Chaste  Release::3.4
CardiacSimulation.cpp
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35 
36 #include "CardiacSimulationArchiver.hpp" // Must go first
37 #include "CardiacSimulation.hpp"
38 
39 
40 boost::shared_ptr<AbstractUntemplatedCardiacProblem> CardiacSimulation::GetSavedProblem()
41 {
42  return mSavedProblem;
43 }
44 
45 std::string CardiacSimulation::BoolToString(bool yesNo)
46 {
47  std::string result;
48  if (yesNo)
49  {
50  result = "yes";
51  }
52  else
53  {
54  result = "no";
55  }
56  return result;
57 }
58 
59 void CardiacSimulation::CreateResumeXmlFile(const std::string& rOutputDirectory, const std::string& rArchiveDirectory)
60 {
61  OutputFileHandler handler(rOutputDirectory, false);
63  {
64  out_stream p_file = handler.OpenOutputFile("ResumeParameters.xml");
65  (*p_file) << "<?xml version='1.0' encoding='UTF-8'?>" << std::endl;
66  (*p_file) << "<ChasteParameters xmlns='https://chaste.comlab.ox.ac.uk/nss/parameters/3_0' "
67  << "xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' "
68  << "xsi:schemaLocation='https://chaste.comlab.ox.ac.uk/nss/parameters/3_0 ChasteParameters_3_0.xsd'>" << std::endl;
69  (*p_file) << std::endl;
70  (*p_file) << " <ResumeSimulation>" << std::endl;
71  (*p_file) << " <ArchiveDirectory relative_to='this_file'>" << rArchiveDirectory << "</ArchiveDirectory>" << std::endl;
72  (*p_file) << " <SpaceDimension>" << HeartConfig::Instance()->GetSpaceDimension() << "</SpaceDimension>" << std::endl;
73  (*p_file) << " <SimulationDuration unit='ms'>0.0</SimulationDuration> <!-- Edit with new simulation duration. Please "
74  << "note that the simulation does not restart at t=0 but at the time where the checkpoint was created.-->" << std::endl;
75  (*p_file) << " <Domain>" << HeartConfig::Instance()->GetDomain() << "</Domain>" << std::endl;
76  (*p_file) << " <CheckpointSimulation timestep='" << HeartConfig::Instance()->GetCheckpointTimestep()
77  << "' unit='ms' max_checkpoints_on_disk='" << HeartConfig::Instance()->GetMaxCheckpointsOnDisk()
78  << "'/> <!-- This is optional; if not given, the loaded simulation will NOT itself be checkpointed -->" << std::endl;
79  (*p_file) << " <OutputVisualizer meshalyzer='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithMeshalyzer())
80  << "' vtk='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithVtk())
81  << "' parallel_vtk='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithParallelVtk())
82  << "' cmgui='" << BoolToString(HeartConfig::Instance()->GetVisualizeWithCmgui()) << "'/>" << std::endl;
83  (*p_file) << " </ResumeSimulation>" << std::endl;
84  (*p_file) << std::endl;
85  (*p_file) << " <!-- These elements must exist, but their contents are ignored -->" << std::endl;
86  (*p_file) << " <Physiological/>" << std::endl;
87  (*p_file) << " <Numerical/>" << std::endl;
88  (*p_file) << "</ChasteParameters>" << std::endl;
89  p_file->close();
90  }
91 
93 }
94 
95 CardiacSimulation::CardiacSimulation(std::string parameterFileName,
96  bool writeProvenanceInfo,
97  bool saveProblemInstance)
98  : mSaveProblemInstance(saveProblemInstance)
99 {
100  // If we have been passed an XML file then parse the XML file, otherwise throw
101  if (parameterFileName == "")
102  {
103  EXCEPTION("No XML file name given");
104  }
105  ReadParametersFromFile(parameterFileName);
106  Run();
109  if (writeProvenanceInfo)
110  {
114  }
115 }
116 
117 void CardiacSimulation::ReadParametersFromFile(std::string parameterFileName)
118 {
119  // Ensure the singleton is in a clean state
121  try
122  {
123  // Try the hardcoded schema location first
125  HeartConfig::Instance()->SetParametersFile(parameterFileName);
126  }
127  catch (Exception& e)
128  {
129  if (e.CheckShortMessageContains("Missing file parsing configuration") == "")
130  {
131  // Try using the schema location given in the XML
134  HeartConfig::Instance()->SetParametersFile(parameterFileName);
135  }
136  else
137  {
138  throw e;
139  }
140  }
141 }
142 
143 
144 #define DOMAIN_CASE(VALUE, CLASS, DIM) \
145  case VALUE: \
146  { \
147  CreateAndRun<CLASS<DIM>, DIM>(); \
148  break; \
149  }
150 
151 #define DOMAIN_SWITCH(DIM) \
152  switch (HeartConfig::Instance()->GetDomain()) \
153  { \
154  DOMAIN_CASE(cp::domain_type::Mono, MonodomainProblem, DIM) \
155  DOMAIN_CASE(cp::domain_type::Bi, BidomainProblem, DIM) \
156  DOMAIN_CASE(cp::domain_type::BiWithBath, BidomainWithBathProblem, DIM) \
157  default: \
158  NEVER_REACHED; \
159  } \
160  break
161 // Note that if the domain is not set correctly then the XML parser will have picked it up before now!
162 // Missing semi-colon after break so we can put it after the macro call.
163 
165 {
166  switch (HeartConfig::Instance()->GetSpaceDimension())
167  {
168  case 3:
169  {
170  DOMAIN_SWITCH(3);
171  }
172  case 2:
173  {
174  DOMAIN_SWITCH(2);
175  }
176  case 1:
177  {
178  DOMAIN_SWITCH(1);
179  }
180  default:
181  // We could check for this too in the XML Schema...
182  EXCEPTION("Space dimension not supported: should be 1, 2 or 3");
183  }
184 }
185 
186 // These aren't needed externally
187 #undef DOMAIN_SWITCH
188 #undef DOMAIN_CASE
189 
CardiacSimulation(std::string parameterFileName, bool writeProvenanceInfo=false, bool saveProblemInstance=false)
double GetCheckpointTimestep() const
#define EXCEPTION(message)
Definition: Exception.hpp:143
static bool AmMaster()
Definition: PetscTools.cpp:120
boost::shared_ptr< AbstractUntemplatedCardiacProblem > mSavedProblem
void SetUseFixedSchemaLocation(bool useFixedSchemaLocation)
std::string GetOutputDirectoryFullPath() const
static void WriteProvenanceInfoFile()
cp::domain_type GetDomain() const
out_stream OpenOutputFile(const std::string &rFileName, std::ios_base::openmode mode=std::ios::out|std::ios::trunc) const
unsigned GetSpaceDimension() const
unsigned GetMaxCheckpointsOnDisk() const
std::string BoolToString(bool yesNo)
void CreateResumeXmlFile(const std::string &rOutputDirectory, const std::string &rArchiveDirectory)
void SetParametersFile(const std::string &rFileName)
boost::shared_ptr< AbstractUntemplatedCardiacProblem > GetSavedProblem()
std::string CheckShortMessageContains(std::string expected) const
Definition: Exception.cpp:107
static void Reset()
static void WriteMachineInfoFile(std::string fileBaseName)
#define TRY_IF_MASTER(method)
Definition: PetscTools.hpp:90
static HeartConfig * Instance()
void ReadParametersFromFile(std::string parameterFileName)
static void SetOutputDirectory(const std::string &rOutputDirectory)