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root/OpenMD/trunk/src/io/DumpReader.cpp
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Comparing trunk/src/io/DumpReader.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1112 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 < */
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 < #define _LARGEFILE_SOURCE64
46 < #define _FILE_OFFSET_BITS 64
47 <
48 < #include <sys/types.h>
49 < #include <sys/stat.h>
50 <
51 < #include <iostream>
52 < #include <math.h>
53 <
54 < #include <stdio.h>
55 < #include <stdlib.h>
56 < #include <string.h>
57 <
58 < #include "io/DumpReader.hpp"
59 < #include "primitives/Molecule.hpp"
60 < #include "utils/simError.h"
61 < #include "utils/MemoryUtils.hpp"
62 < #include "utils/StringTokenizer.hpp"
63 <
64 < #ifdef IS_MPI
65 <
66 < #include <mpi.h>
67 < #define TAKE_THIS_TAG_CHAR 0
68 < #define TAKE_THIS_TAG_INT 1
69 <
70 < #endif // is_mpi
71 <
72 <
73 < namespace oopse {
74 <
75 < DumpReader::DumpReader(SimInfo* info, const std::string& filename)
76 <                     : info_(info), filename_(filename), isScanned_(false), nframes_(0) {
77 <
78 < #ifdef IS_MPI
79 <
80 <    if (worldRank == 0) {
81 < #endif
82 <
83 <        inFile_ = fopen(filename_.c_str(), "r");
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
76 >    
77 >    if (worldRank == 0) {
78 > #endif
79 >      
80 >      inFile_ = new std::ifstream(filename_.c_str());
81 >      
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
91 >      
92 >    }
93 >    
94 >    strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95 >    MPIcheckPoint();
96 >    
97 > #endif
98 >    
99 >    return;
100 >  }
101 >  
102 >  DumpReader::~DumpReader() {
103 >    
104 > #ifdef IS_MPI
105 >    
106 >    if (worldRank == 0) {
107 > #endif
108 >      
109 >      delete inFile_;
110 >      
111 > #ifdef IS_MPI
112 >      
113 >    }
114 >    
115 >    strcpy(checkPointMsg, "Dump file closed successfully.");
116 >    MPIcheckPoint();
117 >    
118 > #endif
119 >    
120 >    return;
121 >  }
122 >  
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 > #ifdef IS_MPI
137 >    
138 >    if (worldRank == 0) {
139 > #endif // is_mpi
140 >      
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 >            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 >        } 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 >        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 >      nframes_ = framePos_.size();
195 >      
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 > #endif // is_mpi
208 >    
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 (inFile_ == NULL) {
245 <            sprintf(painCave.errMsg, "DumpReader: Cannot open file: %s\n", filename_.c_str());
246 <            painCave.isFatal = 1;
247 <            simError();
248 <        }
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 < #ifdef IS_MPI
260 >  }
261 >  
262 >  void DumpReader::readSet(int whichFrame) {    
263 >    std::string line;
264  
265 <    }
265 > #ifndef IS_MPI
266  
267 <    strcpy(checkPointMsg, "Dump file opened for reading successfully.");
268 <    MPIcheckPoint();
267 >    inFile_->clear();  
268 >    inFile_->seekg(framePos_[whichFrame]);
269  
270 < #endif
270 >    std::istream& inputStream = *inFile_;    
271  
272 <    return;
273 < }
272 > #else
273 >    int masterNode = 0;
274 >    std::stringstream sstream;
275 >    if (worldRank == masterNode) {
276 >      std::string sendBuffer;
277  
278 < DumpReader::~DumpReader() {
278 >      inFile_->clear();  
279 >      inFile_->seekg(framePos_[whichFrame]);
280 >      
281 >      while (inFile_->getline(buffer, bufferSize)) {
282  
283 < #ifdef IS_MPI
283 >        line = buffer;
284 >        sendBuffer += line;
285 >        sendBuffer += '\n';
286 >        if (line.find("</Snapshot>") != std::string::npos) {
287 >          break;
288 >        }        
289 >      }
290  
291 <    if (worldRank == 0) {
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 >      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 <        int error;
108 <        error = fclose(inFile_);
