Develop and Download Open Source Software

Powder auto-indexing software Conograph

Browse Subversion Repository

/[conograph]/Conograph/trunk/src/lattice_symmetry/LatticeFigureOfMerit.hh

Annotation of /Conograph/trunk/src/lattice_symmetry/LatticeFigureOfMerit.hh

Parent Directory Parent Directory | Revision Log Revision Log

Revision 33 - (hide annotations) (download) (as text)
Wed Sep 7 04:38:51 2016 UTC (7 years, 6 months ago) by rtomiyasu
File MIME type: text/x-c++hdr
File size: 15355 byte(s) 
The output format for base-centered monoclinic cells was corrected.
1 rtomiyasu 3 /*
2     * The MIT License
3    
4     Conograph (powder auto-indexing program)
5    
6     Copyright (c) <2012> <Ryoko Oishi-Tomiyasu, KEK>
7    
8     Permission is hereby granted, free of charge, to any person obtaining a copy
9     of this software and associated documentation files (the "Software"), to deal
10     in the Software without restriction, including without limitation the rights
11     to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
12     copies of the Software, and to permit persons to whom the Software is
13     furnished to do so, subject to the following conditions:
14    
15     The above copyright notice and this permission notice shall be included in
16     all copies or substantial portions of the Software.
17    
18     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
21     AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22     LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
23     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
24     THE SOFTWARE.
25     *
26     */
27     #ifndef LATTICEFIGUREOFMERIT_HH_
28     #define LATTICEFIGUREOFMERIT_HH_
29    
30     #include "../utility_data_structure/nrutil_nr.hh"
31 rtomiyasu 25 #include "../utility_data_structure/SymMatNplus1N.hh"
32 rtomiyasu 3 #include "../utility_data_structure/VecDat3.hh"
33     #include "../utility_func/transform_sym_matrix.hh"
34     #include "../utility_func/lattice_constant.hh"
35     #include "../utility_func/chToDouble.hh"
36 rtomiyasu 25 #include "../utility_lattice_reduction/matrix_NbyN.hh"
37     #include "../centring_type/enumCentringType.hh"
38 rtomiyasu 3 #include "../point_group/enumPointGroup.hh"
39     #include "../laue_group/LaueGroup.hh"
40     #include "../zparam/ZParawError.hh"
41     #include "../model_function/profile_function/global_function/enumPeakShiftFunctionType.hh"
42     #include "../bravais_type/BravaisType.hh"
43     #include "enumSortCriterion.hh"
44     #include "HKL_Q.hh"
45 rtomiyasu 25 #include "check_equiv.hh"
46 rtomiyasu 3
47    
48 rtomiyasu 25 // Class for outputting information about a lattice in index file.
49     class LatticeFigureOfMerit
50 rtomiyasu 3 {
51 rtomiyasu 25 friend inline bool operator<(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs);
52 rtomiyasu 3
53     public:
54 rtomiyasu 25 class SetOfFigureOfMerit
55 rtomiyasu 3 {
56 rtomiyasu 25 private:
57     Int4 m_num_ref_figure_of_merit;
58     Int4 m_num_q_observed;
59     Double m_num_total_hkl;
60     Double m_figure_of_merit_Wolff;
61     Double m_figure_of_merit_Wu;
62     Double m_reversed_figure_of_merit;
63 rtomiyasu 3
64 rtomiyasu 25 static string putStrFigureOfMeritWolff(const Int4& num_ref_fom){ return putLabel(SCM) + num2str(num_ref_fom); };
65     static string putStrFigureOfMeritWu(const Int4& num_ref_fom){ return putLabel(SCWuM) + num2str(num_ref_fom); };
66     static string putStrReversedFigureOfMeritWolff(const Int4& num_ref_fom){ return putLabel(SCRevM) + num2str(num_ref_fom); };
