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Comparing trunk/OOPSE-4/src/io/DumpReader.cpp (file contents):
Revision 2204 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 3110 by chuckv, Wed Jan 3 20:47:00 2007 UTC

# Line 1 | Line 1
1 < /*
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 {
1 > /*
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 <  DumpReader::DumpReader(SimInfo* info, const std::string& filename)
43 <    : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
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), needCOMprops_(false) {
74      
75 < #ifdef IS_MPI
75 > #ifdef IS_MPI
76      
77 <      if (worldRank == 0) {
78 < #endif
77 >    if (worldRank == 0) {
78 > #endif
79        
80 <        inFile_ = fopen(filename_.c_str(), "r");
80 >      inFile_ = new std::ifstream(filename_.c_str());
81        
82 <        if (inFile_ == NULL) {
83 <          sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
84 <          painCave.isFatal = 1;
85 <          simError();
86 <        }
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 < #ifdef IS_MPI
90 > #ifdef IS_MPI
91        
92 <      }
92 >    }
93      
94 <      strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95 <      MPIcheckPoint();
94 >    strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95 >    MPIcheckPoint();
96      
97 < #endif
97 > #endif
98      
99 <      return;
100 <    }
99 >    return;
100 >  }
101    
102 <  DumpReader::~DumpReader() {
102 >  DumpReader::~DumpReader() {
103      
104 < #ifdef IS_MPI
104 > #ifdef IS_MPI
105      
106 <    if (worldRank == 0) {
107 < #endif
106 >    if (worldRank == 0) {
107 > #endif
108        
109 <      int error;
108 <      error = fclose(inFile_);
109 >      delete inFile_;
110        
111 <      if (error) {
111 <        sprintf(painCave.errMsg, "DumpReader Error: Error closing %s\n", filename_.c_str());
112 <        painCave.isFatal = 1;            
113 <        simError();
114 <      }
111 > #ifdef IS_MPI
112        
113 <      MemoryUtils::deletePointers(framePos_);
117 <      
118 < #ifdef IS_MPI
119 <      
120 <    }
113 >    }
114      
115 <    strcpy(checkPointMsg, "Dump file closed successfully.");
116 <    MPIcheckPoint();
115 >    strcpy(checkPointMsg, "Dump file closed successfully.");
116 >    MPIcheckPoint();
117      
118 < #endif
118 > #endif
119      
120 <    return;
121 <  }
120 >    return;
121 >  }
122    
123 <  int DumpReader::getNFrames(void) {
123 >  int DumpReader::getNFrames(void) {
124 >    
125 >    if (!isScanned_)
126 >      scanFile();
127 >    
128 >    return nframes_;
129 >  }
130 >  
131 >  void DumpReader::scanFile(void) {
132 >    int lineNo = 0;
133 >    std::streampos prevPos;
134 >    std::streampos  currPos;
135      
136 <    if (!isScanned_)
133 <      scanFile();
136 > #ifdef IS_MPI
137      
138 <    return nframes_;
139 <  }
137 <  
138 <  void DumpReader::scanFile(void) {
139 <    int i, j;
140 <    int lineNum = 0;
141 <    char readBuffer[maxBufferSize];
142 <    fpos_t * currPos;
143 <    
144 < #ifdef IS_MPI
145 <    
146 <    if (worldRank == 0) {
147 < #endif // is_mpi
138 >    if (worldRank == 0) {
139 > #endif // is_mpi
140        
141 <      rewind(inFile_);
142 <      
143 <      currPos = new fpos_t;
144 <      fgetpos(inFile_, currPos);
145 <      fgets(readBuffer, sizeof(readBuffer), inFile_);
146 <      lineNum++;
155 <      
156 <      if (feof(inFile_)) {
157 <        sprintf(painCave.errMsg,
158 <                "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
159 <                filename_.c_str(),
160 <                lineNum);
161 <        painCave.isFatal = 1;
162 <        simError();
163 <      }
164 <      
165 <      while (!feof(inFile_)) {
166 <        framePos_.push_back(currPos);
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 <        i = atoi(readBuffer);
149 <        
150 <        fgets(readBuffer, sizeof(readBuffer), inFile_);
151 <        lineNum++;
152 <        
153 <        if (feof(inFile_)) {
154 <          sprintf(painCave.errMsg,
155 <                  "DumpReader Error: File \"%s\" ended unexpectedly at line %d\n",
