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root/OpenMD/trunk/src/applications/staticProps/RadialDistrFunc.cpp
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Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents):
Revision 309 by tim, Thu Feb 10 14:15:52 2005 UTC vs.
Revision 361 by tim, Thu Feb 17 18:30:54 2005 UTC

# Line 42 | Line 42
42   #include <algorithm>
43  
44   #include "RadialDistrFunc.hpp"
45 <
45 > #include "io/DumpReader.hpp"
46 > #include "primitives/Molecule.hpp"
47   namespace oopse {
48  
49 < RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len)
50 <        : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1),
51 <          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info){
49 > RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50 >        : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1),
51 >          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
52 >          seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){
53            
54      evaluator1_.loadScriptString(sele1);
55      evaluator2_.loadScriptString(sele2);
56  
57 <    if (!evaluator1_->isDynamic()) {
58 <            seleMan1_.setSelectionSet(evaluator1_->evaluate());
57 >    if (!evaluator1_.isDynamic()) {
58 >        seleMan1_.setSelectionSet(evaluator1_.evaluate());
59 >        validateSelection1(seleMan1_);
60      }
61 <    if (!evaluator2_->isDynamic()) {
62 <            seleMan2_.setSelectionSet(evaluator2_->evaluate());
61 >    if (!evaluator2_.isDynamic()) {
62 >        seleMan2_.setSelectionSet(evaluator2_.evaluate());
63 >        validateSelection2(seleMan2_);
64      }
65  
66 <    deltaR_ = len_ /nbins_;
66 >    if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
67 >        //if all selections are static,  we can precompute the number of real pairs    
68 >        common_ = seleMan1_ & seleMan2_;
69 >        sele1_minus_common_ = seleMan1_ - common_;
70 >        sele2_minus_common_ = seleMan2_ - common_;      
71 >
72 >        int nSelected1 = seleMan1_.getSelectionCount();
73 >        int nSelected2 = seleMan2_.getSelectionCount();
74 >        int nIntersect = common_.getSelectionCount();
75 >        
76 >        nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;            
77 >    }
78 >    
79   }
80  
81   void RadialDistrFunc::process() {
82 <
82 >    Molecule* mol;
83 >    RigidBody* rb;
84 >    SimInfo::MoleculeIterator mi;
85 >    Molecule::RigidBodyIterator rbIter;
86 >    
87      preProcess();
88      
89      DumpReader reader(info_, dumpFilename_);    
90 <    int nFrames = reader->getNFrames();
91 <    nProcessed_ = nFrames / step_ + 1;
90 >    int nFrames = reader.getNFrames();
91 >    nProcessed_ = nFrames / step_;
92 >
93      for (int i = 0; i < nFrames; i += step_) {
94 <        reader->readFrame(i);
94 >        reader.readFrame(i);
95          currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
96  
97 <        if (evaluator1_->isDynamic()) {
98 <            seleMan1_.setSelectionSet(evaluator1_->evaluate());
97 >        if (evaluator1_.isDynamic()) {
98 >            seleMan1_.setSelectionSet(evaluator1_.evaluate());
99 >            validateSelection1(seleMan1_);
100          }
101 <        if (evaluator2_->isDynamic()) {
102 <            seleMan2_.setSelectionSet(evaluator2_->evaluate());
101 >        if (evaluator2_.isDynamic()) {
102 >            seleMan2_.setSelectionSet(evaluator2_.evaluate());
103 >            validateSelection2(seleMan2_);
104          }
105  
106 +        for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
107 +
108 +            //change the positions of atoms which belong to the rigidbodies
109 +            for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
110 +                rb->updateAtoms();
111 +            }
112 +        }
113 +        
114          initalizeHistogram();
115  
85 –        StuntDouble* sd1;
86 –        int j;
87 –        for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) {
116  
117 <            StuntDouble* sd2;
118 <            int k;
119 <            for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) {
120 <                collectHistogram(sd1, sd2);
121 <            }            
117 >        
118 >        //selections may overlap.
119 >        //
120 >        // |s1 -c | c |
121 >        //            | c |s2 - c|
122 >        //
123 >        // s1 : number of selected stuntdoubles in selection1
124 >        // s2 : number of selected stuntdoubles in selection2
125 >        // c   : number of intersect stuntdouble between selection1 and selection2
126 >        //when loop over the pairs, we can divide the looping into 3 stages
127 >        //stage 1 :     [s1-c]      [s2]
128 >        //stage 2 :     [c]            [s2 - c]
129 >        //stage 3 :     [c]            [c]
130 >        //stage 1 and stage 2 are completly non-overlapping
131 >        //stage 3 are completely overlapping
132 >
133 >        if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
134 >
135 >            common_ = seleMan1_ & seleMan2_;
136 >            sele1_minus_common_ = seleMan1_ - common_;
137 >            sele2_minus_common_ = seleMan2_ - common_;            
138 >            int nSelected1 = seleMan1_.getSelectionCount();
139 >            int nSelected2 = seleMan2_.getSelectionCount();
140 >            int nIntersect = common_.getSelectionCount();
141 >            
142 >            nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;                      
143          }
144  
145 +        processNonOverlapping(sele1_minus_common_, seleMan2_);
146 +        processNonOverlapping(common_, sele2_minus_common_);        
147 +        processOverlapping(common_);
148 +        
149 +        
150          processHistogram();
151          
152      }
# Line 102 | Line 156 | void RadialDistrFunc::process() {
156      writeRdf();
157   }
158  
159 + void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
160 +    StuntDouble* sd1;
161 +    StuntDouble* sd2;
162 +    int i;    
163 +    int j;
164 +    
165 +    for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
166 +
167 +        for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
168 +            collectHistogram(sd1, sd2);
169 +        }            
170 +    }
171 +
172   }
173 +
174 + void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
175 +    StuntDouble* sd1;
176 +    StuntDouble* sd2;
177 +    int i;    
178 +    int j;
179 +
180 +    //basically, it is the same as below loop
181 +    //for (int i = 0;  i < n; ++i )
182 +    //  for (int j = i + 1; j < n; ++j) {}
183 +    
184 +    for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {                    
185 +        for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
186 +            collectHistogram(sd1, sd2);
187 +        }            
188 +    }
189 +
190 + }
191 +
192 + }

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