# 2.5. Colloids¶

## 2.5.1. Introducing colloids¶

If no relevant key words are present, no colloids will be expected at run time. The simulation will progress in the usual fashion with fluid only.

If colloids are required, the colloid_init key word must be present to allow the code to determine where colloid information will come from. The options for the colloid_init key word are summarised below:

colloid_init             none

#  none                  no colloids [DEFAULT]
#  input_one             one colloid from input file
#  input_two             two colloids from input file
#  input_three           three colloids from input file
#  input_random          Small number at random
#  from_file             Read a separate file (including all restarts)


For idealised simulations which require 1, 2, or 3 colloids, relevant initial state information for each particle can be included in the input file. In principle, most of the colloid state as defined in the colloid state structure in colloid.h may be specified. (Some state is reserved for internal use only and cannot be set from the input file.) Furthermore, not all the state is relevant in all simulations — quantities such as charge and wetting parameters may not be required, in which case they a simply ignored.

A minimal initialisation is shown in the following example:

colloid_init              input_one

colloid_one_a0            1.25
colloid_one_ah            1.25
colloid_one_r             12.0_12.0_12.0


This initialises a single colloid with an input radius $$a_0=1.25$$, and a hydrodynamic radius $$a_h=1.25$$; in general both are required, but they do not have to be equal. A valid position is required within the extent of the system $$0.5 < x,y,z < L + 0.5$$ as specified by the size key word. State which is not explicitly defined is initialised to zero.

## 2.5.2. Single colloid initialisation¶

A full list of colloid state-related key words is as follows. All the quantities are floating point numbers unless explicitly stated to be otherwise:

# colloid_one_nbonds      (integer) number of bonds
#   colloid_one_bond1     (integer) index of bond partner 1
#   colloid_one_bond2     (integer) index of bond partner 2
# colloid_one_isfixedr    colloid has fixed position (integer 0 or 1)
# colloid_one_isfixedv    colloid has fixed velocity (integer 0 or 1)
# colloid_one_isfixedw    colloid has fixed angular velocity (0 or 1)
# colloid_one_isfixeds    colloid has fixed spin (0 or 1)
# colloid_one_type        default'' COLLOID_TYPE_DEFAULT
#                         active''  COLLOID_TYPE_ACTIVE
#                         subgrid'' COLLOID_TYPE_SUBGRID
# colloid_one_al          subgrid offset parameter (subgrid only)
# colloid_one_r           position vector
# colloid_one_v           velocity (vector)
# colloid_one_w           angular velocity (vector)
# colloid_one_s           spin (unit vector)
# colloid_one_m           direction of motion (unit) vector for swimmers


Note that for magnetic particles, the appropriate initialisation involves the spin key word colloid_one_s which relates to the dipole moment $$\mu \mathbf{s}_i$$, while colloid_one_m relates to the direction of motion vector. Do not confuse the two. It is possible in principle to have magnetic active particles, in which case the dipole direction or spin ($$\mathbf{s}_i$$) and the direction of swimming motion $$\mathbf{m}_i$$ are allowed to be distinct.

# colloid_one_b1          Squirmer parameter B_1
# colloid_one_b2          Squirmer parameter B_2
# colloid_one_rng         (integer) random number generator state
# colloid_one_q0          charge (charge species 0)
# colloid_one_q1          charge (charge species 1)
# colloid_one_epsilon     Permeativity
# colloid_one_c           Wetting parameter C
# colloid_one_h           Wetting parameter H


### 2.5.2.1. Example: Single active particle (a squirmer)¶

The following example shows a single active particle with initial swimming direction along the $$x$$-axis.

colloid_init              input_one

colloid_one_type          active
colloid_one_a0            7.25
colloid_one_ah            7.25
colloid_one_r             32.0_32.0_32.0
colloid_one_v             0.0_0.0_0.0
colloid_one_m             1.0_0.0_0.0
colloid_one_b1            0.05
colloid_one_b2            0.05


### 2.5.2.2. Fixed position or velocity¶

It is possible to fix the position or velocity of a colloid via

colloid_one_isfixedr       1
colloid_one_isfixedv       1


It is also possible to do this on a per co-ordinate direction basis using

colloid_one_isfixedrxyz    0_0_1
colloid_one_isfixedvxyz    0_0_1


to, for example, fix the $$z$$-poisition and velocity components only.

