Cy_3} 1234 mycylinderinside3 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + v_rcutlj93"
variable lo_2 equal "v_lo - 2*v_rcutlj93"
region mycylinder3 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder3 region mycylinder3
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal 12.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal -12.5
variable hi equal -9.5
region mycylinderinside4 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_4 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 4 random ${n_nodes_Cy_4} 1234 mycylinderinside4 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + v_rcutlj93"
variable lo_2 equal "v_lo - 2*v_rcutlj93"
region mycylinder4 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder4 region mycylinder4
#-------------------------------------------------------------------------#
# Creating the prism
#-------------------------------------------------------------------------#
variable xlo1 equal -5.0
variable xhi1 equal 5.0
variable ylo1 equal -15.0
variable yhi1 equal 15.0
variable zlo1 equal -6.0
variable zhi1 equal 6.0
region myprisminside1 block ${xlo1} ${xhi1} ${ylo1} ${yhi1} ${zlo1} ${zhi1}
variable n_nodes_P_1 equal "(round(v_more*3.4*(6*(10.0)^2)/(PI*v_dx^2)))"
create_atoms 5 random ${n_nodes_P_1} 1234 myprisminside1 units box
variable xlo1_2 equal "v_xlo1 - v_rcutlj93/2"
variable xhi1_2 equal "v_xhi1 + v_rcutlj93/2"
variable ylo1_2 equal "v_ylo1 - v_rcutlj93/2"
variable yhi1_2 equal "v_yhi1 + v_rcutlj93/2"
variable zlo1_2 equal "v_zlo1 - v_rcutlj93/2"
variable zhi1_2 equal "v_zhi1 + v_rcutlj93/2"
region myprism1 block ${xlo1_2} ${xhi1_2} ${ylo1_2} ${yhi1_2} ${zlo1_2} ${zhi1_2}
group gprism1 region myprism1
#-------------------------------------------------------------------------#
# Creating the rear wing
#-------------------------------------------------------------------------#
variable xlo2 equal -10.0
variable xhi2 equal 10.0
variable ylo2 equal 14.0
variable yhi2 equal 22.0
variable zlo2 equal 10.0
variable zhi2 equal 12.0
region myprisminside2 block ${xlo2} ${xhi2} ${ylo2} ${yhi2} ${zlo2} ${zhi2}
variable n_nodes_P_2 equal "(round(v_more*0.93*(6*(7.0)^2)/(PI*v_dx^2)))"
create_atoms 6 random ${n_nodes_P_2} 1234 myprisminside2 units box
variable xlo2_2 equal "v_xlo2 - v_rcutlj93/2"
variable xhi2_2 equal "v_xhi2 + v_rcutlj93/2"
variable ylo2_2 equal "v_ylo2 - v_rcutlj93/2"
variable yhi2_2 equal "v_yhi2 + v_rcutlj93/2"
variable zlo2_2 equal "v_zlo2 - v_rcutlj93/2"
variable zhi2_2 equal "v_zhi2 + v_rcutlj93/2"
region myprism2 block ${xlo2_2} ${xhi2_2} ${ylo2_2} ${yhi2_2} ${zlo2_2} ${zhi2_2}
group gprism2 region myprism2
#-------------------------------------------------------------------------#
# Creating the rear wing stand
#-------------------------------------------------------------------------#
variable xlo3 equal -2.0
variable xhi3 equal 2.0
variable ylo3 equal 17.0
variable yhi3 equal 19.0
variable zlo3 equal -2.0
variable zhi3 equal 7.0
region myprisminside3 block ${xlo3} ${xhi3} ${ylo3} ${yhi3} ${zlo3} ${zhi3}
variable n_nodes_P_3 equal "(round(v_more*0.32*(6*(6.0)^2)/(PI*v_dx^2)))"
create_atoms 7 random ${n_nodes_P_3} 1234 myprisminside3 units box
variable xlo3_2 equal "v_xlo3 - v_rcutlj93/2"
variable xhi3_2 equal "v_xhi3 + v_rcutlj93/2"
variable ylo3_2 equal "v_ylo3 - v_rcutlj93/2"
variable yhi3_2 equal "v_yhi3 + v_rcutlj93/2"
variable zlo3_2 equal "v_zlo3 - v_rcutlj93/2"
variable zhi3_2 equal "v_zhi3 + v_rcutlj93/2"
region myprism3 block ${xlo3_2} ${xhi3_2} ${ylo3_2} ${yhi3_2} ${zlo3_2} ${zhi3_2}
group gprism3 region myprism3
#-------------------------------------------------------------------------#
# Creating the front wing
#-------------------------------------------------------------------------#
variable xlo4 equal -10.0
variable xhi4 equal 10.0
variable ylo4 equal -26.5
variable yhi4 equal -22.0
variable zlo4 equal -5.0
variable zhi4 equal -3.0
region myprisminside4 block ${xlo4} ${xhi4} ${ylo4} ${yhi4} ${zlo4} ${zhi4}
variable n_nodes_P_4 equal "(round(v_more*1.47*(6*(4.0)^2)/(PI*v_dx^2)))"
create_atoms 8 random ${n_nodes_P_4} 1234 myprisminside4 units box
variable xlo4_2 equal "v_xlo4 - v_rcutlj93/2"
variable xhi4_2 equal "v_xhi4 + v_rcutlj93/2"
variable ylo4_2 equal "v_ylo4 - v_rcutlj93/2"
variable yhi4_2 equal "v_yhi4 + v_rcutlj93/2"
variable zlo4_2 equal "v_zlo4 - v_rcutlj93/2"
variable zhi4_2 equal "v_zhi4 + v_rcutlj93/2"
region myprism4 block ${xlo4_2} ${xhi4_2} ${ylo4_2} ${yhi4_2} ${zlo4_2} ${zhi4_2}
group gprism4 region myprism4
#-------------------------------------------------------------------------#
# Creating the front wing stand
#-------------------------------------------------------------------------#
variable xlo5 equal -4.0
variable xhi5 equal 4.0
variable ylo5 equal -20.0
variable yhi5 equal -18.0
variable zlo5 equal -5.0
variable zhi5 equal 3.0
region myprisminside5 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_5 equal "(round(v_more*2.15*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 9 random ${n_nodes_P_5} 1234 myprisminside5 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism5 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism5 region myprism5
#-------------------------------------------------------------------------#
# Creating the driver
#-------------------------------------------------------------------------#
variable radius2 equal 1.0
variable xloc equal 0.0
variable yloc equal 3.0
variable zloc equal 9.5
region mysphereinside2 sphere ${xloc} ${yloc} ${zloc} ${radius2}
variable n_nodes_S_2 equal "(round(v_more*2.0*(2*v_radius2^2/v_dx^2)))"
create_atoms 10 random ${n_nodes_S_2} 1234 mysphereinside2 units box
variable radius2_2 equal "v_radius2 + v_rcutlj93"
region mysphere2 sphere ${xloc} ${yloc} ${zloc} ${radius2_2}
group gball2 region mysphere2
#-------------------------------------------------------------------------#
# Creating the rear wing side
#-------------------------------------------------------------------------#
variable xlo5 equal 12.0
variable xhi5 equal 14.25
variable ylo5 equal 14.0
variable yhi5 equal 22.0
variable zlo5 equal 10.0
variable zhi5 equal 14.0
region myprisminside6 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_6 equal "(round(v_more*1.0*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 11 random ${n_nodes_P_6} 1234 myprisminside6 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism6 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism6 region myprism6
#-------------------------------------------------------------------------#
# Creating the rear wing side
#-------------------------------------------------------------------------#
variable xlo5 equal -14.25
variable xhi5 equal -12.0
variable ylo5 equal 14.0
variable yhi5 equal 22.0
variable zlo5 equal 10.0
variable zhi5 equal 14.0
region myprisminside7 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_7 equal "(round(v_more*1.0*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 12 random ${n_nodes_P_7} 1234 myprisminside7 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism7 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism7 region myprism7
#-------------------------------------------------------------------------#
# Creating the front wing side
#-------------------------------------------------------------------------#
variable xlo5 equal 12.0
variable xhi5 equal 14.25
variable ylo5 equal -26.0
variable yhi5 equal -20.0
variable zlo5 equal -5.0
variable zhi5 equal -1.0
region myprisminside8 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_8 equal "(round(v_more*1.8*(6*(2.0)^2)/(PI*v_dx^2)))"
create_atoms 11 random ${n_nodes_P_8} 1234 myprisminside8 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism8 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism8 region myprism8
#-------------------------------------------------------------------------#
# Creating the front wing side
#-------------------------------------------------------------------------#
variable xlo5 equal -14.25
variable xhi5 equal -12.0
variable ylo5 equal -26.0
variable yhi5 equal -20.0
variable zlo5 equal -5.0
variable zhi5 equal -1.0
region myprisminside9 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_9 equal "(round(v_more*1.8*(6*(2.0)^2)/(PI*v_dx^2)))"
create_atoms 12 random ${n_nodes_P_9} 1234 myprisminside9 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism9 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism9 region myprism9
#------------------------------------------------------------------------#
# creating the union between the regions
#------------------------------------------------------------------------#
group wheels union gcylinder1 gcylinder2 gcylinder3 gcylinder4
group not_wheels union gprism1 gprism2 gprism3 gprism4 gprism5 gball2 gprism6 gprism7 gprism8 gprism9
group aero_group union gprism2 gprism3 gprism4 gprism5 gball2 gprism6 gprism7 gprism8 gprism9
region aero union 9 myprism2 myprism3 myprism4 myprism5 mysphere2 myprism6 myprism7 myprism8 myprism9
group chassis_group union gcylinder1 gcylinder2 gcylinder3 gcylinder4 gprism1
region chassis union 5 mycylinder1 mycylinder2 mycylinder3 mycylinder4 myprism1
group surge_group union aero_group chassis_group
region surge union 2 aero chassis
#------------------------------------------------------------------------#
# Soft Potential
#------------------------------------------------------------------------#
variable softlength equal "0.5*v_rcutlj"
pair_style soft ${softlength}
pair_coeff * * 0.0
variable prefactor equal ramp(0,4.14e-8)
fix 1 all adapt 1 pair soft a * * v_prefactor
#------------------------------------------------------------------------#
# Run parameters and set up dump
#------------------------------------------------------------------------#
timestep 0.2
mass * 1.0e-6
variable nbin equal "v_rcutlj / (4/3)"
neighbor ${nbin} bin
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
thermo 5000
#------------------------------------------------------------------------#
# Computes initial interaction
#------------------------------------------------------------------------#
variable epsilon equal 10.0e-10
variable cutofflj93 equal 7.0
fix wall surge_group wall/region surge lj93 ${epsilon} ${sigma} ${cutofflj93}
fix 3 all langevin 31000000.0 50000.0 100.0 5678
fix 2 all nve
restart 100000 ParticleRestart
run 100000
unfix 1
unfix 2
unfix 3
unfix wall
#------------------------------------------------------------------------#
# Phase 2 : annealing
#------------------------------------------------------------------------#
#------------------------------------------------------------------------#
# Soft Potential
#------------------------------------------------------------------------#
variable softlength equal "0.475*v_rcutlj"
pair_style soft ${softlength}
pair_coeff * * 4.14e-8
#------------------------------------------------------------------------#
# Computes initial interaction
#------------------------------------------------------------------------#
variable epsilon equal 20.0e-10
variable cutofflj93 equal 7.0
fix wall surge_group wall/region surge lj93 ${epsilon} ${sigma} ${cutofflj93}
fix 3 all langevin 100000.0 5000.0 100.0 5678
fix 2 all nve
run 200000
minimize 0.0 1.0e-8 1000 100000
unfix wall
unfix 2
unfix 3
#-------------------------------------------------------------------------#
# The lb/fluid simulation
#
# The sphere travels through the simulation, being pushed by the fluid
#-------------------------------------------------------------------------#
variable number_all equal count(all)
variable node_mass equal "500000 / v_number_all"
mass 5* ${node_mass}
variable wheel_mass equal "v_node_mass/1000"
mass *4 ${wheel_mass}
variable dx equal 1.0
variable density equal 0.001184
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 3.0
pair_style lj/cut 1.2
pair_coeff * * 0.0 0.0
timestep 0.025
reset_timestep 0
#variable total_force equal 0.2
#variable node_force equal "v_total_force / 178"
#fix drag all addforce 0.0 0.0 0.0
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
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
fix 2 all lb/viscous
fix 4 not_wheels nve
fix 3 wheels rigid group 4 gcylinder1 gcylinder2 gcylinder3 gcylinder4 force * off off off torque * on off off
fix 5 not_wheels setforce 0.0 0.0 0.0
thermo_style custom step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
thermo 100
run 5000
#-------------------------------------------------------------------------#

