Updated tutorials and bug fixes

Author: wardsimon

install_spinw.m

@@ -1,4 +1,4 @@
-function install_spinw()
+function install_spinw(varargin)
 % installs SpinW
 %
 % INSTALL_SPINW()
@@ -13,6 +13,15 @@ function install_spinw()
 %     return
 % end
 
+silent = false;
+if nargin == 2
+    if strcmpi(varargin{1},'silent')
+        if isa(varargin{2},'logical')
+            silent = varargin{2};
+        end
+    end
+end
+    
 newline = char(10); %#ok<CHARTEN>
 
 % remove old SpinW installation from path
@@ -91,20 +100,26 @@ function install_spinw()
 
 % create new startup.m file
 if isempty(sfLoc)
+    if ~silent
     answer = getinput(sprintf(['You don''t have a Matlab startup.m file,\n'...
         'do you want it to be created at %s? (y/n)'],esc(uPath)),'yn');
+    else
+        answer = 'n';
+    end
     if answer == 'y'
         fclose(fopen(uPath,'w'));
         sfLoc = uPath;
     end
 end
 
 if ~isempty(sfLoc)
-    
+    if ~silent
     answer = getinput(['Would you like to add the following line:' newline...
         'addpath(genpath('''  esc(folName) '''));' newline 'to the end of '...
         'your Matlab startup file (' esc(sfLoc) ')? (y/n)'],'yn');
-    
+    else
+        answer = 'n';
+    end
     if answer == 'y'
         fid = fopen(sfLoc,'a');
         fprintf(fid,['\n%%###SW_UPDATE\n%% Path to the SpinW installation\n'...
@@ -113,14 +128,17 @@ function install_spinw()
     end
 end
 
+if ~silent
 answer = getinput(...
     ['\nIn order to refresh the internal class definitions of Matlab (to\n'...
     'access the new SpinW version), issuing the "clear classes" command\n'...
     'is necessary. However this command will also clear all your variables\n'...
     'in the Matlab internal memory. Would you like the updater to issue\n'...
     'the command now, otherwise you can do it manually later.\n'...
     'Do you want to issue the command "clear classes" now? (y/n)'],'yn');
-
+else
+    answer = 'n';
+end
 if answer == 'y'
     clear('classes'); %#ok<CLCLS>
     disp('Matlab class memory is refreshed!')

swfiles/+swplot/plotmag.m

@@ -208,6 +208,13 @@
     setappdata(hFigure,'base',obj.basisvector);
 end
 
+if obj.symbolic
+   warning('plotmag:symbolic','A symbolic magnetic structure can not be plotted.')
+   varargout = cell(1:nargout);
+   return
+end
+
+
 % the basis vectors in columns.
 BV = obj.basisvector;
 
@@ -325,8 +332,14 @@
     end
 
     % normalize the longest moment vector to scale*(shortest bond length)
-    M = M/sqrt(max(sum(M.^2,1)))*param.scale*lBond;
-    
+    if isa(M,'sym')
+        warning('sw_plotmag:symcalc','This is a symbolic calculaiton, normalisation can''t be achieved.')
+        temp = cellfun(@(x) M./sqrt(sum(x,1).^2),mat2cell(M,3,[1 1 1 1]),'UniformOutput',false);
+        [m, ind] = min(cellfun(@(x) sum(x(:)),temp));
+        M = temp{ind}*param.scale*lBond;
+    else
+        M = M/sqrt(max(sum(M.^2,1)))*param.scale*lBond;
+    end
     if param.centered
         % double the length for centered moments
         M = 2*M;
@@ -350,7 +363,7 @@
     end
 
     % shift positions
-    vpos = bsxfun(@plus,vpos,BV\param.shift);
+    vpos = bsxfunsym(@plus,vpos,BV\param.shift);
 
