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Wed Sep 7 04:38:51 2016 UTC (7 years, 6 months ago) by rtomiyasu
File MIME type: text/x-c++src
File size: 27855 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     #ifdef _OPENMP
28     #include <omp.h>
29     #endif
30     #include <string>
31     #include "ControlParam.hh"
32     #include "utility_data_structure/qdata.hh"
33     #include "utility_func/zstring.hh"
34     #include "utility_func/zmath.hh"
35     #include "zlog/zlog.hh"
36    
37     const map<eABCaxis, string> ControlParam::ABCaxisLabel = putABCaxisLabel();
38     const map<eRHaxis, string> ControlParam::RHaxisLabel = putRHaxisLabel();
39    
40     static Vec_DP putConvParamRange()
41     {
42     Vec_DP ans(2, 0.0);
43     ans[0] = -I_ReadData::MAX_DP();
44     return ans;
45     }
46    
47     const pair<RWParamProperty, RWParamData<bool> > ControlParam::IsAngleDispersion_Data(
48     RWParamProperty(BOOLFLAG, "IsAngleDispersion"),
49     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) );
50     const pair<RWParamProperty, RWParamData<bool> > ControlParam::OutputSymmetry_Data[NUM_LS]
51     = {
52     pair<RWParamProperty, RWParamData<bool> >(
53     RWParamProperty(BOOLFLAG, "OutputTriclinic"),
54     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
55     pair<RWParamProperty, RWParamData<bool> >(
56     RWParamProperty(BOOLFLAG, "OutputMonoclinicP"),
57     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
58     pair<RWParamProperty, RWParamData<bool> >(
59     RWParamProperty(BOOLFLAG, "OutputMonoclinicB"),
60     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
61     pair<RWParamProperty, RWParamData<bool> >(
62     RWParamProperty(BOOLFLAG, "OutputOrthorhombicP"),
63     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
64     pair<RWParamProperty, RWParamData<bool> >(
65 rtomiyasu 9 RWParamProperty(BOOLFLAG, "OutputOrthorhombicC"),
66 rtomiyasu 3 RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
67     pair<RWParamProperty, RWParamData<bool> >(
68     RWParamProperty(BOOLFLAG, "OutputOrthorhombicI"),
69     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
70     pair<RWParamProperty, RWParamData<bool> >(
71     RWParamProperty(BOOLFLAG, "OutputOrthorhombicF"),
72     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
73     pair<RWParamProperty, RWParamData<bool> >(
74     RWParamProperty(BOOLFLAG, "OutputTetragonalP"),
75     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
76     pair<RWParamProperty, RWParamData<bool> >(
77     RWParamProperty(BOOLFLAG, "OutputTetragonalI"),
78     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
79     pair<RWParamProperty, RWParamData<bool> >(
80     RWParamProperty(BOOLFLAG, "OutputRhombohedral"),
81     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
82     pair<RWParamProperty, RWParamData<bool> >(
83     RWParamProperty(BOOLFLAG, "OutputHexagonal"),
84     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
85     pair<RWParamProperty, RWParamData<bool> >(
86     RWParamProperty(BOOLFLAG, "OutputCubicP"),
87     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
88     pair<RWParamProperty, RWParamData<bool> >(
89     RWParamProperty(BOOLFLAG, "OutputCubicI"),
90     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) ),
91     pair<RWParamProperty, RWParamData<bool> >(
92     RWParamProperty(BOOLFLAG, "OutputCubicF"),
93     RWParamData<bool>(true, REPLACE_NONE<bool>, NULL, false, NULL, false, -1, -1) )
94     };
95    
96     inline Vec_DP put_initial_conv_param()
97     {
98     Vec_DP ans(3,0.0);
99     ans[1] = 1.0;
100     return ans;
101     }
102    
103     const pair<RWParamProperty, RWParamData<Vec_DP> > ControlParam::ConvParam_Data(
104     RWParamProperty(DARRAY, "ConversionParameters"),
105     RWParamData<Vec_DP>(put_initial_conv_param(), REPLACE_VECTOR_NONE<Double>, GTVec<Double>, putConvParamRange(), NULL, Vec_DP(), 2, 6) );
106     const pair<RWParamProperty, RWParamData<Vec_DP> > ControlParam::PeakShiftParam_Data(
107 rtomiyasu 9 RWParamProperty(DARRAY, "ZeroPointShiftParameter"),
108 rtomiyasu 3 RWParamData<Vec_DP>(Vec_DP(1,0.0), REPLACE_VECTOR_NONE<Double>, NULL, Vec_DP(), NULL, Vec_DP(), 1, 1) );
109     const pair<RWParamProperty, RWParamData<Double> > ControlParam::WlengthX_Data(
110     RWParamProperty(DVALUE, "WaveLength"),
111     RWParamData<Double>(1.54056, REPLACE_NONE<Double>, GT<Double>, 0.0, NULL, MAX_DP(), -1, -1) );
112    
113    
114     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MaxPeakNum_Data(
115     RWParamProperty(STRVALUE, "MaxNumberOfPeaks"),
116     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) );
117     const pair<RWParamProperty, RWParamData<Int4> > ControlParam::NumRefFigureOfMerit_Data(
118     RWParamProperty(INT4VALUE, "MaxNumberOfPeaksForFOM"),
119     RWParamData<Int4>(20, REPLACE_NONE<Int4>, GE<Int4>, 1, NULL, MAX_INT(), -1, -1) ); // 20 <= param < INF.
120     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MaxEdgeNum_Data(
121     RWParamProperty(STRVALUE, "MaxNumberOfTwoDimTopographs"),
122     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) ); // 0 < param < INF.
123     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MaxNodeNum_Data(
124     RWParamProperty(STRVALUE, "MaxNumberOfLatticeCandidates"),
125     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) ); // 0 < param < INF.
126     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MaxNumPeakInRange_Data(
127     RWParamProperty(STRVALUE, "MaxNumberOfMillerIndicesInRange"),
128     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) );
129     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MinNumPeakInRange_Data(
130     RWParamProperty(STRVALUE, "MinNumberOfMillerIndicesInRange"),
131     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) ); // 0.0 <= param <= 1.0.
132     const pair<RWParamProperty, RWParamData<Double> > ControlParam::MinFOM_Data(
133     RWParamProperty(DVALUE, "MinFOM"),
134     RWParamData<Double>(3.0, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
135     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MaxUnitCellVolume_Data(
136     RWParamProperty(STRVALUE, "MaxPrimitiveUnitCellVolume"),
137     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) ); // 0 <= param < INF.
138     const pair<RWParamProperty, RWParamData<string> > ControlParam::str_MinUnitCellVolume_Data(
139     RWParamProperty(STRVALUE, "MinPrimitiveUnitCellVolume"),
140     RWParamData<string>("AUTO", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) ); // 0 <= param < INF.
141     const pair<RWParamProperty, RWParamData<Double> > ControlParam::MinUnitCellEdgeABC_Data(
142     RWParamProperty(DVALUE, "MinUnitCellEdgeABC"),
143     RWParamData<Double>(0.0, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
144     const pair<RWParamProperty, RWParamData<Double> > ControlParam::MaxUnitCellEdgeABC_Data(
145     RWParamProperty(DVALUE, "MaxUnitCellEdgeABC"),
146     RWParamData<Double>(1000.0, REPLACE_MAX<Double>, GT<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
147     const pair<RWParamProperty, RWParamData<Double> > ControlParam::CVForLinearSum_Data(
148     RWParamProperty(DVALUE, "CriticalValueForLinearSum"),
149     RWParamData<Double>(1.0, REPLACE_NONE<Double>, GT<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 < param < INF.
150     const pair<RWParamProperty, RWParamData<Double> > ControlParam::Resol_Data(
151     RWParamProperty(DVALUE, "Resolution"),
152     RWParamData<Double>(0.03, REPLACE_NONE<Double>, GE<Double>, 0.0, LE<Double>, 0.25, -1, -1) ); // 0 <= param < INF.
