Updating tutorials

README.md

@@ -1,4 +1,4 @@
-<img src="spinw_logo.png" width="150">
+<img src="spinw3_logo.png" width="150">
 
-**SpinW** is a Matlab library that can calculate magnetic structure using mean field theory and spin wave dispersion and spin-spin correlation function for complex crystal structures.
+**SpinW** is a Matlab library that can optimize magnetic structures using mean field theory and calculate spin wave dispersion and spin-spin correlation function for complex crystal and magnetic structures.
 

swfiles/+swplot/figure.m

@@ -60,12 +60,14 @@
 pbaspect([1 1 1]);
 
 set(hFigure,...
-    'Name',          'swplot',...
-    'DockControls',  'off',...
-    'PaperType',     'A4',...
-    'Tag',           swpref.getpref('tag',[]),...
-    'Toolbar',       'figure',...
-    'DeleteFcn',     @closeSubFigs);
+	'Renderer',     'opengl',...
+    'Name',         'swplot',...
+    'DockControls', 'off',...
+    'PaperType',    'A4',...
+    'Tag',          swpref.getpref('tag',[]),...
+    'Toolbar',      'figure',...
+    'DeleteFcn',    @closeSubFigs...
+    );
 
 hToolbarT = get(hFigure,'children');
 

swfiles/+swplot/logo.m

@@ -18,8 +18,17 @@ function logo(varargin)
 % See also: SPINW.
 %
 
+% determine the version of SpinW
+ver = sw_version;
+
+if ~isempty(ver.Version)
+    verStr = [' ' ver.Version ' ' 'R' ver.Revision];
+else
+    verStr = [' ' 'R' ver.Revision];
+end
+
 hFigure = figure('menubar','none','toolbar','none','name',...
-    'About SpinW','NumberTitle','off','resize','off','Visible','off');
+    ['About SpinW' verStr],'NumberTitle','off','resize','off','Visible','off');
 hold on
 
 % plot wave
@@ -56,10 +65,13 @@ function logo(varargin)
 
 % add name
 text(-2.3,-1.3,2.35,'Spin','fontsize',110,'fontname','Krungthep')
+
+set(hFigure,'Visible','on');
+
 % save logo
 if nargin > 0 && ~isempty(varargin{end})
     print(varargin{end},'-dpng','-r300')
-    close(gcf)
+    close(hFigure)
 else
     % add text
     ver0 = evalc('sw_version');
@@ -82,11 +94,9 @@ function logo(varargin)
     tt = text(0.65,0.5,txt0,'units','normal');
     set(tt,'FontSize',9.2);
 
+    WinOnTop(hFigure, true);
 end
 
-set(hFigure,'Visible','on');
-WinOnTop(hFigure, true);
-
 end
 
 function WasOnTop = WinOnTop(FigureHandle, IsOnTop)

swfiles/+swpref/setpref.m

@@ -18,6 +18,20 @@ function setpref(prefName, varargin)
 % See also SWPREF.SETPREF.
 %
 
+if nargin>0 && mod(nargin,2)==0
+    % check for usemex option
+    mexopt = find(strcmpi('usemex',varargin));
+
+    if ~isempty(mexopt) && varargin{mexopt+1}
+        % check for the existence of the necessary mex files
+        if exist('chol_omp','file')==3 && exist('eig_omp','file')==3
+        else
+            warning('setpref:MissingMex','Necessary mex files are missing, compile them!')
+            varargin{mexopt+1} = false;
+        end
+    end
+end
+
 if nargin<=2
     swpref.pref(prefName,'set',varargin{:});
 elseif mod(nargin,2)==0