346
examples/PACKAGES/latboltz/toycar/toycar.out Normal file
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@ -0,0 +1,346 @@
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

1040
examples/PACKAGES/latboltz/translocation/translocation.data Normal file
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File diff suppressed because it is too large Load Diff

181
examples/PACKAGES/latboltz/translocation/translocation.in Normal file
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@ -0,0 +1,181 @@
#===========================================================================#
# 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, USER-LB, USER-VTK #
# #
#To run this example on N cores, use command: #
# mpirun -n N /LAMMPS/EXE/FILE -in polymer.in > output.out #
# #
# 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 translocation.data
#---------------------------------------------------------------------------
#Creating a atomistic wall on an FCC lattice and removing the block from the
#middle to create the nanopore
#---------------------------------------------------------------------------
lattice fcc 1.0
region wall block 28 38 0 32 0 32
create_atoms 3 region wall
region hole block 28 38 14 18 14 18
delete_atoms region hole compress no
#----------------------------------------------------------------------------
# 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
group FluidAtoms type 2 3
group Polymer type 1 2
group WallAtoms type 3
#---------------------------------------------------------------------------
# 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=15003). 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
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow5252
#----------------------------------------------------------------------------
# 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
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

488
examples/PACKAGES/latboltz/translocation/translocation.out Normal file
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@ -0,0 +1,488 @@
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
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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

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22
src/LATBOLTZ/README
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@ -1,7 +1,7 @@
This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces. Details are described in these two
papers:
influenced by hydrodynamic forces. Details of the original version
of this package are described in these two papers:
Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces
Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer
@ -21,19 +21,18 @@ examples/PACKAGES/latboltz.
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
with MPI (i.e. the serial makefile should not be used to compile the
code). Also, several of the test examples provided make use of the
rigid fix. Therefore, this should be included in the LAMMPS build by
typing "make yes-rigid" prior to the usual compilation (see the
"Including/excluding packages" section of the LAMMPS manual).
rigid fix and molecule packages. Therefore, these should be included
in the LAMMPS build (see the "Including/excluding packages" section of
the LAMMPS manual).
The creators of this package are as follows:
Frances Mackay
Santtu Ollila
Tyson Whitehead
Colin Denniston, cdennist@uwo.ca
University of Western Ontario
fmackay@uwo.ca
Dr. Colin Denniston
University of Western Ontario
cdennist@uwo.ca
--------------------------------------------------------------------------
@ -45,10 +44,5 @@ fix_lb_fluid.cpp: fix used to create the lattice-Boltzmann fluid on a
fix_momentum_lb.cpp: fix used to subtract off the total (atom plus fluid)
linear momentum from the system.
fix_pc.cpp: integration algorithm for individual atoms.
fix_rigid_pc_sphere.cpp: integration algorithm for rigid spherical
collections of atoms.
fix_viscous_lb.cpp: fix to add the fluid force to the atoms when using a
built-in LAMMPS integrator.