153    
154     const pair<RWParamProperty, RWParamData<Int4> > ControlParam::SearchLevel_Data(
155     RWParamProperty(INT4VALUE, "SearchLevel"),
156     RWParamData<Int4>((Int4)ConographQuickSearch, REPLACE_NONE<Int4>, GE<Int4>, (Int4)ConographQuickSearch, LE<Int4>, (Int4)ConographRegularSearch, -1, -1) );
157    
158     const pair<RWParamProperty, RWParamData<string> > ControlParam::MonoBaseAxis_Data(
159 rtomiyasu 9 RWParamProperty(STRVALUE, "AxisForMonoclinicSymmetry"),
160 rtomiyasu 3 RWParamData<string>("B", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) );
161     const pair<RWParamProperty, RWParamData<string> > ControlParam::RhomAxis_Data(
162     RWParamProperty(STRVALUE, "AxisForRhombohedralSymmetry"),
163     RWParamData<string>("Hexagonal", REPLACE_NONE<string>, NULL, "", NULL, "", -1, -1) );
164     const pair<RWParamProperty, RWParamData<Double> > ControlParam::ThresholdNormM_Data(
165     RWParamProperty(DVALUE, "ThresholdOnNormM"),
166     RWParamData<Double>(1.9, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
167     const pair<RWParamProperty, RWParamData<Double> > ControlParam::ThresholdRevM_Data(
168     RWParamProperty(DVALUE, "ThresholdOnRevM"),
169 rtomiyasu 33 RWParamData<Double>(1.0, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
170 rtomiyasu 3 const pair<RWParamProperty, RWParamData<Double> > ControlParam::MinLatticePointDistance_Data(
171     RWParamProperty(DVALUE, "MinDistanceBetweenLatticePoints"),
172     RWParamData<Double>(2.0, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
173 rtomiyasu 25 const pair<RWParamProperty, RWParamData<Double> > ControlParam::ResoltoCheckComputedLines_Data(
174     RWParamProperty(DVALUE, "ResolutionToCheckCoincidenceofComputedLines", NULL, 1, 0),
175     RWParamData<Double>(0.03, REPLACE_NONE<Double>, GE<Double>, 0.0, LE<Double>, 0.05, -1, -1) ); // 0 <= param < INF.
176     const pair<RWParamProperty, RWParamData<Double> > ControlParam::MaxQtoCheckComputedLines_Data(
177     RWParamProperty(DVALUE, "MaxQToCheckCoincidenceofComputedLines", NULL, 1, 0),
178     RWParamData<Double>(3.0, REPLACE_NONE<Double>, GE<Double>, 0.0, NULL, MAX_DP(), -1, -1) ); // 0 <= param < INF.
179     const pair<RWParamProperty, RWParamData<Int4> > ControlParam::MaxSizeForEachBRAVAIS_Data(
180     RWParamProperty(INT4VALUE, "MaxNumberOfSolutionsForEachBravaisLattice", NULL, 1, 0),
181     RWParamData<Int4>(1000, REPLACE_NONE<Int4>, GE<Int4>, 1, NULL, MAX_INT(), -1, -1) );
182 rtomiyasu 3
183     ControlParam::ControlParam()
184 rtomiyasu 6 :
185     #ifdef _OPENMP
186     NumCores_Data(RWParamProperty(INT4VALUE, "NumberOfThreadsToUse"),
187 rtomiyasu 25 RWParamData<Int4>(max(1, omp_get_num_procs()-1), REPLACE_NUM_THREAD, GE<Int4>, 1, NULL, MAX_INT(), -1, -1) ),
188 rtomiyasu 6 #else
189     NumCores_Data(RWParamProperty(INT4VALUE, "NumberOfThreadsToUse"),
190 rtomiyasu 25 RWParamData<Int4>(1, REPLACE_NUM_THREAD, GE<Int4>, 1, NULL, MAX_INT(), -1, -1) ),
191 rtomiyasu 6 #endif
192 rtomiyasu 16 ReadConfigurationParameters(true),
193     IsADorTOF(IsAngleDispersion_Data.second.initial_value),
194 rtomiyasu 3 ConvParam(ConvParam_Data.second.initial_value),
195     PeakShiftParam(PeakShiftParam_Data.second.initial_value),
196     WlengthX(WlengthX_Data.second.initial_value),
197     SearchLevel(SearchLevel_Data.second.initial_value),
198     MaxPeakNum(0),
199     MaxEdgeNum(0),
200     MaxNodeNum(0),
201     MinUnitCellVolume(0.0),
202     MaxUnitCellVolume(0.0),
203     CVForLinearSum(CVForLinearSum_Data.second.initial_value),