swfiles/@spinw/fitspec.m

@@ -1,8 +1,34 @@
-function fitsp = fitspec2(obj, varargin)
+function fitsp = fitspec(obj, varargin)
 % fits spin wave spectra to experimental spectral data
 %
 % fitsp = FITSPEC(obj, 'Option1', Value1, ...)
 %
+% The function uses a heuristic method to fit spin wave spectrum using a
+% few simple rules to define the R-value of the fit:
+%   1 All calculated spin wave modes that are outside of the measured
+%     energy range will be omitted.
+%   2 Spin wave modes that are closer to each other than the given energy
+%     bin will be binned together and considered as one mode in the fit.
+%   3 If the number of calculated spin wave modes after applying rule 1&2 
+%     is larger than the observed number, the weakes simulated modes will
+%     be removed from the fit.
+%   4 If the number of observed spin wave modes is larger than the observed
+%     number, fake spin wave modes are added with energy equal to the
+%     limits of the scan; at the upper or lower limit depending on which is
+%     closer to the observed spin wave mode.
+% After these rules the number of observed and simulated spin wave modes
+% will be equal. The R-value is defined as:
+%
+%           R = sqrt( sum_i_q (E_i_q_sim - E_i_q_meas)^2/sigma_i_q^2 ),
+%
+% where (i,q) indexing the spin wave mode and momentum. E_sim and E_meas
+% are the simulated and measured spin wave energies, sigma is the standard
+% deviation of the measured spin wave energy determined previously by
+% fitting the inelastic peak.
+%
+% The R value is optimized using particle swarm algorithm to find the
+% global minimum.
+%
 % Options:
 %
 % func      Function to change the Hamiltonian in obj, it has the following
@@ -99,10 +125,10 @@
 inpForm.size   = [inpForm.size   {[1 1]  [1 1]    [1 1]    [1 1]   [1 -7]     }];
 inpForm.soft   = [inpForm.soft   {false  false    false    false   false      }];
 
-inpForm.fname  = [inpForm.fname  {'maxiter' 'sw'  'optmem' 'usemex' 'tid' }];
-inpForm.defval = [inpForm.defval {20        1     0        false    tid0  }];
-inpForm.size   = [inpForm.size   {[1 1]  	[1 1] [1 1]    [1 1]    [1 1] }];
-inpForm.soft   = [inpForm.soft   {false  	false false    false    false }];
+inpForm.fname  = [inpForm.fname  {'maxiter' 'sw'  'optmem' 'tid' }];
+inpForm.defval = [inpForm.defval {20        1     0        tid0  }];
+inpForm.size   = [inpForm.size   {[1 1]  	[1 1] [1 1]    [1 1] }];
+inpForm.soft   = [inpForm.soft   {false  	false false    false }];
 
 param = sw_readparam(inpForm, varargin{:});
 
@@ -272,7 +298,7 @@
 
     % calculate spin-spin correlation function
     spec = obj.spinwave(data.Q,'fitmode',true,'hermit',param.hermit,...
-        'tid',0,'optMem',param.optmem,'useMex',param.usemex,'tid',param.tid);
+        'tid',0,'optMem',param.optmem,'tid',param.tid);
     % calculate neutron scattering cross section
     spec = sw_neutron(spec,'n',data.n,'pol',data.corr.type{1}(1) > 1);
     % bin the data along energy

swfiles/@spinw/powspec.m

@@ -3,6 +3,11 @@
 %
 % spectra = POWSPEC(obj, hklA, 'Option1', Value1, ...)
 %
+% The function calculates powder averaged spin wave spectrum by doing a 3D
+% average in momentum space. This method is not efficient for low
+% dimensional (2D, 1D) structures. To speed up the calculation with mex
+% files use the swpref.setpref('usemex',true) option.
+%
 % Input:
 %
 % obj       spinw class object.
@@ -34,9 +39,6 @@
 %           J. Phys. A: Math. Gen. 37 (2004) 11591
 %           The number of points on the sphere is given by the largest
 %           Fibonacci number below nRand. Default is false.
-% useMex        If true, the code will use compiled mex files (if they
-%               exist) to speed up the calculation, for details see
-%               sw_mex() function. Default is false.
 % imagChk   Checks that the imaginary part of the spin wave dispersion is
 %           smaller than the energy bin size. Default is true.
 %
@@ -95,9 +97,9 @@
 inpForm.defval = [inpForm.defval {true     false     title0  @spinwave  true   }];
 inpForm.size   = [inpForm.size   {[1 1]    [1 1]     [1 -3]  [1 1]      [1 1]  }];
 
-inpForm.fname  = [inpForm.fname  {'extrap' 'fibo' 'optmem' 'binType' 'useMex'}];
-inpForm.defval = [inpForm.defval {false    false  0        'ebin'    false   }];
-inpForm.size   = [inpForm.size   {[1 1]    [1 1]  [1 1]    [1 -4]    [1 1]   }];
+inpForm.fname  = [inpForm.fname  {'extrap' 'fibo' 'optmem' 'binType'}];
+inpForm.defval = [inpForm.defval {false    false  0        'ebin'   }];
+inpForm.size   = [inpForm.size   {[1 1]    [1 1]  [1 1]    [1 -4]   }];
 
 param  = sw_readparam(inpForm, varargin{:});
 