156 <                  filename_.c_str(),
157 <                  lineNum);
158 <          painCave.isFatal = 1;
159 <          simError();
160 <        }
181 <        
182 <        for(j = 0; j < i; j++) {
183 <          fgets(readBuffer, sizeof(readBuffer), inFile_);
184 <          lineNum++;
148 >        std::string line = buffer;
149 >        currPos = inFile_->tellg();
150 >        if (line.find("<Snapshot>")!= std::string::npos) {
151 >          if (foundOpenSnapshotTag) {
152 >            sprintf(painCave.errMsg,
153 >                    "DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154 >                    filename_.c_str());
155 >            painCave.isFatal = 1;
156 >            simError();          
157 >          }
158 >          foundOpenSnapshotTag = true;
159 >          foundClosedSnapshotTag = false;
160 >          framePos_.push_back(prevPos);
161            
162 <          if (feof(inFile_)) {
163 <            sprintf(painCave.errMsg,
164 <                    "DumpReader Error: File \"%s\" ended unexpectedly at line %d,"
165 <                    " with atom %d\n", filename_.c_str(),
166 <                    lineNum,
167 <                    j);
168 <            
193 <            painCave.isFatal = 1;
194 <            simError();
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 >            simError();
169            }
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 <        
198 <        currPos = new fpos_t;
199 <        fgetpos(inFile_, currPos);
200 <        fgets(readBuffer, sizeof(readBuffer), inFile_);
201 <        lineNum++;
181 >        prevPos = currPos;
182        }
183        
184 <      delete currPos;
185 <      rewind(inFile_);
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 <      nframes_ = framePos_.size();
208 < #ifdef IS_MPI
209 <    }
210 <    
211 <    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
212 <    
213 <    strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
214 <    MPIcheckPoint();
215 <    
216 < #endif // is_mpi
217 <    
218 <    isScanned_ = true;
219 <  }
220 <  
221 <  void DumpReader::readFrame(int whichFrame) {
222 <    int storageLayout = info_->getSnapshotManager()->getStorageLayout();
223 <    
224 <    if (storageLayout & DataStorage::dslPosition) {
225 <      needPos_ = true;
226 <    } else {
227 <      needPos_ = false;
228 <    }
229 <    
230 <    if (storageLayout & DataStorage::dslVelocity) {
231 <      needVel_ = true;
232 <    } else {
233 <      needVel_ = false;
234 <    }
235 <    
236 <    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
237 <      needQuaternion_ = true;
238 <    } else {
239 <      needQuaternion_ = false;
240 <    }
241 <    
242 <    if (storageLayout & DataStorage::dslAngularMomentum) {
243 <      needAngMom_ = true;
244 <    } else {
245 <      needAngMom_ = false;    
246 <    }
247 <    
248 <    readSet(whichFrame);
249 <  }
250 <  
251 <  void DumpReader::readSet(int whichFrame) {
252 <    int i;
253 <    int nTotObjs;                  // the number of atoms
254 <    char read_buffer[maxBufferSize];  //the line buffer for reading
255 <    char * eof_test;               // ptr to see when we reach the end of the file
256 <    
257 <    Molecule* mol;
258 <    StuntDouble* integrableObject;
259 <    SimInfo::MoleculeIterator mi;
260 <    Molecule::IntegrableObjectIterator ii;
261 <    
262 < #ifndef IS_MPI
263 <    
264 <    fsetpos(inFile_, framePos_[whichFrame]);
265 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266 <    
267 <    if (eof_test == NULL) {
268 <      sprintf(painCave.errMsg,
269 <              "DumpReader error: error reading 1st line of \"%s\"\n",
270 <              filename_.c_str());
271 <      painCave.isFatal = 1;
272 <      simError();
273 <    }
274 <    
275 <    nTotObjs = atoi(read_buffer);
276 <    
277 <    if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
278 <      sprintf(painCave.errMsg,
279 <              "DumpReader error. %s nIntegrable, %d, "
280 <              "does not match the meta-data file's nIntegrable, %d.\n",
281 <              filename_.c_str(),
