From 057b51a0ab19b9c35032681104540f721f36a192 Mon Sep 17 00:00:00 2001
From: Laura Nervo <lnervo@esrf.fr>
Date: Mon, 14 May 2012 09:41:31 +0000
Subject: [PATCH] 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 | 17 ++++++----
zUtil_Cryst/gtCalculateDist.m | 47 +++++++++++---------------
zUtil_Cryst/gtReadSpaceGroup.m | 62 +++++++++++++++++++++++++++-------
3 files changed, 79 insertions(+), 47 deletions(-)
diff --git a/1_preprocessing/gtSetup.m b/1_preprocessing/gtSetup.m
index c403776c..25b1500c 100644
--- a/1_preprocessing/gtSetup.m
+++ b/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');
diff --git a/zUtil_Cryst/gtCalculateDist.m b/zUtil_Cryst/gtCalculateDist.m
index 86f894a8..b46d1a29 100644
--- a/zUtil_Cryst/gtCalculateDist.m
+++ b/zUtil_Cryst/gtCalculateDist.m
@@ -1,11 +1,10 @@
-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
diff --git a/zUtil_Cryst/gtReadSpaceGroup.m b/zUtil_Cryst/gtReadSpaceGroup.m
index ad8d8592..3854db04 100644
--- a/zUtil_Cryst/gtReadSpaceGroup.m
+++ b/zUtil_Cryst/gtReadSpaceGroup.m
@@ -1,17 +1,20 @@
-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
--
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