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Comparing trunk/src/applications/staticProps/GofXyz.cpp (file contents):
Revision 448 by tim, Mon Mar 28 15:54:04 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 "applications/staticProps/GofXyz.hpp"
45   #include "utils/simError.h"
46   #include "primitives/Molecule.hpp"
47 < namespace oopse {
47 > namespace OpenMD {
48  
49 < GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins)
49 >  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
50      : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
51 <    setOutputName(getPrefix(filename) + ".gxyz");
51 >      setOutputName(getPrefix(filename) + ".gxyz");
52  
53 <    evaluator3_.loadScriptString(sele3);
54 <    if (!evaluator3_.isDynamic()) {
53 >      evaluator3_.loadScriptString(sele3);
54 >      if (!evaluator3_.isDynamic()) {
55          seleMan3_.setSelectionSet(evaluator3_.evaluate());
56 <    }    
56 >      }    
57  
58 <    deltaR_ =  len_ / nRBins_;
58 >      deltaR_ =  len_ / nRBins_;
59      
60 <    histogram_.resize(nRBins_);
61 <    for (int i = 0 ; i < nRBins_; ++i) {
60 >      histogram_.resize(nRBins_);
61 >      for (int i = 0 ; i < nRBins_; ++i) {
62          histogram_[i].resize(nRBins_);
63          for(int j = 0; j < nRBins_; ++j) {
64 <            histogram_[i][j].resize(nRBins_);
64 >          histogram_[i][j].resize(nRBins_);
65          }
66 <    }  
66 >      }  
67    
68 < }
68 >    }
69  
70  
71 < void GofXyz::preProcess() {
71 >  void GofXyz::preProcess() {
72      for (int i = 0 ; i < nRBins_; ++i) {
73 <        histogram_[i].resize(nRBins_);
74 <        for(int j = 0; j < nRBins_; ++j) {
75 <            std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76 <        }
73 >      histogram_[i].resize(nRBins_);
74 >      for(int j = 0; j < nRBins_; ++j) {
75 >        std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76 >      }
77      }  
78 < }
78 >  }
79  
80  
81 < void GofXyz::initalizeHistogram() {
81 >  void GofXyz::initalizeHistogram() {
82      //calculate the center of mass of the molecule of selected stuntdouble in selection1
83  
84      if (!evaluator3_.isDynamic()) {
85 <        seleMan3_.setSelectionSet(evaluator3_.evaluate());
85 >      seleMan3_.setSelectionSet(evaluator3_.evaluate());
86      }    
87  
88      assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
# Line 100 | Line 100 | void GofXyz::initalizeHistogram() {
100      StuntDouble* sd3;
101      
102      for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
103 <        sd1 != NULL, sd3 != NULL;
104 <        sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
103 >         sd1 != NULL, sd3 != NULL;
104 >         sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
105  
106 <        Vector3d r3 =sd3->getPos();
107 <        Vector3d r1 = sd1->getPos();
108 <        Vector3d v1 =  r3 - r1;
106 >      Vector3d r3 =sd3->getPos();
107 >      Vector3d r1 = sd1->getPos();
108 >      Vector3d v1 =  r3 - r1;
109 >      if (usePeriodicBoundaryConditions_)
110          info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
111 <        Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
112 <        Vector3d xaxis = cross(v1, zaxis);
113 <        Vector3d yaxis = cross(zaxis, xaxis);
111 >      Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
112 >      Vector3d xaxis = cross(v1, zaxis);
113 >      Vector3d yaxis = cross(zaxis, xaxis);
114  
115 <        xaxis.normalize();
116 <        yaxis.normalize();
117 <        zaxis.normalize();
115 >      xaxis.normalize();
116 >      yaxis.normalize();
117 >      zaxis.normalize();
118  
119 <        RotMat3x3d rotMat;
120 <        rotMat.setRow(0, xaxis);
121 <        rotMat.setRow(1, yaxis);
122 <        rotMat.setRow(2, zaxis);
119 >      RotMat3x3d rotMat;
120 >      rotMat.setRow(0, xaxis);
121 >      rotMat.setRow(1, yaxis);
122 >      rotMat.setRow(2, zaxis);
123          
124 <        rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
124 >      rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
125      }
126  
127 < }
127 >  }
128  
129 < void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
129 >  void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
130  
131      Vector3d pos1 = sd1->getPos();
132      Vector3d pos2 = sd2->getPos();
133      Vector3d r12 = pos2 - pos1;
134 <    currentSnapshot_->wrapVector(r12);
134 >    if (usePeriodicBoundaryConditions_)
135 >      currentSnapshot_->wrapVector(r12);
136  
137      std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
138      assert(i != rotMats_.end());
# Line 144 | Line 146 | void GofXyz::collectHistogram(StuntDouble* sd1, StuntD
146      if (xbin < nRBins_ && xbin >=0 &&
147          ybin < nRBins_ && ybin >= 0 &&
148          zbin < nRBins_ && zbin >=0 ) {
149 <        ++histogram_[xbin][ybin][zbin];
149 >      ++histogram_[xbin][ybin][zbin];
150      }
151      
152 < }
152 >  }
153  
154 < void GofXyz::writeRdf() {
154 >  void GofXyz::writeRdf() {
155      std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
156      if (rdfStream.is_open()) {
157 <        //rdfStream << "#g(x, y, z)\n";
158 <        //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
159 <        //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
160 <        //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
161 <        for (int i = 0; i < histogram_.size(); ++i) {
157 >      //rdfStream << "#g(x, y, z)\n";
158 >      //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
159 >      //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
160 >      //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
161 >      for (int i = 0; i < histogram_.size(); ++i) {
162  
163 <            for(int j = 0; j < histogram_[i].size(); ++j) {
163 >        for(int j = 0; j < histogram_[i].size(); ++j) {
164  
165 <                for(int k = 0;k < histogram_[i][j].size(); ++k) {
166 <                    rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
167 <                }
168 <            }
169 <        }
165 >          for(int k = 0;k < histogram_[i][j].size(); ++k) {
166 >            rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
167 >          }
168 >        }
169 >      }
170          
171      } else {
172  
173 <        sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
174 <        painCave.isFatal = 1;
175 <        simError();  
173 >      sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
174 >      painCave.isFatal = 1;
175 >      simError();  
176      }
177  
178      rdfStream.close();
179 < }
179 >  }
180  
181   }

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