204     NumRefFigureOfMerit(NumRefFigureOfMerit_Data.second.initial_value),
205     MaxNumPeakInRange(0),
206     MinNumPeakInRange(0),
207     MinUnitCellEdgeABC(MinUnitCellEdgeABC_Data.second.initial_value),
208     MaxUnitCellEdgeABC(MaxUnitCellEdgeABC_Data.second.initial_value),
209     MinFOM(MinFOM_Data.second.initial_value),
210     Resol(Resol_Data.second.initial_value),
211     NumCores(NumCores_Data.second.initial_value),
212 rtomiyasu 25 MaxSizeForEachBRAVAIS(MaxSizeForEachBRAVAIS_Data.second.initial_value),
213 rtomiyasu 3 MonoBaseAxis(MonoBaseAxis_Data.second.initial_value),
214     RhomAxis(RhomAxis_Data.second.initial_value),
215     ThresholdNormM(ThresholdNormM_Data.second.initial_value),
216     ThresholdRevM(ThresholdRevM_Data.second.initial_value),
217     MinLatticePointDistance(MinLatticePointDistance_Data.second.initial_value),
218 rtomiyasu 25 ResoltoCheckComputedLines(ResoltoCheckComputedLines_Data.second.initial_value),
219     MaxQtoCheckComputedLines(MaxQtoCheckComputedLines_Data.second.initial_value),
220 rtomiyasu 3 str_MaxPeakNum(str_MaxPeakNum_Data.second.initial_value),
221     str_MaxEdgeNum(str_MaxEdgeNum_Data.second.initial_value),
222     str_MaxNodeNum(str_MaxNodeNum_Data.second.initial_value),
223     str_MinUnitCellVolume(str_MinUnitCellVolume_Data.second.initial_value),
224     str_MaxUnitCellVolume(str_MaxUnitCellVolume_Data.second.initial_value),
225     str_MaxNumPeakInRange(str_MaxNumPeakInRange_Data.second.initial_value),
226     str_MinNumPeakInRange(str_MinNumPeakInRange_Data.second.initial_value)
227     {
228     for(Int4 i=0; i<NUM_LS; i++)
229     {
230     OutputSymmetry[i] = OutputSymmetry_Data[i].second.initial_value;
231     }
232     }
233    
234    
235     ControlParam::~ControlParam()
236     {
237     }
238    
239    
240     const string& ControlParam::putTagLabel() const
241     {
242     static const string label = "ConographParameters";
243     return label;
244     }
245    
246    
247     ZErrorMessageReadingFile ControlParam::readFile(const string& filename, const string& file_label)
248     {
249     ZErrorMessageReadingFile zerr = I_ReadData::readFile(filename, file_label);
250     if( IsAngleDispersion() ) ConvParam.clear();
251     else PeakShiftParam.clear();
252    
253     if( zerr.putErrorType() != ZErrorNoError ) return zerr;
254     if( str_MaxPeakNum!="AUTO" )
255     {
256     if( str_MaxPeakNum=="MAX" )
257     {
258     MaxPeakNum = numeric_limits<Int4>::max();
259     }
260     else
261     {
262     istringstream iss( str_MaxPeakNum );
263     iss >> MaxPeakNum;
264     if( iss.fail() ) return ZErrorMessageReadingFile( filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + str_MaxPeakNum_Data.first.putLabel() + ">:"+str_MaxPeakNum, __FILE__, __LINE__, __FUNCTION__) );
265     if( MaxPeakNum < 3 )
266     {
267     return ZErrorMessageReadingFile( filename, ZErrorMessage("<"+ str_MaxPeakNum_Data.first.putLabel() + "> is too small: "+num2str<Int4>(MaxPeakNum), __FILE__, __LINE__, __FUNCTION__) );
268     }
269     else if( MaxPeakNum > 2000 )
270     {
271     return ZErrorMessageReadingFile( filename, ZErrorMessage("<"+ str_MaxPeakNum_Data.first.putLabel() + "> is too large: "+num2str<Int4>(MaxPeakNum), __FILE__, __LINE__, __FUNCTION__) );
272     }
273     }
274     }
275    
276     if( str_MaxEdgeNum != "AUTO" )
277     {
278     if( str_MaxEdgeNum=="MAX" )
279     {
280     MaxEdgeNum = numeric_limits<Int4>::max();
281     }
282     else
283     {
284     istringstream iss( str_MaxEdgeNum );
285     iss >> MaxEdgeNum;