282 <              nTotObjs,
283 <              info_->getNGlobalIntegrableObjects());
194 >      nframes_ = framePos_.size();
195        
196 <      painCave.isFatal = 1;
197 <      simError();
198 <    }
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 > #ifdef IS_MPI
203 >    }
204 >    
205 >    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206      
207 <    //read the box mat from the comment line
207 > #endif // is_mpi
208      
209 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
210 <    
211 <    if (eof_test == NULL) {
212 <      sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
213 <              filename_.c_str());
214 <      painCave.isFatal = 1;
215 <      simError();
216 <    }
217 <    
218 <    parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
219 <    
220 <    //parse dump lines
221 <    
222 <    i = 0;
223 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
224 <      
225 <      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
226 <           integrableObject = mol->nextIntegrableObject(ii)) {          
227 <        
228 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
229 <        
230 <        if (eof_test == NULL) {
231 <          sprintf(painCave.errMsg,
232 <                  "DumpReader Error: error in reading file %s\n"
233 <                  "natoms  = %d; index = %d\n"
234 <                  "error reading the line from the file.\n",
235 <                  filename_.c_str(),
236 <                  nTotObjs,
237 <                  i);
238 <          
239 <          painCave.isFatal = 1;
240 <          simError();
241 <        }
242 <        
243 <        parseDumpLine(read_buffer, integrableObject);
244 <        i++;
209 >    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 >    if (needCOMprops_) {
245 >      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246 >      Vector3d com;
247 >      Vector3d comvel;
248 >      Vector3d comw;
249 >      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 +      s->setCOMprops(com, comvel, comw);      
258      }
259 <    
260 <    // MPI Section of code..........
261 <    
262 < #else //IS_MPI
263 <    
264 <    // first thing first, suspend fatalities.
259 >
260 >  }
261 >  
262 >  void DumpReader::readSet(int whichFrame) {    
263 >    std::string line;
264 >
265 > #ifndef IS_MPI
266 >
267 >    inFile_->clear();  
268 >    inFile_->seekg(framePos_[whichFrame]);
269 >
270 >    std::istream& inputStream = *inFile_;    
271 >
272 > #else
273      int masterNode = 0;
274 <    int nCurObj;
337 <    painCave.isEventLoop = 1;
338 <    
339 <    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
340 <    int haveError;
341 <    
342 <    MPI_Status istatus;
343 <    int nitems;
344 <    
345 <    nTotObjs = info_->getNGlobalIntegrableObjects();
346 <    haveError = 0;
347 <    
274 >    std::stringstream sstream;
275      if (worldRank == masterNode) {
276 <      fsetpos(inFile_, framePos_[whichFrame]);
277 <      
278 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
276 >      std::string sendBuffer;
277 >
278 >      inFile_->clear();  
279 >      inFile_->seekg(framePos_[whichFrame]);
280        
281 <      if (eof_test == NULL) {
282 <        sprintf(painCave.errMsg, "DumpReader Error: Error reading 1st line of %s \n ",
283 <                filename_.c_str());
284 <        painCave.isFatal = 1;
285 <        simError();
281 >      while (inFile_->getline(buffer, bufferSize)) {
282 >
283 >        line = buffer;
284 >        sendBuffer += line;
285 >        sendBuffer += '\n';
286 >        if (line.find("</Snapshot>") != std::string::npos) {
287 >          break;
288 >        }        
289        }
290 +
291 +      int sendBufferSize = sendBuffer.size();
292 +      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
293 +      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
294        
295 <      nitems = atoi(read_buffer);
296 <      
297 <      // Check to see that the number of integrable objects in the
298 <      // intial configuration file is the same as derived from the
299 <      // meta-data file.
