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Support for Octave (#24)
* Start support for Octave * Put Arenstorf problem in Octave-compatible format * Fix warnings and Andrey's comments * Force consistent line ending * Fix Andrey's comments * More detailed documentation for Arenstorf problem * Add contributing guide * Rewrite installer to support Octave. Currently untested in MATLAB * Conversion of the Lorenz '63 problem to the new style defined by Steven * Made the install script work with matlab, and added stubs for mac and windows * added 'cite as' text as before. * Converted the matlab prj file to use the build directory * converted the find-replace functionality to use matlab built-in commands * Switch from sed to pure matlab preprocessing for installer * Lorenz 96 modified to octave format * added a small test script to help with the conversion to octave. This can be removed later, but is very helpful to keep track of everything now * updated the temp test script to look at all presets * Allen Cahn support for octave * Problem fix for events * change script to validate all presets, and changed format to not do warnings * Converted Bouncing Ball to octave format * Changed solver of nbody to default to ode15s as some of the systems are stiff * Changed the Ascher linear DAE to be octave compatible * Brusselator into octave now * We cusp now * CUSP octave fix * Nbody is octave compatible * Changed Nbody to work with ode23t * Quadratic problem done * QG octave gogogogo * Changes and cleanup to the lienard problem, octave support * Fix for lineard problem * Linear problem should work with octave now * Vanderpol done * Lotka volterra octave * pendulum octave * Trig DAE, simple octave * Update E5 for octave * Vectorization and capitilization fixes for all problems currently in octave format * Updates to docs * PR done * sanz serna octave * ZLA kinetics octave * fixes for zla * Update HIRES for octave * Update inverter chain for octave * Update KPR for octave * Update Oregonator for octave * Transistor amplifier octave * Fixes for validation tests * Fixes for validation tests * renaming jacobian, jvp and javp * Revert "renaming jacobian, jvp and javp" This reverts commit 3e90edd. * jacobian correct renaming * Revert "jacobian correct renaming" This reverts commit e94b5b6. * WIll I ever get this right? * Support linear problem in octave * Modified hessian filenames too * changed install to only use w on windows * changed validatepresets to always find the OTP directory. * fixed matlab parameter validation issues * always use w flag on install * Capitalized RHS * Update README.md * Documentation inprovements * Finish renaming RHS functions * fix warnings Co-authored-by: Andrey A Popov <apopov@vt.edu>
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‎.gitattributes‎

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* text=auto
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*.m text eol=lf
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‎.gitignore‎

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*.asv
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*.m~
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*.mltbx
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build/
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‎DESCRIPTION‎

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Name: ODE Test Problems
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Version: 0.0.1
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Date: 2021-13-12
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Author: Steven Roberts, Andrey Popov, Arash Sarshar, Adrian Sandu
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Maintainer: Steven Roberts, Andrey Popov
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Title: A MATLAB suite of initial value problems
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Description: TODO
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Categories: ODEs
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Url: https://github.com/ComputationalScienceLaboratory/ODE-Test-Problems
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License: MIT
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‎ODE Test Problems.prj‎