67     static string putStrSymmetricFigureOfMeritWolff(const Int4& num_ref_fom){ return putLabel(SCSymM) + num2str(num_ref_fom); };
68 rtomiyasu 3
69 rtomiyasu 25 public:
70     SetOfFigureOfMerit(){ this->reset(); }
71     ~SetOfFigureOfMerit(){}
72 rtomiyasu 3
73 rtomiyasu 25 inline void reset()
74     {
75     m_num_ref_figure_of_merit = 0;
76     m_num_q_observed = 0;
77     m_num_total_hkl = 0.0;
78     m_figure_of_merit_Wolff = 0.0;
79     m_figure_of_merit_Wu = 0.0;
80     m_reversed_figure_of_merit = 0.0;
81     }
82 rtomiyasu 3
83 rtomiyasu 25 inline Int4& putNumberOfReflectionsForFigureOfMerit() { return m_num_ref_figure_of_merit; };
84     inline Int4& putNumQobsAssociatedWithCloseHKL() { return m_num_q_observed; };
85     inline Double& putContinuousNumberOfHKLInRange() { return m_num_total_hkl; };
86 rtomiyasu 3
87 rtomiyasu 25 inline const Int4& putNumQobsAssociatedWithCloseHKL() const { return m_num_q_observed; };
88     inline const Int4& putNumberOfReflectionsForFigureOfMerit() const { return m_num_ref_figure_of_merit; };
89     inline const Double& putContinuousNumberOfHKLInRange() const { return m_num_total_hkl; };
90 rtomiyasu 3
91 rtomiyasu 25 inline Double& putFigureOfMeritWolff() { return m_figure_of_merit_Wolff; };
92     inline Double& putFigureOfMeritWu() { return m_figure_of_merit_Wu; };
93     inline Double& putReversedFigureOfMerit() { return m_reversed_figure_of_merit; };
94 rtomiyasu 3
95 rtomiyasu 25 inline const Double& putFigureOfMeritWolff() const { return m_figure_of_merit_Wolff; };
96     inline const Double& putFigureOfMeritWu() const { return m_figure_of_merit_Wu; };
97     inline const Double& putReversedFigureOfMerit() const { return m_reversed_figure_of_merit; };
98 rtomiyasu 3
99 rtomiyasu 25 inline string putLabel_FigureOfMeritWolff() const { return putStrFigureOfMeritWolff(m_num_ref_figure_of_merit); };
100     inline string putLabel_FigureOfMeritWu() const { return putStrFigureOfMeritWu(m_num_ref_figure_of_merit); };
101     inline string putLabel_ReversedFigureOfMeritWolff() const { return putStrReversedFigureOfMeritWolff(m_num_ref_figure_of_merit); };
102     inline string putLabel_SymmetricFigureOfMeritWolff() const { return putStrSymmetricFigureOfMeritWolff(m_num_ref_figure_of_merit); };
103 rtomiyasu 3
104 rtomiyasu 25 inline Double putSymmetricFigureOfMerit() const { return m_reversed_figure_of_merit * m_figure_of_merit_Wolff; };
105     };
106 rtomiyasu 3
107     private:
108     static const NRMat<Int4> m_tmat_prim_to_face;
109     static const NRMat<Int4> m_tmat_prim_to_body;
110     static const NRMat<Int4> m_tmat_prim_to_rhomhex;
111     static const NRMat<Int4> m_tmat_prim_to_base[3];
112     static const NRMat<Int4> m_tmat_prim_to_prim;
113    
114     BravaisType m_brat;
115    
116     // This matrix is a result of optimization, therefore, it may be not reduced.
117     // m_S_optimized.second * m_S_optimized.first * Transpose(m_S_optimized.second) is obtuse.
118     SymMat43_Double m_S_optimized;
119    
120 rtomiyasu 25 // The inverse of m_S_red is Buerger-reduced.
121 rtomiyasu 3 SymMat<Double> m_S_red;
122    
123     Double m_determ_S_red;
124    
125     SetOfFigureOfMerit m_figures_of_merit;
126    
127     // Sets m_S_red from m_S_optimized.
128 rtomiyasu 25 // On output, trans_mat gives the matrix such that trans_mat * m_S_red * transpose(trans_mat) = m_S_optimized.first.
129     void setInverseOfBuergerReducedForm(NRMat<Int4>& trans_mat);
130 rtomiyasu 3
131 rtomiyasu 25 // Returns unit-cell parameters with other centrings using m_S_red.