300 <      
301 <      if (nTotObjs != nitems) {
302 <        sprintf(painCave.errMsg,
303 <                "DumpReader Error. %s nIntegrable, %d, "
304 <                "does not match the meta-data file's nIntegrable, %d.\n",
305 <                filename_.c_str(),
306 <                nTotObjs,
307 <                info_->getNGlobalIntegrableObjects());
295 >      sstream.str(sendBuffer);
296 >    } else {
297 >      int sendBufferSize;
298 >      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
299 >      char * recvBuffer = new char[sendBufferSize+1];
300 >      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
301 >      sstream.str(recvBuffer);
302 >    }      
303 >
304 >    std::istream& inputStream = sstream;  
305 > #endif
306 >
307 >    inputStream.getline(buffer, bufferSize);
308 >
309 >    line = buffer;
310 >    if (line.find("<Snapshot>") == std::string::npos) {
311 >      sprintf(painCave.errMsg,
312 >              "DumpReader Error: can not find <Snapshot>\n");
313 >      painCave.isFatal = 1;
314 >      simError();
315 >    }
316 >    
317 >    //read frameData
318 >    readFrameProperties(inputStream);
319 >
320 >    //read StuntDoubles
321 >    readStuntDoubles(inputStream);    
322 >
323 >    inputStream.getline(buffer, bufferSize);
324 >    line = buffer;
325 >    if (line.find("</Snapshot>") == std::string::npos) {
326 >      sprintf(painCave.errMsg,
327 >              "DumpReader Error: can not find </Snapshot>\n");
328 >      painCave.isFatal = 1;
329 >      simError();
330 >    }        
331 >  
332 >  }
333 >  
334 >  void DumpReader::parseDumpLine(const std::string& line) {
335 >
336 >      
337 >    StringTokenizer tokenizer(line);
338 >    int nTokens;
339 >    
340 >    nTokens = tokenizer.countTokens();
341 >    
342 >    if (nTokens < 2) {
343 >      sprintf(painCave.errMsg,
344 >              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
345 >      painCave.isFatal = 1;
346 >      simError();
347 >    }
348 >
349 >    int index = tokenizer.nextTokenAsInt();
350 >
351 >    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
352 >
353 >    if (integrableObject == NULL) {
354 >      return;
355 >    }
356 >    std::string type = tokenizer.nextToken();
357 >    int size = type.size();
358 >
359 >    for(int i = 0; i < size; ++i) {
360 >      switch(type[i]) {
361          
362 <        painCave.isFatal = 1;
363 <        simError();
364 <      }
365 <      
366 <      //read the boxMat from the comment line
367 <      
368 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
369 <      
370 <      if (eof_test == NULL) {
371 <        sprintf(painCave.errMsg, "DumpReader Error: error in reading commment in %s\n",
372 <                filename_.c_str());
373 <        painCave.isFatal = 1;
374 <        simError();
375 <      }
376 <      
377 <      //Every single processor will parse the comment line by itself
378 <      //By using this way, we might lose some efficiency, but if we want to add
379 <      //more parameters into comment line, we only need to modify function
380 <      //parseCommentLine
381 <      
382 <      MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
383 <      parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
384 <      
385 <      for(i = 0; i < info_->getNGlobalMolecules(); i++) {
398 <        int which_node = info_->getMolToProc(i);
399 <        
400 <        if (which_node == masterNode) {
401 <          //molecules belong to master node
402 <          
403 <          mol = info_->getMoleculeByGlobalIndex(i);
404 <          
405 <          if (mol == NULL) {
406 <            sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
407 <            painCave.isFatal = 1;
408 <            simError();
409 <          }
