Chaste  Release::2018.1
GeneralisedLinearSpringForce.cpp
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35 
36 #include "GeneralisedLinearSpringForce.hpp"
37 
38 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
40  : AbstractTwoBodyInteractionForce<ELEMENT_DIM,SPACE_DIM>(),
41  mMeinekeSpringStiffness(15.0), // denoted by mu in Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
42  mMeinekeDivisionRestingSpringLength(0.5),
43  mMeinekeSpringGrowthDuration(1.0)
44 {
45  if (SPACE_DIM == 1)
46  {
48  }
49 }
50 
51 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
53  unsigned nodeBGlobalIndex,
55  bool isCloserThanRestLength)
56 {
57  return 1.0;
58 }
59 
60 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
62 {
63 }
64 
65 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
66 c_vector<double, SPACE_DIM> GeneralisedLinearSpringForce<ELEMENT_DIM,SPACE_DIM>::CalculateForceBetweenNodes(unsigned nodeAGlobalIndex,
67  unsigned nodeBGlobalIndex,
69 {
70  // We should only ever calculate the force between two distinct nodes
71  assert(nodeAGlobalIndex != nodeBGlobalIndex);
72 
73  Node<SPACE_DIM>* p_node_a = rCellPopulation.GetNode(nodeAGlobalIndex);
74  Node<SPACE_DIM>* p_node_b = rCellPopulation.GetNode(nodeBGlobalIndex);
75 
76  // Get the node locations
77  const c_vector<double, SPACE_DIM>& r_node_a_location = p_node_a->rGetLocation();
78  const c_vector<double, SPACE_DIM>& r_node_b_location = p_node_b->rGetLocation();
79 
80  // Get the node radii for a NodeBasedCellPopulation
81  double node_a_radius = 0.0;
82  double node_b_radius = 0.0;
83 
84  if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
85  {
86  node_a_radius = p_node_a->GetRadius();
87  node_b_radius = p_node_b->GetRadius();
88  }
89 
90  // Get the unit vector parallel to the line joining the two nodes
91  c_vector<double, SPACE_DIM> unit_difference;
92  /*
93  * We use the mesh method GetVectorFromAtoB() to compute the direction of the
94  * unit vector along the line joining the two nodes, rather than simply subtract
95  * their positions, because this method can be overloaded (e.g. to enforce a
96  * periodic boundary in Cylindrical2dMesh).
97  */
98  unit_difference = rCellPopulation.rGetMesh().GetVectorFromAtoB(r_node_a_location, r_node_b_location);
99 
100  // Calculate the distance between the two nodes
101  double distance_between_nodes = norm_2(unit_difference);
102  assert(distance_between_nodes > 0);
103  assert(!std::isnan(distance_between_nodes));
104 
105  unit_difference /= distance_between_nodes;
106 
107  /*
108  * If mUseCutOffLength has been set, then there is zero force between
109  * two nodes located a distance apart greater than mMechanicsCutOffLength in AbstractTwoBodyInteractionForce.
110  */
111  if (this->mUseCutOffLength)
112  {
113  if (distance_between_nodes >= this->GetCutOffLength())
114  {
115  return zero_vector<double>(SPACE_DIM); // c_vector<double,SPACE_DIM>() is not guaranteed to be fresh memory
116  }
117  }
118 
119  /*
120  * Calculate the rest length of the spring connecting the two nodes with a default
121  * value of 1.0.