## 2.5.3. Many colloid initialisation at random¶

For suspensions with more than few colloids, but still at relatively low volume fraction (10–20% by volume), it is possible to request initialisation at random positions.

The additional key word value pair colloid_random_no determines the total number of particles to be placed in the system. To prevent particles being initialised very close together, which can cause problems in the first few time steps if strong potential interactions are present, a grace'' distance or minimum surface-surface separation may also be specified (colloid_random_dh).

The following example asks for 100 colloids to be initialised at random positions, with a minimum separation of 0.5 lattice spacing.

colloid_init              input_random

colloid_random_no         100             # Total number of colloids
colloid_random_dh         0.5             # Grace'' distance

colloid_random_a0         2.30
colloid_random_ah         2.40


An input radius and hydrodynamic radius must be provided: these are the same for all colloids. If specific initialisations of the colloid state (excepting the position) other than the radii are wanted, values should be provided as for the single particle case in the preceding section, but using colloid_random_a0 in place of colloid_one_a0 and so on.

The code will try to initialise the requested number in the current system size, but only makes a finite number of attempts to place particles at random with no overlaps. (The initialisation will also take into account the presence of any solid walls, using the same grace distance.) If the the number of particles is too large, the code will halt with a message to that effect.

In general, colloid information for a arbitrary configuration with many particles should be read from a pre-prepared file. See the section on File I/O for further information on reading files.

## 2.5.4. Colloid interactions¶

Note that two-body pair-potential interactions are defined uniformly for all colloids in a simulation. The same is true for lubrication corrections. There are a number of constraints related to the computation of interactions discussed below.

### 2.5.4.1. Boundary-colloid lubrication correction¶

Lubrication corrections (here the normal force) between a flat wall are required to prevent overlap between colloid and the wall. The cutoff distance is set via the key word value pair

boundary_lubrication_rcnormal    0.5    # normal cut-off distance
# Note this is 'rcnormal'


It is recommended that this is used in all cases involving walls. A reasonable value for the cut off is in the range $$0.1 < h_c < 0.5$$ in lattice units, and should be calibrated for particle hydrodynamic radius and fluid viscosity $$\eta$$ if exact results are important.

The form of the lubrication correction for a colloid of hydrodynamic radius $$a_h$$ and velocity $$U_\alpha$$ is based on the analytical expression for the lubrication force between a place wall and a sphere:

$f_\alpha = - 6\pi \eta a_h \left( \frac{1}{h} - \frac{1}{h_c} \right) {\hat n}_\beta U_\beta {\hat n}_\alpha \quad\quad (h < h_c)$

where $${\hat n}_\alpha$$ is the unit normal between the wall and the centre of the colloid. The correction is zero for $$h > h_c$$. The surface-surface separation is $$h$$ and the cut off is $$h_c$$ as illustrated in the following diagram on the left. In this illustration, the wall position (full line) is at the default value of $$x = 0.5for the lower end of the system in the :math:x$$-direction.

In some situations it may be useful to prevent colloids approaching the wall to within some fixed separation. It is possible to provide a uniform offset the apparent position of the wall by a fixed amount $$\delta h$$. This is illustrated on the right above. The lubrication correction will then diverge at the new wall position (dotted line). This can be useful to maintain clear fluid lattice sites between wall and colloid.

The relevant input key is

boundary_lubrication_dhnormal    0.2    # normal offset distance (+ve)
# [Default: 0]


For both the cut-off, and the offset distance, there is a single input value which takes effect in all three co-ordinate directions if a wall is present in the corresponding direction. In practice, the lubrication correction between wall and colloid should be very robust.