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<deployment-project plugin="plugin.toolbox" plugin-version="1.0">
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<configuration name="ODE Test Problems" target="target.toolbox" target-name="Package Toolbox">
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<param.appname>ODE Test Problems</param.appname>
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<param.authnamewatermark>Steven Roberts, Andrey Popov, Ardian Sandu</param.authnamewatermark>
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<param.email />
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<param.company>Computational Science Laboratory</param.company>
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<param.summary>A MATLAB suite of initial value problems</param.summary>
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<param.description />
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<param.screenshot />
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<param.version>0.0.1</param.version>
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<param.output>${PROJECT_ROOT}/ODE Test Problems.mltbx</param.output>
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<param.examples />
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<param.release.current.only>false</param.release.current.only>
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<param.compatiblity.windows>true</param.compatiblity.windows>
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<param.compatiblity.macos>true</param.compatiblity.macos>
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<param.compatiblity.linux>true</param.compatiblity.linux>
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<param.compatiblity.matlabonline>true</param.compatiblity.matlabonline>
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<param.installation.map />
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<file>${PROJECT_ROOT}/src</file>
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</deployment-project>
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<deployment-project plugin="plugin.toolbox" plugin-version="1.0">
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<configuration name="ODE Test Problems" target="target.toolbox" target-name="Package Toolbox">
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<param.appname>ODE Test Problems</param.appname>
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<param.authnamewatermark>Steven Roberts, Andrey Popov, Arash Sarshar, Ardian Sandu</param.authnamewatermark>
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<param.email />
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<param.company>Computational Science Laboratory</param.company>
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<param.summary>A MATLAB suite of initial value problems</param.summary>
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<param.description />
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<param.screenshot />
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<param.version>0.0.1</param.version>
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<param.output>${PROJECT_ROOT}/ODE Test Problems.mltbx</param.output>
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<param.products.name />
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<param.exported.on.package>false</param.exported.on.package>
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<param.required.addons />
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<param.matlab.project.id />
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<param.matlab.project.name />
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<param.release.start />
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<param.release.end />
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<param.release.current.only>false</param.release.current.only>
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<param.compatiblity.windows>true</param.compatiblity.windows>
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<param.compatiblity.macos>true</param.compatiblity.macos>
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<param.compatiblity.linux>true</param.compatiblity.linux>
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<param.compatiblity.matlabonline>true</param.compatiblity.matlabonline>
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<param.installation.map />
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<param.additional.sw.names />
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<param.additional.sw.licenses />
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<param.additional.sw.win.url />
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<param.additional.sw.mac.url />
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<param.additional.sw.linux.url />
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<unset>
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<param.email />
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<param.description />
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<param.screenshot />
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<param.output />
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<param.products.name />
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<param.platforms />
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<param.exclude.pcodedmfiles />
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<param.demosxml />
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<param.apps />
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<param.registered.apps />
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<param.docs />
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<param.getting.started.guide />
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<param.javaclasspath.excludes />
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<param.required.addons />
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<param.matlab.project.id />
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<param.matlab.project.name />
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<param.release.start />
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<param.release.end />
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<param.release.current.only />
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<param.compatiblity.windows />
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<param.compatiblity.macos />
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<param.compatiblity.linux />
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<param.compatiblity.matlabonline />
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<param.installation.map />
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<param.additional.sw.names />
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<param.additional.sw.licenses />
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<param.additional.sw.win.url />
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<param.additional.sw.mac.url />
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<param.additional.sw.linux.url />
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</unset>
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<fileset.rootdir>
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<file>${PROJECT_ROOT}/build</file>
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</fileset.rootdir>
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<fileset.rootfiles>
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<file>${PROJECT_ROOT}/build/+otp</file>
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</fileset.rootfiles>
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<fileset.depfun.included />
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<fileset.depfun.excluded />
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<fileset.package />
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</configuration>
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</deployment-project>