307 >    inputStream.getline(buffer, bufferSize);
308  
309 <        if (error) {
310 <            sprintf(painCave.errMsg, "Error closing %s\n", filename_.c_str());
311 <            painCave.isFatal = 1;            
312 <            simError();
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 >        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 <        MemoryUtils::deleteVectorOfPointer(framePos_);
383 >        case 'q' : {
384 >           Quat4d q;
385 >           if (integrableObject->isDirectional()) {
386 >              
387 >             q[0] = tokenizer.nextTokenAsDouble();
388 >             q[1] = tokenizer.nextTokenAsDouble();
389 >             q[2] = tokenizer.nextTokenAsDouble();
390 >             q[3] = tokenizer.nextTokenAsDouble();
391 >              
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 < #ifdef IS_MPI
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      }
449 +    
450 +  }
451 +  
452  
453 <    strcpy(checkPointMsg, "Dump file closed successfully.");
123 <    MPIcheckPoint();
453 >  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
454  
455 < #endif
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 <    return;
466 < }
465 >    while(inputStream.getline(buffer, bufferSize)) {
466 >      line = buffer;
467 >      
468 >      if(line.find("</StuntDoubles>") != std::string::npos) {
469 >        break;
470 >      }
471  
472 < int DumpReader::getNFrames(void) {
472 >      parseDumpLine(line);
473 >    }
474 >  
475 >  }
476 >
477 >  void DumpReader::readFrameProperties(std::istream& inputStream) {
478  
479 <    if (!isScanned_)
480 <        scanFile();
479 >    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
480 >    inputStream.getline(buffer, bufferSize);
481 >    std::string line(buffer);
482  
483 <    return nframes_;
484 < }
485 <
486 < void DumpReader::scanFile(void) {
487 <  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
148 <
149 <        rewind(inFile_);
150 <
151 <        currPos = new fpos_t;
152 <        fgetpos(inFile_, currPos);
153 <        fgets(readBuffer, sizeof(readBuffer), inFile_);
154 <        lineNum++;
155 <
156 <        if (feof(inFile_)) {
157 <            sprintf(painCave.errMsg,
158 <                    "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);
167 <
168 <            i = atoi(readBuffer);
169 <
170 <            fgets(readBuffer, sizeof(readBuffer), inFile_);
171 <            lineNum++;
172 <
173 <            if (feof(inFile_)) {
174 <                sprintf(painCave.errMsg,
175 <                        "File \"%s\" ended unexpectedly at line %d\n",
176 <                        filename_.c_str(),
177 <                        lineNum);
178 <                painCave.isFatal = 1;
179 <                simError();
180 <            }
181 <
182 <            for(j = 0; j < i; j++) {
183 <                fgets(readBuffer, sizeof(readBuffer), inFile_);
184 <                lineNum++;
185 <
186 <                if (feof(inFile_)) {
187 <                    sprintf(painCave.errMsg,
188 <                            "File \"%s\" ended unexpectedly at line %d,"
189 <                                " with atom %d\n", filename_.c_str(),
190 <                            lineNum,
191 <                            j);
192 <
193 <                    painCave.isFatal = 1;
194 <                    simError();
195 <                }
196 <            }
197 <
198 <            currPos = new fpos_t;
199 <            fgetpos(inFile_, currPos);
200 <            fgets(readBuffer, sizeof(readBuffer), inFile_);
201 <            lineNum++;
202 <        }
203 <
204 <        delete currPos;
205 <        rewind(inFile_);
206 <        
207 <        nframes_ = framePos_.size();
208 < #ifdef IS_MPI
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 <    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
490 >    while(inputStream.getline(buffer, bufferSize)) {
491 >      line = buffer;
492 >      
493 >      if(line.find("</FrameData>") != std::string::npos) {
494 >        break;
495 >      }
496 >      