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src/LATBOLTZ/fix_lb_fluid.h
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@ -13,7 +13,7 @@
#ifdef FIX_CLASS
// clang-format off
FixStyle(lb/fluid,FixLbFluid);
FixStyle(lb/fluid,FixLbFluid)
// clang-format on
#else
@ -28,138 +28,377 @@ FixStyle(lb/fluid,FixLbFluid);
namespace LAMMPS_NS {
class FixLbFluid : public Fix {
friend class FixLbMomentum;
friend class FixLbRigidPCSphere;
friend class FixLbPC;
friend class FixLbViscous;
static const double kappa_lb=0.0;
public:
FixLbFluid(class LAMMPS *, int, char **);
~FixLbFluid();
int setmask();
void init();
void initial_integrate(int);
void setup(int);
void post_force(int);
void end_of_step();
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
private:
double viscosity, densityinit_real, a_0_real, T;
int setdx, seta0;
int numvel;
double dm_lb, dx_lb, dt_lb; // Lattice units for mass, distance, time.
int Nbx, Nby, Nbz; // Total # of x,y,z grid points.
int subNbx, subNby, subNbz; // # of x,y,z, grid points (including buffer)
// on local processor.
int me, nprocs; // MPI variables: processor ID, # of processors
MPI_Datatype oneslice; // MPI datatypes to pass arrays.
MPI_Datatype passxu, passyu, passzu;
MPI_Datatype passxf, passyf, passzf;
MPI_Datatype passxrho, passyrho, passzrho;
MPI_Datatype passxtemp, passytemp, passztemp;
double kB, densityinit, a_0; // Boltzmann constant, initial density,
// and a_0 all in lattice units.
double *Gamma;
double *NodeArea;
int setGamma, setArea;
double **hydroF;
int groupbit_viscouslb, groupbit_pc, groupbit_rigid_pc_sphere;
double ***density_lb; // fluid density
double ****u_lb; // fluid velocity
double ****f_lb; // distributions
double ****fnew; // used in the calculation of the new
// distributions.
double ****feq; // equilibrium distributions
double ****feqold; // equilibrium distributions from previous
// timestep
double ****feqn; // equilibrium distributions without noise.
double ****feqoldn; // equilibrium distributions from previous
// timestep without noise.
double ****Ff; // Force from the MD particles on the fluid.
double ****Fftempx;
double ****Fftempy;
double ****Fftempz;
double *Ng_lb; // Lattice Boltzmann variables.
double *w_lb;
double **mg_lb;
int **e;
double tau;
double expminusdtovertau;
double Dcoeff;
double K_0;
double dtoverdtcollision;
int step;
double ****buf; // arrays used to output data.
double ****buf2;
double ****altogether;
double ****altogether2;
double bodyforcex, bodyforcey, bodyforcez; // Body Forces acting on the fluid (default=0)
double vwtp, vwbt; // Velocities of the z walls in the y
// direction. (must have fixed boundary
// conditions in z)
int noisestress; // 1 to include noise in the system,
// 0 otherwise.
double namp, noisefactor;
int seed;
class RanMars *random;
int force_diagnostic; // 1 to print out the force action on a group
// of particles, 0 otherwise.
int igroupforce; // the group for which the force is to be
// printed.
int typeLB;
int trilinear_stencil; // 1 to use the trilinear stencil, 0 to use the
// peskin stencil.
int readrestart; // 1 to read in data from a restart file.
MPI_File pFileRead;
int printrestart; // 1 to write data to a restart file.
MPI_File pFileWrite;
int printfluid;
int fixviscouslb;
void rescale();
void (FixLbFluid::*initializeLB)();
void initializeLB15();
void initializeLB19();
void initialize_feq();
void (FixLbFluid::*equilibriumdist)(int, int, int, int, int, int);
void equilibriumdist15(int, int, int, int, int, int);
void equilibriumdist19(int, int, int, int, int, int);
void parametercalc_part(int, int, int, int, int, int);
void parametercalc_full();
void update_periodic(int, int, int, int, int, int);
void (FixLbFluid::*update_full)();
void update_full15();
void update_full19();
void streamout();
void read_restartfile();
void write_restartfile();
void peskin_interpolation(int);
void trilinear_interpolation(int);
void calc_fluidforce();
// 15-velocity lattice propogation vectors
static const int e15[15][3] = {
{ 0, 0, 0},
{ 1, 0, 0},
{ 0, 1, 0},
{-1, 0, 0},
{ 0,-1, 0},
{ 0, 0, 1},
{ 0, 0,-1},
{ 1, 1, 1},
{-1, 1, 1},
{-1,-1, 1},
{ 1,-1, 1},
{ 1, 1,-1},
{-1, 1,-1},
{-1,-1,-1},
{ 1,-1,-1}
};
// 15-velocity weights
static const double w_lb15[15] =
{ 2./9., 1./9., 1./9., 1./9., 1./9., 1./9., 1./9., 1./72., 1./72., 1./72., 1./72., 1./72., 1./72., 1./72., 1./72.};
// 15-velocity normalizations
static const double Ng_lb15[15] =
{ 1., 3., 3., 3., 9./2., 9./2., 9./2., 9., 9., 9., 27./2., 27./2., 27./2., 9., 1.};
// 15-velcity transformation matrix for f_i to moments
static const double mg_lb15[15][15] = {
{ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.},
{ 0., 1., 0., -1., 0., 0., 0., 1., -1., -1., 1., 1., -1., -1., 1.},
{ 0., 0., 1., 0., -1., 0., 0., 1., 1., -1., -1., 1., 1., -1., -1.},
{ 0., 0., 0., 0., 0., 1., -1., 1., 1., 1., 1., -1., -1., -1., -1.},
{ -1./3., 2./3., -1./3., 2./3., -1./3., -1./3., -1./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3.},
{ -1./3., -1./3., 2./3., -1./3., 2./3., -1./3., -1./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3.},
{ -1./3., -1./3., -1./3., -1./3., -1./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3.},
{ 0., 0., 0., 0., 0., 0., 0., 1., -1., 1., -1., 1., -1., 1., -1.},
{ 0., 0., 0., 0., 0., 0., 0., 1., 1., -1., -1., -1., -1., 1., 1.},
{ 0., 0., 0., 0., 0., 0., 0., 1., -1., -1., 1., -1., 1., 1., -1.},
{ 0., 0., -1./3., 0., 1./3., 0., 0., 2./3., 2./3., -2./3., -2./3., 2./3., 2./3., -2./3., -2./3.},
{ 0., 0., 0., 0., 0., -1./3., 1./3., 2./3., 2./3., 2./3., 2./3., -2./3., -2./3., -2./3., -2./3.},
{ 0., -1./3., 0., 1./3., 0., 0., 0., 2./3., -2./3., -2./3., 2./3., 2./3., -2./3., -2./3., 2./3.},
{ 0., 0., 0., 0., 0., 0., 0., 1., -1., 1., -1., -1., 1., -1., 1.},
{M_SQRT2,-M_SQRT1_2,-M_SQRT1_2,-M_SQRT1_2,-M_SQRT1_2,-M_SQRT1_2,-M_SQRT1_2,M_SQRT2,M_SQRT2,M_SQRT2,M_SQRT2,M_SQRT2,M_SQRT2,M_SQRT2,M_SQRT2}
