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Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents):
Revision 351 by tim, Tue Feb 15 19:36:07 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <algorithm>
# Line 44 | Line 44
44   #include "RadialDistrFunc.hpp"
45   #include "io/DumpReader.hpp"
46   #include "primitives/Molecule.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
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 <    }
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 88 | Line 91 | void RadialDistrFunc::process() {
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  
111 –        StuntDouble* sd1;
112 –        int j;
113 –        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 >        common_ = seleMan1_ & seleMan2_;
135 >        sele1_minus_common_ = seleMan1_ - common_;
136 >        sele2_minus_common_ = seleMan2_ - common_;            
137 >        int nSelected1 = seleMan1_.getSelectionCount();
138 >        int nSelected2 = seleMan2_.getSelectionCount();
139 >        int nIntersect = common_.getSelectionCount();
140 >            
141 >        nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
142 >      }
143 >      processNonOverlapping(sele1_minus_common_, seleMan2_);
144 >      processNonOverlapping(common_, sele2_minus_common_);        
145 >      processOverlapping(common_);
146 >      
147 >      processHistogram();
148          
149      }
150  
151      postProcess();
152  
153      writeRdf();
154 < }
154 >  }
155  
156 < int RadialDistrFunc::getNRealPairs() {
157 <    if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
158 <        //if one of the selection is dynamic,  need to recompute it    
156 >  void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
157 >    StuntDouble* sd1;
158 >    StuntDouble* sd2;
159 >    int i;    
160 >    int j;
161 >    
162 >    for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
163  
164 <        int nSelected1 = seleMan1_.getSelectionCount();
165 <        int nSelected2 = seleMan2_.getSelectionCount();
164 >      for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
165 >        collectHistogram(sd1, sd2);
166 >      }            
167 >    }
168  
169 <        BitSet bs = seleMan1_.getSelectionSet();
141 <        bs &= seleMan2_.getSelectionSet();
142 <        int nIntersect = bs.countBits();
169 >  }
170  
171 <        nRealPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
171 >  void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
172 >    StuntDouble* sd1;
173 >    StuntDouble* sd2;
174 >    int i;    
175 >    int j;
176 >
177 >    //basically, it is the same as below loop
178 >    //for (int i = 0;  i < n; ++i )
179 >    //  for (int j = i + 1; j < n; ++j) {}
180 >    
181 >    for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {                    
182 >      for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
183 >        collectHistogram(sd1, sd2);
184 >      }            
185      }
186  
187 <    return nRealPairs_;
148 < }
187 >  }
188  
189   }

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