     % prepare legend labels
     mAtom.name = obj.unit_cell.label(mAtom.idx);

swfiles/@spinw/energy.m

@@ -1,21 +1,21 @@
 function  Eout = energy(obj, varargin)
 % calculates the ground state energy
-% 
+%
 % ### Syntax
-% 
+%
 % `E = energy(obj,Name,Value)`
-% 
+%
 % ### Description
-% 
+%
 % `E = energy(obj,Name,Value)` calculates the classical ground state energy
 % per spin. The calculation correctly takes into account the magnetic
 % supercell. The function gives correct results on single-k magnetic
 % structures even defined on magnetic supercells. For multi-k magnetic
 % structures first a definition of a larger supercell is necessary where an
 % effective $k=0$ representation is possible.
-% 
+%
 % ### Examples
-% 
+%
 % After optimising the magnetic structure (by minimizing the ground state
 % energy), the energy per spin is calculated. This can be compared to
 % different ground state structures to decide which is the right classical
@@ -31,20 +31,20 @@
 % >>cryst.optmagsteep('nRun',10)
 % >>cryst.energy>>
 % ```
-% 
+%
 % ### Input Arguments
-% 
+%
 % `obj`
 % : [spinw] object.
-% 
+%
 % ### Name-Value Pair Arguments
-% 
+%
 % `'epsilon'`
-% : The smallest value of incommensurability that is tolerated 
+% : The smallest value of incommensurability that is tolerated
 %   without warning. Default is $10^{-5}$.
-% 
+%
 % ### Output Arguments
-% 
+%
 % `E`
 % : Energy per moment (anisotropy + exchange + Zeeman energy).
 %
@@ -59,9 +59,9 @@
 % ion anisotropy one has to be carefull! In the triangular case one has to
 % extend the unit cell to `nExt = [3 3 1]` (in the hexagonal setting), in
 % this case the energy will be correct.}}
-% 
+%
 % ### See Also
-% 
+%
 % [spinw] \| [spinw.anneal] \| [spinw.newcell]
 %
 
@@ -103,7 +103,7 @@
 end
 
 if nMagExt>0
-
+    
     dR    = [SS.all(1:3,:) zeros(3,nMagExt)];
     atom1 = [SS.all(4,:)   1:nMagExt];
     atom2 = [SS.all(5,:)   1:nMagExt];
@@ -127,8 +127,19 @@
 
     Ml = repmat(permute(M1,[1 3 2]),[1 3 1]);
     Mr = repmat(permute(M2,[3 1 2]),[3 1 1]);
-    
-    exchE   =  sum(sum(sum(Ml.*JJ.*Mr,3),2),1);
+
+    Q = Ml.*JJ.*Mr;
+    if isa(Ml,'sym') || isa(Ml,'sym') || isa(Ml,'sym')
+        [n1, n2, n3] = size(Q);
+        sum_3 = 0;
+        for k = 1:n3
+            sum_3 = sum_3 + Q(:,:,k);
+        end
+    else
+        sum_3 = sum(Q,3);
+    end
+    exchE   =  sum(sum(sum_3,2),1);
+
     % TODO
     % correct energy for twins
     ZeemanE = -sum(SI.field*permute(mmat(SI.g,permute(M0,[1 3 2])),[1 3 2]),2)*obj.unit.muB;

swfiles/@spinw/genmagstr.m

@@ -341,7 +341,7 @@ function genmagstr(obj, varargin)
         % Create random spin directions and use a single k-vector
         S  = randn(nMagExt,3);
         S  = bsxfun(@rdivide,S,sqrt(sum(S.^2,2)));
-        S  = bsxfun(@times,S,mAtom.Sext')';
+        S  = bsxfunsym(@times,S,mAtom.Sext')';
         if noK
             k  = [0 0 0];
         end
@@ -387,11 +387,11 @@ function genmagstr(obj, varargin)
         if addPhase
             % additional phase for each spin in the magnetic supercell
             %phi = sum(bsxfun(@times,2*pi*kExt',r),1);
-            phi = sum(bsxfun(@times,2*pi*permute(kExt,[2 3 1]),r),1);
+            phi = sum(bsxfunsym(@times,2*pi*permute(kExt,[2 3 1]),r),1);
 