### 2.5.4.2. Boundary-colloid soft sphere potential¶

In some circumstances it may be desirable to use a conservative potential at a boundary wall in place of the lubrication correction. In this case a cut-and-shifted soft sphere potential is available. Foe example:

wall_ss_cut_on       yes                    # Switch
wall_ss_cut_epsilon  0.001                  # Energy scale
wall_ss_cut_sigma    0.1                    # Length scale
wall_ss_cut_nu       2.0                    # Exponent
wall_ss_cut_hc       0.5                    # wall-surface cut off


Both the exponent and the wall-surface cut off should be positive. The potential will take effect at boundary walls in all directions.

### 2.5.4.3. Colloid-colloid lubrication corrections¶

The key words to activate the calculation of lubrication corrections are:

lubrication_on                   1
lubrication_normal_cutoff        0.5
lubrication_tangential_cutoff    0.05


### 2.5.4.4. Soft-sphere potential¶

A cut-and-shifted soft-sphere potential of the form $$v \sim \epsilon (\sigma/r)^\nu$$ is available. Some trial-and-error with the parameters may be required in any given situation to ensure simulation stability in the long run. The following gives an example of the relevant input key words:

soft_sphere_on            1                 # integer 0/1 for off/on
soft_sphere_epsilon       0.0004            # energy units
soft_sphere_sigma         1.0               # a length
soft_sphere_nu            1.0               # exponent is positive
soft_sphere_cutoff        2.25              # a surface-surface separation


### 2.5.4.5. Soft-sphere potential (type-specific)¶

This potential is of the same form as the basic cut-and-shifted soft-sphere potential described above, but allows different parameters to be specified for colloids with different interaction type. The interaction type is an integer specified by the appropriate element of the colloid structure, e.g., via input

colloid_one_interact_type   0
...
colloid_two_interact_type   1


specifying two different types (0 and 1). The first type must have index 0. Interactions between different pairs then all have the form $$v_{ij} \sim \epsilon_{ij} (\sigma_{ij}/r)^{\nu_{ij}}$$.

The type specific pair interaction is then introduced via

pair_ss_cut_ij          yes
pair_ss_cut_ij_ntypes   2


the second key value pair giving the number of types expected. The parameters then form a symmetric matrix, for which we specific the upper triangle as a flattened vector. In the case of two types, there are three independent parameters, e.g.,

pair_ss_cut_ij_epsilon  0.2_0.1_0.05  # epsilon_00, _01, _11 in order


where we specify $$\epsilon_{00}, \epsilon_{01}$$ and $$\epsilon_{11}$$, being the interaction energies for interactions bewtween pairs of type (0,0), (0,1), and (1,1) respectively. The value $$\epsilon_{10}$$ is set to be the same as $$\epsilon_{01}$$ internally. A full set of key value pairs might be

pair_ss_cut_ij          yes           # Switch on
pair_ss_cut_ij_ntypes   2             # Number of types n
pair_ss_cut_ij_epsilon  0.0_0.1_0.0   # n(n+1)/2 epsilon parameters
pair_ss_cut_ij_sigma    0.0_2.0_0.0   # n(n+1)/2 sigma parameters
pair_ss_cut_ij_nu       1.0_1.0_3.0   # n(n+1)/2 nu exponents
pair_ss_cut_ij_hc       0.1_0.4_0.1   # n(n+1)/2 surface-surface cut offs


The user must ensure all colloids have appropriate interaction types, i.e., the interaction type does not exceed 1 in this case.