};
// 15-velocity opposite lattice directions for bounce-back, i.e. od[i] = j such that e15[j]=-e15[i]
static const int od[15] =
{ 0, 3, 4, 1, 2, 6, 5, 13, 14, 11, 12, 9, 10, 7, 8};
// 15-velocity bounce-back list
// bbl[i][0] = number of bounce-back directions for orientation i
// bbl[i][j]...bbl[i][bbl[i][0]] directions that would be coming from inside the wall so need to come from bounce-back
// bbl[i][[bbl[i][0]+1]...bbl[i][16] directions where standard propogation can proceed (pointing into or along wall)
// inside edge has 1/4 inside domain, 3/4 outside domain
// outside edge has 3/4 outside domain, 1/4 inside domain
// Note: 1. This list is not exhaustive (eg. there should be 12 inside and 12 outside edges possible, it just covers cases
// accessible in the pit routines. Could be generalized to include other geometries
// 2. Need better labelling for corners (particularly in-out) that distinguishes different cases (e.g. 10 and 29 are NOT same, also 11,31)
// ori wall normals (point into domain)
// 0 not relevent, ori==0 only for lattice type 0 (standard bulk fluid) and 2 (outside domain)
// 1 wall +x
// 2 wall +y
// 3 wall +z
// 4 outside edge +x,+z
// 5 inside edge +x,+z
// 6 inside edge +y,+z
// 7 outside edge +y,+z
// 8 inside edge -x,-y
// 9 inside edge -x,+y
// 10 in-out corner +x,+y,+z
// 11 in-out corner +x,-y,+z
// 12 inside corner -x,+y,+z
// 13 inside corner -x,-y,+z
// 14 wall -x
// 15 wall -y
// 16 wall -z
// 17 outside edge -x,+z
// 18 inside edge -x,+z
// 19 inside edge -y,+z
// 20 outside edge -y,+z
// 21 inside edge +x,-y
// 22 inside edge +x,+y
// 23 in-out corner -x,+y,+z
// 24 in-out corner -x,-y,+z
// 25 inside corner +x,+y,+z
// 26 inside corner +x,-y,+z
// 27 inside edge +y,-z
// 28 inside edge -y,-z
// 29 in-out corner +x,+y,+z
// 30 in-out corner +x,-y,+z
// 31 in-out corner -x,+y,+z
// 32 in-out corner -x,-y,+z
static const int bbl[33][16] = {
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
{ 5, 1, 7, 10, 11, 14, 0, 2, 3, 4, 5, 6, 8, 9, 12, 13},
{ 5, 2, 7, 8, 11, 12, 0, 1, 3, 4, 5, 6, 9, 10, 13, 14},
{ 5, 5, 7, 8, 9, 10, 0, 1, 2, 3, 4, 6, 11, 12, 13, 14},
{ 4, 7, 10, 1, 5, 0, 2, 3, 4, 6, 8, 9, 11, 12, 13, 14},
{ 8, 1, 5, 7, 10, 8, 9, 11, 14, 0, 2, 3, 4, 6, 12, 13},
{ 8, 2, 5, 7, 8, 9, 10, 11, 12, 0, 1, 3, 4, 6, 13, 14},
{ 4, 2, 5, 7, 8, 0, 1, 3, 4, 6, 9, 10, 11, 12, 13, 14},
{ 8, 3, 4, 9, 13, 8, 10, 12, 14, 0, 1, 2, 5, 6, 7, 11},
{ 8, 2, 3, 8, 12, 7, 9, 11, 13, 0, 1, 4, 5, 6, 10, 14},
{ 3, 7, 8, 10, 0, 1, 2, 3, 4, 5, 6, 9, 11, 12, 13, 14},
{ 3, 7, 9, 10, 0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14},
{10, 2, 3, 5, 8, 7, 9, 10, 11, 12, 13, 0, 1, 4, 6, 14},
{10, 3, 4, 5, 9, 7, 8, 10, 12, 13, 14, 0, 1, 2, 6, 11},
{ 5, 3, 8, 9, 12, 13, 0, 1, 2, 4, 5, 6, 7, 10, 11, 14},
{ 5, 4, 9, 10, 13, 14, 0, 1, 2, 3, 5, 6, 7, 8, 11, 12},
{ 5, 6, 11, 12, 13, 14, 0, 1, 2, 3, 4, 5, 7, 8, 9, 10},
{ 4, 8, 9, 3, 5, 0, 1, 2, 4, 6, 7, 10, 11, 12, 13, 14},
{ 8, 3, 5, 8, 9, 7, 10, 12, 13, 0, 1, 2, 4, 6, 11, 14},
{ 8, 4, 5, 9, 10, 7, 8, 13, 14, 0, 1, 2, 3, 6, 11, 12},
{ 4, 4, 5, 9, 10, 0, 1, 2, 3, 6, 7, 8, 11, 12, 13, 14},
{ 8, 1, 4, 10, 14, 7, 9, 11, 13, 0, 2, 3, 5, 6, 8, 12},
{ 8, 1, 2, 7, 11, 8, 10, 12, 14, 0, 3, 4, 5, 6, 9, 13},
{ 3, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14},
{ 3, 8, 9, 10, 0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14},
{10, 1, 2, 5, 7, 8, 9, 10, 11, 12, 14, 0, 3, 4, 6, 13},
{10, 1, 4, 5, 10, 7, 8, 9, 11, 13, 14, 0, 2, 3, 6, 12},
{ 8, 2, 6, 11, 12, 7, 8, 13, 14, 0, 1, 3, 4, 5, 9, 10},
{ 8, 4, 6, 13, 14, 9, 10, 11, 12, 0, 1, 2, 3, 5, 7, 8},
{ 6, 2, 7, 8, 11, 10, 12, 0, 1, 3, 4, 5, 6, 9, 13, 14},
{ 6, 4, 9, 10, 14, 7, 13, 0, 1, 2, 3, 5, 6, 8, 11, 12},
{ 6, 2, 7, 8, 12, 9, 11, 0, 1, 3, 4, 5, 6, 10, 13, 14},
{ 6, 4, 9, 10, 13, 8, 14, 0, 1, 2, 3, 5, 6, 7, 11, 12}
};
// 19-velocity lattice propogation vectors
static const int e19[19][3] = {
{ 0, 0, 0},
{ 1, 0, 0},
{ 0, 1, 0},
{-1, 0, 0},
{ 0,-1, 0},
{ 0, 0, 1},
{ 0, 0,-1},
{ 1, 1, 0},
{1, -1, 0},
{-1, 1, 0},
{-1,-1, 0},
{ 1, 0, 1},
{ 1, 0,-1},
{-1, 0, 1},
{-1, 0,-1},
{ 0, 1, 1},
{ 0, 1,-1},
{ 0,-1, 1},
{ 0,-1,-1}
};
static const double w_lb19[19] =
{1./3.,1./18.,1./18.,1./18.,1./18.,1./18.,1./18.,1./36.,1./36.,1./36.,1./36.,1./36.,1./36.,1./36.,1./36.,1./36., 1./36., 1./36.,1./36.};
static const double Ng_lb19[19] =
{ 1., 3., 3., 3., 9./2., 9./2., 9./2., 9., 9., 9.,27./2.,27./2.,27./2., 18., 18., 18.,162./7.,126./5., 30.};
static const double mg_lb19[19][19] = {
{ 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.},
{ 0., 1., 0., -1., 0., 0., 0., 1., 1., -1., -1., 1., 1., -1., -1., 0., 0., 0., 0.},
{ 0., 0., 1., 0., -1., 0., 0., 1., -1., 1., -1., 0., 0., 0., 0., 1., 1., -1., -1.},
{ 0., 0., 0., 0., 0., 1., -1., 0., 0., 0., 0., 1., -1., 1., -1., 1., -1., 1., -1.},
{-1./3., 2./3., -1./3., 2./3., -1./3., -1./3., -1./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3.,-1./3.,-1./3.,-1./3.,-1./3.},
{-1./3., -1./3., 2./3., -1./3., 2./3., -1./3., -1./3., 2./3., 2./3., 2./3., 2./3.,-1./3.,-1./3.,-1./3.,-1./3., 2./3., 2./3., 2./3., 2./3.},
{-1./3., -1./3., -1./3., -1./3., -1./3., 2./3., 2./3.,-1./3.,-1./3.,-1./3.,-1./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3., 2./3.},
{ 0., 0., 0., 0., 0., 0., 0., 1., -1., -1., 1., 0., 0., 0., 0., 0., 0., 0., 0.},
{ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., -1., -1., 1., 0., 0., 0., 0.},
{ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., -1., -1., 1.},
{ 0., -1./3., 0., 1./3., 0., 0., 0., 2./3., 2./3.,-2./3.,-2./3.,-1./3.,-1./3., 1./3., 1./3., 0., 0., 0., 0.},
{ 0., 0., -1./3., 0., 1./3., 0., 0., 2./3.,-2./3., 2./3.,-2./3., 0., 0., 0., 0.,-1./3.,-1./3., 1./3., 1./3.},
{ 0., 0., 0., 0., 0., -1./3., 1./3., 0., 0., 0., 0., 2./3.,-2./3., 2./3.,-2./3.,-1./3., 1./3.,-1./3., 1./3.},
{ 0., -0.5, 0., 0.5, 0., 0., 0., 0., 0., 0., 0., 0.5, 0.5, -0.5, -0.5, 0., 0., 0., 0.},
{ 0., 0., 0., 0., 0., -0.5, 0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0.5, -0.5, 0.5, -0.5},
{ 0., 0., -0.5, 0., 0.5, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0.5, 0.5, -0.5, -0.5},
{1./18.,-5./18.,-5./18.,-5./18.,-5./18., 2./9., 2./9.,7./18.,7./18.,7./18.,7./18.,-1./9.,-1./9.,-1./9.,-1./9.,-1./9.,-1./9.,-1./9.,-1./9.},
{1./14.,-5./14., 1./7.,-5./14., 1./7.,-3./14.,-3./14., 0., 0., 0., 0.,5./14.,5./14.,5./14.,5./14.,-1./7.,-1./7.,-1./7.,-1./7.},
{1./10., 0.,-3./10., 0.,-3./10.,-3./10.,-3./10., 0., 0., 0., 0., 0., 0., 0., 0.,3./10.,3./10.,3./10.,3./10.}
};
class Site {
public:
int type;
int orientation;
};
class FixLbFluid : public Fix {
friend class FixLbMomentum;
friend class FixLbViscous;
public:
FixLbFluid(class LAMMPS *, int, char **);
~FixLbFluid();
int setmask();
void init();
void initial_integrate(int);
void setup(int);
void pre_force(int);
void post_force(int);
void final_integrate();
void end_of_step();
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
double compute_scalar();
double compute_vector(int);
void dump(int);
private:
double viscosity,densityinit_real,a_0_real,T;
int setdx,seta0,setdof;
int numvel;
double dm_lb,dx_lb,dt_lb; // Lattice units for mass, distance, time.
int Nbx,Nby,Nbz; // Total # of x,y,z grid points.
int subNbx,subNby,subNbz; // # of x,y,z, grid points (including buffer)
// on local processor.
int fluid_local_n0[3]; // Size of local including both lower and upper end points
int fluid_global_o0[3]; // Offset of local in global from lower end point
int fluid_global_n0[3]; // Size of global including both lower and upper end points
int me, nprocs; // MPI variables: processor ID, # of processors
MPI_Datatype oneslice; // MPI datatypes to pass arrays.
MPI_Datatype passxu,passyu,passzu;
MPI_Datatype passxf,passyf,passzf;
MPI_Datatype passxrho,passyrho,passzrho;
MPI_Datatype passxtemp,passytemp,passztemp;
MPI_Datatype passxWtemp,passyWtemp,passzWtemp;
MPI_Datatype fluid_density_2_mpitype;
MPI_Datatype fluid_velocity_2_mpitype;
MPI_Datatype realType3_mpitype; // MPI type for a 3-vector
double kB,densityinit,a_0; // Boltzmann constant, initial density,
// and a_0 all in lattice units.
double *Gamma;
double **hydroF;
double *massp;
int dump_interval, dump_time_index;
std::string dump_file_name_xdmf;
std::string dump_file_name_raw;
FILE* dump_file_handle_xdmf;
MPI_File dump_file_handle_raw;
MPI_Datatype dump_file_mpitype;
int groupbit_viscouslb;
double ***density_lb; // fluid density
double ****u_lb; // fluid velocity
double ****f_lb; // distributions
double ****fnew; // used in the calculation of the new
// distributions.
double ****feq; // equilibrium distributions
double ****Ff,***Wf; // Force, total weight, from the MD particles on the fluid.
double ****Fftempx,***Wftempx;
double ****Fftempy,***Wftempy;
double ****Fftempz,***Wftempz;
double tau; // Lattice Boltzmann variables.
double K_0;
int step;
int n_stencil=2; // Number of points for spread/interpolate stencil
double bodyforcex,bodyforcey,bodyforcez; // Body Forces acting on the fluid (default=0)
double vwtp,vwbt; // Velocities of the z walls in the y
// direction. (must have fixed boundary
// conditions in z)
int pressure; // pressure boundary conditions on/off
double rhofactor; // factor for density/pressure jump at boundary
double rhoH,rhoL; // density target for high/low side of jump
double meanrho1,meanrhoLx; // current densities at boundary on high/low side of jump
int noisestress; // 1 to include noise in the system,
// 0 otherwise.
int lin_init; // 1 to initialize with linear interpolation
// between boundaries.
// 0 initialize to uniform density, 0.0 velocities.
double namp,noisefactor;
int seed;
class RanMars *random;
int readrestart; // 1 to read in data from a restart file.
MPI_File pFileRead;
int printrestart; // 1 to write data to a restart file.
MPI_File pFileWrite;
double timeEqb,timeUpdate,timePCalc,timefluidForce,timeCorrectU;
double dof_lb=0;
int fixviscouslb;
void rescale(void);
void SetupBuffers(void);
void InitializeFirstRun(void);
void initializeLB(void);
void initialize_feq(void);
void (FixLbFluid::*equilibriumdist)(int,int,int,int,int,int);
void equilibriumdist15(int,int,int,int,int,int);
void equilibriumdist19(int,int,int,int,int,int);
void parametercalc_part(int,int,int,int,int,int);
void correctu_part(int,int,int,int,int,int);
void parametercalc_full(void);
void update_periodic(int,int,int,int,int,int);
void correctu_full(void);
void calc_mass_momentum(double& totalmass, double totalmomentum[3]);
void calc_MPT(double& totalmass, double totalmomentum[3], double& Tave);
void (FixLbFluid::*update_full)(void);
void update_full15(void);
void update_full19(void);
void read_restartfile(void);
void write_restartfile(void);
void (FixLbFluid::*interpolate)(int, int);
void (FixLbFluid::*interpolationweight)(int);
void keys_interpolation(int, int);
void keys_interpolationweight(int);
void trilinear_interpolation(int, int);
void trilinear_interpolationweight(int);
void IBM3_interpolation(int, int);
void IBM3_interpolationweight(int);
void calc_fluidforceI(void);
void calc_fluidforceII(void);
void calc_fluidforceweight(void);
int adjust_dof_fix();
double dof_compute();
/* nanopit parameters */
int npits; // number of nanopits
int h_s; // slit height
int h_p; // pit height
int w_p; // pit width
int l_p; // pit length
int l_pp; // distance between consecutive pits
int l_e; // length of end segments
int sw; // side walls on/off
int openingsites; // Number of active fluid sites at x=0
Site ***sublattice, ***wholelattice; // lattice geometry
/* nanopit routines */
void addslit(int &,int,int,int,int);
void addpit(int &,int,int,int,int,int);
void initializeGeometry(void);
void initializeGlobalGeometry(void);
};
} // namespace LAMMPS_NS
#endif
#endif