122  */
123  double rest_length_final = 1.0;
124 
125  if (bool(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)))
126  {
127  rest_length_final = static_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)->GetRestLength(nodeAGlobalIndex, nodeBGlobalIndex);
128  }
129  else if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
130  {
131  assert(node_a_radius > 0 && node_b_radius > 0);
132  rest_length_final = node_a_radius+node_b_radius;
133  }
134 
135  double rest_length = rest_length_final;
136 
137  CellPtr p_cell_A = rCellPopulation.GetCellUsingLocationIndex(nodeAGlobalIndex);
138  CellPtr p_cell_B = rCellPopulation.GetCellUsingLocationIndex(nodeBGlobalIndex);
139 
140  double ageA = p_cell_A->GetAge();
141  double ageB = p_cell_B->GetAge();
142 
143  assert(!std::isnan(ageA));
144  assert(!std::isnan(ageB));
145 
146  /*
147  * If the cells are both newly divided, then the rest length of the spring
148  * connecting them grows linearly with time, until 1 hour after division.
149  */
150  if (ageA < mMeinekeSpringGrowthDuration && ageB < mMeinekeSpringGrowthDuration)
151  {
153 
154  std::pair<CellPtr,CellPtr> cell_pair = p_static_cast_cell_population->CreateCellPair(p_cell_A, p_cell_B);
155 
156  if (p_static_cast_cell_population->IsMarkedSpring(cell_pair))
157  {
158  // Spring rest length increases from a small value to the normal rest length over 1 hour
159  double lambda = mMeinekeDivisionRestingSpringLength;
160  rest_length = lambda + (rest_length_final - lambda) * ageA/mMeinekeSpringGrowthDuration;
161  }
162  if (ageA + SimulationTime::Instance()->GetTimeStep() >= mMeinekeSpringGrowthDuration)
163  {
164  // This spring is about to go out of scope
165  p_static_cast_cell_population->UnmarkSpring(cell_pair);
166  }
167  }
168 
169  /*
170  * For apoptosis, progressively reduce the radius of the cell
171  */
172  double a_rest_length = rest_length*0.5;
173  double b_rest_length = a_rest_length;
174 
175  if (bool(dynamic_cast<NodeBasedCellPopulation<SPACE_DIM>*>(&rCellPopulation)))
176  {
177  assert(node_a_radius > 0 && node_b_radius > 0);
178  a_rest_length = (node_a_radius/(node_a_radius+node_b_radius))*rest_length;
179  b_rest_length = (node_b_radius/(node_a_radius+node_b_radius))*rest_length;
180  }
181 
182  /*
183  * If either of the cells has begun apoptosis, then the length of the spring
184  * connecting them decreases linearly with time.
185  */
186  if (p_cell_A->HasApoptosisBegun())
187  {
188  double time_until_death_a = p_cell_A->GetTimeUntilDeath();
189  a_rest_length = a_rest_length * time_until_death_a / p_cell_A->GetApoptosisTime();
190  }
191  if (p_cell_B->HasApoptosisBegun())
192  {
193  double time_until_death_b = p_cell_B->GetTimeUntilDeath();
194  b_rest_length = b_rest_length * time_until_death_b / p_cell_B->GetApoptosisTime();
195  }
196 
197  rest_length = a_rest_length + b_rest_length;
198  //assert(rest_length <= 1.0+1e-12); ///\todo #1884 Magic number: would "<= 1.0" do?
