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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 128 | Line 128 | namespace OpenMD {
128    }
129    
130    void DumpReader::scanFile(void) {
131 <    int lineNo = 0;
131 >
132      std::streampos prevPos;
133      std::streampos  currPos;
134      
# Line 142 | Line 142 | namespace OpenMD {
142        bool foundOpenSnapshotTag = false;
143        bool foundClosedSnapshotTag = false;
144  
145 +      int lineNo = 0;
146        while(inFile_->getline(buffer, bufferSize)) {
147          ++lineNo;
148          
# Line 227 | Line 228 | namespace OpenMD {
228        needVel_ = false;
229      }
230      
231 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
231 >    if (storageLayout & DataStorage::dslAmat ||
232 >        storageLayout & DataStorage::dslDipole ||
233 >        storageLayout & DataStorage::dslQuadrupole) {
234        needQuaternion_ = true;
235      } else {
236        needQuaternion_ = false;
# Line 525 | Line 528 | namespace OpenMD {
528  
529      StringTokenizer tokenizer(line);
530      int nTokens;
531 <    
531 >        
532      nTokens = tokenizer.countTokens();
533      
534      if (nTokens < 2) {  
# Line 645 | Line 648 | namespace OpenMD {
648  
649    void  DumpReader::readSiteData(std::istream& inputStream) {
650  
648 –    inputStream.getline(buffer, bufferSize);
651      std::string line(buffer);
650 –    
651 –    if (line.find("<SiteData>") == std::string::npos) {
652 –      // site data isn't required for a simulation, so skip
653 –      return;
654 –    }
652  
653 +    // We already found the starting <SiteData> tag or we wouldn't be
654 +    // here, so just start parsing until we get to the ending
655 +    // </SiteData> tag:
656 +    
657      while(inputStream.getline(buffer, bufferSize)) {
658        line = buffer;
659        

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