410 <          
411 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
412 <               integrableObject = mol->nextIntegrableObject(ii)){
413 <            
414 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
415 <            
416 <            if (eof_test == NULL) {
417 <              sprintf(painCave.errMsg,
418 <                      "DumpReader Error: error in reading file %s\n"
419 <                      "natoms  = %d; index = %d\n"
420 <                      "error reading the line from the file.\n",
421 <                      filename_.c_str(),
422 <                      nTotObjs,
423 <                      i);
362 >        case 'p': {
363 >            Vector3d pos;
364 >            pos[0] = tokenizer.nextTokenAsDouble();
365 >            pos[1] = tokenizer.nextTokenAsDouble();
366 >            pos[2] = tokenizer.nextTokenAsDouble();
367 >            if (needPos_) {
368 >              integrableObject->setPos(pos);
369 >            }            
370 >            break;
371 >        }
372 >        case 'v' : {
373 >            Vector3d vel;
374 >            vel[0] = tokenizer.nextTokenAsDouble();
375 >            vel[1] = tokenizer.nextTokenAsDouble();
376 >            vel[2] = tokenizer.nextTokenAsDouble();
377 >            if (needVel_) {
378 >              integrableObject->setVel(vel);
379 >            }
380 >            break;
381 >        }
382 >
383 >        case 'q' : {
384 >           Quat4d q;
385 >           if (integrableObject->isDirectional()) {
386                
387 <              painCave.isFatal = 1;
388 <              simError();
389 <            }
390 <            
429 <            parseDumpLine(read_buffer, integrableObject);
430 <          }
431 <        } else {
432 <          //molecule belongs to slave nodes
433 <          
434 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
435 <                   MPI_COMM_WORLD, &istatus);
436 <          
437 <          for(int j = 0; j < nCurObj; j++) {
438 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
439 <            
440 <            if (eof_test == NULL) {
441 <              sprintf(painCave.errMsg,
442 <                      "DumpReader Error: error in reading file %s\n"
443 <                      "natoms  = %d; index = %d\n"
444 <                      "error reading the line from the file.\n",
445 <                      filename_.c_str(),
446 <                      nTotObjs,
447 <                      i);
387 >             q[0] = tokenizer.nextTokenAsDouble();
388 >             q[1] = tokenizer.nextTokenAsDouble();
389 >             q[2] = tokenizer.nextTokenAsDouble();
390 >             q[3] = tokenizer.nextTokenAsDouble();
391                
392 <              painCave.isFatal = 1;
393 <              simError();
394 <            }
395 <            
396 <            MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
397 <                     TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
392 >             RealType qlen = q.length();
393 >             if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
394 >                
395 >               sprintf(painCave.errMsg,
396 >                       "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
397 >               painCave.isFatal = 1;
398 >               simError();
399 >                
400 >             }  
401 >              
402 >             q.normalize();
403 >             if (needQuaternion_) {            
404 >               integrableObject->setQ(q);
405 >             }              
406 >           }            
407 >           break;
408 >        }  
409 >        case 'j' : {
410 >          Vector3d ji;
411 >          if (integrableObject->isDirectional()) {
412 >             ji[0] = tokenizer.nextTokenAsDouble();
