src/io/DumpReader.cpp

/*
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
  
#define _LARGEFILE_SOURCE64 
#define _FILE_OFFSET_BITS 64 
 
#include <sys/types.h> 
#include <sys/stat.h> 
 
#include <iostream> 
#include <math.h> 
 
#include <stdio.h> 
#include <stdlib.h> 
#include <string.h> 
 
#include "io/DumpReader.hpp" 
#include "primitives/Molecule.hpp" 
#include "utils/simError.h" 
#include "utils/MemoryUtils.hpp" 
#include "utils/StringTokenizer.hpp" 
 
#ifdef IS_MPI 
 
#include <mpi.h> 
#define TAKE_THIS_TAG_CHAR 0 
#define TAKE_THIS_TAG_INT 1 
 
#endif // is_mpi 
 
 
namespace OpenMD { 
   
  DumpReader::DumpReader(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif 
      
      inFile_ = new std::ifstream(filename_.c_str()); 
      
      if (inFile_->fail()) { 
        sprintf(painCave.errMsg, 
                "DumpReader: Cannot open file: %s\n", 
                filename_.c_str()); 
        painCave.isFatal = 1; 
        simError(); 
      } 
      
#ifdef IS_MPI 
      
    } 
    
    strcpy(checkPointMsg, "Dump file opened for reading successfully."); 
    errorCheckPoint(); 
    
#endif 
    
    return; 
  } 
  
  DumpReader::~DumpReader() { 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif 
      
      delete inFile_; 
      
#ifdef IS_MPI 
      
    } 
    
    strcpy(checkPointMsg, "Dump file closed successfully."); 
    errorCheckPoint(); 
    
#endif 
    
    return; 
  } 
  
  int DumpReader::getNFrames(void) { 
     
    if (!isScanned_) 
      scanFile(); 
     
    return nframes_; 
  } 
   
  void DumpReader::scanFile(void) { 
    int lineNo = 0; 
    std::streampos prevPos;
    std::streampos  currPos; 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif // is_mpi 
      
      currPos = inFile_->tellg();
      prevPos = currPos;
      bool foundOpenSnapshotTag = false;
      bool foundClosedSnapshotTag = false;
      while(inFile_->getline(buffer, bufferSize)) {
        ++lineNo;
        
        std::string line = buffer;
        currPos = inFile_->tellg(); 
        if (line.find("<Snapshot>")!= std::string::npos) {
          if (foundOpenSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError();           
          }
          foundOpenSnapshotTag = true;
          foundClosedSnapshotTag = false;
          framePos_.push_back(prevPos);
          
        } else if (line.find("</Snapshot>") != std::string::npos){
          if (!foundOpenSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError(); 
          }
          
          if (foundClosedSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError(); 
          }
          foundClosedSnapshotTag = true;
          foundOpenSnapshotTag = false;
        }
        prevPos = currPos;
      }
      
      // only found <Snapshot> for the last frame means the file is corrupted, we should discard
      // it and give a warning message
      if (foundOpenSnapshotTag) {
        sprintf(painCave.errMsg, 
                "DumpReader: last frame in %s is invalid\n", filename_.c_str()); 
        painCave.isFatal = 0; 
        simError();       
        framePos_.pop_back();
      }
      
      nframes_ = framePos_.size(); 
      
      if (nframes_ == 0) {
        sprintf(painCave.errMsg, 
                "DumpReader: %s does not contain a valid frame\n", filename_.c_str()); 
        painCave.isFatal = 1; 
        simError();      
      }
#ifdef IS_MPI 
    } 
     
    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); 
    
#endif // is_mpi 
    
    isScanned_ = true; 
  } 
   
  void DumpReader::readFrame(int whichFrame) { 
    if (!isScanned_) 
      scanFile(); 
         
    int storageLayout = info_->getSnapshotManager()->getStorageLayout(); 
     
    if (storageLayout & DataStorage::dslPosition) { 
      needPos_ = true; 
    } else { 
      needPos_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslVelocity) { 
      needVel_ = true; 
    } else { 
      needVel_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { 
      needQuaternion_ = true; 
    } else { 
      needQuaternion_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslAngularMomentum) { 
      needAngMom_ = true; 
    } else { 
      needAngMom_ = false;     
    } 
     
    readSet(whichFrame); 

    if (needCOMprops_) {
      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
      Vector3d com;
      Vector3d comvel;
      Vector3d comw;
      if (needPos_ && needVel_){
        info_->getComAll(com, comvel);
        comw = info_->getAngularMomentum();
      }else{
        com = info_->getCom();
        comvel = 0.0;
        comw   = 0.0;
      }
      s->setCOMprops(com, comvel, comw);      
    }

  } 
   
  void DumpReader::readSet(int whichFrame) {     
    std::string line;

#ifndef IS_MPI 
    inFile_->clear();  
    inFile_->seekg(framePos_[whichFrame]); 

    std::istream& inputStream = *inFile_;     

#else 
    int masterNode = 0;
    std::stringstream sstream;
    if (worldRank == masterNode) {
      std::string sendBuffer;

      inFile_->clear();  
      inFile_->seekg(framePos_[whichFrame]); 
      
      while (inFile_->getline(buffer, bufferSize)) {

        line = buffer;
        sendBuffer += line;
        sendBuffer += '\n';
        if (line.find("</Snapshot>") != std::string::npos) {
          break;
        }        
      }

      int sendBufferSize = sendBuffer.size();
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      
      sstream.str(sendBuffer);
    } else {
      int sendBufferSize;
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      char * recvBuffer = new char[sendBufferSize+1];
      assert(recvBuffer);
      recvBuffer[sendBufferSize] = '\0';
      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      sstream.str(recvBuffer);
      delete [] recvBuffer;
    }      

    std::istream& inputStream = sstream;  
#endif

    inputStream.getline(buffer, bufferSize);

    line = buffer;
    if (line.find("<Snapshot>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader Error: can not find <Snapshot>\n"); 
      painCave.isFatal = 1; 
      simError(); 
    } 
    
    //read frameData
    readFrameProperties(inputStream);

    //read StuntDoubles
    readStuntDoubles(inputStream);     

    inputStream.getline(buffer, bufferSize);
    line = buffer;
    if (line.find("</Snapshot>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader Error: can not find </Snapshot>\n"); 
      painCave.isFatal = 1; 
      simError(); 
    }        
   
  } 
   
  void DumpReader::parseDumpLine(const std::string& line) { 

       
    StringTokenizer tokenizer(line); 
    int nTokens; 
     
    nTokens = tokenizer.countTokens(); 
     
    if (nTokens < 2) {  
      sprintf(painCave.errMsg, 
              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); 
      painCave.isFatal = 1; 
      simError(); 
    } 

    int index = tokenizer.nextTokenAsInt();
 
    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);

    if (integrableObject == NULL) {
      return;
    }
    std::string type = tokenizer.nextToken(); 
    int size = type.size();

    size_t found;
    
    if (needPos_) {
      found = type.find("p");      
      if (found == std::string::npos) {
        sprintf(painCave.errMsg, 
                "DumpReader Error: StuntDouble %d has no Position\n"
                "\tField (\"p\") specified.\n%s\n", index, 
                line.c_str());  
        painCave.isFatal = 1; 
        simError(); 
      }
    }
    
    if (integrableObject->isDirectional()) {
      if (needQuaternion_) {
        found = type.find("q");      
        if (found == std::string::npos) {
          sprintf(painCave.errMsg, 
                  "DumpReader Error: Directional StuntDouble %d has no\n"
                  "\tQuaternion Field (\"q\") specified.\n%s\n", index, 
                  line.c_str());  
          painCave.isFatal = 1; 
          simError(); 
        }
      }      
    }

    for(int i = 0; i < size; ++i) {
      switch(type[i]) {
        
        case 'p': {
            Vector3d pos;
            pos[0] = tokenizer.nextTokenAsDouble(); 
            pos[1] = tokenizer.nextTokenAsDouble(); 
            pos[2] = tokenizer.nextTokenAsDouble(); 
            if (needPos_) { 
              integrableObject->setPos(pos); 
            }             
            break;
        }
        case 'v' : {
            Vector3d vel;
            vel[0] = tokenizer.nextTokenAsDouble(); 
            vel[1] = tokenizer.nextTokenAsDouble(); 
            vel[2] = tokenizer.nextTokenAsDouble(); 
            if (needVel_) { 
              integrableObject->setVel(vel); 
            } 
            break;
        }

        case 'q' : {
           Quat4d q;
           if (integrableObject->isDirectional()) { 
              
             q[0] = tokenizer.nextTokenAsDouble(); 
             q[1] = tokenizer.nextTokenAsDouble(); 
             q[2] = tokenizer.nextTokenAsDouble(); 
             q[3] = tokenizer.nextTokenAsDouble(); 
              
             RealType qlen = q.length(); 
             if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 
                
               sprintf(painCave.errMsg, 
                       "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); 
               painCave.isFatal = 1; 
               simError(); 
                
             }  
              
             q.normalize(); 
             if (needQuaternion_) {            
               integrableObject->setQ(q); 
             }               
           }            
           break;
        }  
        case 'j' : {
          Vector3d ji;
          if (integrableObject->isDirectional()) {
             ji[0] = tokenizer.nextTokenAsDouble(); 
             ji[1] = tokenizer.nextTokenAsDouble(); 
             ji[2] = tokenizer.nextTokenAsDouble(); 
             if (needAngMom_) { 
               integrableObject->setJ(ji); 
             } 
          }
          break;
        }  
        case 'f': {

          Vector3d force;
          force[0] = tokenizer.nextTokenAsDouble(); 
          force[1] = tokenizer.nextTokenAsDouble(); 
          force[2] = tokenizer.nextTokenAsDouble();           
          integrableObject->setFrc(force); 
          break;
        }
        case 't' : {

           Vector3d torque;
           torque[0] = tokenizer.nextTokenAsDouble(); 
           torque[1] = tokenizer.nextTokenAsDouble(); 
           torque[2] = tokenizer.nextTokenAsDouble();           
           integrableObject->setTrq(torque);          
           break;
        }
        case 'u' : {

           RealType particlePot;
           particlePot = tokenizer.nextTokenAsDouble(); 
           integrableObject->setParticlePot(particlePot);          
           break;
        }
        default: {
               sprintf(painCave.errMsg, 
                       "DumpReader Error: %s is an unrecognized type\n", type.c_str()); 
               painCave.isFatal = 1; 
               simError(); 
          break;   
        }

      }
    }
     
  } 
   

  void  DumpReader::readStuntDoubles(std::istream& inputStream) {

    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);
    
    if (line.find("<StuntDoubles>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader Error: Missing <StuntDoubles>\n"); 
      painCave.isFatal = 1; 
      simError(); 
    }

    while(inputStream.getline(buffer, bufferSize)) {
      line = buffer;
      
      if(line.find("</StuntDoubles>") != std::string::npos) {
        break;
      }

      parseDumpLine(line);
    }
  
  }

  void DumpReader::readFrameProperties(std::istream& inputStream) {

    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);

    if (line.find("<FrameData>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader Error: Missing <FrameData>\n"); 
      painCave.isFatal = 1; 
      simError(); 
    }

    while(inputStream.getline(buffer, bufferSize)) {
      line = buffer;
      
      if(line.find("</FrameData>") != std::string::npos) {
        break;
      }
      
      StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
      if (!tokenizer.hasMoreTokens()) {
        sprintf(painCave.errMsg, 
                "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); 
        painCave.isFatal = 1; 
        simError();      
      }

      std::string propertyName = tokenizer.nextToken();
      if (propertyName == "Time") {
        RealType currTime = tokenizer.nextTokenAsDouble(); 
        s->setTime(currTime); 
      } else if (propertyName == "Hmat"){
        Mat3x3d hmat;
        hmat(0, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(0, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(0, 2) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 2) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 2) = tokenizer.nextTokenAsDouble(); 
        s->setHmat(hmat);      
      } else if (propertyName == "Thermostat") {
        RealType chi = tokenizer.nextTokenAsDouble();
        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
        s->setChi(chi); 
        s->setIntegralOfChiDt(integralOfChiDt);        
     } else if (propertyName == "Barostat") {
        Mat3x3d eta;
        eta(0, 0) = tokenizer.nextTokenAsDouble(); 
        eta(0, 1) = tokenizer.nextTokenAsDouble(); 
        eta(0, 2) = tokenizer.nextTokenAsDouble(); 
        eta(1, 0) = tokenizer.nextTokenAsDouble(); 
        eta(1, 1) = tokenizer.nextTokenAsDouble(); 
        eta(1, 2) = tokenizer.nextTokenAsDouble(); 
        eta(2, 0) = tokenizer.nextTokenAsDouble(); 
        eta(2, 1) = tokenizer.nextTokenAsDouble(); 
        eta(2, 2) = tokenizer.nextTokenAsDouble(); 
        s->setEta(eta); 
      } else {
        sprintf(painCave.errMsg, 
                "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); 
        painCave.isFatal = 0; 
        simError();         
      }
      
    }

  }

   
}//end namespace OpenMD 
Revision:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 7 months ago) by gezelter
File size:	17375 byte(s)
Log Message:	Merging changes from old branch into development branch
#	User	Rev	Content
1	gezelter	1390	/*
2			* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
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.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	chrisfen	721
42			#define _LARGEFILE_SOURCE64
43			#define _FILE_OFFSET_BITS 64
44
45			#include <sys/types.h>
46			#include <sys/stat.h>
47
48			#include <iostream>
49			#include <math.h>
50
51			#include <stdio.h>
52			#include <stdlib.h>
53			#include <string.h>
54
55			#include "io/DumpReader.hpp"
56			#include "primitives/Molecule.hpp"
57			#include "utils/simError.h"
58			#include "utils/MemoryUtils.hpp"
59			#include "utils/StringTokenizer.hpp"
60
61			#ifdef IS_MPI
62
63			#include <mpi.h>
64			#define TAKE_THIS_TAG_CHAR 0
65			#define TAKE_THIS_TAG_INT 1
66
67			#endif // is_mpi
68
69
70	gezelter	1390	namespace OpenMD {
71	chrisfen	721
72			DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	gezelter	1104	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74	chrisfen	996
75	chrisfen	721	#ifdef IS_MPI
76	chrisfen	996
77			if (worldRank == 0) {
78	chrisfen	721	#endif
79	chrisfen	996
80	chrisfen	721	inFile_ = new std::ifstream(filename_.c_str());
81	chrisfen	996
82			if (inFile_->fail()) {
83			sprintf(painCave.errMsg,
84			"DumpReader: Cannot open file: %s\n",
85			filename_.c_str());
86			painCave.isFatal = 1;
87			simError();
88			}
89
90	chrisfen	721	#ifdef IS_MPI
91	chrisfen	996
92			}
93
94			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	gezelter	1241	errorCheckPoint();
96	chrisfen	996
97	chrisfen	721	#endif
98	chrisfen	996
99			return;
100			}
101
102	chrisfen	721	DumpReader::~DumpReader() {
103	chrisfen	996
104	chrisfen	721	#ifdef IS_MPI
105	chrisfen	996
106	chrisfen	721	if (worldRank == 0) {
107			#endif
108	chrisfen	996
109	chrisfen	721	delete inFile_;
110	chrisfen	996
111	chrisfen	721	#ifdef IS_MPI
112	chrisfen	996
113	chrisfen	721	}
114	chrisfen	996
115	chrisfen	721	strcpy(checkPointMsg, "Dump file closed successfully.");
116	gezelter	1241	errorCheckPoint();
117	chrisfen	996
118	chrisfen	721	#endif
119	chrisfen	996
120	chrisfen	721	return;
121			}
122	chrisfen	996
123	chrisfen	721	int DumpReader::getNFrames(void) {
124
125			if (!isScanned_)
126			scanFile();
127
128			return nframes_;
129			}
130
131			void DumpReader::scanFile(void) {
132	tim	1024	int lineNo = 0;
133			std::streampos prevPos;
134	chrisfen	721	std::streampos currPos;
135	tim	1024
136	chrisfen	721	#ifdef IS_MPI
137	tim	1024
138	chrisfen	721	if (worldRank == 0) {
139			#endif // is_mpi
140	tim	1024
141			currPos = inFile_->tellg();
142			prevPos = currPos;
143			bool foundOpenSnapshotTag = false;
144			bool foundClosedSnapshotTag = false;
145			while(inFile_->getline(buffer, bufferSize)) {
146			++lineNo;
147
148			std::string line = buffer;
149			currPos = inFile_->tellg();
150			if (line.find("<Snapshot>")!= std::string::npos) {
151			if (foundOpenSnapshotTag) {
152	chrisfen	721	sprintf(painCave.errMsg,
153	tim	1024	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154			filename_.c_str());
155	chrisfen	721	painCave.isFatal = 1;
156	tim	1024	simError();
157			}
158			foundOpenSnapshotTag = true;
159			foundClosedSnapshotTag = false;
160			framePos_.push_back(prevPos);
161
162			} else if (line.find("</Snapshot>") != std::string::npos){
163			if (!foundOpenSnapshotTag) {
164			sprintf(painCave.errMsg,
165			"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166			filename_.c_str());
167			painCave.isFatal = 1;
168	chrisfen	721	simError();
169	tim	1024	}
170
171			if (foundClosedSnapshotTag) {
172			sprintf(painCave.errMsg,
173			"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174			filename_.c_str());
175			painCave.isFatal = 1;
176			simError();
177			}
178			foundClosedSnapshotTag = true;
179			foundOpenSnapshotTag = false;
180			}
181			prevPos = currPos;
182			}
183
184			// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185			// it and give a warning message
186			if (foundOpenSnapshotTag) {
187			sprintf(painCave.errMsg,
188			"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189			painCave.isFatal = 0;
190			simError();
191			framePos_.pop_back();
192			}
193
194	chrisfen	721	nframes_ = framePos_.size();
195	tim	1024
196			if (nframes_ == 0) {
197			sprintf(painCave.errMsg,
198			"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199			painCave.isFatal = 1;
200			simError();
201			}
202	chrisfen	721	#ifdef IS_MPI
203			}
204
205			MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	tim	1024
207	chrisfen	721	#endif // is_mpi
208	tim	1024
209	chrisfen	721	isScanned_ = true;
210			}
211
212			void DumpReader::readFrame(int whichFrame) {
213			if (!isScanned_)
214			scanFile();
215
216			int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217
218			if (storageLayout & DataStorage::dslPosition) {
219			needPos_ = true;
220			} else {
221			needPos_ = false;
222			}
223
224			if (storageLayout & DataStorage::dslVelocity) {
225			needVel_ = true;
226			} else {
227			needVel_ = false;
228			}
229
230			if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
231			needQuaternion_ = true;
232			} else {
233			needQuaternion_ = false;
234			}
235
236			if (storageLayout & DataStorage::dslAngularMomentum) {
237			needAngMom_ = true;
238			} else {
239			needAngMom_ = false;
240			}
241
242			readSet(whichFrame);
243	gezelter	1104
244			if (needCOMprops_) {
245			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246			Vector3d com;
247			Vector3d comvel;
248			Vector3d comw;
249	chuckv	1112	if (needPos_ && needVel_){
250			info_->getComAll(com, comvel);
251			comw = info_->getAngularMomentum();
252			}else{
253			com = info_->getCom();
254			comvel = 0.0;
255			comw = 0.0;
256			}
257	gezelter	1104	s->setCOMprops(com, comvel, comw);
258			}
259
260	chrisfen	721	}
261
262	tim	1024	void DumpReader::readSet(int whichFrame) {
263			std::string line;
264
265	chrisfen	721	#ifndef IS_MPI
266			inFile_->clear();
267			inFile_->seekg(framePos_[whichFrame]);
268	tim	1024
269			std::istream& inputStream = *inFile_;
270
271			#else
272			int masterNode = 0;
273			std::stringstream sstream;
274			if (worldRank == masterNode) {
275			std::string sendBuffer;
276
277			inFile_->clear();
278			inFile_->seekg(framePos_[whichFrame]);
279
280			while (inFile_->getline(buffer, bufferSize)) {
281
282			line = buffer;
283			sendBuffer += line;
284			sendBuffer += '\n';
285			if (line.find("</Snapshot>") != std::string::npos) {
286			break;
287			}
288			}
289
290			int sendBufferSize = sendBuffer.size();
291			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292			MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293
294			sstream.str(sendBuffer);
295			} else {
296			int sendBufferSize;
297			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298			char * recvBuffer = new char[sendBufferSize+1];
299	gezelter	1313	assert(recvBuffer);
300			recvBuffer[sendBufferSize] = '\0';
301	tim	1024	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302			sstream.str(recvBuffer);
303	gezelter	1313	delete [] recvBuffer;
304	tim	1024	}
305
306			std::istream& inputStream = sstream;
307			#endif
308
309			inputStream.getline(buffer, bufferSize);
310
311			line = buffer;
312			if (line.find("<Snapshot>") == std::string::npos) {
313	chrisfen	721	sprintf(painCave.errMsg,
314	tim	1024	"DumpReader Error: can not find <Snapshot>\n");
315	chrisfen	721	painCave.isFatal = 1;
316			simError();
317			}
318	tim	1024
319			//read frameData
320			readFrameProperties(inputStream);
321
322			//read StuntDoubles
323			readStuntDoubles(inputStream);
324
325			inputStream.getline(buffer, bufferSize);
326			line = buffer;
327			if (line.find("</Snapshot>") == std::string::npos) {
328	chrisfen	721	sprintf(painCave.errMsg,
329	tim	1024	"DumpReader Error: can not find </Snapshot>\n");
330	chrisfen	721	painCave.isFatal = 1;
331			simError();
332	tim	1024	}
333
334	chrisfen	721	}
335
336	tim	1024	void DumpReader::parseDumpLine(const std::string& line) {
337
338
339	chrisfen	721	StringTokenizer tokenizer(line);
340			int nTokens;
341
342			nTokens = tokenizer.countTokens();
343
344	gezelter	1450	if (nTokens < 2) {
345	chrisfen	721	sprintf(painCave.errMsg,
346	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347	chrisfen	721	painCave.isFatal = 1;
348			simError();
349			}
350	tim	1024
351			int index = tokenizer.nextTokenAsInt();
352
353			StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354
355			if (integrableObject == NULL) {
356			return;
357			}
358			std::string type = tokenizer.nextToken();
359			int size = type.size();
360	gezelter	1037
361	gezelter	1450	size_t found;
362
363			if (needPos_) {
364			found = type.find("p");
365			if (found == std::string::npos) {
366			sprintf(painCave.errMsg,
367			"DumpReader Error: StuntDouble %d has no Position\n"
368			"\tField (\"p\") specified.\n%s\n", index,
369			line.c_str());
370			painCave.isFatal = 1;
371			simError();
372			}
373			}
374
375			if (integrableObject->isDirectional()) {
376			if (needQuaternion_) {
377			found = type.find("q");
378			if (found == std::string::npos) {
379			sprintf(painCave.errMsg,
380			"DumpReader Error: Directional StuntDouble %d has no\n"
381			"\tQuaternion Field (\"q\") specified.\n%s\n", index,
382			line.c_str());
383			painCave.isFatal = 1;
384			simError();
385			}
386			}
387			}
388
389	tim	1024	for(int i = 0; i < size; ++i) {
390			switch(type[i]) {
391
392			case 'p': {
393			Vector3d pos;
394			pos[0] = tokenizer.nextTokenAsDouble();
395			pos[1] = tokenizer.nextTokenAsDouble();
396			pos[2] = tokenizer.nextTokenAsDouble();
397			if (needPos_) {
398			integrableObject->setPos(pos);
399			}
400			break;
401			}
402			case 'v' : {
403			Vector3d vel;
404			vel[0] = tokenizer.nextTokenAsDouble();
405			vel[1] = tokenizer.nextTokenAsDouble();
406			vel[2] = tokenizer.nextTokenAsDouble();
407			if (needVel_) {
408			integrableObject->setVel(vel);
409			}
410			break;
411			}
412
413			case 'q' : {
414			Quat4d q;
415			if (integrableObject->isDirectional()) {
416
417			q[0] = tokenizer.nextTokenAsDouble();
418			q[1] = tokenizer.nextTokenAsDouble();
419			q[2] = tokenizer.nextTokenAsDouble();
420			q[3] = tokenizer.nextTokenAsDouble();
421
422			RealType qlen = q.length();
423	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
424	tim	1024
425			sprintf(painCave.errMsg,
426			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
427			painCave.isFatal = 1;
428			simError();
429
430			}
431
432			q.normalize();
433			if (needQuaternion_) {
434			integrableObject->setQ(q);
435			}
436			}
437			break;
438			}
439			case 'j' : {
440			Vector3d ji;
441			if (integrableObject->isDirectional()) {
442			ji[0] = tokenizer.nextTokenAsDouble();
443			ji[1] = tokenizer.nextTokenAsDouble();
444			ji[2] = tokenizer.nextTokenAsDouble();
445			if (needAngMom_) {
446			integrableObject->setJ(ji);
447			}
448			}
449	gezelter	1037	break;
450	tim	1024	}
451			case 'f': {
452
453			Vector3d force;
454			force[0] = tokenizer.nextTokenAsDouble();
455			force[1] = tokenizer.nextTokenAsDouble();
456			force[2] = tokenizer.nextTokenAsDouble();
457			integrableObject->setFrc(force);
458			break;
459			}
460			case 't' : {
461
462			Vector3d torque;
463			torque[0] = tokenizer.nextTokenAsDouble();
464			torque[1] = tokenizer.nextTokenAsDouble();
465			torque[2] = tokenizer.nextTokenAsDouble();
466			integrableObject->setTrq(torque);
467			break;
468			}
469	gezelter	1629	case 'u' : {
470
471			RealType particlePot;
472			particlePot = tokenizer.nextTokenAsDouble();
473			integrableObject->setParticlePot(particlePot);
474			break;
475			}
476	tim	1024	default: {
477			sprintf(painCave.errMsg,
478			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
479			painCave.isFatal = 1;
480			simError();
481			break;
482			}
483
484			}
485			}
486	chrisfen	721
487	tim	1024	}
488
489
490			void DumpReader::readStuntDoubles(std::istream& inputStream) {
491
492			inputStream.getline(buffer, bufferSize);
493			std::string line(buffer);
494
495			if (line.find("<StuntDoubles>") == std::string::npos) {
496	chrisfen	721	sprintf(painCave.errMsg,
497	tim	1024	"DumpReader Error: Missing <StuntDoubles>\n");
498	chrisfen	721	painCave.isFatal = 1;
499	tim	1024	simError();
500			}
501
502			while(inputStream.getline(buffer, bufferSize)) {
503			line = buffer;
504
505			if(line.find("</StuntDoubles>") != std::string::npos) {
506			break;
507			}
508
509			parseDumpLine(line);
510			}
511
512			}
513
514			void DumpReader::readFrameProperties(std::istream& inputStream) {
515
516			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
517			inputStream.getline(buffer, bufferSize);
518			std::string line(buffer);
519
520			if (line.find("<FrameData>") == std::string::npos) {
521			sprintf(painCave.errMsg,
522			"DumpReader Error: Missing <FrameData>\n");
523			painCave.isFatal = 1;
524			simError();
525			}
526
527			while(inputStream.getline(buffer, bufferSize)) {
528			line = buffer;
529
530			if(line.find("</FrameData>") != std::string::npos) {
531			break;
532			}
533
534			StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
535			if (!tokenizer.hasMoreTokens()) {
536	chrisfen	721	sprintf(painCave.errMsg,
537	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
538	chrisfen	721	painCave.isFatal = 1;
539	tim	1024	simError();
540			}
541
542			std::string propertyName = tokenizer.nextToken();
543			if (propertyName == "Time") {
544			RealType currTime = tokenizer.nextTokenAsDouble();
545			s->setTime(currTime);
546			} else if (propertyName == "Hmat"){
547			Mat3x3d hmat;
548			hmat(0, 0) = tokenizer.nextTokenAsDouble();
549			hmat(0, 1) = tokenizer.nextTokenAsDouble();
550			hmat(0, 2) = tokenizer.nextTokenAsDouble();
551			hmat(1, 0) = tokenizer.nextTokenAsDouble();
552			hmat(1, 1) = tokenizer.nextTokenAsDouble();
553			hmat(1, 2) = tokenizer.nextTokenAsDouble();
554			hmat(2, 0) = tokenizer.nextTokenAsDouble();
555			hmat(2, 1) = tokenizer.nextTokenAsDouble();
556			hmat(2, 2) = tokenizer.nextTokenAsDouble();
557			s->setHmat(hmat);
558			} else if (propertyName == "Thermostat") {
559			RealType chi = tokenizer.nextTokenAsDouble();
560			RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
561			s->setChi(chi);
562			s->setIntegralOfChiDt(integralOfChiDt);
563			} else if (propertyName == "Barostat") {
564			Mat3x3d eta;
565			eta(0, 0) = tokenizer.nextTokenAsDouble();
566			eta(0, 1) = tokenizer.nextTokenAsDouble();
567			eta(0, 2) = tokenizer.nextTokenAsDouble();
568			eta(1, 0) = tokenizer.nextTokenAsDouble();
569			eta(1, 1) = tokenizer.nextTokenAsDouble();
570			eta(1, 2) = tokenizer.nextTokenAsDouble();
571			eta(2, 0) = tokenizer.nextTokenAsDouble();
572			eta(2, 1) = tokenizer.nextTokenAsDouble();
573			eta(2, 2) = tokenizer.nextTokenAsDouble();
574			s->setEta(eta);
575			} else {
576			sprintf(painCave.errMsg,
577			"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
578			painCave.isFatal = 0;
579			simError();
580			}
581
582			}
583
584			}
585
586	chrisfen	721
587	gezelter	1390	}//end namespace OpenMD