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 <    strcpy(checkPointMsg, "Successfully scanned DumpFile\n");
506 <    MPIcheckPoint();
507 <
508 < #endif // is_mpi
509 <
510 <    isScanned_ = true;
511 < }
512 <
513 < void DumpReader::readFrame(int whichFrame) {
514 <    readSet(whichFrame);
515 < }
516 <
517 < void DumpReader::readSet(int whichFrame) {
518 <  int i;
519 <  int nTotObjs;                  // the number of atoms
520 <  char read_buffer[maxBufferSize];  //the line buffer for reading
521 <  char * eof_test;               // ptr to see when we reach the end of the file
522 <
523 <  Molecule* mol;
524 <  StuntDouble* integrableObject;
525 <  SimInfo::MoleculeIterator mi;
526 <  Molecule::IntegrableObjectIterator ii;
527 <
528 < #ifndef IS_MPI
529 <
530 <    fsetpos(inFile_, framePos_[whichFrame]);
531 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
532 <
533 <    if (eof_test == NULL) {
534 <        sprintf(painCave.errMsg,
535 <                "DumpReader error: error reading 1st line of \"%s\"\n",
536 <                filename_.c_str());
537 <        painCave.isFatal = 1;
538 <        simError();
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 >      
545      }
546  
547 <    nTotObjs = atoi(read_buffer);
547 >  }
548  
549 <    if (nTotObjs != info_->getNGlobalIntegrableObjects()) {
550 <        sprintf(painCave.errMsg,
253 <                "DumpReader error. %s nIntegrable, %d, "
254 <                    "does not match the meta-data file's nIntegrable, %d.\n",
255 <                filename_.c_str(),
256 <                nTotObjs,
257 <                info_->getNGlobalIntegrableObjects());
258 <
259 <        painCave.isFatal = 1;
260 <        simError();
261 <    }
262 <
263 <    //read the box mat from the comment line
264 <
265 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
266 <
267 <    if (eof_test == NULL) {
268 <        sprintf(painCave.errMsg, "error in reading commment in %s\n",
269 <                filename_.c_str());
270 <        painCave.isFatal = 1;
271 <        simError();
272 <    }
273 <
274 <    parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
275 <
276 <    //parse dump lines
277 <
278 <    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
279 <
280 <        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
281 <            integrableObject = mol->nextIntegrableObject(ii)) {          
282 <
283 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
284 <
285 <            if (eof_test == NULL) {
286 <                sprintf(painCave.errMsg,
287 <                        "error in reading file %s\n"
288 <                            "natoms  = %d; index = %d\n"
289 <                            "error reading the line from the file.\n",
290 <                        filename_.c_str(),
291 <                        nTotObjs,
292 <                        i);
293 <
294 <                painCave.isFatal = 1;
295 <                simError();
296 <            }
297 <
298 <            parseDumpLine(read_buffer, integrableObject);
299 <            
300 <            }
301 <    }
302 <
303 <    // MPI Section of code..........
304 <
305 < #else //IS_MPI
306 <
307 <    // first thing first, suspend fatalities.
308 <    int masterNode = 0;
309 <    int nCurObj;
310 <    painCave.isEventLoop = 1;
311 <
312 <    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
313 <    int haveError;
314 <
315 <    MPI_Status istatus;
316 <    int nitems;
317 <
318 <    nTotObjs = info_->getNGlobalIntegrableObjects();
319 <    haveError = 0;
320 <
321 <    if (worldRank == masterNode) {
322 <        fsetpos(inFile_, framePos_[whichFrame]);
323 <
324 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
325 <
326 <        if (eof_test == NULL) {
327 <            sprintf(painCave.errMsg, "Error reading 1st line of %s \n ",
328 <                    filename_.c_str());
329 <            painCave.isFatal = 1;
330 <            simError();
331 <        }
332 <
333 <        nitems = atoi(read_buffer);
334 <
335 <        // Check to see that the number of integrable objects in the
336 <        // intial configuration file is the same as derived from the
337 <        // meta-data file.
