Trying to update hossein's branch

.gitignore

@@ -10,5 +10,5 @@ Thumbs.db
 
 # Sysplotter data and configuration files #
 ######################
-sysplotterconfig.mat
+sysplotter_config.mat
 sysplotter_data

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "suresh-submodule1"]
+	path = suresh-submodule1
+	url = https://github.com/sureshr14/suresh-submodule.git

ProgramFiles/v4.2/Utilities/GetFullPath.m

@@ -0,0 +1,326 @@
+function File = GetFullPath(File, Style)
+% GetFullPath - Get absolute canonical path of a file or folder
+% Absolute path names are safer than relative paths, when e.g. a GUI or TIMER
+% callback changes the current directory. Only canonical paths without "." and
+% ".." can be recognized uniquely.
+% Long path names (>259 characters) require a magic initial key "\\?\" to be
+% handled by Windows API functions, e.g. for Matlab's FOPEN, DIR and EXIST.
+%
+% FullName = GetFullPath(Name, Style)
+% INPUT:
+%   Name:  String or cell string, absolute or relative name of a file or
+%          folder. The path need not exist. Unicode strings, UNC paths and long
+%          names are supported.
+%   Style: Style of the output as string, optional, default: 'auto'.
+%          'auto': Add '\\?\' or '\\?\UNC\' for long names on demand.
+%          'lean': Magic string is not added.
+%          'fat':  Magic string is added for short names also.
+%          The Style is ignored when not running under Windows.
+%
+% OUTPUT:
+%   FullName: Absolute canonical path name as string or cell string.
+%          For empty strings the current directory is replied.
+%          '\\?\' or '\\?\UNC' is added on demand.
+%
+% NOTE: The M- and the MEX-version create the same results, the faster MEX
+%   function works under Windows only.
+%   Some functions of the Windows-API still do not support long file names.
+%   E.g. the Recycler and the Windows Explorer fail even with the magic '\\?\'
+%   prefix. Some functions of Matlab accept 260 characters (value of MAX_PATH),
+%   some at 259 already. Don't blame me.
+%   The 'fat' style is useful e.g. when Matlab's DIR command is called for a
+%   folder with les than 260 characters, but together with the file name this
+%   limit is exceeded. Then "dir(GetFullPath([folder, '\*.*], 'fat'))" helps.
+%
+% EXAMPLES:
+%   cd(tempdir);                    % Assumed as 'C:\Temp' here
+%   GetFullPath('File.Ext')         % 'C:\Temp\File.Ext'
+%   GetFullPath('..\File.Ext')      % 'C:\File.Ext'
+%   GetFullPath('..\..\File.Ext')   % 'C:\File.Ext'
+%   GetFullPath('.\File.Ext')       % 'C:\Temp\File.Ext'
+%   GetFullPath('*.txt')            % 'C:\Temp\*.txt'
+%   GetFullPath('..')               % 'C:\'
+%   GetFullPath('..\..\..')         % 'C:\'
+%   GetFullPath('Folder\')          % 'C:\Temp\Folder\'
+%   GetFullPath('D:\A\..\B')        % 'D:\B'
+%   GetFullPath('\\Server\Folder\Sub\..\File.ext')
+%                                   % '\\Server\Folder\File.ext'
+%   GetFullPath({'..', 'new'})      % {'C:\', 'C:\Temp\new'}
+%   GetFullPath('.', 'fat')         % '\\?\C:\Temp\File.Ext'
+%
+% COMPILE:
+%   Automatic: InstallMex GetFullPath.c uTest_GetFullPath
+%   Manual:    mex -O GetFullPath.c
+%   Download:  http://www.n-simon.de/mex
+% Run the unit-test uTest_GetFullPath after compiling.
+%
+% Tested: Matlab 6.5, 7.7, 7.8, 7.13, WinXP/32, Win7/64
+%         Compiler: LCC2.4/3.8, BCC5.5, OWC1.8, MSVC2008/2010
+% Assumed Compatibility: higher Matlab versions
+% Author: Jan Simon, Heidelberg, (C) 2009-2013 matlab.THISYEAR(a)nMINUSsimon.de
+%
+% See also: CD, FULLFILE, FILEPARTS.
+
+% $JRev: R-G V:032 Sum:7Xd/JS0+yfax Date:15-Jan-2013 01:06:12 $
+% $License: BSD (use/copy/change/redistribute on own risk, mention the author) $
+% $UnitTest: uTest_GetFullPath $
+% $File: Tools\GLFile\GetFullPath.m $
+% History:
+% 001: 20-Apr-2010 22:28, Successor of Rel2AbsPath.
+% 010: 27-Jul-2008 21:59, Consider leading separator in M-version also.
+% 011: 24-Jan-2011 12:11, Cell strings, '~File' under linux.
+%      Check of input types in the M-version.
+% 015: 31-Mar-2011 10:48, BUGFIX: Accept [] as input as in the Mex version.
+%      Thanks to Jiro Doke, who found this bug by running the test function for
+%      the M-version.
+% 020: 18-Oct-2011 00:57, BUGFIX: Linux version created bad results.
+%      Thanks to Daniel.
+% 024: 10-Dec-2011 14:00, Care for long names under Windows in M-version.
+%      Improved the unittest function for Linux. Thanks to Paul Sexton.