303
src/LATBOLTZ/fix_lb_momentum.cpp
View File

@ -20,14 +20,13 @@
------------------------------------------------------------------------- */
#include "fix_lb_momentum.h"
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "error.h"
#include "fix_lb_fluid.h"
#include "modify.h"
#include "comm.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -39,7 +38,7 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal fix lb/momentum command");
nevery = atoi(arg[3]);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);;
if (nevery <= 0) error->all(FLERR,"Illegal fix lb/momentum command");
linear = 1;
@ -52,9 +51,9 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"linear") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix lb/momentum command");
linear = 1;
xflag = atoi(arg[iarg+1]);
yflag = atoi(arg[iarg+2]);
zflag = atoi(arg[iarg+3]);
xflag = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
yflag = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
zflag = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
iarg += 4;
} else error->all(FLERR,"Illegal fix lb/momentum command");
}
@ -64,19 +63,8 @@ FixLbMomentum::FixLbMomentum(LAMMPS *lmp, int narg, char **arg) :
if (linear)
if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
zflag < 0 || zflag > 1) error->all(FLERR,"Illegal fix lb/momentum command");
// cannot have 0 atoms in group
if (group->count(igroup) == 0.0)
error->all(FLERR,"Fix lb/momentum group has no atoms");
for (int ifix=0; ifix<modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"lb/fluid")==0)
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
zflag < 0 || zflag > 1)
error->all(FLERR,"Illegal fix lb/momentum command");
}
/* ---------------------------------------------------------------------- */
@ -92,208 +80,111 @@ int FixLbMomentum::setmask()
void FixLbMomentum::init()
{
masstotal = group->mass(igroup);
// warn if 0 atoms in group
if ((count = group->count(igroup)) == 0)
error->warning(FLERR,"Fix lb/momentum group has no atoms: Only fluid momentum affected");
for(int ifix=0; ifix<modify->nfix; ifix++)
if(strcmp(modify->fix[ifix]->style,"lb/fluid")==0)
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
count ? masstotal = group->mass(igroup) : 0;
}
/* ---------------------------------------------------------------------- */
void FixLbMomentum::end_of_step()
{
double masslb,masslbloc;
double momentumlbloc[3],momentumlb[3];
double vcmtotal[3];
const int numvel = fix_lb_fluid->numvel;
double etacov[19]; // = double etacov[numvel]; i.e. 15 or 19
double rho;
// particle com velcity
double vcmp[3] = {0, 0, 0};
if (count) group->vcm(igroup,masstotal,vcmp);
if (linear) {
double vcm[3];
group->vcm(igroup,masstotal,vcm);
// total fluid mass and momentum.
double masslb,momentumlb[3];
fix_lb_fluid->calc_mass_momentum(masslb, momentumlb);
//Calculate the center of mass velocity of the particles + fluid.
double vcmall[3];
vcmall[0] = (masstotal*vcmp[0] + momentumlb[0])/(masslb + masstotal);
vcmall[1] = (masstotal*vcmp[1] + momentumlb[1])/(masslb + masstotal);
vcmall[2] = (masstotal*vcmp[2] + momentumlb[2])/(masslb + masstotal);
// adjust velocities by vcm to zero linear momentum
// only adjust a component if flag is set
// adjust velocities to zero net linear momentum
// only adjust a component if flag is set
//Subtract vcmall from the particles.
if (count) {
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int typeLB = fix_lb_fluid->typeLB;
int subNbx = fix_lb_fluid->subNbx;
int subNby = fix_lb_fluid->subNby;
int subNbz = fix_lb_fluid->subNbz;
double ***density_lb = fix_lb_fluid->density_lb;
double ****f_lb = fix_lb_fluid->f_lb;
double ****u_lb = fix_lb_fluid->u_lb;
double dm_lb = fix_lb_fluid->dm_lb;
double dx_lb = fix_lb_fluid->dx_lb;
double dt_lb = fix_lb_fluid->dt_lb;
double *Ng_lb = fix_lb_fluid->Ng_lb;
double *w_lb = fix_lb_fluid->w_lb;
double **mg_lb = fix_lb_fluid->mg_lb;
double ucmx,ucmy,ucmz;
//Calculate the total fluid mass and momentum.
masslbloc = 0.0;
momentumlbloc[0] = momentumlbloc[1] = momentumlbloc[2] = 0.0;
for (int i = 1; i<subNbx-1; i++)
for (int j = 1; j<subNby-1; j++)
for (int k = 1; k<subNbz-1; k++) {
masslbloc += density_lb[i][j][k];
momentumlbloc[0] += density_lb[i][j][k]*u_lb[i][j][k][0];
momentumlbloc[1] += density_lb[i][j][k]*u_lb[i][j][k][1];
momentumlbloc[2] += density_lb[i][j][k]*u_lb[i][j][k][2];
}
MPI_Allreduce(&masslbloc,&masslb,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&momentumlbloc[0],&momentumlb[0],3,MPI_DOUBLE,MPI_SUM,world);
momentumlb[0] *= dm_lb*dx_lb/dt_lb;
momentumlb[1] *= dm_lb*dx_lb/dt_lb;
momentumlb[2] *= dm_lb*dx_lb/dt_lb;
masslb *= dm_lb;
//Calculate the center of mass velocity of the entire system.
vcmtotal[0] = (masstotal*vcm[0] + momentumlb[0])/(masslb + masstotal);
vcmtotal[1] = (masstotal*vcm[1] + momentumlb[1])/(masslb + masstotal);
vcmtotal[2] = (masstotal*vcm[2] + momentumlb[2])/(masslb + masstotal);
//Subtract vcm from the particles.
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (xflag) v[i][0] -= vcmtotal[0];
if (yflag) v[i][1] -= vcmtotal[1];
if (zflag) v[i][2] -= vcmtotal[2];
if (xflag) v[i][0] -= vcmall[0];
if (yflag) v[i][1] -= vcmall[1];
if (zflag) v[i][2] -= vcmall[2];
}
vcmtotal[0] *= dt_lb/dx_lb;
vcmtotal[1] *= dt_lb/dx_lb;
vcmtotal[2] *= dt_lb/dx_lb;
ucmx = ucmy = ucmz = 0.0;
double density_old;
double u_old[3];
int **e = fix_lb_fluid->e;
//Subtract vcm from the fluid.
for (int i=0; i<subNbx; i++)
for (int j=0; j<subNby; j++)
for (int k=0; k<subNbz; k++) {
rho = density_lb[i][j][k];
if (xflag) ucmx = vcmtotal[0];
if (yflag) ucmy = vcmtotal[1];
if (zflag) ucmz = vcmtotal[2];
if (numvel==15) {
etacov[0]=0.0;
etacov[1]=rho*ucmx;
etacov[2]=rho*ucmy;
etacov[3]=rho*ucmz;
etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
etacov[7]=rho*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8]=rho*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
etacov[9]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
etacov[10]=0.0;
etacov[11]=0.0;
etacov[12]=0.0;
etacov[13]=rho*(u_lb[i][j][k][0]*u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][0]*ucmy*u_lb[i][j][k][2]-
u_lb[i][j][k][0]*ucmy*ucmz+ucmx*u_lb[i][j][k][1]*u_lb[i][j][k][2]-
ucmx*u_lb[i][j][k][1]*ucmz-ucmx*ucmy*u_lb[i][j][k][2]+
ucmx*ucmy*ucmz);
etacov[14]=0.0;
} else {
etacov[0] = 0.0;
etacov[1] = rho*ucmx;
etacov[2] = rho*ucmy;
etacov[3] = rho*ucmz;
etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
etacov[7]=rho*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
etacov[9]=rho*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
etacov[10] = 0.0;
etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = 0.0;
etacov[14] = 0.0;
etacov[15] = 0.0;
etacov[16] = 0.0;
etacov[17] = 0.0;
etacov[18] = 0.0;
}
for (int l=0; l<numvel; l++)
for (int ii=0; ii<numvel; ii++) {
f_lb[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
}
if (typeLB == 2) {
double ****feqold = fix_lb_fluid->feqold;
double ****feqoldn = fix_lb_fluid->feqoldn;
density_old = 0.0;
u_old[0] = u_old[1] = u_old[2] = 0.0;
for (int l=0; l<numvel; l++) {
density_old += feqold[i][j][k][l];
u_old[0] += feqold[i][j][k][l]*e[l][0];
u_old[1] += feqold[i][j][k][l]*e[l][1];
u_old[2] += feqold[i][j][k][l]*e[l][2];
}
u_old[0] = u_old[0]/density_old;
u_old[1] = u_old[1]/density_old;
u_old[2] = u_old[2]/density_old;
if (numvel==15) {
etacov[0]=0.0;
etacov[1]=density_old*ucmx;
etacov[2]=density_old*ucmy;
etacov[3]=density_old*ucmz;
etacov[4]=density_old*(2.*u_old[0]*ucmx-ucmx*ucmx);
etacov[5]=density_old*(2.*u_old[1]*ucmy-ucmy*ucmy);
etacov[6]=density_old*(2.*u_old[2]*ucmz-ucmz*ucmz);
etacov[7]=density_old*(u_old[0]*ucmy+u_old[1]*ucmx-ucmx*ucmy);
etacov[8]=density_old*(u_old[1]*ucmz+u_old[2]*ucmy-ucmy*ucmz);
etacov[9]=density_old*(u_old[0]*ucmz+u_old[2]*ucmx-ucmx*ucmz);
etacov[10]=0.0;
etacov[11]=0.0;
etacov[12]=0.0;
etacov[13]=density_old*(u_old[0]*u_old[1]*ucmz+u_old[0]*ucmy*u_old[2]-
u_old[0]*ucmy*ucmz+ucmx*u_old[1]*u_old[2]-
ucmx*u_old[1]*ucmz-ucmx*ucmy*u_old[2]+
ucmx*ucmy*ucmz);
etacov[14]=0.0;
} else {
etacov[0] = 0.0;
etacov[1] = density_old*ucmx;
etacov[2] = density_old*ucmy;
etacov[3] = density_old*ucmz;
etacov[4] = density_old*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
etacov[5] = density_old*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
etacov[6] = density_old*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
etacov[7] = density_old*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8] = density_old*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
etacov[9] = density_old*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
etacov[10] = 0.0;
etacov[11] = 0.0;
etacov[12] = 0.0;
etacov[13] = 0.0;
etacov[14] = 0.0;
etacov[15] = 0.0;
etacov[16] = 0.0;
etacov[17] = 0.0;
etacov[18] = 0.0;
}
for (int l=0; l<numvel; l++)
for (int ii=0; ii<numvel; ii++) {
feqold[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
feqoldn[i][j][k][l] -= w_lb[l]*mg_lb[ii][l]*etacov[ii]*Ng_lb[ii];
}
}
}
}
fix_lb_fluid->parametercalc_full();
//Subtract vcmall from the fluid.
// convert vcmall to lattice units used in lb/fluid
double dx_lb = fix_lb_fluid->dx_lb;
double dt_lb = fix_lb_fluid->dt_lb;
vcmall[0] *= dt_lb/dx_lb;
vcmall[1] *= dt_lb/dx_lb;
vcmall[2] *= dt_lb/dx_lb;
double ucmx, ucmy, ucmz;
ucmx = xflag ? vcmall[0] : 0.0;
ucmy = yflag ? vcmall[1] : 0.0;
ucmz = zflag ? vcmall[2] : 0.0;
int numvel = fix_lb_fluid->numvel;
double etacov[14]; // This is for changes and only moments up to 13 are affected
double rho;
int subNbx = fix_lb_fluid->subNbx;
int subNby = fix_lb_fluid->subNby;
int subNbz = fix_lb_fluid->subNbz;
double ***density_lb = fix_lb_fluid->density_lb;
double ****f_lb = fix_lb_fluid->f_lb;
double ****u_lb = fix_lb_fluid->u_lb;
etacov[0] = etacov[10] = etacov[11] = etacov[12] = etacov[13] = 0.0;
for(int i=0; i<subNbx; i++)
for(int j=0; j<subNby; j++)
for(int k=0; k<subNbz; k++){
rho = density_lb[i][j][k];
etacov[1]=rho*ucmx;
etacov[2]=rho*ucmy;
etacov[3]=rho*ucmz;
etacov[4]=rho*(2.*u_lb[i][j][k][0]*ucmx-ucmx*ucmx);
etacov[5]=rho*(2.*u_lb[i][j][k][1]*ucmy-ucmy*ucmy);
etacov[6]=rho*(2.*u_lb[i][j][k][2]*ucmz-ucmz*ucmz);
etacov[7]=rho*(u_lb[i][j][k][0]*ucmy+u_lb[i][j][k][1]*ucmx-ucmx*ucmy);
etacov[8]=rho*(u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][2]*ucmy-ucmy*ucmz);
etacov[9]=rho*(u_lb[i][j][k][0]*ucmz+u_lb[i][j][k][2]*ucmx-ucmx*ucmz);
if (numvel==15) {
etacov[13]=rho*(u_lb[i][j][k][0]*u_lb[i][j][k][1]*ucmz+u_lb[i][j][k][0]*ucmy*u_lb[i][j][k][2]-
u_lb[i][j][k][0]*ucmy*ucmz+ucmx*u_lb[i][j][k][1]*u_lb[i][j][k][2]-
ucmx*u_lb[i][j][k][1]*ucmz-ucmx*ucmy*u_lb[i][j][k][2]+
ucmx*ucmy*ucmz);
for(int l=0; l<15; l++)
for(int ii=1; ii<14; ii++){
f_lb[i][j][k][l] -= w_lb15[l]*mg_lb15[ii][l]*etacov[ii]*Ng_lb15[ii];
}
}
else // 19-velocity model
for(int l=0; l<19; l++)
for(int ii=1; ii<14; ii++){
f_lb[i][j][k][l] -= w_lb19[l]*mg_lb19[ii][l]*etacov[ii]*Ng_lb19[ii];
}
if(xflag) u_lb[i][j][k][0] -= vcmall[0];
if(yflag) u_lb[i][j][k][1] -= vcmall[1];
if(zflag) u_lb[i][j][k][2] -= vcmall[2];
}
}

