Crystallography :

- add to gtReadSpaceGroup the crystal_system info
- adapt gtSetup code
- remove from gtCalculateDist the crystal_system calculation

Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@406 4c865b51-4357-4376-afb4-474e03ccb993

1_preprocessing/gtSetup.m

@@ -2,6 +2,10 @@ function gtSetup()
 % GTSETUP  Sets up the parameters file for the experiment
 %     gtSetup()
 %     ---------
+%
+%     Version 011 14-05-2012 by LNervo
+%       Modify gtReadSpaceGroup to give lattice and crystal systems
+%
 %     Version 010.1 03-05-2012 by LNervo
 %       Add lab2sam and sam2lab definition in samgeo
 %
@@ -342,13 +346,12 @@ for ii = 1 : parameters.acq.nof_phases
     parameters.cryst(ii) = gtAddMatFile(parameters.cryst(ii),cif,true,true,false);
     clear cif
     
-    [lattice,~] = gtReadSpaceGroup(parameters.cryst(ii).spacegroup);
-    if isempty(lattice)
-        parameters.cryst(ii).lattice_system = parameters.cryst(ii).crystal_system;
-    else
-        parameters.cryst(ii).lattice_system = lattice;
-    end
-    clear lattice
+    % crystal_system should be read from .cif file
+    % it is overwritten here
+    [lattice_system, crystal_system, ~] = gtReadSpaceGroup(parameters.cryst(ii).spacegroup);
+    parameters.cryst(ii).lattice_system = lattice_system;
+    parameters.cryst(ii).crystal_system = crystal_system;
+    clear lattice_system crystal_system
     
     disp('Saving parameters.mat in the analysis directory...')
     save(parameters_name,'parameters');

zUtil_Cryst/gtCalculateDist.m

-function [dsp,twotheta,crystal_system] = gtCalculateDist(hkl,cryst,energy)
+function [dsp,twotheta] = gtCalculateDist(hkl,cryst,energy)
 
-% GTCALCULATEDIST  Calculates d-spacing and twice the Bragg angle for a
-%     given hkl. Also gives crystal and lattice system of the spacegroup. 
-%     [dsp,twotheta,crystal_system] = gtCalculateDist(hkl,cryst,energy)
-%     -----------------------------------------------------------------
+% GTCALCULATEDIST  Calculates d-spacing and twice the Bragg angle for a given hkl
+%     [dsp,twotheta] = gtCalculateDist(hkl,cryst,energy)
+%     --------------------------------------------------
 %    
-%     INPUT
+%     INPUT:
 %       hkl                    - row vector of Miller indices;
 %                                size 1x3 or 1x4 for hexagonal
 %       cryst.latticepar       - lattice parameters
@@ -13,14 +12,15 @@ function [dsp,twotheta,crystal_system] = gtCalculateDist(hkl,cryst,energy)
 %       cryst.hermann_mauguin  - Hermann-Mauguin symbol
 %       energy                 - beam energy in keV 
 % 
-%     OUTPUT
+%     OUTPUT:
 %       dsp            - d-spacing of the specified hkl family
 %       twotheta       - twice the Bragg angle of the specified hkl family
-%       crystal_system - crystallographic crystal system of the specified
-%                        spacegroup
 %     
+%     Version 005 14-05-2012 by LNervo
+%       Remove crystal_system calculation
+%
 %     Version 004 14-03-2012 by PReischig
-%       Addition of lattice system as output; formatting.
+%       formatting.
 %
 %     Version 003 08-03-2012 by PReischig
 %       Seperated 'parameters' input into 'cryst' and 'energy'.
@@ -69,8 +69,7 @@ end
 
 % Spacegroups
 
-if between(spacegroup,1,2)
-    crystal = 'triclinic'; % a ~= b ~= c;  alpha ~= beta ~= gamma ~= 90
+if between(spacegroup,1,2) % crystal_system = 'triclinic'; % a ~= b ~= c;  alpha ~= beta ~= gamma ~= 90
     
     Y = h^2/a^2*(sind(alpha))^2 + k^2/b^2*(sind(beta))^2 + l^2/c^2*(sind(gamma))^2;
     Z = 2*k*l/b/c*(cosd(beta) *cosd(gamma) - cosd(alpha)) + ...
@@ -81,34 +80,30 @@ if between(spacegroup,1,2)
               2*cosd(alpha)*cosd(beta)*cosd(gamma))*(Y+Z);
 end
 
-if between(spacegroup,3,15)
-    crystal = 'monoclinic'; % a ~= b ~= c;  alpha = gamma = 90 ~= beta
+if between(spacegroup,3,15) % crystal_system = 'monoclinic'; % a ~= b ~= c;  alpha = gamma = 90 ~= beta
     
     invdsp2 = h^2/(a*sind(beta))^2 + k^2/b^2 + l^2/(c*sind(beta))^2 - ...
               (2*h*l*cosd(beta)) / (a*c*(sind(beta))^2);
 end
 
