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root/OpenMD/trunk/src/applications/staticProps/SurfaceDiffusion.cpp
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Comparing trunk/src/applications/staticProps/SurfaceDiffusion.cpp (file contents):
Revision 2032 by jmichalk, Fri Oct 31 18:57:19 2014 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

# Line 96 | Line 96 | namespace OpenMD {
96      frames_ = 0;
97      nProcessed_ = nFrames/step_;
98  
99 <    //positions_ and moBool_ are 2D arrays, need the second dimension filled as well
99 >    // positions_ and moBool_ are 2D arrays, need the second dimension
100 >    // filled as well
101      for(int i = 0; i < selectionCount_; i++){
102        moBool_[i].resize(nFrames);
103        positions_[i].resize(nFrames);
# Line 105 | Line 106 | namespace OpenMD {
106      int iterator;
107      int index = 0;
108      /* Loop over all frames storing the positions in a vec< vec<pos> >
109 <     * At the end, positions.length() should equal seleMan1_.size() or w/e
110 <     * And positions[index].length() should equal nFrames (or nFrames/istep)
109 >     * At the end, positions.length() should equal seleMan1_.size() or
110 >     * w/e And positions[index].length() should equal nFrames (or
111 >     * nFrames/istep)
112       */
113      for(int istep = 0; istep < nFrames; istep += step_){
114        frames_++;
115        reader.readFrame(istep);
116        currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
117  
118 <      for(mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)){
118 >      for(mol = info_->beginMolecule(mi); mol != NULL;
119 >          mol = info_->nextMolecule(mi)){
120          //change the positions of atoms which belong to the rigidbodies
121 <        for(rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)){
121 >        for(rb = mol->beginRigidBody(rbIter); rb != NULL;
122 >            rb = mol->nextRigidBody(rbIter)){
123            rb->updateAtoms();
124          }
125        }
126        
127 <      index = 0; //count over atoms since iterators aren't the most friendly for such plebian things
128 <      for(sd = seleMan1_.beginSelected(iterator); sd != NULL; sd = seleMan1_.nextSelected(iterator)){
127 >      index = 0; // count over atoms since iterators aren't the most
128 >                 // friendly for such plebian things
129 >      for(sd = seleMan1_.beginSelected(iterator); sd != NULL;
130 >          sd = seleMan1_.nextSelected(iterator)){
131          Vector3d pos = sd->getPos();
132          positions_[index][istep] = pos;
133          index++;
134        }      
135      }
136  
131 –
137      cout << "Position Array size: " << positions_.size() << "\n";
138      cout << "Frames analyzed: " << positions_[0].size() << "\n";
139        
140 <
136 <    for(int i = 0; i < positions_.size(); i++){
140 >    for(std::size_t i = 0; i < positions_.size(); i++){
141        int frameIndex = positions_[i].size();
142        for(int j = 1; j < frameIndex; j++){
143          Vector3d posF1 = positions_[i][j-1];
# Line 152 | Line 156 | namespace OpenMD {
156      }
157  
158      int mobileAtomCount = 0;
159 <    for(int i = 0; i < moBool_.size(); i++){
159 >    for(std::size_t i = 0; i < moBool_.size(); i++){
160        int frameIndex = moBool_[i].size();
161        bool mobileAtom = false;
162        for(int j = 0; j < frameIndex; j++){
163          mobileAtom = mobileAtom || moBool_[i][j];
164        }
165 <      moBool_[i][0] = mobileAtom; //is true if any value later in the array is true, false otherwise
165 >      moBool_[i][0] = mobileAtom; // is true if any value later in the
166 >                                  // array is true, false otherwise
167        if(mobileAtom){
168          mobileAtomCount++;
169        }
# Line 166 | Line 171 | namespace OpenMD {
171  
172      cout << "Mobile atom count: " << mobileAtomCount << "\n";
173  
174 <    //Here I shrink the size of the arrays, why look through 3888, when you only need ~800.
175 <    //Additionally, all of these are mobile at some point in time, the others aren't, dead weight and
176 <    //memory
174 >    // Here I shrink the size of the arrays, why look through 3888,
175 >    // when you only need ~800.  Additionally, all of these are mobile
176 >    // at some point in time, the others aren't, dead weight and
177 >    // memory
178      positions2_.resize(mobileAtomCount);
179      moBool2_.resize(mobileAtomCount);
180      int pos2index = 0;
181 <    for(int i = 0; i < positions_.size(); i++){
181 >    for(std::size_t i = 0; i < positions_.size(); i++){
182        int frameCount = positions_[i].size();
183        if(moBool_[i][0]){
184          for(int j = 0; j < frameCount; j++){
# Line 200 | Line 206 | namespace OpenMD {
206      diffStream.open(outputFilename_.c_str());
207      diffStream << "#X&Y diffusion amounts\n";
208      diffStream << "#singleMoveDistance_: " << singleMoveDistance_ << "\n";
203 –
209      diffStream << "#Number of mobile atoms: " << positions2_.size() << "\n";
205 –
210      diffStream << "#time, <x(t)-x(0)>, <y(t)-y(0)>, <r(t)-r(0)>\n";
211 <    for(int i = 0; i < xHist_.size(); i++){
212 <      diffStream << i << ", " << xHist_[i] << ", " << yHist_[i] << ", " << rHist_[i] << "\n";
211 >
212 >    for(std::size_t i = 0; i < xHist_.size(); i++){
213 >      diffStream << i << ", " << xHist_[i] << ", " << yHist_[i] << ", "
214 >                 << rHist_[i] << "\n";
215      }
216      diffStream.close();
217  
# Line 231 | Line 237 | namespace OpenMD {
237      //loop over particles
238      // loop over frames starting at j
239      //  loop over frames starting at k = j (time shift of 0)
240 <    for(int i = 0; i < positions2_.size(); i++){
241 <      int frames = positions2_[i].size() - 1; //for counting properly, otherwise moBool2_[i][j+1] will
242 <      // go over  
240 >    for(std::size_t i = 0; i < positions2_.size(); i++){
241 >      int frames = positions2_[i].size() - 1; // for counting
242 >                                              // properly, otherwise
243 >                                              // moBool2_[i][j+1] will
244 >                                              // go over
245        for(int j = 0; j < frames; j++){
246 <        //if the particle is mobile between j and j + 1, then count it for all timeShifts
246 >        // if the particle is mobile between j and j + 1, then count
247 >        // it for all timeShifts
248          if(moBool2_[i][j+1]){
249 <          for(int k = j; k < positions2_[0].size(); k++){
249 >          for(std::size_t k = j; k < positions2_[0].size(); k++){
250              //<x(t)-x(0)>  <y(t)-y(0)>  <r(t)-r(0)>
251 <            //The positions stored are not wrapped, thus I don't need to worry about pbc          
251 >            //The positions stored are not wrapped, thus I don't need
252 >            //to worry about pbc          
253              //Mean square displacement
254              //So I do want the squared distances
255            
# Line 265 | Line 275 | namespace OpenMD {
275      }
276      cout << "X, Y, R calculated\n";
277  
278 <    for(int i = 0; i < xHist_.size(); i++){
278 >    for(std::size_t i = 0; i < xHist_.size(); i++){
279        xHist_[i] = xHist_[i]/(count_[i]);
280        yHist_[i] = yHist_[i]/(count_[i]);
281        rHist_[i] = rHist_[i]/(count_[i]);

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