413 >             ji[1] = tokenizer.nextTokenAsDouble();
414 >             ji[2] = tokenizer.nextTokenAsDouble();
415 >             if (needAngMom_) {
416 >               integrableObject->setJ(ji);
417 >             }
418            }
419 +          break;
420 +        }  
421 +        case 'f': {
422 +
423 +          Vector3d force;
424 +          force[0] = tokenizer.nextTokenAsDouble();
425 +          force[1] = tokenizer.nextTokenAsDouble();
426 +          force[2] = tokenizer.nextTokenAsDouble();          
427 +          integrableObject->setFrc(force);
428 +          break;
429          }
430 +        case 't' : {
431 +
432 +           Vector3d torque;
433 +           torque[0] = tokenizer.nextTokenAsDouble();
434 +           torque[1] = tokenizer.nextTokenAsDouble();
435 +           torque[2] = tokenizer.nextTokenAsDouble();          
436 +           integrableObject->setTrq(torque);          
437 +           break;
438 +        }
439 +        default: {
440 +               sprintf(painCave.errMsg,
441 +                       "DumpReader Error: %s is an unrecognized type\n", type.c_str());
442 +               painCave.isFatal = 1;
443 +               simError();
444 +          break;  
445 +        }
446 +
447        }
448 <    } else {
449 <      //actions taken at slave nodes
450 <      MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
451 <      
452 <      /**@todo*/
453 <      parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
448 >    }
449 >    
450 >  }
451 >  
452 >
453 >  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
454 >
455 >    inputStream.getline(buffer, bufferSize);
456 >    std::string line(buffer);
457 >    
458 >    if (line.find("<StuntDoubles>") == std::string::npos) {
459 >      sprintf(painCave.errMsg,
460 >              "DumpReader Error: Missing <StuntDoubles>\n");
461 >      painCave.isFatal = 1;
462 >      simError();
463 >    }
464 >
465 >    while(inputStream.getline(buffer, bufferSize)) {
466 >      line = buffer;
467        
468 <      for(i = 0; i < info_->getNGlobalMolecules(); i++) {
469 <        int which_node = info_->getMolToProc(i);
467 <        
468 <        if (which_node == worldRank) {
469 <          //molecule with global index i belongs to this processor
470 <          
471 <          mol = info_->getMoleculeByGlobalIndex(i);
472 <          if (mol == NULL) {
473 <            sprintf(painCave.errMsg, "DumpReader Error: Molecule not found on node %d!", worldRank);
474 <            painCave.isFatal = 1;
475 <            simError();
476 <          }
477 <          
478 <          nCurObj = mol->getNIntegrableObjects();
479 <          
480 <          MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
481 <                   MPI_COMM_WORLD);
482 <          
483 <          for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
484 <               integrableObject = mol->nextIntegrableObject(ii)){
485 <            
486 <            MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
487 <                     TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
488 <            
489 <            parseDumpLine(read_buffer, integrableObject);
490 <          }
491 <          
492 <        }
493 <        
468 >      if(line.find("</StuntDoubles>") != std::string::npos) {
469 >        break;
470        }
471 <      
471 >
472 >      parseDumpLine(line);
473      }
497 –    
498 – #endif
499 –    
500 –  }
474    
475 <  void DumpReader::parseDumpLine(char *line, StuntDouble *integrableObject) {
476 <    
477 <    Vector3d pos;  // position place holders
478 <    Vector3d vel;  // velocity placeholders
479 <    Quat4d q;    // the quaternions
480 <    Vector3d ji;   // angular velocity placeholders;
481 <    StringTokenizer tokenizer(line);
