Chaste
Commit::baa90ac2819b962188b7562f2326be23c47859a7
CellBasedSimulationArchiver.hpp
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/*
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Copyright (c) 2005-2024, University of Oxford.
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All rights reserved.
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University of Oxford means the Chancellor, Masters and Scholars of the
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University of Oxford, having an administrative office at Wellington
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Square, Oxford OX1 2JD, UK.
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This file is part of Chaste.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the University of Oxford nor the names of its
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contributors may be used to endorse or promote products derived from this
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software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
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GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
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OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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#ifndef CELLBASEDSIMULATIONARCHIVER_HPP_
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#define CELLBASEDSIMULATIONARCHIVER_HPP_
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// Must be included before any other serialization headers
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#include "
CheckpointArchiveTypes.hpp
"
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#include <string>
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// The headers below are needed by the templated implementation, which is in this header
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#include <fstream>
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#include <sstream>
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#include "ArchiveLocationInfo.hpp"
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#include "ArchiveOpener.hpp"
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#include "FileFinder.hpp"
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#include "SimulationTime.hpp"
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template
<
unsigned
ELEMENT_DIM,
class
SIM,
unsigned
SPACE_DIM=ELEMENT_DIM>
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class
CellBasedSimulationArchiver
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{
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public
:
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static
SIM*
Load
(
const
std::string& rArchiveDirectory,
const
double
& rTimeStamp);
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static
void
Save
(SIM* pSim);
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};
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template
<
unsigned
ELEMENT_DIM,
class
SIM,
unsigned
SPACE_DIM>
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SIM*
CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM>::Load
(
const
std::string& rArchiveDirectory,
const
double
& rTimeStamp)
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{
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std::ostringstream time_stamp;
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time_stamp << rTimeStamp;
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std::string archive_filename =
"cell_population_sim_at_time_"
+ time_stamp.str() +
".arch"
;
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std::string mesh_filename =
"mesh_"
+ time_stamp.str();
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FileFinder
archive_dir(rArchiveDirectory +
"/archive/"
,
RelativeTo::ChasteTestOutput
);
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ArchiveLocationInfo::SetMeshPathname
(archive_dir, mesh_filename);
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// Create an input archive
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ArchiveOpener<boost::archive::text_iarchive, std::ifstream>
arch_opener(archive_dir, archive_filename);
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boost::archive::text_iarchive* p_arch = arch_opener.
GetCommonArchive
();
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// Load the simulation
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SIM* p_sim;
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(*p_arch) >> p_sim;
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return
p_sim;
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}
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template
<
unsigned
ELEMENT_DIM,
class
SIM,
unsigned
SPACE_DIM>
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void
CellBasedSimulationArchiver<ELEMENT_DIM, SIM, SPACE_DIM>::Save
(SIM* pSim)
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{
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// Get the simulation time as a string
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const
SimulationTime
* p_sim_time =
SimulationTime::Instance
();
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assert(p_sim_time->
IsStartTimeSetUp
());
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std::ostringstream time_stamp;
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time_stamp << p_sim_time->
GetTime
();
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// Set up folder and filename of archive
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FileFinder
archive_dir(pSim->GetOutputDirectory() +
"/archive/"
,
RelativeTo::ChasteTestOutput
);
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std::string archive_filename =
"cell_population_sim_at_time_"
+ time_stamp.str() +
".arch"
;
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ArchiveLocationInfo::SetMeshFilename
(std::string(
"mesh_"
) + time_stamp.str());
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// Create output archive
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ArchiveOpener<boost::archive::text_oarchive, std::ofstream>
arch_opener(archive_dir, archive_filename);
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boost::archive::text_oarchive* p_arch = arch_opener.
GetCommonArchive
();
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// Archive the simulation (const-ness would be a pain here)
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(*p_arch) & pSim;
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}
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#endif
/*CELLBASEDSIMULATIONARCHIVER_HPP_*/
CheckpointArchiveTypes.hpp
ArchiveLocationInfo::SetMeshFilename
static void SetMeshFilename(const std::string &rFilename)
Definition
ArchiveLocationInfo.cpp:69
ArchiveLocationInfo::SetMeshPathname
static void SetMeshPathname(const FileFinder &rDirectory, const std::string &rFilename)
Definition
ArchiveLocationInfo.cpp:46
ArchiveOpener
Definition
ArchiveOpener.hpp:62
ArchiveOpener::GetCommonArchive
Archive * GetCommonArchive()
Definition
ArchiveOpener.hpp:98
CellBasedSimulationArchiver
Definition
CellBasedSimulationArchiver.hpp:60
CellBasedSimulationArchiver::Load
static SIM * Load(const std::string &rArchiveDirectory, const double &rTimeStamp)
Definition
CellBasedSimulationArchiver.hpp:90
CellBasedSimulationArchiver::Save
static void Save(SIM *pSim)
Definition
CellBasedSimulationArchiver.hpp:118
FileFinder
Definition
FileFinder.hpp:71
SimulationTime
Definition
SimulationTime.hpp:56
SimulationTime::IsStartTimeSetUp
bool IsStartTimeSetUp() const
Definition
SimulationTime.cpp:136
SimulationTime::GetTime
double GetTime() const
Definition
SimulationTime.cpp:92
SimulationTime::Instance
static SimulationTime * Instance()
Definition
SimulationTime.cpp:46
RelativeTo::ChasteTestOutput
@ ChasteTestOutput
Definition
FileFinder.hpp:57
cell_based
src
simulation
CellBasedSimulationArchiver.hpp
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