@@ -157,7 +159,7 @@
         specQ = param.specfun(obj,hkl,'fitmode',true,'notwin',true,...
             'Hermit',param.hermit,'formfact',param.formfact,...
             'formfactfun',param.formfactfun,'gtensor',param.gtensor,...
-            'optmem',param.optmem,'useMex',param.useMex,'tid',0,'fid',0);
+            'optmem',param.optmem,'tid',0,'fid',0);
     end
     specQ = sw_neutron(specQ,'pol',false);
     specQ.obj = obj;

swfiles/@spinw/spinwave.m

@@ -13,6 +13,11 @@
 % calculated using a coordinate system rotating from cell to cell. In this
 % case the spin Hamiltonian has to fulfill this extra rotational symmetry.
 %
+% Some of the code of the function can run faster is mex files are used. To
+% switch on mex files, use the swpref.setpref('usemex',true) command. For
+% details see the <a href="matlab:help('sw_mex.m')">sw_mex</a> function.
+%
+%
 % Input:
 %
 % obj           Input structure, spinw class object.
@@ -97,9 +102,6 @@
 %               frame is saved S'(k,omega). Default is false.
 % title         Gives a title string to the simulation that is saved in the
 %               output.
-% useMex        If true, the code will use compiled mex files (if they
-%               exist) to speed up the calculation, for details see
-%               sw_mex() function. Default is false.
 %
 % Output:
 %
@@ -153,7 +155,7 @@
 % triangular lattice antiferromagnet (S=1, J=1) along the [H H 0] direction
 % in reciprocal space.
 %
-% See also SPINW, SPINW.SPINWAVESYM, SW_NEUTRON, SPINW.POWSPEC, SPINW.OPTMAGSTR, SPINW.FILEID, SW_INSTRUMENT.
+% See also SPINW, SPINW.SPINWAVESYM, SW_MEX, SPINW.POWSPEC.
 %
 
 % for linear scans create the Q line(s)
@@ -166,6 +168,9 @@
 % save warning of eigorth
 orthWarn0 = false;
 
+% use mex file by default?
+useMex = swpref.getpref('usemex',[]);
+
 % calculate symbolic spectrum if obj is in symbolic mode
 if obj.symbolic
     if numel(hkl) == 3
@@ -209,9 +214,9 @@
 inpForm.defval = [inpForm.defval {false       @sw_mff      title0  false    }];
 inpForm.size   = [inpForm.size   {[1 -1]      [1 1]        [1 -2]  [1 1]    }];
 
-inpForm.fname  = [inpForm.fname  {'useMex' 'cmplxBase' 'tid' 'fid' }];
-inpForm.defval = [inpForm.defval {false    false       -1    nan   }];
-inpForm.size   = [inpForm.size   {[1 1]    [1 1]       [1 1] [1 1] }];
+inpForm.fname  = [inpForm.fname  {'cmplxBase' 'tid' 'fid' }];
+inpForm.defval = [inpForm.defval {false       -1    nan   }];
+inpForm.size   = [inpForm.size   {[1 1]       [1 1] [1 1] }];
 
 param = sw_readparam(inpForm, varargin{:});
 
@@ -236,17 +241,6 @@
     param.tid = swpref.getpref('tid',[]);
 end
 
-if param.useMex == -1
-    % don't check files (takes too much time)
-    param.useMex = true;
-    % elseif ~(param.useMex && exist('chol_omp','file')==3 && ...
-    %         exist('eig_omp','file')==3 && exist('mtimesx','file')==3)
-elseif ~(param.useMex && exist('chol_omp','file')==3 && ...
-        exist('eig_omp','file')==3)
-    % check if mex files exist
-    param.useMex = false;
-end
-
 % generate magnetic structure in the rotating noation
 magStr = obj.magstr;
 
@@ -711,7 +705,7 @@
         % basis functions of the magnon modes
         V = zeros(2*nMagExt,2*nMagExt,nHklMEM);
 