11
src/LATBOLTZ/fix_lb_momentum.h
View File

@ -1,6 +1,6 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
http://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -13,7 +13,7 @@
#ifdef FIX_CLASS
// clang-format off
FixStyle(lb/momentum,FixLbMomentum);
FixStyle(lb/momentum,FixLbMomentum)
// clang-format on
#else
@ -23,7 +23,7 @@ FixStyle(lb/momentum,FixLbMomentum);
#include "fix.h"
namespace LAMMPS_NS {
class FixLbMomentum : public Fix {
public:
FixLbMomentum(class LAMMPS *, int, char **);
@ -33,13 +33,14 @@ class FixLbMomentum : public Fix {
private:
int linear;
int xflag, yflag, zflag;
int xflag,yflag,zflag;
double masstotal;
int count;
class FixLbFluid *fix_lb_fluid;
};
} // namespace LAMMPS_NS
} // namespace LAMMPS_NS
#endif
#endif

469
src/LATBOLTZ/fix_lb_pc.cpp
View File

@ -1,469 +0,0 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
#include "fix_lb_pc.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "error.h"
#include "memory.h"
#include "domain.h"
#include "fix_lb_fluid.h"
#include "modify.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixLbPC::FixLbPC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 3)
error->all(FLERR,"Illegal fix lb/pc command");
time_integrate = 1;
// perform initial allocation of atom-based array
// register with Atom class
force_old = nullptr;
up = nullptr;
up_old = nullptr;
grow_arrays(atom->nmax);
atom->add_callback(Atom::GROW);
Gamma_MD = new double[atom->ntypes+1];
int groupbit_lb_fluid = 0;
for (int ifix=0; ifix<modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"lb/fluid")==0) {
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
groupbit_lb_fluid = group->bitmask[modify->fix[ifix]->igroup];
}
if (groupbit_lb_fluid == 0)
error->all(FLERR,"the lb/fluid fix must also be used if using the lb/pc fix");
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int j=0; j<nlocal; j++) {
if ((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
error->one(FLERR,"can only use the lb/pc fix for an atom if also using the lb/fluid fix for that atom");
}
}
/* ---------------------------------------------------------------------- */
FixLbPC::~FixLbPC() {
atom->delete_callback(id,Atom::GROW);
memory->destroy(force_old);
memory->destroy(up);
memory->destroy(up_old);
delete [] Gamma_MD;
}
/* ---------------------------------------------------------------------- */
int FixLbPC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::init()
{
double *Gamma = fix_lb_fluid->Gamma;
double dm_lb = fix_lb_fluid->dm_lb;
double dt_lb = fix_lb_fluid->dt_lb;
MPI_Comm_rank(world,&me);
dtv = update->dt;
dtf = update->dt * force->ftm2v;
for (int i=0; i<=atom->ntypes; i++)
Gamma_MD[i] = Gamma[i]*dm_lb/dt_lb;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::initial_integrate(int /*vflag*/) {
double dtfm;
double **x = atom->x;
double dx[3];
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
compute_up();
for (int i=0; i<nlocal; i++) {
up_old[i][0] = up[i][0];
up_old[i][1] = up[i][1];
up_old[i][2] = up[i][2];
force_old[i][0] = f[i][0];
force_old[i][1] = f[i][1];
force_old[i][2] = f[i][2];
}
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/rmass[i];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/rmass[i];
dx[2] = dtv*v[i][2] + 0.5*(f[i][2]*force->ftm2v - Gamma_MD[type[i]]*(v[i][2]-up[i][2]))*dtv*dtv/rmass[i];
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
// Approximation for v
if (Gamma_MD[type[i]] == 0.0) {
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
} else {
v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
}
}
}
} else {
// this does NOT take varying masses into account
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/mass[type[i]];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/mass[type[i]];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/mass[type[i]];
dx[2] = dtv*v[i][2] + 0.5*(f[i][2]*force->ftm2v - Gamma_MD[type[i]]*(v[i][2]-up[i][2]))*dtv*dtv/mass[type[i]];
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
// Approximation for v
if (Gamma_MD[type[i]] == 0.0) {
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
} else {
v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixLbPC::final_integrate()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
compute_up();
if (rmass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
DMDcoeff = (dtv - rmass[i]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
if (Gamma_MD[type[i]] == 0.0) {
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
} else {
v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv;
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
}
}
}
} else {
// this does NOT take varying masses into account
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/mass[type[i]];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
DMDcoeff = (dtv - mass[type[i]]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
if (Gamma_MD[type[i]] == 0.0) {
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
} else {
v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv;
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixLbPC::grow_arrays(int nmax)
{
memory->grow(force_old,nmax,3,"FixLbPC:force_old");
memory->grow(up_old,nmax,3,"FixLbPC:up_old");
memory->grow(up,nmax,3,"FixLbPC:up");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixLbPC::copy_arrays(int i, int j, int /*delflag*/)
{
force_old[j][0] = force_old[i][0];
force_old[j][1] = force_old[i][1];
force_old[j][2] = force_old[i][2];
up_old[j][0] = up_old[i][0];
up_old[j][1] = up_old[i][1];
up_old[j][2] = up_old[i][2];
up[j][0] = up[i][0];
up[j][1] = up[i][1];
up[j][2] = up[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixLbPC::pack_exchange(int i, double *buf)
{
buf[0] = force_old[i][0];
buf[1] = force_old[i][1];
buf[2] = force_old[i][2];
buf[3] = up_old[i][0];
buf[4] = up_old[i][1];
buf[5] = up_old[i][2];
buf[6] = up[i][0];
buf[7] = up[i][1];
buf[8] = up[i][2];
return 9;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixLbPC::unpack_exchange(int nlocal, double *buf)
{
force_old[nlocal][0] = buf[0];
force_old[nlocal][1] = buf[1];
force_old[nlocal][2] = buf[2];
up_old[nlocal][0] = buf[3];
up_old[nlocal][1] = buf[4];
up_old[nlocal][2] = buf[5];
up[nlocal][0] = buf[6];
up[nlocal][1] = buf[7];
up[nlocal][2] = buf[8];
return 9;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::compute_up()
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double **x = atom->x;
int i,k;
int ix,iy,iz;
int ixp,iyp,izp;
double dx1,dy1,dz1;
int isten,ii,jj,kk;
double r,rsq,weightx,weighty,weightz;
double ****u_lb = fix_lb_fluid->u_lb;
int subNbx = fix_lb_fluid->subNbx;
int subNby = fix_lb_fluid->subNby;
int subNbz = fix_lb_fluid->subNbz;
double dx_lb = fix_lb_fluid->dx_lb;
double dt_lb = fix_lb_fluid->dt_lb;
double FfP[64];
int trilinear_stencil = fix_lb_fluid->trilinear_stencil;
for (i=0; i<nlocal; i++) {
if (mask[i] & groupbit) {
//Calculate nearest leftmost grid point.
//Since array indices from 1 to subNb-2 correspond to the
// local subprocessor domain (not indices from 0), use the
// ceiling value.
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
//Calculate distances to the nearest points.
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
dz1 = x[i][2] - (domain->sublo[2] + (iz-1)*dx_lb);
// Need to convert these to lattice units:
dx1 = dx1/dx_lb;
dy1 = dy1/dx_lb;
dz1 = dz1/dx_lb;
up[i][0]=0.0; up[i][1]=0.0; up[i][2]=0.0;
if (trilinear_stencil==0) {
isten=0;
for (ii=-1; ii<3; ii++) {
rsq=(-dx1+ii)*(-dx1+ii);
if (rsq>=4) {
weightx=0.0;
} else {
r=sqrt(rsq);
if (rsq>1) {
weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else {
weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
for (jj=-1; jj<3; jj++) {
rsq=(-dy1+jj)*(-dy1+jj);
if (rsq>=4) {
weighty=0.0;
} else {
r=sqrt(rsq);
if (rsq>1) {
weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else {
weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
for (kk=-1; kk<3; kk++) {
rsq=(-dz1+kk)*(-dz1+kk);
if (rsq>=4) {
weightz=0.0;
} else {
r=sqrt(rsq);
if (rsq>1) {
weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else {
weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
ixp = ix+ii;
iyp = iy+jj;
izp = iz+kk;
if (ixp==-1) ixp=subNbx+2;
if (iyp==-1) iyp=subNby+2;
if (izp==-1) izp=subNbz+2;
FfP[isten] = weightx*weighty*weightz;
// interpolated velocity based on delta function.
for (k=0; k<3; k++) {
up[i][k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
}
}
}
}
} else {
FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1);
FfP[1] = (1.-dx1)*(1.-dy1)*dz1;
FfP[2] = (1.-dx1)*dy1*(1.-dz1);
FfP[3] = (1.-dx1)*dy1*dz1;
FfP[4] = dx1*(1.-dy1)*(1.-dz1);
FfP[5] = dx1*(1.-dy1)*dz1;
FfP[6] = dx1*dy1*(1.-dz1);
FfP[7] = dx1*dy1*dz1;
ixp = (ix+1);
iyp = (iy+1);
izp = (iz+1);
for (k=0; k<3; k++) { // tri-linearly interpolated velocity at node
up[i][k] = u_lb[ix][iy][iz][k]*FfP[0]
+ u_lb[ix][iy][izp][k]*FfP[1]
+ u_lb[ix][iyp][iz][k]*FfP[2]
+ u_lb[ix][iyp][izp][k]*FfP[3]
+ u_lb[ixp][iy][iz][k]*FfP[4]
+ u_lb[ixp][iy][izp][k]*FfP[5]
+ u_lb[ixp][iyp][iz][k]*FfP[6]
+ u_lb[ixp][iyp][izp][k]*FfP[7];
}
}
for (k=0; k<3; k++)
up[i][k] = up[i][k]*dx_lb/dt_lb;
}
}
}