338 <
339 <        if (nTotObjs != nitems) {
340 <            sprintf(painCave.errMsg,
341 <                    "DumpReader Error. %s nIntegrable, %d, "
342 <                        "does not match the meta-data file's nIntegrable, %d.\n",
343 <                    filename_.c_str(),
344 <                    nTotObjs,
345 <                    info_->getNGlobalIntegrableObjects());
346 <
347 <            painCave.isFatal = 1;
348 <            simError();
349 <        }
350 <
351 <        //read the boxMat from the comment line
352 <
353 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
354 <
355 <        if (eof_test == NULL) {
356 <            sprintf(painCave.errMsg, "error in reading commment in %s\n",
357 <                    filename_.c_str());
358 <            painCave.isFatal = 1;
359 <            simError();
360 <        }
361 <
362 <        //Every single processor will parse the comment line by itself
363 <        //By using this way, we might lose some efficiency, but if we want to add
364 <        //more parameters into comment line, we only need to modify function
365 <        //parseCommentLine
366 <
367 <        MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
368 <        parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
369 <
370 <        for(i = 0; i < info_->getNGlobalMolecules(); i++) {
371 <            int which_node = info_->getMolToProc(i);
372 <
373 <            if (which_node == masterNode) {
374 <                //molecules belong to master node
375 <
376 <                mol = info_->getMoleculeByGlobalIndex(i);
377 <
378 <                if (mol == NULL) {
379 <                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
380 <                        painCave.isFatal = 1;
381 <                    simError();
382 <                }
383 <
384 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
385 <                       integrableObject = mol->nextIntegrableObject(ii)){
386 <                        
387 <                    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
388 <
389 <                    if (eof_test == NULL) {
390 <                        sprintf(painCave.errMsg,
391 <                                "error in reading file %s\n"
392 <                                    "natoms  = %d; index = %d\n"
393 <                                    "error reading the line from the file.\n",
394 <                                filename_.c_str(),
395 <                                nTotObjs,
396 <                                i);
397 <
398 <                        painCave.isFatal = 1;
399 <                        simError();
400 <                    }
401 <
402 <                    parseDumpLine(read_buffer, integrableObject);
403 <                }
404 <            } else {
405 <                //molecule belongs to slave nodes
406 <
407 <                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
408 <                         MPI_COMM_WORLD, &istatus);
409 <
410 <                for(int j = 0; j < nCurObj; j++) {
411 <                    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile_);
412 <
413 <                    if (eof_test == NULL) {
414 <                        sprintf(painCave.errMsg,
415 <                                "error in reading file %s\n"
416 <                                    "natoms  = %d; index = %d\n"
417 <                                    "error reading the line from the file.\n",
418 <                                filename_.c_str(),
419 <                                nTotObjs,
420 <                                i);
421 <
422 <                        painCave.isFatal = 1;
423 <                        simError();
424 <                    }
425 <                    
426 <                    MPI_Send(read_buffer, maxBufferSize, MPI_CHAR, which_node,
427 <                             TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
428 <                }
429 <            }
430 <        }
431 <    } else {
432 <        //actions taken at slave nodes
433 <        MPI_Bcast(read_buffer, maxBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
434 <
435 <        /**@todo*/
436 <        parseCommentLine(read_buffer, info_->getSnapshotManager()->getCurrentSnapshot());
437 <
438 <        for(i = 0; i < info_->getNGlobalMolecules(); i++) {
439 <            int which_node = info_->getMolToProc(i);
440 <
441 <            if (which_node == worldRank) {
442 <                //molecule with global index i belongs to this processor
443 <                
444 <                mol = info_->getMoleculeByGlobalIndex(i);
445 <                if (mol == NULL) {
446 <                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
447 <                    painCave.isFatal = 1;
448 <                    simError();
449 <                }
450 <                
451 <                nCurObj = mol->getNIntegrableObjects();