+% 025: 09-Aug-2012 14:00, In MEX: Paths starting with "\\" can be non-UNC.
+%      The former version treated "\\?\C:\<longpath>\file" as UNC path and
+%      replied "\\?\UNC\?\C:\<longpath>\file".
+% 032: 12-Jan-2013 21:16, 'auto', 'lean' and 'fat' style.
+
+% Initialize: ==================================================================
+% Do the work: =================================================================
+
+% #############################################
+% ### USE THE MUCH FASTER MEX ON WINDOWS!!! ###
+% #############################################
+
+% Difference between M- and Mex-version:
+% - Mex does not work under MacOS/Unix.
+% - Mex calls Windows API function GetFullPath.
+% - Mex is much faster.
+
+% Magix prefix for long Windows names:
+if nargin < 2
+   Style = 'auto';
+end
+
+% Handle cell strings:
+% NOTE: It is faster to create a function @cell\GetFullPath.m under Linux, but
+% under Windows this would shadow the fast C-Mex.
+if isa(File, 'cell')
+   for iC = 1:numel(File)
+      File{iC} = GetFullPath(File{iC}, Style);
+   end
+   return;
+end
+
+% Check this once only:
+isWIN    = strncmpi(computer, 'PC', 2);
+MAX_PATH = 260;
+
+% Warn once per session (disable this under Linux/MacOS):
+persistent hasDataRead
+if isempty(hasDataRead)
+   % Test this once only - there is no relation to the existence of DATAREAD!
+   %if isWIN
+   %   Show a warning, if the slower Matlab version is used - commented, because
+   %   this is not a problem and it might be even useful when the MEX-folder is
+   %   not inlcuded in the path yet.
+   %   warning('JSimon:GetFullPath:NoMex', ...
+   %      ['GetFullPath: Using slow Matlab-version instead of fast Mex.', ...
+   %       char(10), 'Compile: InstallMex GetFullPath.c']);
+   %end
+
+   % DATAREAD is deprecated in 2011b, but still available. In Matlab 6.5, REGEXP
+   % does not know the 'split' command, therefore DATAREAD is preferred:
+   hasDataRead = ~isempty(which('dataread'));
+end
+
+if isempty(File)  % Accept empty matrix as input:
+   if ischar(File) || isnumeric(File)
+      File = cd;
+      return;
+   else
+      error(['JSimon:', mfilename, ':BadTypeInput1'], ...
+         ['*** ', mfilename, ': Input must be a string or cell string']);
+   end
+end
+
+if ischar(File) == 0  % Non-empty inputs must be strings
+   error(['JSimon:', mfilename, ':BadTypeInput1'], ...
+      ['*** ', mfilename, ': Input must be a string or cell string']);
+end
+
+if isWIN  % Windows: --------------------------------------------------------
+   FSep = '\';
+   File = strrep(File, '/', FSep);
+
+   % Remove the magic key on demand, it is appended finally again:
+   if strncmp(File, '\\?\', 4)
+      if strncmpi(File, '\\?\UNC\', 8)
+         File = ['\', File(7:length(File))];  % Two leading backslashes!
+      else
+         File = File(5:length(File));
+      end
+   end
+
+   isUNC   = strncmp(File, '\\', 2);
+   FileLen = length(File);
+   if isUNC == 0                        % File is not a UNC path
+      % Leading file separator means relative to current drive or base folder:
+      ThePath = cd;
+      if File(1) == FSep
+         if strncmp(ThePath, '\\', 2)   % Current directory is a UNC path
+            sepInd  = strfind(ThePath, '\');
+            ThePath = ThePath(1:sepInd(4));
+         else
+            ThePath = ThePath(1:3);     % Drive letter only
+         end
+      end
+
+      if FileLen < 2 || File(2) ~= ':'  % Does not start with drive letter
+         if ThePath(length(ThePath)) ~= FSep
+            if File(1) ~= FSep
+               File = [ThePath, FSep, File];
+            else                        % File starts with separator:
+               File = [ThePath, File];
+            end
+         else                           % Current path ends with separator:
+            if File(1) ~= FSep
+               File = [ThePath, File];
+            else                        % File starts with separator:
+               ThePath(length(ThePath)) = [];
+               File = [ThePath, File];
+            end
+         end
+
+      elseif FileLen == 2 && File(2) == ':'   % "C:" current directory on C!
+         % "C:" is the current directory on the C-disk, even if the current
+         % directory is on another disk! This was ignored in Matlab 6.5, but
+         % modern versions considers this strange behaviour.
+         if strncmpi(ThePath, File, 2)
+            File = ThePath;
+         else
+            try
+               File = cd(cd(File));