286     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + str_MaxEdgeNum_Data.first.putLabel() + ">: "+str_MaxEdgeNum, __FILE__, __LINE__, __FUNCTION__) );
287     if( MaxEdgeNum < 1 )
288     {
289     return ZErrorMessageReadingFile(filename, nerror_arg("<"+ str_MaxEdgeNum_Data.first.putLabel() + "> is too small: "+num2str<Int4>(MaxEdgeNum), __FILE__, __LINE__, __FUNCTION__) );
290     }
291     }
292     }
293    
294     if( str_MaxNodeNum != "AUTO" )
295     {
296     if( str_MaxNodeNum=="MAX" )
297     {
298     MaxNodeNum = numeric_limits<Int4>::max();
299     }
300     else
301     {
302     istringstream iss( str_MaxNodeNum );
303     iss >> MaxNodeNum;
304     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string in <" + str_MaxNodeNum_Data.first.putLabel() + "> is not replaced: "+str_MaxNodeNum, __FILE__, __LINE__, __FUNCTION__) );
305     if( MaxNodeNum < 1 )
306     {
307     return ZErrorMessageReadingFile(filename, nerror_arg("<"+ str_MaxNodeNum_Data.first.putLabel() + "> is too small: "+num2str<Int4>(MaxNodeNum), __FILE__, __LINE__, __FUNCTION__) );
308     }
309     }
310     }
311    
312     if( str_MinUnitCellVolume != "AUTO" )
313     {
314     istringstream iss( str_MinUnitCellVolume );
315     iss >> MinUnitCellVolume;
316     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + putMinUnitCellVolumeLabel() + ">: "+str_MinUnitCellVolume, __FILE__, __LINE__, __FUNCTION__) );
317     if( MinUnitCellVolume < 1.0 )
318     {
319     return ZErrorMessageReadingFile(filename, nerror_arg("<"+ putMinUnitCellVolumeLabel() + "> is less than 1: "+num2str<Double>(MinUnitCellVolume), __FILE__, __LINE__, __FUNCTION__) );
320     }
321     }
322    
323     if( str_MaxUnitCellVolume != "AUTO" )
324     {
325     istringstream iss( str_MaxUnitCellVolume );
326     iss >> MaxUnitCellVolume;
327     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + putMaxUnitCellVolumeLabel() + ">: "+str_MaxUnitCellVolume, __FILE__, __LINE__, __FUNCTION__) );
328     if( MaxUnitCellVolume <= MinUnitCellVolume )
329     {
330     return ZErrorMessageReadingFile(filename, nerror_arg("<"+ putMaxUnitCellVolumeLabel() + "> is not larger than <"+ putMinUnitCellVolumeLabel() + "> : "+num2str<Double>(MaxUnitCellVolume), __FILE__, __LINE__, __FUNCTION__) );
331     }
332     }
333    
334     if( str_MaxNumPeakInRange != "AUTO" )
335     {
336     if( str_MaxNumPeakInRange =="MAX" )
337     {
338     MaxNumPeakInRange = numeric_limits<Int4>::max();
339     }
340     else
341     {
342     istringstream iss( str_MaxNumPeakInRange );
343     iss >> MaxNumPeakInRange;
344     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + str_MaxNumPeakInRange_Data.first.putLabel() + ">: "+str_MaxNumPeakInRange, __FILE__, __LINE__, __FUNCTION__) );
345     if( MaxNumPeakInRange < 1 )
346     {
347     return ZErrorMessageReadingFile(filename, ZErrorMessage("<"+ str_MaxNumPeakInRange_Data.first.putLabel() + "> is less than 1: "+num2str<Double>(MaxNumPeakInRange), __FILE__, __LINE__, __FUNCTION__) );
348     }
349     }
350     }
351    
352     if( str_MinNumPeakInRange != "AUTO" )
353     {
354     istringstream iss( str_MinNumPeakInRange );
355     iss >> MinNumPeakInRange;
356     if( iss.fail() ) return ZErrorMessageReadingFile(filename, ZErrorMessage(ZErrorFileFormatBroken, "The string cannot be replaced for <" + str_MinNumPeakInRange_Data.first.putLabel() + ">: "+str_MinNumPeakInRange, __FILE__, __LINE__, __FUNCTION__) );
357     if( MinNumPeakInRange < 1 )
358     {
359     return ZErrorMessageReadingFile(filename, ZErrorMessage("<"+ str_MinNumPeakInRange_Data.first.putLabel() + "> is less than 1: "+num2str<Double>(MinNumPeakInRange), __FILE__, __LINE__, __FUNCTION__) );