482 <    int nTokens;
483 <    
484 <    nTokens = tokenizer.countTokens();
485 <    
486 <    if (nTokens < 14) {
487 <      sprintf(painCave.errMsg,
515 <              "DumpReader Error: Not enough Tokens.\n%s\n", line);
516 <      painCave.isFatal = 1;
517 <      simError();
475 >  }
476 >
477 >  void DumpReader::readFrameProperties(std::istream& inputStream) {
478 >
479 >    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
480 >    inputStream.getline(buffer, bufferSize);
481 >    std::string line(buffer);
482 >
483 >    if (line.find("<FrameData>") == std::string::npos) {
484 >      sprintf(painCave.errMsg,
485 >              "DumpReader Error: Missing <FrameData>\n");
486 >      painCave.isFatal = 1;
487 >      simError();
488      }
489 <    
490 <    std::string name = tokenizer.nextToken();
491 <    
522 <    if (name != integrableObject->getType()) {
489 >
490 >    while(inputStream.getline(buffer, bufferSize)) {
491 >      line = buffer;
492        
493 <      sprintf(painCave.errMsg,
494 <              "DumpReader Error: Atom type [%s] in %s does not match Atom Type [%s] in .md file.\n",
526 <              name.c_str(), filename_.c_str(), integrableObject->getType().c_str());
527 <      painCave.isFatal = 1;
528 <      simError();        
529 <    }
530 <    
531 <    pos[0] = tokenizer.nextTokenAsDouble();
532 <    pos[1] = tokenizer.nextTokenAsDouble();
533 <    pos[2] = tokenizer.nextTokenAsDouble();
534 <    if (needPos_) {
535 <      integrableObject->setPos(pos);
536 <    }
537 <    
538 <    vel[0] = tokenizer.nextTokenAsDouble();
539 <    vel[1] = tokenizer.nextTokenAsDouble();
540 <    vel[2] = tokenizer.nextTokenAsDouble();
541 <    if (needVel_) {
542 <      integrableObject->setVel(vel);
543 <    }
544 <    
545 <    if (integrableObject->isDirectional()) {
546 <      
547 <      q[0] = tokenizer.nextTokenAsDouble();
548 <      q[1] = tokenizer.nextTokenAsDouble();
549 <      q[2] = tokenizer.nextTokenAsDouble();
550 <      q[3] = tokenizer.nextTokenAsDouble();
551 <      
552 <      double qlen = q.length();
553 <      if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
554 <        
555 <        sprintf(painCave.errMsg,
556 <                "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
557 <        painCave.isFatal = 1;
558 <        simError();
559 <        
560 <      }
561 <      
562 <      q.normalize();
563 <      if (needQuaternion_) {          
564 <        integrableObject->setQ(q);
493 >      if(line.find("</FrameData>") != std::string::npos) {
494 >        break;
495        }
496        
497 <      ji[0] = tokenizer.nextTokenAsDouble();
498 <      ji[1] = tokenizer.nextTokenAsDouble();
499 <      ji[2] = tokenizer.nextTokenAsDouble();
500 <      if (needAngMom_) {
501 <        integrableObject->setJ(ji);
497 >      StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
498 >      if (!tokenizer.hasMoreTokens()) {
499 >        sprintf(painCave.errMsg,
500 >                "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
501 >        painCave.isFatal = 1;
502 >        simError();      
503        }
504 <    }
505 <    
506 <  }
507 <  
508 <  
509 <  void DumpReader::parseCommentLine(char* line, Snapshot* s) {
510 <    double currTime;
511 <    Mat3x3d hmat;
512 <    double chi;
513 <    double integralOfChiDt;
514 <    Mat3x3d eta;
515 <    
516 <    StringTokenizer tokenizer(line);
517 <    int nTokens;
518 <    
519 <    nTokens = tokenizer.countTokens();
520 <    
521 <    //comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
522 <    if (nTokens < 10) {
523 <      sprintf(painCave.errMsg,
524 <              "DumpReader Error: Not enough tokens in comment line: %s", line);
525 <      painCave.isFatal = 1;
