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Fergus Cooper
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| build/ | ||
|
|
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>TemplateProject</name> | ||
| <comment></comment> | ||
| <projects> | ||
| <project>Chaste</project> | ||
| </projects> | ||
| <buildSpec> | ||
| <buildCommand> | ||
| <name>org.python.pydev.PyDevBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.cdt.make.core.makeBuilder</name> | ||
| <triggers>clean,full,incremental,</triggers> | ||
| <arguments> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.core.errorOutputParser</key> | ||
| <value>org.eclipse.cdt.core.MakeErrorParser;org.eclipse.cdt.core.GCCErrorParser;org.eclipse.cdt.core.GASErrorParser;org.eclipse.cdt.core.GLDErrorParser;org.eclipse.cdt.core.VCErrorParser;</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.append_environment</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.autoBuildTarget</key> | ||
| <value>all</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.arguments</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.command</key> | ||
| <value>scons</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.location</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.target.auto</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.target.clean</key> | ||
| <value>-c</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.build.target.inc</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.buildArguments</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.buildCommand</key> | ||
| <value>scons</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.buildLocation</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.cleanBuildTarget</key> | ||
| <value>-c</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.enableAutoBuild</key> | ||
| <value>false</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.enableCleanBuild</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.enableFullBuild</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.enabledIncrementalBuild</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.environment</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.fullBuildTarget</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.incrementalBuildTarget</key> | ||
| <value></value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.stopOnError</key> | ||
| <value>false</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key> | ||
| <value>false</value> | ||
| </dictionary> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.cdt.make.core.ScannerConfigBuilder</name> | ||
| <arguments> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.ScannerConfigDiscoveryEnabled</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.esiProviderCommandEnabled</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.esiProviderParserId</key> | ||
| <value>org.eclipse.cdt.make.core.GCCSpecsConsoleParser</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.makeBuilderParserEnabled</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.makeBuilderParserId</key> | ||
| <value>org.eclipse.cdt.make.core.GCCScannerInfoConsoleParser</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.siProblemGenerationEnabled</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| <dictionary> | ||
| <key>org.eclipse.cdt.make.core.useDefaultESIProviderCmd</key> | ||
| <value>true</value> | ||
| </dictionary> | ||
| </arguments> | ||
| </buildCommand> | ||
| </buildSpec> | ||
| <natures> | ||
| <nature>org.eclipse.cdt.core.cnature</nature> | ||
| <nature>org.eclipse.cdt.make.core.makeNature</nature> | ||
| <nature>org.eclipse.cdt.make.core.ScannerConfigNature</nature> | ||
| <nature>org.eclipse.cdt.core.ccnature</nature> | ||
| <nature>org.python.pydev.pythonNature</nature> | ||
| </natures> | ||
| </projectDescription> |
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| # Copyright (c) 2005-2017, University of Oxford. | ||
| # All rights reserved. | ||
| # | ||
| # University of Oxford means the Chancellor, Masters and Scholars of the | ||
| # University of Oxford, having an administrative office at Wellington | ||
| # Square, Oxford OX1 2JD, UK. | ||
| # | ||
| # This file is part of Chaste. | ||
| # | ||
| # Redistribution and use in source and binary forms, with or without | ||
| # modification, are permitted provided that the following conditions are met: | ||
| # * Redistributions of source code must retain the above copyright notice, | ||
| # this list of conditions and the following disclaimer. | ||
| # * Redistributions in binary form must reproduce the above copyright notice, | ||
| # this list of conditions and the following disclaimer in the documentation | ||
| # and/or other materials provided with the distribution. | ||
