Modified grain.strain field names and function help.

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@572 4c865b51-4357-4376-afb4-474e03ccb993

zUtil_Indexter/gtINDEXDrawGrainCubes.m

@@ -169,10 +169,10 @@ end
 ggrain = Rod2g(grain.R_vector);
 grain_vertices = ga*cube_vertices*ggrain';
 
-if isfield(grain,'strain') && ~any(isnan(grain.strain.ST(:)))
+if isfield(grain,'strain') && ~any(isnan(grain.strain.strainT(:)))
 	grain_vertices_st = repmat(gc,8,1) + ...
-                        ((eye(3) + grain.strain.ST*strainscale)*grain_vertices')';
-	facecolor = grain.strain.ST(3,3);
+                        ((eye(3) + grain.strain.strainT*strainscale)*grain_vertices')';
+	facecolor = grain.strain.strainT(3,3);
 else
 	grain_vertices_st = repmat(gc,8,1) + (eye(3)*grain_vertices')';
 	facecolor = 0;

zUtil_Strain2/gtStrainGrainsGeneral.m

@@ -37,12 +37,12 @@ parfor ii = 1:length(grain)
     % Strain tensor
     ST = gtStrainSingleGrain(grain{ii}, cryst, lambda, Bmat);
     
-    grain{ii}.strain.ST  = ST;
+    grain{ii}.strain.strainT = ST;
     
     grain{ii}.strain.Eps = [ST(1,1) ST(2,2) ST(3,3) ST(2,3) ST(1,3) ST(1,2)];
     
     % Principal strains - eigenvalues and eigenvectors        
-    [ivec, ival] = eig(grain{ii}.strain.ST);
+    [ivec, ival] = eig(grain{ii}.strain.strainT);
     
     [ivalsort, ivalinds] = sort([ival(1,1), ival(2,2), ival(3,3)], 2, 'descend');
     
@@ -68,7 +68,7 @@ parfor ii = 1:length(grain)
     if (grain{ii}.strain.pstrain(1) > med_ps + stdlim*std_ps) || ...
        (grain{ii}.strain.pstrain(1) < med_ps - stdlim*std_ps)   
         
-        grain{ii}.strain.ST(:)         = NaN;
+        grain{ii}.strain.strainT(:)    = NaN;
         grain{ii}.strain.Eps(:)        = NaN(1,6);
         grain{ii}.strain.pstrain(:)    = NaN;
         grain{ii}.strain.pstraindir(:) = NaN;

zUtil_Strain2/gtStrainPlaneNormals.m

 function [pldef, drel] = gtStrainPlaneNormals(pl, G)
-% FUNCTION [pldef, drel] = gtStrainPlaneNormals(pl, G)
+% GTSTRAINPLANENORMALS Given a deformation tensor, calculates new plane 
+% normals with no approximations.
+% 
+%   [pldef, drel] = gtStrainPlaneNormals(pl, G)
 %
 % Returns the new orientations of plane normals 'pl' after a deformation 
 % described by the deformation tensor 'G' (9 distinct components).
 % Also returns the elongations 'drel' due to the deformation in the 
 % directions of the plane normals. In a crystal this equals to the ratios 
 % of the d-spacings after and before the deformation.
-% The results are exact, no linear approximation is used.
+% The results are exact, no approximation is used.
 % The 'pl' and 'G' coordinates must be given in the same reference frame.
 %
+% INPUT
+%   pl - normalised coordinates of plane normals (3xn)
+%   G  - deformation tensor (3x3)
+%
+% OUTPUT
+%   pldef - plane normals in deformed state
+%   drel  - relative elongations along the (deformed) plane normals
+%
 
 
 % Get an arbitrary vector e1 perpendicular to n:

zUtil_Strain2/gtStrainSingleGrain.m

 function ST = gtStrainSingleGrain(grain, cryst, lambda, Bmat)
-% GTSTRAINSINGLEGRAIN  ST = gtStrainSingleGrain(grain, cryst, lambda, Bmat)
+% GTSTRAINSINGLEGRAIN  Computes the strain tensor for a single grain.
+%  
+%   ST = gtStrainSingleGrain(grain, cryst, lambda, Bmat)
 % 
 % Computes the strain tensor 'ST' for a single indexed grain
 % (crystal system is irrelevant). The 6 strain matrix components are
 % computed in the same reference as the plane normals.
 % The deformation components are found by fitting all the interplanar 
-% angles and distances observed (no weighting of the equations). No linear
+% angles and distances observed (no weighting of the equations).
+%
+% Small deformations are assumed so that the strain tensor is considered to
+% be the symmetric part of the deformation tensor, but no further 
 % approximation is used.
-% If 'Bmat' is empty, it will be calculated inside the function. 
+%
+% It uses the function 'lsqnonlin' from Matlab's Optimization Toolbox.
+%
+%
+% INPUT
+%   grain  - a single grain data as from Indexter
+%   cryst  - crystallography data as in parameters file
+%   lambda - X-ray beam wavelength
+%   Bmat   - matrix to transform HKL indices into Cartesian coordinates
+%            (if empty, it will be calculated inside the function)
+% OUTPUT
+%   ST     - strain tensor (approximated as the symmetric part of the
+%            deformation tensor)
 %