-if between(spacegroup,16,74)
-    crystal = 'orthorhombic'; % a ~= b ~= c;  alpha = beta = gamma = 90
+if between(spacegroup,16,74) % crystal_system = 'orthorhombic'; % a ~= b ~= c;  alpha = beta = gamma = 90
     
     invdsp2 = h^2/a^2 + k^2/b^2 + l^2/c^2;
 end
 
-if between(spacegroup,75,142)
-    crystal = 'tetragonal'; % a = b ~= c;  alpha = beta = gamma = 90
+if between(spacegroup,75,142) % crystal_system = 'tetragonal'; % a = b ~= c;  alpha = beta = gamma = 90
  
     invdsp2=(h^2+k^2)/a^2+l^2/c^2;
 end
 
-if between(spacegroup,143,167)
-    crystal = 'trigonal';
+if between(spacegroup,143,167) % crystal_system = 'trigonal';
     
-    if ~isempty(strfind(hermann,'P')) % hexagonal lattice 
+    if ~isempty(strfind(hermann,'P')) % hexagonal lattice_system
         % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
         
         invdsp2 = 4/(3*a^2) * (h^2 + k^2 + h*k) + l^2/c^2;
     
-    elseif ~isempty(strfind(hermann,'R')) % rhombohedral lattice
+    elseif ~isempty(strfind(hermann,'R')) % rhombohedral lattice_system
         % a = b = c;  alpha = beta = gamma ~= 90
         
         Y1 = h^2 + k^2 + h*k;
@@ -121,14 +116,12 @@ if between(spacegroup,143,167)
     end
 end
 
-if between(spacegroup,168,194) || spacegroup==663 % snow case
-    crystal = 'hexagonal'; % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
+if between(spacegroup,168,194) || spacegroup==663 % crystal_system = 'hexagonal'; % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
     
     invdsp2 = 4/(3*a^2)*(h^2 + k^2 + h*k) + l^2/c^2;
 end
 
-if between(spacegroup,195,230)
-    crystal = 'cubic'; % a = b = c;  alpha = beta = gamma = 90
+if between(spacegroup,195,230) % crystal_system = 'cubic'; % a = b = c;  alpha = beta = gamma = 90
     
     invdsp2 = (h^2+k^2+l^2)/a^2;
 end
@@ -140,6 +133,4 @@ dsp = 1/(invdsp2)^0.5;
 % 2theta
 twotheta = 2*asind(lambda/(2*dsp));
 
-crystal_system = crystal;
-
 end % end of function

zUtil_Cryst/gtReadSpaceGroup.m

-function [lattice,table]=gtReadSpaceGroup(sg)
+function [lattice, crystal, table] = gtReadSpaceGroup(sg)
 % GTREADSPACEGROUP  Read the spacegroup and give the hermann_mauguin symbol
-%     [lattice,table]=gtReadSpaceGroup(sg)
-%     ------------------------------------
+%     [lattice, crystal, table] = gtReadSpaceGroup(sg)
+%     ------------------------------------------------
 %
 %     INPUT:
 %       sg = spacegroup to look at <double>
 %
 %     OUTPUT:
 %       lattice = lattice system for this spacegroup
-%       table   = mhashtable with spacegroup,hermann_mauguin
-%
+%       crystal = crystal system for this spacegroup
+%       table   = mhashtable with 'spacegroup' : hermann_mauguin symbol
+%                 
+%     Version 003 14-05-2012 by LNervo
+%       Add lattice system calculation
 
-fid=fopen('spacegroups.dat','r');
+fid=fopen( fullfile( getenv('USER'), 'matlabDCT', 'zUtil_Cryst','spacegroups.dat' ),'r');
 C=textscan(fid,'%s %d','delimiter','\t','commentstyle','matlab');
 fclose(fid);
 
@@ -29,15 +32,50 @@ end
 table.remove('0');
 herm=table.get(num2str(sg));
 
-if between(sg,143,167) 
-    if ~isempty(strfind(herm,'P')) % hexagonal lattice
-        lattice = 'hexagonal'; % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
+% Spacegroups
+
+if between(sg,1,2)
+    crystal = 'triclinic'; % a ~= b ~= c;  alpha ~= beta ~= gamma ~= 90
+    lattice = 'triclinic';
+end
+
+if between(sg,3,15)
+    crystal = 'monoclinic'; % a ~= b ~= c;  alpha = gamma = 90 ~= beta
+    lattice = 'monoclinic';
+end
+
+if between(sg,16,74)
+    crystal = 'orthorhombic'; % a ~= b ~= c;  alpha = beta = gamma = 90
+    lattice = 'orthorhombic';
+end
+
+if between(sg,75,142)
+    crystal = 'tetragonal'; % a = b ~= c;  alpha = beta = gamma = 90
+    lattice = 'tetragonal';
+end
+
+if between(sg,143,167)
+    crystal = 'trigonal';
+    
+    if ~isempty(strfind(herm,'P')) % hexagonal lattice 
+        % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
+        lattice = 'hexagonal';
     elseif ~isempty(strfind(herm,'R')) % rhombohedral lattice
-        lattice = 'rhombohedral'; % a = b = c;  alpha = beta = gamma ~= 90
+        % a = b = c;  alpha = beta = gamma ~= 90
+        lattice = 'rhombohedral';
     end
-else
-    lattice ='';
 end
+
+if between(sg,168,194) || sg==663 % snow case
+    crystal = 'hexagonal'; % a1 = a2 = a3 ~= c;  alpha = beta = 90; gamma = 120
+    lattice = 'hexagonal';
+end
+
+if between(sg,195,230)
+    crystal = 'cubic'; % a = b = c;  alpha = beta = gamma = 90
+    lattice = 'cubic';
+end
+
         
         
 end % end of function
\ No newline at end of file