Chaste  Release::2018.1
AbstractOdeBasedCellCycleModel.cpp
1 /*
2 
3 Copyright (c) 2005-2018, University of Oxford.
4 All rights reserved.
5 
6 University of Oxford means the Chancellor, Masters and Scholars of the
7 University of Oxford, having an administrative office at Wellington
8 Square, Oxford OX1 2JD, UK.
9 
10 This file is part of Chaste.
11 
12 Redistribution and use in source and binary forms, with or without
13 modification, are permitted provided that the following conditions are met:
14  * Redistributions of source code must retain the above copyright notice,
15  this list of conditions and the following disclaimer.
16  * Redistributions in binary form must reproduce the above copyright notice,
17  this list of conditions and the following disclaimer in the documentation
18  and/or other materials provided with the distribution.
19  * Neither the name of the University of Oxford nor the names of its
20  contributors may be used to endorse or promote products derived from this
21  software without specific prior written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29 GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30 HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31 LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32 OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 
34 */
35 
36 #include "AbstractOdeBasedCellCycleModel.hpp"
37 
39  boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
40  : CellCycleModelOdeHandler(lastTime, pOdeSolver),
41  mDivideTime(lastTime)
42 {
44 }
45 
47 {
48 }
49 
51  : AbstractCellCycleModel(rModel),
53  mDivideTime(rModel.mDivideTime)
54 {
55  /*
56  * Initialize only those member variables defined in this class.
57  *
58  * The member variables mBirthTime, mReadyToDivide and mDimension
59  * are initialized in the AbstractCellCycleModel constructor.
60  */
61 }
62 
64 {
66  mLastTime = birthTime;
67  mDivideTime = birthTime;
68 }
69 
71 {
72  assert(mpCell != nullptr);
73 
74  if (!mReadyToDivide)
75  {
76  assert(mpOdeSystem != nullptr);
77 
78  double current_time = SimulationTime::Instance()->GetTime();
79 
80  if (current_time > mLastTime)
81  {
82  // Update whether a stopping event has occurred
83  mReadyToDivide = SolveOdeToTime(current_time);
84 
85  // Check no concentrations have gone negative
86  for (unsigned i=0; i<mpOdeSystem->GetNumberOfStateVariables(); i++)
87  {
88  if (mpOdeSystem->rGetStateVariables()[i] < -DBL_EPSILON)
89  {
90  // LCOV_EXCL_START
91  EXCEPTION("A protein concentration " << i << " has gone negative (" <<
92  mpOdeSystem->rGetStateVariables()[i] << ")\n"
93  << "Chaste predicts that the CellCycleModel numerical method is probably unstable.");
94  // LCOV_EXCL_STOP
95  }
96  }
97  if (mReadyToDivide)
98  {
100  }
101  }
102  }
103  return mReadyToDivide;
104 }
105 
107 {
108  assert(mReadyToDivide);
112  mDivideTime = DBL_MAX;
113 }
114 
116 {
117  double stop_time = DOUBLE_UNSET;
118  if (mpOdeSolver->StoppingEventOccurred())
119  {
120  stop_time = mpOdeSolver->GetStoppingTime();
121  }
122  return stop_time;
123 }
124 
126 {
127  // No new parameters to output, so just call method on direct parent class
129 }
boost::shared_ptr< AbstractCellCycleModelOdeSolver > mpOdeSolver
virtual void SetBirthTime(double birthTime)
#define EXCEPTION(message)
Definition: Exception.hpp:143
static SimulationTime * Instance()
const double DOUBLE_UNSET
Definition: Exception.hpp:56
AbstractOdeBasedCellCycleModel(const AbstractOdeBasedCellCycleModel &rModel)
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)=0
double GetTime() const
virtual void OutputCellCycleModelParameters(out_stream &rParamsFile)
bool SolveOdeToTime(double currentTime)