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root/OpenMD/trunk/src/io/RestReader.cpp
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Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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   */
41 –
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46 +
47   #include <sys/types.h>
48   #include <sys/stat.h>
49  
# Line 58 | Line 62
62   #include "utils/StringTokenizer.hpp"
63   #include "restraints/ObjectRestraint.hpp"
64   #include "restraints/MolecularRestraint.hpp"
61 –
62 – #ifdef IS_MPI
63 –
64 – #include <mpi.h>
65 – #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 81 | 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 96 | Line 95 | namespace OpenMD {
95        
96   #ifdef IS_MPI
97      }
98 <    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
98 >    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
99   #endif // is_mpi
100    }
101  
# Line 131 | 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_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
134 >      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
135 >                MPI_CHAR, masterNode, MPI_COMM_WORLD);
136        
137        sstream.str(sendBuffer);
138      } else {
139        int sendBufferSize;
140 <      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
140 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
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_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode,
145 >                MPI_COMM_WORLD);
146        sstream.str(recvBuffer);
147        delete [] recvBuffer;
148      }      
# Line 279 | Line 280 | namespace OpenMD {
280  
281      int index = tokenizer.nextTokenAsInt();
282  
283 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
283 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284  
285 <    if (integrableObject == NULL) {
285 >    if (sd == NULL) {
286        return;
287      }
288    
# Line 309 | Line 310 | namespace OpenMD {
310        }
311  
312        case 'q' : {
313 <        if (integrableObject->isDirectional()) {
313 >        if (sd->isDirectional()) {
314            
315            q[0] = tokenizer.nextTokenAsDouble();
316            q[1] = tokenizer.nextTokenAsDouble();
# Line 331 | Line 332 | namespace OpenMD {
332        }  
333        case 'j' : {
334          Vector3d ji;
335 <        if (integrableObject->isDirectional()) {
335 >        if (sd->isDirectional()) {
336            ji[0] = tokenizer.nextTokenAsDouble();
337            ji[1] = tokenizer.nextTokenAsDouble();
338            ji[2] = tokenizer.nextTokenAsDouble();
# Line 365 | Line 366 | namespace OpenMD {
366        all_pos_[index] = pos;      
367          
368        // is this io restrained?
369 <      GenericData* data = integrableObject->getPropertyByName("Restraint");
369 <      ObjectRestraint* oRest;
369 >      GenericData* data = sd->getPropertyByName("Restraint");
370        
371        if (data != NULL) {
372          // make sure we can reinterpret the generic data as restraint data:
# Line 374 | Line 374 | namespace OpenMD {
374          if (restData != NULL) {
375            // make sure we can reinterpet the restraint data as a pointer to
376              // an ObjectRestraint:
377 <          oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
377 >          ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
378            if (oRest != NULL) {          
379 <            if (integrableObject->isDirectional()) {
379 >            if (sd->isDirectional()) {
380                oRest->setReferenceStructure(pos, q.toRotationMatrix3());
381              } else {                          
382                oRest->setReferenceStructure(pos);

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