+            catch    % No MException to support Matlab6.5...
+               if exist(File, 'dir')  % No idea what could cause an error then!
+                  rethrow(lasterror);
+               else  % Reply "K:\" for not existing disk:
+                  File = [File, FSep];
+               end
+            end
+         end
+      end
+   end
+
+else         % Linux, MacOS: ---------------------------------------------------
+   FSep = '/';
+   File = strrep(File, '\', FSep);
+
+   if strcmp(File, '~') || strncmp(File, '~/', 2)  % Home directory:
+      HomeDir = getenv('HOME');
+      if ~isempty(HomeDir)
+         File(1) = [];
+         File    = [HomeDir, File];
+      end
+
+   elseif strncmpi(File, FSep, 1) == 0
+      % Append relative path to current folder:
+      ThePath = cd;
+      if ThePath(length(ThePath)) == FSep
+         File = [ThePath, File];
+      else
+         File = [ThePath, FSep, File];
+      end
+   end
+end
+
+% Care for "\." and "\.." - no efficient algorithm, but the fast Mex is
+% recommended at all!
+if ~isempty(strfind(File, [FSep, '.']))
+   if isWIN
+      if strncmp(File, '\\', 2)  % UNC path
+         index = strfind(File, '\');
+         if length(index) < 4    % UNC path without separator after the folder:
+            return;
+         end
+         Drive            = File(1:index(4));
+         File(1:index(4)) = [];
+      else
+         Drive     = File(1:3);
+         File(1:3) = [];
+      end
+   else  % Unix, MacOS:
+      isUNC   = false;
+      Drive   = FSep;
+      File(1) = [];
+   end
+
+   hasTrailFSep = (File(length(File)) == FSep);
+   if hasTrailFSep
+      File(length(File)) = [];
+   end
+
+   if hasDataRead
+      if isWIN  % Need "\\" as separator:
+         C = dataread('string', File, '%s', 'delimiter', '\\');  %#ok<REMFF1>
+      else
+         C = dataread('string', File, '%s', 'delimiter', FSep);  %#ok<REMFF1>
+      end
+   else  % Use the slower REGEXP, when DATAREAD is not available anymore:
+      C = regexp(File, FSep, 'split');
+   end
+
+   % Remove '\.\' directly without side effects:
+   C(strcmp(C, '.')) = [];
+
+   % Remove '\..' with the parent recursively:
+   R = 1:length(C);
+   for dd = reshape(find(strcmp(C, '..')), 1, [])
+      index    = find(R == dd);
+      R(index) = [];
+      if index > 1
+         R(index - 1) = [];
+      end
+   end
+
+   if isempty(R)
+      File = Drive;
+      if isUNC && ~hasTrailFSep
+         File(length(File)) = [];
+      end
+
+   elseif isWIN
+      % If you have CStr2String, use the faster:
+      %   File = CStr2String(C(R), FSep, hasTrailFSep);
+      File = sprintf('%s\\', C{R});
+      if hasTrailFSep
+         File = [Drive, File];
+      else
+         File = [Drive, File(1:length(File) - 1)];
+      end
+
+   else  % Unix:
+      File = [Drive, sprintf('%s/', C{R})];
+      if ~hasTrailFSep
+         File(length(File)) = [];
+      end
+   end
+end
+
+% "Very" long names under Windows:
+if isWIN
+   if ~ischar(Style)
+      error(['JSimon:', mfilename, ':BadTypeInput2'], ...
+         ['*** ', mfilename, ': Input must be a string or cell string']);
+   end
+
+   if (strncmpi(Style, 'a', 1) && length(File) >= MAX_PATH) || ...
+         strncmpi(Style, 'f', 1)
+      % Do not use [isUNC] here, because this concerns the input, which can
+      % '.\File', while the current directory is an UNC path.
+      if strncmp(File, '\\', 2)  % UNC path
+         File = ['\\?\UNC', File(2:end)];
+      else
+         File = ['\\?\', File];
+      end
+   end
+end
+
+% return;

ProgramFiles/v4.2/Utilities/LowRe_toolbox/LowRE_dissipation_metric_from_curvature_bases.m

@@ -1,14 +1,14 @@
-function Mp = LowRE_dissipation_metric_from_curvature_bases(kappa_basis_input,r,L,c)
+function Mp = LowRE_dissipation_metric_from_curvature_bases(kappa_basis_input,r,L,c,drag_ratio)
 % Calculate the dissipation power metric for a set of curvature bases
 
 	% Specified integration limits
 	int_limit = L*[-0.5 0.5];
 
 	% Define the tangential, lateral drag matrix for unit/double drag
-	drag = [1 0; 0 2]*c;
+	drag = [1 0; 0 drag_ratio]*c;
 
 	% Get the backbone locus, Jacobian, and Local Connection functions
-	[A, h, J] = LowRE_local_connection_from_curvature_bases(kappa_basis_input,r,L,c);
+	[A, h, J] = LowRE_local_connection_from_curvature_bases(kappa_basis_input,r,L,c,drag_ratio);
 
 	% Integrate along the body for the power metric
 	Mp_sol = ode_multistart(@ode45,@(s,Mp) dMetric(s,Mp,A,h,J,drag),int_limit,int_limit(1),zeros(length(r)^2,1));