| # * Neither the name of the University of Oxford nor the names of its | ||
| # contributors may be used to endorse or promote products derived from this | ||
| # software without specific prior written permission. | ||
| # | ||
| # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE | ||
| # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE | ||
| # GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) | ||
| # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT | ||
| # LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT | ||
| # OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
|
|
||
|
|
||
| # Example CMake build configuration file for a Chaste user project. | ||
| # See also https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeBuildGuide for full documentation. | ||
|
|
||
| # You can set which Chaste components (or other projects) your project depends on by editing the | ||
| # find_package() call for Chaste. E.g. | ||
| # find_package(Chaste COMPONENTS cell_based) | ||
| # for a project just using the cell_based component (and its dependencies), or | ||
| # find_package(Chaste COMPONENTS heart lung) | ||
| # for a project combining heart & lung simulations. | ||
| # | ||
| # Note that the order in which components are specified does not matter. | ||
|
|
||
| # Here we just depend on core components (nothing application-specific). | ||
| find_package(Chaste COMPONENTS continuum_mechanics global io linalg mesh ode pde) | ||
|
|
||
| # Alternatively, to specify a Chaste installation directory use a line like that below. | ||
| # This is needed if your project is not contained in the projects folder within a Chaste source tree. | ||
| #find_package(Chaste COMPONENTS heart crypt PATHS /path/to/chaste-install NO_DEFAULT_PATH) | ||
|
|
||
| # Change the project name in the line below to match the folder this file is in, | ||
| # i.e. the name of your project. | ||
| chaste_do_project(template_project) |
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| """Copyright (c) 2005-2017, University of Oxford. | ||
| All rights reserved. | ||
| University of Oxford means the Chancellor, Masters and Scholars of the | ||
| University of Oxford, having an administrative office at Wellington | ||
| Square, Oxford OX1 2JD, UK. | ||
| This file is part of Chaste. | ||
| Redistribution and use in source and binary forms, with or without | ||
| modification, are permitted provided that the following conditions are met: | ||
| * Redistributions of source code must retain the above copyright notice, | ||
| this list of conditions and the following disclaimer. | ||
| * Redistributions in binary form must reproduce the above copyright notice, | ||
| this list of conditions and the following disclaimer in the documentation | ||
| and/or other materials provided with the distribution. | ||
| * Neither the name of the University of Oxford nor the names of its | ||
| contributors may be used to endorse or promote products derived from this | ||
| software without specific prior written permission. | ||
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE | ||
| LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE | ||
| GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) | ||
| HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT | ||
| LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT | ||
| OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| """ | ||
|
|
||
| # Example SCons build script for user projects. | ||
|
|
||
| import os | ||
|
|
||
| # Get variables exported from the SConstruct file | ||
| Import("*") | ||
|
|
||
| # Get our project directory name. | ||
| # This assumes that this project is located at <chasteRoot>/projects/<project>. | ||
| # Other things will probably go wrong if this is not the case... | ||
| project_name = os.path.basename(os.path.dirname(os.path.dirname(os.getcwd()))) | ||
|
|
||
| # Chaste libraries used by this project. | ||
| # Select which line to uncomment based on what your project needs, or alter as required. | ||
| chaste_libs_used = ['core'] | ||
| #chaste_libs_used = ['cell_based'] | ||
| #chaste_libs_used = ['heart'] | ||
| #chaste_libs_used = ['cell_based', 'heart'] | ||
|
|
||
| # Do the build magic | ||
| result = SConsTools.DoProjectSConscript(project_name, chaste_libs_used, globals()) | ||
| Return("result") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| # Copyright (c) 2005-2017, University of Oxford. | ||
| # All rights reserved. | ||
| # | ||
| # University of Oxford means the Chancellor, Masters and Scholars of the | ||
| # University of Oxford, having an administrative office at Wellington | ||
| # Square, Oxford OX1 2JD, UK. | ||
| # | ||
| # This file is part of Chaste. | ||
| # | ||
| # Redistribution and use in source and binary forms, with or without | ||
