Chaste  Release::3.4
DiffusionForce.cpp
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34 */
35 
36 #include "DiffusionForce.hpp"
37 #include "NodeBasedCellPopulation.hpp"
38 
39 //Static constant is instantiated here.
40 template<unsigned DIM>
41 const double DiffusionForce<DIM>::msBoltzmannConstant = 4.97033568e-7;
42 
43 template<unsigned DIM>
45  : AbstractForce<DIM>(),
46  mAbsoluteTemperature(296.0), // default to room temperature
47  mViscosity(3.204e-6) // default to viscosity of water at room temperature in (using 10 microns and hours)
48 {
49 }
50 
51 template<unsigned DIM>
53 {
54 }
55 
56 template<unsigned DIM>
58 {
59  assert(newValue > 0.0);
60  mAbsoluteTemperature = newValue;
61 }
62 
63 template<unsigned DIM>
65 {
66  return mAbsoluteTemperature;
67 }
68 
69 template<unsigned DIM>
70 void DiffusionForce<DIM>::SetViscosity(double newValue)
71 {
72  assert(newValue > 0.0);
73  mViscosity = newValue;
74 }
75 
76 template<unsigned DIM>
78 {
79  return mViscosity;
80 }
81 
82 template<unsigned DIM>
84 {
85  return msBoltzmannConstant*mAbsoluteTemperature/(6.0*mViscosity*M_PI);
86 }
87 
88 template<unsigned DIM>
90 {
91  double dt = SimulationTime::Instance()->GetTimeStep();
92 
93  // Iterate over the nodes
94  for (typename AbstractMesh<DIM, DIM>::NodeIterator node_iter = rCellPopulation.rGetMesh().GetNodeIteratorBegin();
95  node_iter != rCellPopulation.rGetMesh().GetNodeIteratorEnd();
96  ++node_iter)
97  {
98  // Get the index, radius and damping constant of this node
99  unsigned node_index = node_iter->GetIndex();
100  double node_radius = node_iter->GetRadius();
101 
102  // If the node radius is zero, then it has not been set...
103  if (node_radius == 0.0)
104  {
105  // ...so throw an exception to avoid dividing by zero when we compute diffusion_constant below
106  EXCEPTION("SetRadius() must be called on each Node before calling DiffusionForce::AddForceContribution() to avoid a division by zero error");
107  }
108 
109  double nu = dynamic_cast<AbstractOffLatticeCellPopulation<DIM>*>(&rCellPopulation)->GetDampingConstant(node_index);
110 
111  /*
112  * Compute the diffusion coefficient D as D = k*T/(6*pi*eta*r), where
113  *
114  * k = Boltzmann's constant,
115  * T = absolute temperature,
116  * eta = dynamic viscosity,
117  * r = cell radius.
118  */
119  double diffusion_const_scaling = GetDiffusionScalingConstant();
120  double diffusion_constant = diffusion_const_scaling/node_radius;
121 
122  c_vector<double, DIM> force_contribution;
123  for (unsigned i=0; i<DIM; i++)
124  {
125  /*
126  * The force on this cell is scaled with the timestep such that when it is
127  * used in the discretised equation of motion for the cell, we obtain the
128  * correct formula
129  *
130  * x_new = x_old + sqrt(2*D*dt)*W
131  *
132  * where W is a standard normal random variable.
133  */
135 
136  force_contribution[i] = (nu*sqrt(2.0*diffusion_constant*dt)/dt)*xi;
137  }
138  node_iter->AddAppliedForceContribution(force_contribution);
139  }
140 }
141 
142 template<unsigned DIM>
143 void DiffusionForce<DIM>::OutputForceParameters(out_stream& rParamsFile)
144 {
145  *rParamsFile << "\t\t\t<AbsoluteTemperature>" << mAbsoluteTemperature << "</AbsoluteTemperature> \n";
146  *rParamsFile << "\t\t\t<Viscosity>" << mViscosity << "</Viscosity> \n";
147 
148  // Call direct parent class
150 }
151 
152 // Explicit instantiation
153 template class DiffusionForce<1>;
154 template class DiffusionForce<2>;
155 template class DiffusionForce<3>;
156 
157 // Serialization for Boost >= 1.36
#define EXCEPTION(message)
Definition: Exception.hpp:143
static SimulationTime * Instance()
double GetAbsoluteTemperature()
NodeIterator GetNodeIteratorEnd()
double GetTimeStep() const
double GetViscosity()
#define EXPORT_TEMPLATE_CLASS_SAME_DIMS(CLASS)
static RandomNumberGenerator * Instance()
NodeIterator GetNodeIteratorBegin(bool skipDeletedNodes=true)
double GetDiffusionScalingConstant()
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh()
void AddForceContribution(AbstractCellPopulation< DIM > &rCellPopulation)
void SetViscosity(double viscosity)
void OutputForceParameters(out_stream &rParamsFile)
virtual void OutputForceParameters(out_stream &rParamsFile)=0
void SetAbsoluteTemperature(double absoluteTemperature)