132     void putEquivalentLatticeConstantsDegreeWithOtherCentring(const eABCaxis& abc_axis,
133     const eRHaxis& rh_axis,
134     const Double& resol,
135     vector< pair< eBravaisType, SymMat<Double> > >& ans) const;
136    
137 rtomiyasu 3 protected:
138     static const Double m_cv2;
139    
140     public:
141     LatticeFigureOfMerit();
142     LatticeFigureOfMerit(const Double& rhs); // Sets only m_determ_GramMat = rhs;
143     LatticeFigureOfMerit(const BravaisType& ebrat,
144     const SymMat43_Double& S_red);
145     virtual ~LatticeFigureOfMerit(){};
146    
147 rtomiyasu 25 void putMillerIndicesInRange(const Double& qrange_end,
148 rtomiyasu 33 const Int4& irc_type,
149 rtomiyasu 3 vector<HKL_Q>& cal_hkl_tray) const;
150    
151 rtomiyasu 33 void setDeWolffFigureOfMerit(const Int4& num_ref_figure_of_merit, const Int4& irc_type, const vector<QData>& qdata);
152 rtomiyasu 25
153 rtomiyasu 3 void setWuFigureOfMerit(const Int4& num_ref_figure_of_merit, const vector<QData>& qdata,
154     const Double& min_thred_num_hkl,
155     const Double& max_thred_num_hkl);
156    
157     // Return false if Qdata is not set or
158     // the number of unindexed reflections is larger max_num_false_peak.
159     void setFigureOfMerit(const Int4& num_ref_figure_of_merit, const vector<QData>& qdata,
160     vector< VecDat3<Int4> >& closest_hkl_tray,
161     Vec_BOOL& Q_observed_flag);
162 rtomiyasu 25
163 rtomiyasu 3 inline void setFigureOfMerit(const Int4& num_ref_figure_of_merit, const vector<QData>& qdata)
164     {
165     vector< VecDat3<Int4> > closest_hkl_tray;
166     Vec_BOOL Q_observed_flag;
167     setFigureOfMerit(num_ref_figure_of_merit, qdata, closest_hkl_tray, Q_observed_flag);
168     };
169    
170     // true : NormM has been improved.
171     // false : NormM has not been improved.
172     pair<bool, ZErrorMessage> fitLatticeParameterLinear(const vector<QData>& qdata,
173     const vector< VecDat3<Int4> >& hkl_to_fit,
174     const vector<bool>& fix_or_fit_flag,
175     const bool& output_view_flag);
176    
177     // Change the lattice constants to string.
178     inline string printOptimizedLatticeConstants(const eABCaxis& axis1,
179     const eRHaxis& axis2,
180     const Int4& precision) const;
181    
182     // Output information on the lattice.
183     void printLatticeInformation(const eABCaxis& abc_axis,
184     const eRHaxis& rh_axis,
185 rtomiyasu 25 const Double& resol,
186 rtomiyasu 3 const Int4& label_start0,
187     ostream* os) const;
188    
189     // Set-functions.
190     // This method assumes that S.second * S.first * Transpose(S.second) is obtuse.
191     void setLatticeConstants43(const BravaisType& brat, const SymMat43_Double& S);
192    
193     ZErrorMessage setLatticeConstants(const BravaisType& brat, const SymMat<Double>& S);
194    
195     Int4 checkDominantZone() const;
196    
197     // Replace m_S_optimized by m_S_red.
198     // On output, trans_mat gives the matrix such that trans_mat * m_S_red * transpose(trans_mat) equals the original m_S_optimized.
199     inline void reduceLatticeConstants(NRMat<Int4>& trans_mat);
200    
201     // The unit of alpha, beta, gamma is degree.
202     inline ZErrorMessage setLatticeConstantsDegree(const BravaisType& brat,
203     const VecDat3<Double>& length_axis,
204     const VecDat3<Double>& angle_axis);
205    
206     static void putLatticeConstantsDegree(const BravaisType& brat,
207     const SymMat<Double>& S,
208     const eABCaxis& axis1,
209     const eRHaxis& axis2,
210     VecDat3<Double>& length, VecDat3<Double>& angle);
211    
212     // Put-functions (Returns a value.)