60
src/LATBOLTZ/fix_lb_pc.h
View File

@ -1,60 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
// clang-format off
FixStyle(lb/pc,FixLbPC);
// clang-format on
#else
#ifndef LMP_FIX_LB_PC_H
#define LMP_FIX_LB_PC_H
#include "fix.h"
namespace LAMMPS_NS {
class FixLbPC : public Fix {
public:
FixLbPC(class LAMMPS *, int, char **);
~FixLbPC();
int setmask();
void init();
void initial_integrate(int);
void final_integrate();
void grow_arrays(int);
void copy_arrays(int, int, int);
// void set_arrays(int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
private:
double dtv, dtf;
int me;
double *Gamma_MD;
double expminusdttimesgamma;
double DMDcoeff;
double **force_old;
double **up;
double **up_old;
void compute_up();
class FixLbFluid *fix_lb_fluid;
};
} // namespace LAMMPS_NS
#endif
#endif

1671
src/LATBOLTZ/fix_lb_rigid_pc_sphere.cpp
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File diff suppressed because it is too large Load Diff

109
src/LATBOLTZ/fix_lb_rigid_pc_sphere.h
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@ -1,109 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
// clang-format off
FixStyle(lb/rigid/pc/sphere,FixLbRigidPCSphere);
// clang-format on
#else
#ifndef LMP_FIX_LB_RIGID_PC_SPHERE_H
#define LMP_FIX_LB_RIGID_PC_SPHERE_H
#include "fix.h"
namespace LAMMPS_NS {
class FixLbRigidPCSphere : public Fix {
public:
FixLbRigidPCSphere(class LAMMPS *, int, char **);
virtual ~FixLbRigidPCSphere();
virtual int setmask();
virtual void init();
virtual void setup(int);
virtual void initial_integrate(int);
virtual void final_integrate();
virtual double compute_scalar();
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
void set_arrays(int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
void pre_neighbor();
int dof(int);
void reset_dt();
double compute_array(int, int);
private:
double **up;
double **up_old;
double *Gamma_MD;
double expminusdttimesgamma, DMDcoeff;
double expminusdttimesgammadiv2;
double force_factor, torque_factor;
double dtv, dtf;
int nbody; // # of rigid bodies
int *nrigid; // # of atoms in each rigid body
int *nrigid_shell;
double *masstotal; // total mass of each rigid body
double *masstotal_shell;
double *sphereradius;
double **xcm; // coords of center-of-mass of each rigid body
double **xcm_old;
double **vcm; // velocity of center-of-mass of each
double **ucm;
double **ucm_old;
double **fcm; // force on center-of-mass of each
double **fcm_old;
double **fcm_fluid;
double **omega; // angular momentum of each in space coords
double **torque; // torque on each rigid body in space coords
double **torque_old;
double **torque_fluid;
double **torque_fluid_old;
double **rotate;
imageint *imagebody; // image flags of xcm of each rigid body
double **fflag; // flag for on/off of center-of-mass force
double **tflag; // flag for on/off of center-of-mass torque
int *body; // which body each atom is part of (-1 if none)
double **sum, **all; // work vectors for each rigid body
int **remapflag; // PBC remap flags for each rigid body
double tfactor; // scale factor on temperature of rigid bodies
int inner_nodes; // ==1 if certain particle are inside the rigid
// body and should not interact with the fluid.
// ==0 otherwise.
int igroupinner; // specifies the particles which are inside the
// spherical rigid body, and do not interact with
// the fluid.
void set_xv();
void set_v();
void compute_up();
class FixLbFluid *fix_lb_fluid;
};
} // namespace LAMMPS_NS
#endif
#endif

51
src/LATBOLTZ/fix_lb_viscous.cpp
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@ -17,7 +17,6 @@
------------------------------------------------------------------------- */
#include "fix_lb_viscous.h"
#include <cstring>
#include "atom.h"
#include "update.h"
#include "respa.h"
@ -38,22 +37,27 @@ FixLbViscous::FixLbViscous(LAMMPS *lmp, int narg, char **arg) :
int groupbit_lb_fluid = 0;
for (int ifix=0; ifix<modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"lb/fluid")==0) {
for(int ifix=0; ifix<modify->nfix; ifix++)
if(strcmp(modify->fix[ifix]->style,"lb/fluid")==0){
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
groupbit_lb_fluid = group->bitmask[modify->fix[ifix]->igroup];
}
if (groupbit_lb_fluid == 0)
if(groupbit_lb_fluid == 0)
error->all(FLERR,"the lb/fluid fix must also be used if using the lb/viscous fix");
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int j=0; j<nlocal; j++) {
if ((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
for(int j=0; j<nlocal; j++){
if((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
error->one(FLERR,"to apply a fluid force onto an atom, the lb/fluid fix must be used for that atom.");
}
}
/* ---------------------------------------------------------------------- */
FixLbViscous::~FixLbViscous()
{
}
@ -73,7 +77,7 @@ int FixLbViscous::setmask()
void FixLbViscous::init()
{
if (utils::strmatch(update->integrate_style,"^respa"))
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
@ -89,7 +93,6 @@ void FixLbViscous::setup(int vflag)
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
@ -108,17 +111,36 @@ void FixLbViscous::post_force(int /*vflag*/)
// magnitude depends on atom type
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double *massp = fix_lb_fluid->massp;
double massfactor;
double **hydroF = fix_lb_fluid->hydroF;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
f[i][0] += hydroF[i][0];
f[i][1] += hydroF[i][1];
f[i][2] += hydroF[i][2];
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfactor = rmass[i]/(rmass[i]+massp[i]);
}
f[i][0] = hydroF[i][0] + massfactor*f[i][0];
f[i][1] = hydroF[i][1] + massfactor*f[i][1];
f[i][2] = hydroF[i][2] + massfactor*f[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massfactor = mass[type[i]]/(mass[type[i]]+massp[i]);
f[i][0] = hydroF[i][0] + massfactor*f[i][0];
f[i][1] = hydroF[i][1] + massfactor*f[i][1];
f[i][2] = hydroF[i][2] + massfactor*f[i][2];
}
}
}
@ -136,3 +158,4 @@ void FixLbViscous::min_post_force(int vflag)
post_force(vflag);
}

4
src/LATBOLTZ/fix_lb_viscous.h
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@ -13,7 +13,7 @@
#ifdef FIX_CLASS
// clang-format off
FixStyle(lb/viscous,FixLbViscous);
FixStyle(lb/viscous,FixLbViscous)
// clang-format on
#else
@ -27,7 +27,7 @@ namespace LAMMPS_NS {
class FixLbViscous : public Fix {
public:
FixLbViscous(class LAMMPS *, int, char **);
virtual ~FixLbViscous() = default;
~FixLbViscous();
int setmask();
void init();
void setup(int);