-        if param.useMex && nHklMEM>1
+        if useMex && nHklMEM>1
             % use mex files to speed up the calculation
             % mex file will return an error if the matrix is not positive definite.
             [K2, invK] = chol_omp(ham,'Colpa','tol',param.omega_tol);
@@ -773,7 +767,7 @@
         gham = mmat(gComm,ham);
         %gham = mtimesx(gComm,ham);
 
-        [V, D, orthWarn] = eigorth(gham,param.omega_tol, param.sortMode,param.useMex);
+        [V, D, orthWarn] = eigorth(gham,param.omega_tol, param.sortMode,useMex);
 
         orthWarn0 = orthWarn || orthWarn0;
 

swfiles/@spinw/table.m

@@ -37,7 +37,7 @@
 % T         Matlab table object.
 %
 
-if verLessThan('MATLAB','R2013b')
+if verLessThan('MATLAB','8.2')
     warning('spinw:table:Version','This function is supported only on MATLAB R2013b or newer!')
     return
 end

swfiles/Contents.m

@@ -103,3 +103,4 @@
 %   sw_uniquetol     - returns the unique column vectors within tolerance
 %   sw_update        - updates the SpinW installation from the internet
 %   sw_version       - returns the installed version of SpinW
+%   sw_mex           - compiles the mex files and test them

dev/sw_mex.m → swfiles/sw_mex.m

@@ -3,13 +3,20 @@ function sw_mex(varargin)
 %
 % SW_MEX('Option1',Value1, ...)
 %
+% The compiled mex files will speed up the spinw.spinwave function. The
+% expected speedup is larger for smaller magnetic unit cells. Once the mex
+% files are compiled, use the swpref.setpref('usemex',true) command to
+% switch to mex in spinw.spinwave.
+%
 % Options:
 %
 % test      If true, the compiled .mex files will be tested. Default is
 %           false.
 % swtest    If true, 3 spin wave calculation will run with and without .mex
 %           files and the results will be compared. Default is false.
 %
+% See also SWPREF.
+%
 
 inpForm.fname  = {'test' 'compile' 'swtest' };
 inpForm.defval = {false  true      false    };

swfiles/sw_plotspec.m

@@ -263,7 +263,7 @@
 
     if any(strfind(get(get(param.aHandle,'Parent'),'Tag'),'sw_crystal'))
         % don't plot into the crystal structure window
-        fHandle = figure;
+        fHandle = figure('color','w');
         param.aHandle = gca;
     else
         fHandle = get(gca,'Parent');
@@ -272,7 +272,7 @@
 else
     fHandle = sw_getfighandle('sw_spectra');
     if isempty(fHandle)
-        fHandle = figure;
+        fHandle = figure('color','w');
     end
 end
 % set Tag to find window later easily

swfiles/sw_version.m

@@ -5,7 +5,7 @@
 %
 
 % read file header from sw.m file
-fid = fopen('spinw.m');
+fid = fopen('sw_version.m');
 
 % first line
 fgets(fid);
@@ -54,9 +54,11 @@
 if nField == 0
     aDir = pwd;
     cd(sw_rootdir);
-    [~, revNum] = system('svn info |grep Revision: |cut -c11-');
+    [~, revNum] = system('git rev-list --count HEAD');
+    revNum = strtrim(revNum);
+    %[~, revNum] = system('svn info |grep Revision: |cut -c11-');
     cd(aDir);
-    revNum = str2double(revNum);
+    revNum = str2double(revNum)+1e3;
 end
 
 % Matlab version & Symbolic Toolbox
@@ -90,15 +92,23 @@
     fprintf(['MATLAB version: ' version ', ' strSym '\n']);
 
 else
+    ver0 = struct;
+    ver0.Name     = 'SpinW';
+    ver0.Version  = '';
+    ver0.Author   = 'S. Toth';
+    ver0.Contact  = '[email protected]';
+    ver0.Revision = '';
+    ver0.Date     = datestr(now,'dd-mmm-yyyy');
+    ver0.License  = 'GNU GENERAL PUBLIC LICENSE';
+
     if nField == 0
         if any(revNum)
-            varargout{1}.Revision = num2str(revNum);
-        else
-            varargout{1} = struct;
+            ver0.Revision = num2str(revNum);
         end
+        varargout{1} = ver0;
     else
-        if isempty(verStruct)
-            varargout{1} = 'beta';
+        if isempty(fieldnames(verStruct))
+            varargout{1} = ver0;
         else
             varargout{1} = verStruct;
         end