             % add the extra phase for each spin in the unit cell
             % TODO check
-            S = bsxfun(@times,S0(:,mod(0:(nMagExt-1),nSpin)+1,:),exp(-1i*phi));
+            S = bsxfunsym(@times,S0(:,mod(0:(nMagExt-1),nSpin)+1,:),exp(-1i*phi));
         else
             S = S0;
         end

swfiles/sw_cartesian.m

@@ -1,29 +1,29 @@
 function [vyOut, vzOut, vxOut] = sw_cartesian(n)
 % creates a right handed Cartesian coordinate system
-% 
+%
 % ### Syntax
-% 
+%
 % `[vy, vz, vx] = sw_cartesian(n)`
 %
 % `V = sw_cartesian(n)`
-% 
+%
 % ### Description
-% 
+%
 % `[vy, vz, vx] = sw_cartesian(n)` creates an $(x,y,z)$ right handed
 % Cartesian coordinate system with $v_x$, $v_y$ and $v_z$ defining the
-% basis vectors. 
+% basis vectors.
 %
 % `V = sw_cartesian(n)` the generated basis vectors are stored in the `V`
 % matrix: `V = [vx vy vz]` as column vectors.
-% 
+%
 % ### Input Arguments
-% 
+%
 % `n`
 % : Either a 3 element row/column vector or a $[3\times 3]$ matrix with
 %   columns defining 3 vectors.
-% 
+%
 % ### Output Arguments
-% 
+%
 % `vy,vz,vx`
 % : Vectors defining the right handed coordinate system. They are
 %           either column of row vectors depending on the shape of the
@@ -43,7 +43,14 @@
     z = [0; 0;-1];
     y = [0;-1; 0];
 
-    if any(cross(n,z))
+    c = cross(n,z);
+    if isa(n,'sym')
+        opt = any(sw_always(c));
+    else
+        opt = any(c);
+    end
+    
+    if opt
         vy = cross(n,z);
     else
         vy = cross(n,y);
@@ -54,12 +61,12 @@
     if det(n) == 0
         error('sw_cartesian:WrongInput','The input vectors are not linearly independent!')
     end
-
+    
     nShape = [3 1];
     vz = cross(n(:,1),n(:,2));
     vy = cross(vz,n(:,1));
     n = n(:,1);
-   
+    
 else
     error('sw_cartesian:WrongInput','Wrong size of n!')
 end
@@ -73,7 +80,6 @@
     vyOut = reshape(vy/norm(vy),nShape);
     vzOut = reshape(vz/norm(vz),nShape);
     vxOut = reshape(n/norm(n),nShape);
-
 end
 
 end

tutorials/publish/tutorial1.m

@@ -55,6 +55,7 @@
 % value is dinamically calculated at every call.
 
 FMchain.energy
+assert(FMchain.energy == -1)
 
 %% Calculate spin wave dispersion and spin-spin correlation function
 % We calculate spin wave dispersion and correlation function along the

tutorials/publish/tutorial10.m

@@ -77,6 +77,10 @@
 % ranges in momentum and energy. Second we call Horace to fill up the empty
 % d3d object with the simulated spin wave data and finally we plot a
 % constant energy cut.
+if ~exist('sqw','file')
+    fprintf('Horace is not installed. Exiting....\n');
+    return
+end
 
 Ebin   = [0,0.01,5];
 fwhm0  = 0.1; 

tutorials/publish/tutorial12.m

@@ -72,6 +72,11 @@
 % Horace is installed and setup. Calculate spectra using disp2sqw_eval
 % Horace function.
 
+if ~exist('sqw','file')
+    fprintf('Horace is not installed. Exiting....\n');
+    return
+end
+
 horaceObj = d3d(tri.abc,[1 0 0 0],[0,0.005,1],[0 1 0 0],[0,0.005,1],[0 0 0 1],[0,0.1,10]);
 horaceObj = disp2sqw_eval(horaceObj,@tri.horace,{'component','Sperp'},dE);
 cut1 = cut(horaceObj,[],[],[3.0 3.5]);

tutorials/publish/tutorial17.m

@@ -44,7 +44,7 @@
 % also created using symbolic input variables, for example incommensurate
 % k-vector, etc.
 
-FMchain.genmagstr('mode','helical','S',[0 1 0])
+FMchain.genmagstr('mode','helical','S',[0; 1; 0])
 FMchain.magtable.M
 plot(FMchain,'range',[3 0.5 0.5],'zoom',1)
 

tutorials/publish/tutorial31.m

@@ -78,7 +78,7 @@
 % Check spinw.formula() to see how much the new cell is smaller
 
 licroR = copy(licro);
-T = licroR.newcell({[-1 1 1]/3 [2 1 1]/3 [-1 -2 1]/3})
+T = licroR.newcell('bvect',{[-1 1 1]/3 [2 1 1]/3 [-1 -2 1]/3})
 plot(licroR,'cellMode','outside')
 swplot.zoom(1.5)