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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 347 by tim, Tue Feb 15 17:11:35 2005 UTC vs.
Revision 543 by tim, Thu May 26 22:45:00 2005 UTC

# Line 46 | Line 46 | namespace oopse {
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)
50 <        : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), step_(1),
51 <          selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), seleMan1_(info), seleMan2_(info){
49 >  RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
50 >    : StaticAnalyser(info, filename),
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);
54 >      evaluator1_.loadScriptString(sele1);
55 >      evaluator2_.loadScriptString(sele2);
56  
57 <    if (!evaluator1_.isDynamic()) {
58 <            seleMan1_.setSelectionSet(evaluator1_.evaluate());
59 <    }
60 <    if (!evaluator2_.isDynamic()) {
61 <            seleMan2_.setSelectionSet(evaluator2_.evaluate());
62 <    }
57 >      if (!evaluator1_.isDynamic()) {
58 >        seleMan1_.setSelectionSet(evaluator1_.evaluate());
59 >        validateSelection1(seleMan1_);
60 >      }
61 >      if (!evaluator2_.isDynamic()) {
62 >        seleMan2_.setSelectionSet(evaluator2_.evaluate());
63 >        validateSelection2(seleMan2_);
64 >      }
65  
66 <    if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
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 <
75 <        BitSet bs = seleMan1_.getSelectionSet();
76 <        bs &= seleMan2_.getSelectionSet();
77 <        int nIntersect = bs.countBits();
72 <
73 <        nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
74 <    }
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 < }
79 >    }
80  
81 < void RadialDistrFunc::process() {
81 >  void RadialDistrFunc::process() {
82      Molecule* mol;
83      RigidBody* rb;
84      SimInfo::MoleculeIterator mi;
# Line 85 | Line 88 | void RadialDistrFunc::process() {
88      
89      DumpReader reader(info_, dumpFilename_);    
90      int nFrames = reader.getNFrames();
91 <    nProcessed_ = nFrames / step_ + 1;
91 >    nProcessed_ = nFrames / step_;
92 >
93      for (int i = 0; i < nFrames; i += step_) {
94 <        reader.readFrame(i);
95 <        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
94 >      reader.readFrame(i);
95 >      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
96  
97 <        if (evaluator1_.isDynamic()) {
98 <            seleMan1_.setSelectionSet(evaluator1_.evaluate());
99 <        }
100 <        if (evaluator2_.isDynamic()) {
101 <            seleMan2_.setSelectionSet(evaluator2_.evaluate());
102 <        }
97 >      if (evaluator1_.isDynamic()) {
98 >        seleMan1_.setSelectionSet(evaluator1_.evaluate());
99 >        validateSelection1(seleMan1_);
100 >      }
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)) {
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 <        }
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();
114 >      initalizeHistogram();
115  
110 –        StuntDouble* sd1;
111 –        int j;
112 –        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 <                if (sd1 != sd2) {
121 <                    collectHistogram(sd1, sd2);
122 <                }
123 <            }            
124 <        }
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 <        processHistogram();
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      }
153  
154      postProcess();
155  
156      writeRdf();
157 < }
157 >  }
158  
159 < int RadialDistrFunc::getNRealPairs() {
160 <    if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
161 <        //if one of the selection is static,  need to recompute it    
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 <        int nSelected1 = seleMan1_->getSelectionCount();
168 <        int nSelected2 = seleMan2_->getSelectionCount();
167 >      for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
168 >        collectHistogram(sd1, sd2);
169 >      }            
170 >    }
171  
172 <        BitSet bs = seleMan1_.getSelectionSet();
140 <        bs &= seleMan2_.getSelectionSet();
141 <        int nIntersect = bs.countBits();
172 >  }
173  
174 <        nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
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 <    return nRealPairs_
147 < }
190 >  }
191  
192   }

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