199 
200  // Although in this class the 'spring constant' is a constant parameter, in
201  // subclasses it can depend on properties of each of the cells
202  double overlap = distance_between_nodes - rest_length;
203  bool is_closer_than_rest_length = (overlap <= 0);
204  double multiplication_factor = VariableSpringConstantMultiplicationFactor(nodeAGlobalIndex, nodeBGlobalIndex, rCellPopulation, is_closer_than_rest_length);
205  double spring_stiffness = mMeinekeSpringStiffness;
206 
207  if (bool(dynamic_cast<MeshBasedCellPopulation<ELEMENT_DIM,SPACE_DIM>*>(&rCellPopulation)))
208  {
209  return multiplication_factor * spring_stiffness * unit_difference * overlap;
210  }
211  else
212  {
213  // A reasonably stable simple force law
214  if (is_closer_than_rest_length) //overlap is negative
215  {
216  //log(x+1) is undefined for x<=-1
217  assert(overlap > -rest_length_final);
218  c_vector<double, SPACE_DIM> temp = multiplication_factor*spring_stiffness * unit_difference * rest_length_final* log(1.0 + overlap/rest_length_final);
219  return temp;
220  }
221  else
222  {
223  double alpha = 5.0;
224  c_vector<double, SPACE_DIM> temp = multiplication_factor*spring_stiffness * unit_difference * overlap * exp(-alpha * overlap/rest_length_final);
225  return temp;
226  }
227  }
228 }
229 
230 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
232 {
233  return mMeinekeSpringStiffness;
234 }
235 
236 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
238 {
239  return mMeinekeDivisionRestingSpringLength;
240 }
241 
242 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
244 {
245  return mMeinekeSpringGrowthDuration;
246 }
247 
248 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
250 {
251  assert(springStiffness > 0.0);
252  mMeinekeSpringStiffness = springStiffness;
253 }
254 
255 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
257 {
258  assert(divisionRestingSpringLength <= 1.0);
259  assert(divisionRestingSpringLength >= 0.0);
260 
261  mMeinekeDivisionRestingSpringLength = divisionRestingSpringLength;
262 }
263 
264 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
266 {
267  assert(springGrowthDuration >= 0.0);
268 
269  mMeinekeSpringGrowthDuration = springGrowthDuration;
270 }
271 
272 template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
274 {
275  *rParamsFile << "\t\t\t<MeinekeSpringStiffness>" << mMeinekeSpringStiffness << "</MeinekeSpringStiffness>\n";
276  *rParamsFile << "\t\t\t<MeinekeDivisionRestingSpringLength>" << mMeinekeDivisionRestingSpringLength << "</MeinekeDivisionRestingSpringLength>\n";
277  *rParamsFile << "\t\t\t<MeinekeSpringGrowthDuration>" << mMeinekeSpringGrowthDuration << "</MeinekeSpringGrowthDuration>\n";
278 
279  // Call method on direct parent class
281 }
282 
283 // Explicit instantiation
284 template class GeneralisedLinearSpringForce<1,1>;
285 template class GeneralisedLinearSpringForce<1,2>;
286 template class GeneralisedLinearSpringForce<2,2>;
287 template class GeneralisedLinearSpringForce<1,3>;
288 template class GeneralisedLinearSpringForce<2,3>;
289 template class GeneralisedLinearSpringForce<3,3>;
290 
291 // Serialization for Boost >= 1.36
virtual Node< SPACE_DIM > * GetNode(unsigned index)=0
virtual void OutputForceParameters(out_stream &rParamsFile)
void UnmarkSpring(std::pair< CellPtr, CellPtr > &rCellPair)
virtual CellPtr GetCellUsingLocationIndex(unsigned index)
Definition: Node.hpp:58
c_vector< double, SPACE_DIM > CalculateForceBetweenNodes(unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
static SimulationTime * Instance()
double GetTimeStep() const
std::pair< CellPtr, CellPtr > CreateCellPair(CellPtr pCell1, CellPtr pCell2)
#define EXPORT_TEMPLATE_CLASS_ALL_DIMS(CLASS)
void SetMeinekeDivisionRestingSpringLength(double divisionRestingSpringLength)
bool IsMarkedSpring(const std::pair< CellPtr, CellPtr > &rCellPair)
void SetMeinekeSpringGrowthDuration(double springGrowthDuration)
const c_vector< double, SPACE_DIM > & rGetLocation() const
Definition: Node.cpp:139
virtual double VariableSpringConstantMultiplicationFactor(unsigned nodeAGlobalIndex, unsigned nodeBGlobalIndex, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool isCloserThanRestLength)
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh()
virtual void OutputForceParameters(out_stream &rParamsFile)
void SetMeinekeSpringStiffness(double springStiffness)
double GetRadius()
Definition: Node.cpp:248