213     inline void putOptimizedLatticeConstantsDegree(const eABCaxis& axis1,
214     const eRHaxis& axis2,
215     VecDat3<Double>& length, VecDat3<Double>& angle) const;
216    
217     inline void putReducedLatticeConstantsDegree(const eABCaxis& axis1,
218     const eRHaxis& axis2,
219     VecDat3<Double>& length, VecDat3<Double>& angle) const;
220    
221     inline Double putLatticeVolume() const { return 1.0 / sqrt(m_determ_S_red); };
222    
223     // Put-functions (Returns a constant reference.)
224     inline const Double& putCriticalValueSquare() const { return m_cv2; };
225    
226 rtomiyasu 17 inline const ePointGroup& enumLaueGroup() const { return m_brat.enumLaueGroup(); };
227 rtomiyasu 25 inline const eCentringType& enumCentringType() const { return m_brat.enumCentringType(); };
228     inline const eBravaisType& enumBravaisType() const { return m_brat.enumBravaisType(); };
229 rtomiyasu 3 inline const BravaisType& putBravaisType() const { return m_brat; };
230    
231 rtomiyasu 25 // The returned matrix is Buerger-reduced matrix equivalent with m_S_red_optimized.
232     inline const SymMat<Double>& putInverseOfBuergerReducedForm() const { return m_S_red; };
233 rtomiyasu 3
234     inline const SymMat43_Double& putOptimizedForm() const { return m_S_optimized; };
235     inline SymMat<Double> putSellingReducedForm() const { return transform_sym_matrix(m_S_optimized.second, m_S_optimized.first); };
236    
237     inline const Double& putDeterminantOfGramMatrix() const { return m_determ_S_red; };
238     inline const SetOfFigureOfMerit& putFiguresOfMerit() const { return m_figures_of_merit; };
239    
240     // Put-functions (Returns a non-constant reference.)
241 rtomiyasu 25 // Returns almost equivalent unit-cell parameters of different centring-types.
242     void putEquivalentLatticeConstantsDegreeWithOtherCentring(const eABCaxis& abc_axis,
243     const eRHaxis& rh_axis,
244     const Double& resol,
245     vector< pair< eBravaisType, pair< VecDat3<Double>, VecDat3<Double> > > >& ans) const;
246 rtomiyasu 3
247     static bool cmpFOMdeWolff(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs)
248     {
249     return lhs.m_figures_of_merit.putFigureOfMeritWolff() > rhs.m_figures_of_merit.putFigureOfMeritWolff();
250     }
251    
252     static bool cmpFOMWu(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs)
253     {
254     return lhs.m_figures_of_merit.putFigureOfMeritWu() > rhs.m_figures_of_merit.putFigureOfMeritWu();
255     }
256    
257     static bool cmpFOMReversed(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs)
258     {
259     return lhs.m_figures_of_merit.putReversedFigureOfMerit() > rhs.m_figures_of_merit.putReversedFigureOfMerit();
260     }
261    
262     static bool cmpFOMSymmetric(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs)
263     {
264     return lhs.m_figures_of_merit.putSymmetricFigureOfMerit() > rhs.m_figures_of_merit.putSymmetricFigureOfMerit();
265     }
266    
267     // For GUI
268     const BravaisType &getref_m_brat() const {return m_brat;}
269     BravaisType &getref_m_brat() {return m_brat;}
270     const SetOfFigureOfMerit &getref_m_figures_of_merit() const {return m_figures_of_merit;}
271     SetOfFigureOfMerit &getref_m_figures_of_merit() {return m_figures_of_merit;}
272     const SymMat43_Double &getref_m_S_red_optimized() const {return m_S_optimized;}
273     SymMat43_Double &getref_m_S_red_optimized() {return m_S_optimized;}
274     const Double &getref_m_determ_S_red() const {return m_determ_S_red;}
275     Double &getref_m_determ_S_red() {return m_determ_S_red;}
276 rtomiyasu 16 const SymMat<Double> &getref_m_S_red() const {return m_S_red;}
277     SymMat<Double> &getref_m_S_red() {return m_S_red;}
278    
279 rtomiyasu 3 };
280    
281    
282     inline string LatticeFigureOfMerit::printOptimizedLatticeConstants(const eABCaxis& axis1,
283     const eRHaxis& axis2,
284     const Int4& precision) const
285     {
286     VecDat3<Double> length_axis, angle_axis;
287     putOptimizedLatticeConstantsDegree(axis1, axis2, length_axis, angle_axis);
288     return chToString(length_axis, angle_axis, precision);
289     }
290    
291    
292     inline void LatticeFigureOfMerit::putOptimizedLatticeConstantsDegree(const eABCaxis& axis1,
293     const eRHaxis& axis2,
294     VecDat3<Double>& length_axis, VecDat3<Double>& angle_axis) const
295     {
296     putLatticeConstantsDegree( m_brat, m_S_optimized.first, axis1, axis2, length_axis, angle_axis );
297     }
298    
299    
300     inline void LatticeFigureOfMerit::putReducedLatticeConstantsDegree(
301     const eABCaxis& axis1,
302     const eRHaxis& axis2, VecDat3<Double>& length_axis, VecDat3<Double>& angle_axis) const
303     {
304 rtomiyasu 25 putLatticeConstantsDegree( m_brat, this->putInverseOfBuergerReducedForm(),
305 rtomiyasu 3 axis1, axis2, length_axis, angle_axis );
306     }
307    
308    
309    
310     inline ZErrorMessage LatticeFigureOfMerit::setLatticeConstantsDegree(const BravaisType& brat,
311     const VecDat3<Double>& length,
312     const VecDat3<Double>& angle)
313     {
314 rtomiyasu 17 LaueGroup lg(brat.enumLaueGroup());
315 rtomiyasu 3 ZErrorMessage zerr = lg->checkLatticeConstantError(length, angle);
316     if( zerr.putErrorType() != ZErrorNoError ) return zerr;
317    
318     SymMat<Double> Sval(3);
319     calCoParameter(length, angle, Sval);
320    
321     return this->setLatticeConstants(brat, Sval);
322     }
323    
324     inline void LatticeFigureOfMerit::reduceLatticeConstants(NRMat<Int4>& trans_mat)
325     {
326 rtomiyasu 33 // trans_mat * m_S_red * transpose(trans_mat) = m_S_optimized.first(old).
327 rtomiyasu 25 setInverseOfBuergerReducedForm(trans_mat);
328 rtomiyasu 33 // m_S_optimized.first(new) = m_S_red.
329 rtomiyasu 3 m_S_optimized.first = m_S_red;
330 rtomiyasu 33
331     // m_S_optimized.second(new) * m_S_optimized.first(new) * transpose(m_S_optimized.second(new))
332     // = m_S_optimized.second(old) * m_S_optimized.first(old) * transpose(m_S_optimized.second(old)) is Delone reduced.
333 rtomiyasu 3 m_S_optimized.second = mprod(m_S_optimized.second, trans_mat);
334     }
335    
336    
337     template<class T>
338     inline T norm(const VecDat3<Int4>& lhs, const SymMat<T>& rhs)
339     {
340     assert( rhs.size() >= 3 );
341    
342     return rhs(0,0)*(lhs[0]*lhs[0]) + rhs(1,1)*(lhs[1]*lhs[1]) + rhs(2,2)*(lhs[2]*lhs[2])
343     + ( rhs(0,1)*(lhs[0]*lhs[1]) + rhs(0,2)*(lhs[0]*lhs[2]) + rhs(1,2)*(lhs[1]*lhs[2]) )*2.0;
344     }
345    
346    
347     inline bool operator<(const LatticeFigureOfMerit& lhs, const LatticeFigureOfMerit& rhs)
348     {
349     return lhs.m_determ_S_red < rhs.m_determ_S_red;
350     }
351    
352 rtomiyasu 25 void putTransformMatrixToBuergerReduced(const SymMat<Double>& S, NRMat<Int4>& trans_mat);
353 rtomiyasu 3
354     #endif /*LATTICEFIGUREOFMERIT_HH_*/
Back to OSDN">Back to OSDN
 ViewVC Help
Powered by ViewVC 1.1.26  
About OSDN
Find Software
Develop Software
Help