‎OTP.m‎

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classdef OTP
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properties (Access = private, Constant)
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Octave = exist('OCTAVE_VERSION', 'builtin') > 0
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Name = 'ODE Test Problems';
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SrcDir = 'src';
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BuildDir = 'build';
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end
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methods (Static)
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function clean()
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[~] = rmdir(OTP.BuildDir, 's');
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end
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function build()
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OTP.clean();
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if OTP.Octave
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OTP.processFiles(OTP.SrcDir, fullfile(OTP.BuildDir, 'inst'), ...
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{}, {});
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copyfile('DESCRIPTION', OTP.BuildDir);
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copyfile('LICENSE', fullfile(OTP.BuildDir, 'COPYING'));
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zip(OTP.packagePath(), OTP.BuildDir);
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else
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OTP.processFiles(OTP.SrcDir, OTP.BuildDir, ...
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'\s*%\s*MATLAB ONLY:\s*', ' ');
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matlab.addons.toolbox.packageToolbox( ...
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strcat(OTP.Name, '.prj'), OTP.packagePath());
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end
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end
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function install()
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OTP.build();
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if OTP.Octave
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pkg('install', OTP.packagePath());
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else
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matlab.addons.toolbox.installToolbox(OTP.packagePath());
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end
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fprintf('ODE Test Problems sucessfully installed\n');
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end
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function uninstall()
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if OTP.Octave
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pkg('uninstall', lower(OTP.Name));
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else
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tbxs = matlab.addons.toolbox.installedToolboxes;
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otp = tbxs(arrayfun(@(t) strcmp(t.Name, OTP.Name), tbxs));
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if ~isempty(otp)
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matlab.addons.toolbox.uninstallToolbox(otp);
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end
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end
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end
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end
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methods (Static, Access = private)
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function processFiles(src, dest, str, replacement)
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list = dir(src);
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mkdir(dest);
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for i = 1:length(list)
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item = list(i);
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newSrc = fullfile(src, item.name);
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newDest = fullfile(dest, item.name);
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if ~item.isdir
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[~, ~, ext] = fileparts(item.name);
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if strcmp(ext, '.m')
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content = regexprep(fileread(newSrc), str, replacement);
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fid = fopen(newDest, 'w');
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fprintf(fid, '%s', content);
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fclose(fid);
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else
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copyfile(newSrc, newDest);
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end
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elseif ~any(strcmp(item.name, {'.', '..'}))
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OTP.processFiles(newSrc, newDest, str, replacement);
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end
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end
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end
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function path = packagePath()
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if OTP.Octave
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ext = '.zip';
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else
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ext = '.mltbx';
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end
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path = fullfile(OTP.BuildDir, strcat(OTP.Name, ext));
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end
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end
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methods (Access = private)
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function obj = OTP()
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end
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end
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end

‎README.md‎

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# ODE Test Problems
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A MATLAB suite of initial value problems
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ODE Test Problems (OTP) is an object-oriented MATLAB/GNU Octave package offering
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a broad range of ordinary differential equations, partial differential
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equations, and differential algebraic equations which can be used to test
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numerical methods such as time-steppers and data assimilation methods. It
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contains problems that are linear and nonlinear, autonomous and nonautonomous,
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scalar and high-dimensional, and stiff and nonstiff. OTP also supports
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partitioned systems for testing IMEX methods, multirate methods, and other
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partitioned schemes. Many problems come from real-world applications in fields
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such as chemistry, astrophysics, meteorology, and electrical engineering. OTP's
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interface provides a simple and standardized way to access problem parameters,
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the right-hand side function, the Jacobian matrix, and other properties. Each
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problem is equipped with functions for computing the solution, plotting the
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solution, and creating a movie.
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Although OTP is currently under development, the public API is quite stable. We
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are currently writing full documentation in order to release version `1.0.0`.
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If there is a test problem, additional RHS property, or new functionality you
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would like added to OTP, we encourage you to let us know via a
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[GitHub issue](https://github.com/ComputationalScienceLaboratory/ODE-Test-Problems/issues).
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We also accept pull requests that adhere to our
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[contributing guide](./docs/CONTRIBUTING.md).
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## Installation
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ODE Test Problems can be installed by running the MATLAB script `install` from the root directory of the project.
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OTP can be installed as a local MATLAB toolbox or Octave package by running
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```matlab
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OTP.install
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```
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from the root directory of the project. If no longer needed, it can be
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uninstalled with `OTP.uninstall`.
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## Example
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problem.plot(sol);
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% Adjust a parameter
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problem.Parameters.preyDeathRate = 2;
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problem.Parameters.PreyDeathRate = 2;
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% Manually use a MATLAB ODE solver to solve the problem
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options = odeset('Jacobian', problem.Rhs.Jacobian);
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[t, y] = ode15s(problem.Rhs.F, problem.TimeSpan, problem.Y0, options);
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options = odeset('Jacobian', problem.RHS.Jacobian);
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[t, y] = ode15s(problem.RHS.F, problem.TimeSpan, problem.Y0, options);
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% Plot the phase space with a custom title
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problem.plotPhaseSpace(t, y, 'Title', 'The Circle of Life');

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