| # modification, are permitted provided that the following conditions are met: | ||
| # * Redistributions of source code must retain the above copyright notice, | ||
| # this list of conditions and the following disclaimer. | ||
| # * Redistributions in binary form must reproduce the above copyright notice, | ||
| # this list of conditions and the following disclaimer in the documentation | ||
| # and/or other materials provided with the distribution. | ||
| # * Neither the name of the University of Oxford nor the names of its | ||
| # contributors may be used to endorse or promote products derived from this | ||
| # software without specific prior written permission. | ||
| # | ||
| # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE | ||
| # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE | ||
| # GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) | ||
| # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT | ||
| # LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT | ||
| # OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
|
|
||
|
|
||
| # Example CMake build configuration file for a Chaste user project. | ||
| # See also https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeBuildGuide for full documentation. | ||
|
|
||
| # This allows us to build executables (apps) using the project. | ||
| # Simply set the project name in the line below. | ||
| chaste_do_apps_project(template_project) |
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| /* | ||
| Copyright (c) 2005-2017, University of Oxford. | ||
| All rights reserved. | ||
| University of Oxford means the Chancellor, Masters and Scholars of the | ||
| University of Oxford, having an administrative office at Wellington | ||
| Square, Oxford OX1 2JD, UK. | ||
| This file is part of Chaste. | ||
| Redistribution and use in source and binary forms, with or without | ||
| modification, are permitted provided that the following conditions are met: | ||
| * Redistributions of source code must retain the above copyright notice, | ||
| this list of conditions and the following disclaimer. | ||
| * Redistributions in binary form must reproduce the above copyright notice, | ||
| this list of conditions and the following disclaimer in the documentation | ||
| and/or other materials provided with the distribution. | ||
| * Neither the name of the University of Oxford nor the names of its | ||
| contributors may be used to endorse or promote products derived from this | ||
| software without specific prior written permission. | ||
| THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE | ||
| LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | ||
| CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE | ||
| GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) | ||
| HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT | ||
| LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT | ||
| OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| */ | ||
|
|
||
| /** | ||
| * @file | ||
| * | ||
| * This file gives an example of how you can create your own executable | ||
| * in a user project. | ||
| */ | ||
|
|
||
| #include <iostream> | ||
| #include <string> | ||
|
|
||
| #include "ExecutableSupport.hpp" | ||
| #include "Exception.hpp" | ||
| #include "PetscTools.hpp" | ||
| #include "PetscException.hpp" | ||
|
|
||
| #include "Hello.hpp" | ||
|
|
||
| int main(int argc, char *argv[]) | ||
| { | ||
| // This sets up PETSc and prints out copyright information, etc. | ||
| ExecutableSupport::StandardStartup(&argc, &argv); | ||
|
|
||
| int exit_code = ExecutableSupport::EXIT_OK; | ||
|
|
||
| // You should put all the main code within a try-catch, to ensure that | ||
| // you clean up PETSc before quitting. | ||
| try | ||
| { | ||
| if (argc<2) | ||
| { | ||
| ExecutableSupport::PrintError("Usage: ExampleApp arguments ...", true); | ||
| exit_code = ExecutableSupport::EXIT_BAD_ARGUMENTS; | ||
| } | ||
| else | ||
| { | ||
| for (int i=1; i<argc; i++) | ||
| { | ||
| if (PetscTools::AmMaster()) | ||
| { | ||
| std::string arg_i(argv[i]); | ||
| Hello world(arg_i); | ||
| std::cout << "Argument " << i << " is " << world.GetMessage() << std::endl << std::flush; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| catch (const Exception& e) | ||
| { | ||
| ExecutableSupport::PrintError(e.GetMessage()); | ||
| exit_code = ExecutableSupport::EXIT_ERROR; | ||
| } | ||
|
|
||
| // Optional - write the machine info to file. | ||
| ExecutableSupport::WriteMachineInfoFile("machine_info"); | ||
|
|
||
| // End by finalizing PETSc, and returning a suitable exit code. | ||
| // 0 means 'no error' | ||
| ExecutableSupport::FinalizePetsc(); | ||
| return exit_code; | ||
| } |
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