ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/staticProps/RadialDistrFunc.cpp
(Generate patch)

Comparing trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents):
Revision 309 by tim, Thu Feb 10 14:15:52 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>
43  
44   #include "RadialDistrFunc.hpp"
45 + #include "io/DumpReader.hpp"
46 + #include "primitives/Molecule.hpp"
47 + namespace OpenMD {
48  
49 < namespace oopse {
50 <
51 < RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len)
52 <        : info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1),
50 <          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 >    : 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 <    deltaR_ = len_ /nbins_;
67 < }
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 < void RadialDistrFunc::process() {
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 +    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);
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 <        initalizeHistogram();
106 >      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
107  
108 <        StuntDouble* sd1;
109 <        int j;
110 <        for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) {
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  
89 –            StuntDouble* sd2;
90 –            int k;
91 –            for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) {
92 –                collectHistogram(sd1, sd2);
93 –            }            
94 –        }
116  
96 –        processHistogram();
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 +        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 +  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 +      for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
165 +        collectHistogram(sd1, sd2);
166 +      }            
167 +    }
168 +
169 +  }
170 +
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 +  }
188 +
189   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines