src/io/DumpReader.cpp

/* 
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any 
 *    publication of scientific results based in part on use of the 
 *    program.  An acceptable form of acknowledgement is citation of 
 *    the article in which the program was described (Matthew 
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher 
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented 
 *    Parallel Simulation Engine for Molecular Dynamics," 
 *    J. Comput. Chem. 26, pp. 252-271 (2005)) 
 * 
 * 2. Redistributions of source code must retain the above copyright 
 *    notice, this list of conditions and the following disclaimer. 
 * 
 * 3. 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. 
 */ 
  
#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 oopse { 
   
  DumpReader::DumpReader(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename), isScanned_(false), nframes_(0) { 
    
#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."); 
    MPIcheckPoint(); 
    
#endif 
    
    return; 
  } 
  
  DumpReader::~DumpReader() { 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif 
      
      delete inFile_; 
      
#ifdef IS_MPI 
      
    } 
    
    strcpy(checkPointMsg, "Dump file closed successfully."); 
    MPIcheckPoint(); 
    
#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); 
  } 
   
  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);
      std::cerr << sendBuffer;
    } else {
      int sendBufferSize;
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      char * recvBuffer = new char[sendBufferSize+1];
      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      sstream.str(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();
    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 < oopse::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); 
             } 
          }
        }  
        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;
        }
        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 oopse 
Revision:	2982
Committed:	Wed Aug 30 18:42:29 2006 UTC (17 years, 10 months ago) by tim
File size:	15818 byte(s)
Log Message:	Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
#	User	Rev	Content
1	chrisfen	2420	/*
2			* Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
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			namespace oopse {
71
72			DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73			: info_(info), filename_(filename), isScanned_(false), nframes_(0) {
74	chrisfen	2903
75	chrisfen	2420	#ifdef IS_MPI
76	chrisfen	2903
77			if (worldRank == 0) {
78	chrisfen	2420	#endif
79	chrisfen	2903
80	chrisfen	2420	inFile_ = new std::ifstream(filename_.c_str());
81	chrisfen	2903
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	2420	#ifdef IS_MPI
91	chrisfen	2903
92			}
93
94			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95			MPIcheckPoint();
96
97	chrisfen	2420	#endif
98	chrisfen	2903
99			return;
100			}
101
102	chrisfen	2420	DumpReader::~DumpReader() {
103	chrisfen	2903
104	chrisfen	2420	#ifdef IS_MPI
105	chrisfen	2903
106	chrisfen	2420	if (worldRank == 0) {
107			#endif
108	chrisfen	2903
109	chrisfen	2420	delete inFile_;
110	chrisfen	2903
111	chrisfen	2420	#ifdef IS_MPI
112	chrisfen	2903
113	chrisfen	2420	}
114	chrisfen	2903
115	chrisfen	2420	strcpy(checkPointMsg, "Dump file closed successfully.");
116			MPIcheckPoint();
117	chrisfen	2903
118	chrisfen	2420	#endif
119	chrisfen	2903
120	chrisfen	2420	return;
121			}
122	chrisfen	2903
123	chrisfen	2420	int DumpReader::getNFrames(void) {
124
125			if (!isScanned_)
126			scanFile();
127
128			return nframes_;
129			}
130
131			void DumpReader::scanFile(void) {
132	tim	2982	int lineNo = 0;
133			std::streampos prevPos;
134	chrisfen	2420	std::streampos currPos;
135	tim	2982
136	chrisfen	2420	#ifdef IS_MPI
137	tim	2982
138	chrisfen	2420	if (worldRank == 0) {
139			#endif // is_mpi
140	tim	2982
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	2420	sprintf(painCave.errMsg,
153	tim	2982	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154			filename_.c_str());
155	chrisfen	2420	painCave.isFatal = 1;
156	tim	2982	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	2420	simError();
169	tim	2982	}
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	2420	nframes_ = framePos_.size();
195	tim	2982
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	2420	#ifdef IS_MPI
203			}
204
205			MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	tim	2982
207	chrisfen	2420	#endif // is_mpi
208	tim	2982
209	chrisfen	2420	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			}
244
245	tim	2982	void DumpReader::readSet(int whichFrame) {
246			std::string line;
247
248	chrisfen	2420	#ifndef IS_MPI
249	tim	2982
250	chrisfen	2420	inFile_->clear();
251			inFile_->seekg(framePos_[whichFrame]);
252	tim	2982
253			std::istream& inputStream = *inFile_;
254
255			#else
256			int masterNode = 0;
257			std::stringstream sstream;
258			if (worldRank == masterNode) {
259			std::string sendBuffer;
260
261			inFile_->clear();
262			inFile_->seekg(framePos_[whichFrame]);
263
264			while (inFile_->getline(buffer, bufferSize)) {
265
266			line = buffer;
267			sendBuffer += line;
268			sendBuffer += '\n';
269			if (line.find("</Snapshot>") != std::string::npos) {
270			break;
271			}
272			}
273
274			int sendBufferSize = sendBuffer.size();
275			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
276			MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
277
278			sstream.str(sendBuffer);
279			std::cerr << sendBuffer;
280			} else {
281			int sendBufferSize;
282			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
283			char * recvBuffer = new char[sendBufferSize+1];
284			MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
285			sstream.str(recvBuffer);
286			}
287
288			std::istream& inputStream = sstream;
289			#endif
290
291			inputStream.getline(buffer, bufferSize);
292
293			line = buffer;
294			if (line.find("<Snapshot>") == std::string::npos) {
295	chrisfen	2420	sprintf(painCave.errMsg,
296	tim	2982	"DumpReader Error: can not find <Snapshot>\n");
297	chrisfen	2420	painCave.isFatal = 1;
298			simError();
299			}
300	tim	2982
301			//read frameData
302			readFrameProperties(inputStream);
303
304			//read StuntDoubles
305			readStuntDoubles(inputStream);
306
307			inputStream.getline(buffer, bufferSize);
308			line = buffer;
309			if (line.find("</Snapshot>") == std::string::npos) {
310	chrisfen	2420	sprintf(painCave.errMsg,
311	tim	2982	"DumpReader Error: can not find </Snapshot>\n");
312	chrisfen	2420	painCave.isFatal = 1;
313			simError();
314	tim	2982	}
315
316	chrisfen	2420	}
317
318	tim	2982	void DumpReader::parseDumpLine(const std::string& line) {
319
320
321	chrisfen	2420	StringTokenizer tokenizer(line);
322			int nTokens;
323
324			nTokens = tokenizer.countTokens();
325
326	tim	2982	if (nTokens < 2) {
327	chrisfen	2420	sprintf(painCave.errMsg,
328	tim	2982	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
329	chrisfen	2420	painCave.isFatal = 1;
330			simError();
331			}
332	tim	2982
333			int index = tokenizer.nextTokenAsInt();
334
335			StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
336
337			if (integrableObject == NULL) {
338			return;
339			}
340			std::string type = tokenizer.nextToken();
341			int size = type.size();
342			for(int i = 0; i < size; ++i) {
343			switch(type[i]) {
344
345			case 'p': {
346			Vector3d pos;
347			pos[0] = tokenizer.nextTokenAsDouble();
348			pos[1] = tokenizer.nextTokenAsDouble();
349			pos[2] = tokenizer.nextTokenAsDouble();
350			if (needPos_) {
351			integrableObject->setPos(pos);
352			}
353			break;
354			}
355			case 'v' : {
356			Vector3d vel;
357			vel[0] = tokenizer.nextTokenAsDouble();
358			vel[1] = tokenizer.nextTokenAsDouble();
359			vel[2] = tokenizer.nextTokenAsDouble();
360			if (needVel_) {
361			integrableObject->setVel(vel);
362			}
363			break;
364			}
365
366			case 'q' : {
367			Quat4d q;
368			if (integrableObject->isDirectional()) {
369
370			q[0] = tokenizer.nextTokenAsDouble();
371			q[1] = tokenizer.nextTokenAsDouble();
372			q[2] = tokenizer.nextTokenAsDouble();
373			q[3] = tokenizer.nextTokenAsDouble();
374
375			RealType qlen = q.length();
376			if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
377
378			sprintf(painCave.errMsg,
379			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
380			painCave.isFatal = 1;
381			simError();
382
383			}
384
385			q.normalize();
386			if (needQuaternion_) {
387			integrableObject->setQ(q);
388			}
389			}
390			break;
391			}
392			case 'j' : {
393			Vector3d ji;
394			if (integrableObject->isDirectional()) {
395			ji[0] = tokenizer.nextTokenAsDouble();
396			ji[1] = tokenizer.nextTokenAsDouble();
397			ji[2] = tokenizer.nextTokenAsDouble();
398			if (needAngMom_) {
399			integrableObject->setJ(ji);
400			}
401			}
402			}
403			case 'f': {
404
405			Vector3d force;
406			force[0] = tokenizer.nextTokenAsDouble();
407			force[1] = tokenizer.nextTokenAsDouble();
408			force[2] = tokenizer.nextTokenAsDouble();
409			integrableObject->setFrc(force);
410			break;
411			}
412			case 't' : {
413
414			Vector3d torque;
415			torque[0] = tokenizer.nextTokenAsDouble();
416			torque[1] = tokenizer.nextTokenAsDouble();
417			torque[2] = tokenizer.nextTokenAsDouble();
418			integrableObject->setTrq(torque);
419			break;
420			}
421			default: {
422			sprintf(painCave.errMsg,
423			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
424			painCave.isFatal = 1;
425			simError();
426			break;
427			}
428
429			}
430			}
431	chrisfen	2420
432	tim	2982	}
433
434
435			void DumpReader::readStuntDoubles(std::istream& inputStream) {
436
437			inputStream.getline(buffer, bufferSize);
438			std::string line(buffer);
439
440			if (line.find("<StuntDoubles>") == std::string::npos) {
441	chrisfen	2420	sprintf(painCave.errMsg,
442	tim	2982	"DumpReader Error: Missing <StuntDoubles>\n");
443	chrisfen	2420	painCave.isFatal = 1;
444	tim	2982	simError();
445			}
446
447			while(inputStream.getline(buffer, bufferSize)) {
448			line = buffer;
449
450			if(line.find("</StuntDoubles>") != std::string::npos) {
451			break;
452			}
453
454			parseDumpLine(line);
455			}
456
457			}
458
459			void DumpReader::readFrameProperties(std::istream& inputStream) {
460
461			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
462			inputStream.getline(buffer, bufferSize);
463			std::string line(buffer);
464
465			if (line.find("<FrameData>") == std::string::npos) {
466			sprintf(painCave.errMsg,
467			"DumpReader Error: Missing <FrameData>\n");
468			painCave.isFatal = 1;
469			simError();
470			}
471
472			while(inputStream.getline(buffer, bufferSize)) {
473			line = buffer;
474
475			if(line.find("</FrameData>") != std::string::npos) {
476			break;
477			}
478
479			StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
480			if (!tokenizer.hasMoreTokens()) {
481	chrisfen	2420	sprintf(painCave.errMsg,
482	tim	2982	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
483	chrisfen	2420	painCave.isFatal = 1;
484	tim	2982	simError();
485			}
486
487			std::string propertyName = tokenizer.nextToken();
488			if (propertyName == "Time") {
489			RealType currTime = tokenizer.nextTokenAsDouble();
490			s->setTime(currTime);
491			} else if (propertyName == "Hmat"){
492			Mat3x3d hmat;
493			hmat(0, 0) = tokenizer.nextTokenAsDouble();
494			hmat(0, 1) = tokenizer.nextTokenAsDouble();
495			hmat(0, 2) = tokenizer.nextTokenAsDouble();
496			hmat(1, 0) = tokenizer.nextTokenAsDouble();
497			hmat(1, 1) = tokenizer.nextTokenAsDouble();
498			hmat(1, 2) = tokenizer.nextTokenAsDouble();
499			hmat(2, 0) = tokenizer.nextTokenAsDouble();
500			hmat(2, 1) = tokenizer.nextTokenAsDouble();
501			hmat(2, 2) = tokenizer.nextTokenAsDouble();
502			s->setHmat(hmat);
503			} else if (propertyName == "Thermostat") {
504			RealType chi = tokenizer.nextTokenAsDouble();
505			RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
506			s->setChi(chi);
507			s->setIntegralOfChiDt(integralOfChiDt);
508			} else if (propertyName == "Barostat") {
509			Mat3x3d eta;
510			eta(0, 0) = tokenizer.nextTokenAsDouble();
511			eta(0, 1) = tokenizer.nextTokenAsDouble();
512			eta(0, 2) = tokenizer.nextTokenAsDouble();
513			eta(1, 0) = tokenizer.nextTokenAsDouble();
514			eta(1, 1) = tokenizer.nextTokenAsDouble();
515			eta(1, 2) = tokenizer.nextTokenAsDouble();
516			eta(2, 0) = tokenizer.nextTokenAsDouble();
517			eta(2, 1) = tokenizer.nextTokenAsDouble();
518			eta(2, 2) = tokenizer.nextTokenAsDouble();
519			s->setEta(eta);
520			} else {
521			sprintf(painCave.errMsg,
522			"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
523			painCave.isFatal = 0;
524			simError();
525			}
526
527			}
528
529			}
530
531	chrisfen	2420
532			}//end namespace oopse