### 2.5.4.6. Lennard-Jones potential¶

The Lennard-Jones potential is controlled by the following key words:

lennard_jones_on          1                 # integer 0/1 off/on
lj_epsilon                0.1               # energy units
lj_sigma                  2.6               # potential length scale
lj_cutoff                 8.0               # a centre-centre separation


### 2.5.4.7. Yukawa potential¶

A cut-and-shifted Yukawa potential of the form $$v \sim \epsilon \exp(-\kappa r)/r$$ is available using the following key word value pairs:

yukawa_on                 1                 # integer 0/1 off/on
yukawa_epsilon            1.330             # energy units
yukawa_kappa              0.725             # an inverse length
yukawa_cutoff             16.0              # a centre-centre cutoff


### 2.5.4.8. Dipole-dipole interaction and the Ewald sum¶

The Ewald sum is completely specified in the input file by the uniform dipole strength $mu$ and the real-space cut off $$r_c$$.

ewald_sum                 1                 # integer 0/1 off/on
ewald_mu                  0.285             # dipole strength mu
ewald_rc                  16.0              # real space cut off


If short range interactions are required, particle information is stored in a cell list, which allows efficient computation of the potentially $$N^2$$ interactions present. This gives rise to a constraint that the width of the cells must be large enough that all relevant interactions are included. This generally means that the cells must be at least $$2a_h + h_c$$ where $$h_c$$ is the largest relevant cut off distance.

The requirement for at least two cells per local domain in parallel means that there is a associated minimum local domain size. This is computed at run time on the basis of the input. If the local domain is too small, the code will terminate with an error message. The local domain size should be increased.

### 2.5.4.9. External forces¶

The following example requests a uniform body force in the negative $$z$$-direction on all particles.

colloid_gravity           0.0_0.0_-0.001    # vector


The counterbalancing body force on the fluid which enforces the constraint of momentum conservation for the system as a whole is computed automatically by the code at each time step.

Note: in a real system, a gravitation force on a colloid is related to buoyancy $$F \propto \Delta\rho g$$, where the density difference is that between the colloid and the surrounding fluid, and $$g$$ is an acceleration. In a system where there is no density contrast, as we have here (typically), the “gravity” is the product $$\Delta\rho g$$. Formally, this may be viewed as the limit that $$\Delta\rho \rightarrow 0$$, combined with the limit $$g \rightarrow \infty$$, but the limit of the product is finite.

## 2.5.5. Liquid crystal anchoring at colloid surfaces¶

The preferred orientation of the liquid crystal director at the surface of a colloid can be of one of two different types:

lc_anchoring_coll        normal
lc_anchoring_coll        planar


For both cases, the chosen condition appliess to all colloids in the system in the same way.

The liquid crystal anchoring boundary condition is implemented via the calculation of the tensor order parameter gradients at the surface of the colloid. We assume there is a surface free energy density (per unit area)

$f_s = f_s(Q_{\alpha\beta}, Q^0_{\alpha\beta})$

where $$Q_{\alpha\beta}$$ us the adjacent fluid order parameter, and $$Q^0_{\alpha\beta}$$ is some preferred otder parameter determined by the type of anchoring.

The boundary condition is derived from the Euler-Lagrange equation, and contains gradient terms in the bulk free energy density and the surface free energy density $$f$$ and $$f_s$$, along with the outward unit normal at the surface $$\hat{n}_\gamma$$:

A suitable gradient computation must be selected (see below).

### 2.5.5.1. Normal (or homoetropic) anchoring at colloid surfaces¶

If the preferred orientation of order at the colloid surface is normal to the surface (also referred to as homoetropic anchoring), the surface free energy density per unit area may be written

$f_s = {\textstyle\frac{1}{2}} w_1 (Q_{\alpha\beta} - Q^0_{\alpha\beta})^2.$

Here, $$w_1$$ is a parameter, and $$Q_{\alpha\beta}$$ is the local fluid order parameter. The preferred orientation is based on the outward normal $$\hat{n}_\gamma$$ at the surface (in the direction from the centre of the colloid to the relevant fluid site at the surface). The order parameter tensor

$Q^0_{\alpha\beta} = {\textstyle\frac{1}{2}} A (3\hat{n}_\alpha \hat{n}_\beta - \delta_{\alpha\beta})$

The value of $$A$$ corresponds to that which minimises the bulk free energy (depending on the temperature $$\gamma$$). The full boundary condition for the order parameter gradient at the colloid surface then contains the term