452 <
453 <                MPI_Send(&nCurObj, 1, MPI_INT, masterNode, TAKE_THIS_TAG_INT,
454 <                         MPI_COMM_WORLD);
455 <
456 <                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
457 <                       integrableObject = mol->nextIntegrableObject(ii)){
458 <                        
459 <                    MPI_Recv(read_buffer, maxBufferSize, MPI_CHAR, masterNode,
460 <                             TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
461 <
462 <                    parseDumpLine(read_buffer, integrableObject);
463 <                }
464 <                      
465 <            }
466 <            
467 <        }
468 <        
469 <    }
470 <
471 < #endif
472 <
473 < }
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,
488 <                    "Not enough Tokens.\n");
489 <            painCave.isFatal = 1;
490 <            simError();
491 <    }
492 <
493 <    std::string name = tokenizer.nextToken();
494 <
495 <    if (name != integrableObject->getType()) {
496 <        
497 <    }
498 <
499 <    pos[0] = tokenizer.nextTokenAsDouble();
500 <    pos[1] = tokenizer.nextTokenAsDouble();
501 <    pos[2] = tokenizer.nextTokenAsDouble();
502 <    integrableObject->setPos(pos);
503 <    
504 <    vel[0] = tokenizer.nextTokenAsDouble();
505 <    vel[1] = tokenizer.nextTokenAsDouble();
506 <    vel[2] = tokenizer.nextTokenAsDouble();
507 <    integrableObject->setVel(vel);
508 <
509 <    if (integrableObject->isDirectional()) {
510 <        
511 <        q[0] = tokenizer.nextTokenAsDouble();
512 <        q[1] = tokenizer.nextTokenAsDouble();
513 <        q[2] = tokenizer.nextTokenAsDouble();
514 <        q[3] = tokenizer.nextTokenAsDouble();
515 <
516 <        double qlen = q.length();
517 <        if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
518 <            
519 <            sprintf(painCave.errMsg,
520 <                    "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
521 <            painCave.isFatal = 1;
522 <            simError();
523 <            
524 <        }
525 <
526 <        q.normalize();
527 <              
528 <        integrableObject->setQ(q);
529 <        
530 <        ji[0] = tokenizer.nextTokenAsDouble();
531 <        ji[1] = tokenizer.nextTokenAsDouble();
532 <        ji[2] = tokenizer.nextTokenAsDouble();
533 <        integrableObject->setJ(ji);
534 <    }
535 <
536 < }
537 <
538 <
539 < void DumpReader::parseCommentLine(char* line, Snapshot* s) {
540 <    double currTime;
541 <    Mat3x3d hmat;
542 <    double chi;
543 <    double integralOfChiDt;
544 <    Mat3x3d eta;
545 <
546 <    StringTokenizer tokenizer(line);
547 <    int nTokens;
548 <
549 <    nTokens = tokenizer.countTokens();
550 <
551 <    //comment line should at least contain 10 tokens: current time(1 token) and  h-matrix(9 tokens)
552 <    if (nTokens < 10) {
553 <            sprintf(painCave.errMsg,
554 <                    "Not enough tokens in comment line: %s", line);
555 <            painCave.isFatal = 1;
556 <            simError();  
557 <    }
558 <
559 <    //read current time
560 <    currTime = tokenizer.nextTokenAsDouble();
561 <    s->setTime(currTime);
562 <    
563 <    //read h-matrix
564 <    hmat(0, 0) = tokenizer.nextTokenAsDouble();
565 <    hmat(0, 1) = tokenizer.nextTokenAsDouble();
566 <    hmat(0, 2) = tokenizer.nextTokenAsDouble();
567 <    hmat(1, 0) = tokenizer.nextTokenAsDouble();
568 <    hmat(1, 1) = tokenizer.nextTokenAsDouble();
569 <    hmat(1, 2) = tokenizer.nextTokenAsDouble();
570 <    hmat(2, 0) = tokenizer.nextTokenAsDouble();
571 <    hmat(2, 1) = tokenizer.nextTokenAsDouble();
572 <    hmat(2, 2) = tokenizer.nextTokenAsDouble();
573 <    s->setHmat(hmat);
574 <    
575 <    //read chi and integrablOfChidt, they should apprear in pair
576 <    if (tokenizer.countTokens() >= 2) {
577 <        chi = tokenizer.nextTokenAsDouble();
578 <        integralOfChiDt = tokenizer.nextTokenAsDouble();            
579 <
580 <        s->setChi(chi);
581 <        s->setIntegralOfChiDt(integralOfChiDt);
582 <    }
583 <    
584 <    //read eta (eta is 3x3 matrix)
585 <    if (tokenizer.countTokens() >= 9) {
586 <        eta(0, 0) = tokenizer.nextTokenAsDouble();
587 <        eta(0, 1) = tokenizer.nextTokenAsDouble();
588 <        eta(0, 2) = tokenizer.nextTokenAsDouble();
589 <        eta(1, 0) = tokenizer.nextTokenAsDouble();
590 <        eta(1, 1) = tokenizer.nextTokenAsDouble();
591 <        eta(1, 2) = tokenizer.nextTokenAsDouble();
592 <        eta(2, 0) = tokenizer.nextTokenAsDouble();
593 <        eta(2, 1) = tokenizer.nextTokenAsDouble();
594 <        eta(2, 2) = tokenizer.nextTokenAsDouble();      
595 <
596 <        s->setEta(eta);
597 <    }
598 <
599 <    
600 < }
601 <
602 < }//end namespace oopse
549 >  
550 > }//end namespace oopse

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