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root/OpenMD/trunk/src/io/RestReader.cpp
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Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 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   */
42 –
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46 +
47   #include <sys/types.h>
48   #include <sys/stat.h>
49  
# Line 59 | Line 62
62   #include "utils/StringTokenizer.hpp"
63   #include "restraints/ObjectRestraint.hpp"
64   #include "restraints/MolecularRestraint.hpp"
62 –
63 – #ifdef IS_MPI
64 –
65 – #include <mpi.h>
66 – #endif
65  
66   namespace OpenMD {
67  
68    void RestReader::scanFile(){
69 <    int lineNo = 0;
69 >
70      std::streampos prevPos;
71      std::streampos  currPos;
72      
# Line 82 | Line 80 | namespace OpenMD {
80        prevPos = currPos;
81        
82        bool foundOpenSnapshotTag = false;
83 <      
83 >      int lineNo = 0;      
84        while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
85          ++lineNo;
86          
# Line 97 | Line 95 | namespace OpenMD {
95        
96   #ifdef IS_MPI
97      }
98 <    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
98 >    MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
99   #endif // is_mpi
100    }
101  
# Line 132 | Line 130 | namespace OpenMD {
130        }
131        
132        int sendBufferSize = sendBuffer.size();
133 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
134 <      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
133 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
134 >      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
135 >                            MPI::CHAR, masterNode);
136        
137        sstream.str(sendBuffer);
138      } else {
139        int sendBufferSize;
140 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
140 >      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
141        char * recvBuffer = new char[sendBufferSize+1];
142        assert(recvBuffer);
143        recvBuffer[sendBufferSize] = '\0';
144 <      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
144 >      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
145        sstream.str(recvBuffer);
146        delete [] recvBuffer;
147      }      
# Line 367 | Line 366 | namespace OpenMD {
366          
367        // is this io restrained?
368        GenericData* data = sd->getPropertyByName("Restraint");
370 –      ObjectRestraint* oRest;
369        
370        if (data != NULL) {
371          // make sure we can reinterpret the generic data as restraint data:
# Line 375 | Line 373 | namespace OpenMD {
373          if (restData != NULL) {
374            // make sure we can reinterpet the restraint data as a pointer to
375              // an ObjectRestraint:
376 <          oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
376 >          ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
377            if (oRest != NULL) {          
378              if (sd->isDirectional()) {
379                oRest->setReferenceStructure(pos, q.toRotationMatrix3());

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