360     }
361    
362     if( str_MaxNumPeakInRange != "AUTO" && MaxNumPeakInRange < MinNumPeakInRange )
363     {
364     return ZErrorMessageReadingFile(filename, ZErrorMessage( "<" + str_MaxNumPeakInRange_Data.first.putLabel() + "> is less than <" + str_MinNumPeakInRange_Data.first.putLabel() + ">",
365     __FILE__, __LINE__, __FUNCTION__) );
366     }
367     }
368    
369     return ZErrorMessageReadingFile();
370     }
371    
372    
373    
374     void ControlParam::setData(const RWParamProperty& parent_prop,
375     vector<RWParam_void>& tray)
376     {
377     if( parent_prop.putLabel() == this->putTagLabel() )
378     {
379     tray.push_back( RWParam_void(IsAngleDispersion_Data, &IsADorTOF) );
380     for(Int4 i=0; i<NUM_LS; i++)
381     {
382     tray.push_back( RWParam_void(OutputSymmetry_Data[i], &OutputSymmetry[i]) );
383     }
384     tray.push_back( RWParam_void(ConvParam_Data, &ConvParam) );
385     tray.push_back( RWParam_void(PeakShiftParam_Data, &PeakShiftParam) );
386     tray.push_back( RWParam_void(WlengthX_Data, &WlengthX) );
387     tray.push_back( RWParam_void(Resol_Data, &Resol) );
388     tray.push_back( RWParam_void(CVForLinearSum_Data, &CVForLinearSum) );
389     tray.push_back( RWParam_void(str_MaxPeakNum_Data, &str_MaxPeakNum) );
390     tray.push_back( RWParam_void(str_MaxEdgeNum_Data, &str_MaxEdgeNum) );
391     tray.push_back( RWParam_void(str_MaxNodeNum_Data, &str_MaxNodeNum) );
392     tray.push_back( RWParam_void(str_MinUnitCellVolume_Data, &str_MinUnitCellVolume) );
393     tray.push_back( RWParam_void(str_MaxUnitCellVolume_Data, &str_MaxUnitCellVolume) );
394    
395     tray.push_back( RWParam_void(MinUnitCellEdgeABC_Data, &MinUnitCellEdgeABC) );
396     tray.push_back( RWParam_void(MaxUnitCellEdgeABC_Data, &MaxUnitCellEdgeABC) );
397     tray.push_back( RWParam_void(MinFOM_Data, &MinFOM) );
398     tray.push_back( RWParam_void(str_MaxNumPeakInRange_Data, &str_MaxNumPeakInRange) );
399     tray.push_back( RWParam_void(str_MinNumPeakInRange_Data, &str_MinNumPeakInRange) );
400     tray.push_back( RWParam_void(NumRefFigureOfMerit_Data, &NumRefFigureOfMerit) );
401    
402     tray.push_back( RWParam_void(SearchLevel_Data, &SearchLevel) );
403 rtomiyasu 16
404     if( ReadConfigurationParameters )
405     {
406     tray.push_back( RWParam_void(NumCores_Data, &NumCores) );
407 rtomiyasu 25 MaxSizeForEachBRAVAIS = MaxSizeForEachBRAVAIS_Data.second.initial_value;
408     tray.push_back( RWParam_void(MaxSizeForEachBRAVAIS_Data, &MaxSizeForEachBRAVAIS) );
409    
410 rtomiyasu 16 tray.push_back( RWParam_void(MonoBaseAxis_Data, &MonoBaseAxis) );
411     tray.push_back( RWParam_void(RhomAxis_Data, &RhomAxis) );
412     tray.push_back( RWParam_void(ThresholdNormM_Data, &ThresholdNormM) );
413     tray.push_back( RWParam_void(ThresholdRevM_Data, &ThresholdRevM) );
414     tray.push_back( RWParam_void(MinLatticePointDistance_Data, &MinLatticePointDistance) );
415 rtomiyasu 25 tray.push_back( RWParam_void(ResoltoCheckComputedLines_Data, &ResoltoCheckComputedLines) );
416     tray.push_back( RWParam_void(MaxQtoCheckComputedLines_Data, &MaxQtoCheckComputedLines) );
417 rtomiyasu 16 }
418 rtomiyasu 3 }
419     }
420    
421    
422     ZErrorMessage ControlParam::checkData(const RWParam_void& param) const
423     {
424     const string Label = param.putLabel();
425     if( IsEqualTag(param.putProperty(), ConvParam_Data.first ) )
426     {
427     if( IsADorTOF )
428     {
429     return ZErrorMessage();
430     }
431     }
432     else if( IsEqualTag(param.putProperty(), PeakShiftParam_Data.first)
433     || IsEqualTag(param.putProperty(), WlengthX_Data.first) )
434     {
435     if( !IsADorTOF )
436     {
437     return ZErrorMessage();
438     }
439     }
440     else if( IsEqualTag(param.putProperty(), MonoBaseAxis_Data.first) )
441     {
442     if( find_key(ABCaxisLabel, MonoBaseAxis) == eABCaxis(-1) )
443     {
444     return nerror_out_range(param.putLabel(), MonoBaseAxis, __FILE__, __LINE__, __FUNCTION__ );
445     }
446     else return ZErrorMessage();
447     }
448     else if( IsEqualTag(param.putProperty(), RhomAxis_Data.first) )
449     {
450     if( find_key(RHaxisLabel, RhomAxis) == eRHaxis(-1) )
451     {
452     return nerror_out_range(param.putLabel(), RhomAxis, __FILE__, __LINE__, __FUNCTION__ );
453     }
454     else return ZErrorMessage();
455     }
456     return I_ReadData::checkData(param);
457     }
458    
459    
460    
461     ZErrorMessage ControlParam::checkIfDataAreSet(const RWParam_void& param, const Int4& num) const
462     {
463     const string Label = param.putLabel();
464     if( IsEqualTag(param.putProperty(), ConvParam_Data.first) )
465     {
466     if( IsADorTOF )
467     {
468     return ZErrorMessage();
469     }
470     }
471     else if( IsEqualTag(param.putProperty(), PeakShiftParam_Data.first)
472     || IsEqualTag(param.putProperty(), WlengthX_Data.first) )
473     {
474     if( !IsADorTOF )
475     {
476     return ZErrorMessage();
477     }
478     }
479     else if( IsEqualTag(param.putProperty(), MaxUnitCellEdgeABC_Data.first) )
480     {
481     if( MaxUnitCellEdgeABC < MinUnitCellEdgeABC )
482     {
483     return ZErrorMessage( "<" + MaxUnitCellEdgeABC_Data.first.putLabel() + "> is less than <" + MinUnitCellEdgeABC_Data.first.putLabel() + ">",
484     __FILE__, __LINE__, __FUNCTION__);
485     }
486     }
487    
488     return I_ReadData::checkIfDataAreSet(param, num);
489     }
490    
491    
492     inline Int4 put_automatic_peak_num(const eConographAnalysisMode& search_level, const vector<QData>& qdata,
493     const Int4& num_ref_figure_of_merit, const Double& min_length_edge)
494     {
495     assert( num_ref_figure_of_merit <= (Int4)qdata.size() );
496     if( qdata.empty() ) return 0;
497     return max(num_ref_figure_of_merit, min(48, (Int4)distance( qdata.begin(),
498     upper_bound( qdata.begin(), qdata.end(), QData( 10.0 /(min_length_edge*min_length_edge), 0.0 ) ) ) ) );
499     }
500    
501    
502     inline Int4 put_automatic_edge_num(const eConographAnalysisMode& search_level, const Int4& MaxPeakNum)
503     {
504 rtomiyasu 33 if( search_level == ConographQuickSearch ) return max(100, MaxPeakNum*2);
505 rtomiyasu 3 return MaxPeakNum * (MaxPeakNum+1) / 2;
506     }
507    
508    
509     inline Int4 put_automatic_node_num(const eConographAnalysisMode& search_level, const Int4& MaxPeakNum)
510     {
511 rtomiyasu 33 if( search_level == ConographQuickSearch ) return 64000;
512 rtomiyasu 3 return min(MaxPeakNum * (MaxPeakNum+1) * (MaxPeakNum+2) * 2 / 3, 32000);
513     }
514    
515    
516     inline pair<Double, Double> put_automatic_unit_cell_volume(const vector<QData>& qData, const Int4& MaxPeakNum)
517     {
518     Double ans = 1.0/put_maximum_counitcell_volume(qData, 20);
519     return pair<Double, Double>(max(5.0, ans), ans*30.0);
520     }
521    
522    
523     ZErrorMessage ControlParam::setAutomaticallyComputedParam(const vector<QData>& qData)
524     {
525     // Set the automatically calculated number of peaks to utilize for indexing.