526 <      simError();  
527 <    }
528 <    
529 <    //read current time
530 <    currTime = tokenizer.nextTokenAsDouble();
531 <    s->setTime(currTime);
532 <    
533 <    //read h-matrix
534 <    hmat(0, 0) = tokenizer.nextTokenAsDouble();
535 <    hmat(0, 1) = tokenizer.nextTokenAsDouble();
536 <    hmat(0, 2) = tokenizer.nextTokenAsDouble();
537 <    hmat(1, 0) = tokenizer.nextTokenAsDouble();
538 <    hmat(1, 1) = tokenizer.nextTokenAsDouble();
539 <    hmat(1, 2) = tokenizer.nextTokenAsDouble();
540 <    hmat(2, 0) = tokenizer.nextTokenAsDouble();
541 <    hmat(2, 1) = tokenizer.nextTokenAsDouble();
542 <    hmat(2, 2) = tokenizer.nextTokenAsDouble();
543 <    s->setHmat(hmat);
613 <    
614 <    //read chi and integralOfChidt, they should apprear in pair
615 <    if (tokenizer.countTokens() >= 2) {
616 <      chi = tokenizer.nextTokenAsDouble();
617 <      integralOfChiDt = tokenizer.nextTokenAsDouble();            
504 >
505 >      std::string propertyName = tokenizer.nextToken();
506 >      if (propertyName == "Time") {
507 >        RealType currTime = tokenizer.nextTokenAsDouble();
508 >        s->setTime(currTime);
509 >      } else if (propertyName == "Hmat"){
510 >        Mat3x3d hmat;
511 >        hmat(0, 0) = tokenizer.nextTokenAsDouble();
512 >        hmat(0, 1) = tokenizer.nextTokenAsDouble();
513 >        hmat(0, 2) = tokenizer.nextTokenAsDouble();
514 >        hmat(1, 0) = tokenizer.nextTokenAsDouble();
515 >        hmat(1, 1) = tokenizer.nextTokenAsDouble();
516 >        hmat(1, 2) = tokenizer.nextTokenAsDouble();
517 >        hmat(2, 0) = tokenizer.nextTokenAsDouble();
518 >        hmat(2, 1) = tokenizer.nextTokenAsDouble();
519 >        hmat(2, 2) = tokenizer.nextTokenAsDouble();
520 >        s->setHmat(hmat);      
521 >      } else if (propertyName == "Thermostat") {
522 >        RealType chi = tokenizer.nextTokenAsDouble();
523 >        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
524 >        s->setChi(chi);
525 >        s->setIntegralOfChiDt(integralOfChiDt);        
526 >     } else if (propertyName == "Barostat") {
527 >        Mat3x3d eta;
528 >        eta(0, 0) = tokenizer.nextTokenAsDouble();
529 >        eta(0, 1) = tokenizer.nextTokenAsDouble();
530 >        eta(0, 2) = tokenizer.nextTokenAsDouble();
531 >        eta(1, 0) = tokenizer.nextTokenAsDouble();
532 >        eta(1, 1) = tokenizer.nextTokenAsDouble();
533 >        eta(1, 2) = tokenizer.nextTokenAsDouble();
534 >        eta(2, 0) = tokenizer.nextTokenAsDouble();
535 >        eta(2, 1) = tokenizer.nextTokenAsDouble();
536 >        eta(2, 2) = tokenizer.nextTokenAsDouble();
537 >        s->setEta(eta);
538 >      } else {
539 >        sprintf(painCave.errMsg,
540 >                "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
541 >        painCave.isFatal = 0;
542 >        simError();        
543 >      }
544        
619 –      s->setChi(chi);
620 –      s->setIntegralOfChiDt(integralOfChiDt);
545      }
546 <    
623 <    //read eta (eta is 3x3 matrix)
624 <    if (tokenizer.countTokens() >= 9) {
625 <      eta(0, 0) = tokenizer.nextTokenAsDouble();
626 <      eta(0, 1) = tokenizer.nextTokenAsDouble();
627 <      eta(0, 2) = tokenizer.nextTokenAsDouble();
628 <      eta(1, 0) = tokenizer.nextTokenAsDouble();
629 <      eta(1, 1) = tokenizer.nextTokenAsDouble();
630 <      eta(1, 2) = tokenizer.nextTokenAsDouble();
631 <      eta(2, 0) = tokenizer.nextTokenAsDouble();
632 <      eta(2, 1) = tokenizer.nextTokenAsDouble();
633 <      eta(2, 2) = tokenizer.nextTokenAsDouble();      
634 <      
635 <      s->setEta(eta);
636 <    }
637 <    
638 <    
546 >
547    }
548 <  
549 < }//end namespace oopse
548 >
549 >  
550 > }//end namespace oopse

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