$\frac{\partial f_s}{\partial Q_{\alpha\beta}} = -w_1 (Q_{\alpha\beta} - Q^0_{\alpha\beta}).$

The relevant input key/value pairs for normal colloid anchoring are:

lc_coll_anchoring      normal     # anchoring type
lc_coll_anchoring_w1   0.002      # free energy parameter w_1


It is often appropriate to set the value of the surface free energy parameter in the context of the bulk elastic constant, e.g., by considering the dimensionless group $$w_1/\kappa a$$, where $$a$$ is the radius of the colloid.

As an example, an ordinary nematic is initialised with the director along the $$x$$-direction, and a single stationary sphereical colloid with normal anchoring introduced to the system. The nematic is allowed to relax with no hydrodynamics. A section of the resulting director field is shown for a “weak” anchoring case (left), and a “strong” anchoring case (right). The $$x$$-direction is in the horizontal. In the strong anchoring case, it can be seen that a defect in the orientational order has appeared above and below the surface of the colloid. In three dimensions, this defect is present all around the circumference of the colloid and forms a “Saturn ring”.

While the nominal radius of the colloid is indicated by the circle, it should be remembered that the discrete shape is block-like, as indicated by the presence of director in individual grid cells.

### 2.5.5.2. Planar (or degenerate) anchoring at colloid surfaces¶

For planar anchoring, the preferred orientation is in the local tangent plane at the surface: this is a degenerate case as any orientation in the plane is energetically equivalent. An appropriate boundary condition is described by Fournier and Galatola [FournierGalatola2005], which we write as

$f_s = \textstyle{\frac{1}{2}} w_1 (\tilde{Q}_{\alpha\beta} - \tilde{Q}^\perp_{\alpha\beta})^2 + \textstyle{\frac{1}{2}} w_2 (\tilde{Q}^2 - S_0^2)^2.$

To compute this term we take the local fluid order parameter $$Q_{\alpha\beta}$$, form the quantity

$\tilde{Q} = Q_{\alpha\beta} + \textstyle{\frac{1}{2}} A \delta_{\alpha\beta}$

which is then projected onto the tangent plane via $$\tilde{Q}^\perp_{\alpha\beta} = P_{\alpha\gamma} \tilde{Q}_{\gamma\sigma} P_{\sigma\beta}$$ with the local surface normal entering through $$P_{\alpha\beta} = \delta_{\alpha\beta} - \hat{n}_\alpha \hat{n}_\beta$$. (Again, the normal at the colloid surface is based on the displacement from the colloid centre.) The full boundary condition arising from the surface free energy contains the terms

$\frac{\partial f_s}{\partial Q_{\alpha\beta}} = - w_1(\tilde{Q}_{\alpha\beta} - \tilde{Q}^\perp_{\alpha\beta}) - 2w_2(\tilde{Q}^2_{\alpha\beta} - S_0^2) \tilde{Q}_{\alpha\beta}.$

The term $$S_0 = 3A/2$$, with amplitude $$A$$ as described above for normal anchoring.

Relevant input parameters are:

lc_coll_anchoring      planar
lc_coll_anchoring_w1   0.01        # both w1 and w2 must be present
lc_coll_anchoring_w2   0.005


Following the example for normal anchoring, the illustration below shows the result for planar anchoring with $$w_1 = w_2$$ (weak and strong cases are left and right, respectively). In the strong case one can identify a pair of point defects at either side of the colloid, usually referred to as “boojums”. Note that the director has actually rotated into the third dimension at these points and so appears forshortened.

### 2.5.5.3. Anchoring when more than one colloid is present¶

If more than one colloid is present in the system, then the surface normal can become poorly defined if adjacent lattice sites are occupied by different colloids. If such cases the anchoring term is set to zero in the boundary condition. The advice here is to prevent close approaches between colloids by means of, e.g., a soft-sphere potential. This should ensure that fluid sites are always present in the gap.