526     if( this->putNumberOfReflectionsForFigureOfMerit() > (Int4)qData.size() )
527     {
528     this->setNumberOfReflectionsForFigureOfMerit(qData.size());
529     ZLOG_INFO( "\"" + ControlParam::putNumberOfReflectionsForFigureOfMeritLabel() + "\" is more than the number of peaks. It is replaced by the number of peaks.\n" );
530     }
531    
532     if( this->putStrMaxPeakNum()=="AUTO" )
533     {
534     MaxPeakNum = put_automatic_peak_num( this->putSearchLevel(), qData, NumRefFigureOfMerit, MinLatticePointDistance);
535     ZLOG_INFO( "<" + str_MaxPeakNum_Data.first.putLabel() + "> is set to " + num2str<Int4>(MaxPeakNum) + "\n" );
536     }
537     else
538     {
539     if( this->putMaxPeakNum() > (Int4)qData.size() )
540     {
541     this->setMaxPeakNum(qData.size());
542     ZLOG_INFO( "\"" + str_MaxPeakNum_Data.first.putLabel() + "\" is more than the number of peaks. It is replaced by the number of peaks.\n" );
543     }
544     }
545    
546     if( str_MaxEdgeNum == "AUTO" )
547     {
548     MaxEdgeNum = put_automatic_edge_num( this->putSearchLevel(), this->putMaxPeakNum() );
549     ZLOG_INFO( "<" + str_MaxEdgeNum_Data.first.putLabel() + "> is set to " + num2str(MaxEdgeNum) + ".\n" );
550     }
551    
552     if( str_MaxNodeNum == "AUTO" )
553     {
554     MaxNodeNum = put_automatic_node_num( this->putSearchLevel(), this->putMaxPeakNum() );
555     ZLOG_INFO( "<" + str_MaxNodeNum_Data.first.putLabel() + "> is set to " + num2str(MaxNodeNum) + ".\n" );
556     }
557    
558     if( str_MinUnitCellVolume == "AUTO" || str_MaxUnitCellVolume == "AUTO" )
559     {
560     pair<Double, Double> unit_cell_vol_range = put_automatic_unit_cell_volume(qData, this->putMaxPeakNum());
561     if( str_MinUnitCellVolume == "AUTO" )
562     {
563     MinUnitCellVolume = unit_cell_vol_range.first;
564     ZLOG_INFO( "<" + putMinUnitCellVolumeLabel() + "> is set to " + num2str(MinUnitCellVolume) + ".\n" );
565     }
566     if( str_MaxUnitCellVolume == "AUTO" )
567     {
568     MaxUnitCellVolume = unit_cell_vol_range.second;
569     ZLOG_INFO( "<" + putMaxUnitCellVolumeLabel() + "> is set to " + num2str(MaxUnitCellVolume) + ".\n" );
570     }
571     }
572    
573     if( str_MaxNumPeakInRange == "AUTO" )
574     {
575 rtomiyasu 16 MaxNumPeakInRange = ifloor( pow(this->putNumberOfReflectionsForFigureOfMerit(), 1.62) );
576 rtomiyasu 3 ZLOG_INFO( "<" + str_MaxNumPeakInRange_Data.first.putLabel() + "> is set to " + num2str(MaxNumPeakInRange) + ".\n" );
577     }
578    
579     if( str_MinNumPeakInRange == "AUTO" )
580     {
581     MinNumPeakInRange = this->putNumberOfReflectionsForFigureOfMerit() * 3 / 5;
582     ZLOG_INFO( "<" + str_MinNumPeakInRange_Data.first.putLabel() + "> is set to " + num2str(MinNumPeakInRange) + ".\n" );
583     }
584    
585     if( MaxNumPeakInRange < MinNumPeakInRange )
586     {
587     return ZErrorMessage("<" + str_MinNumPeakInRange_Data.first.putLabel() + "> : " + num2str<Int4>(MinNumPeakInRange) +'\n'
588     + str_MaxNumPeakInRange_Data.first.putLabel() + "> : " + num2str<Int4>(MaxNumPeakInRange) +'\n'
589     + "<" + str_MaxNumPeakInRange_Data.first.putLabel() + "> is less than <" + str_MinNumPeakInRange_Data.first.putLabel() + ">", __FILE__, __LINE__, __FUNCTION__);
590     }
591    
592     return ZErrorMessage();
593     }
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