src/io/RestReader.cpp

/* 
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. 
 * 
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */ 

 
#include <sys/types.h> 
#include <sys/stat.h> 
 
#include <math.h> 
#include <string>
#include <sstream>
#include <iostream> 
#include <stdio.h> 
#include <stdlib.h> 
#include <string.h> 
 
#include "io/RestReader.hpp" 
#include "primitives/Molecule.hpp" 
#include "utils/simError.h" 
#include "utils/MemoryUtils.hpp" 
#include "utils/StringTokenizer.hpp"
#include "restraints/ObjectRestraint.hpp"
#include "restraints/MolecularRestraint.hpp" 
 
#ifdef IS_MPI 
 
#include <mpi.h> 
#endif

namespace OpenMD { 

  void RestReader::scanFile(){
    int lineNo = 0; 
    std::streampos prevPos;
    std::streampos  currPos;
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif // is_mpi 

      inFile_->clear();
      currPos = inFile_->tellg();
      prevPos = currPos;
      
      bool foundOpenSnapshotTag = false;
      
      while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
        ++lineNo;
        
        std::string line = buffer;
        currPos = inFile_->tellg(); 
        if (line.find("<Snapshot>")!= std::string::npos) {
          foundOpenSnapshotTag = true;
          framePos_ = prevPos;
        }
        prevPos = currPos;
      }
      
#ifdef IS_MPI 
    }
    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD); 
#endif // is_mpi 
  } 


  void RestReader::readSet(){
    std::string line;
    
#ifndef IS_MPI
    
    inFile_->clear();
    inFile_->seekg(framePos_);
    
    std::istream& inputStream = *inFile_;
#else
    
    int masterNode = 0;
    std::stringstream sstream;
    if (worldRank == masterNode) {
      std::string sendBuffer;
      
      inFile_->clear();  
      inFile_->seekg(framePos_); 
      
      while (inFile_->getline(buffer, bufferSize)) {
        
        line = buffer;
        sendBuffer += line;
        sendBuffer += '\n';
        if (line.find("</Snapshot>") != std::string::npos) {
          break;
        }        
      }
      
      int sendBufferSize = sendBuffer.size();
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      
      sstream.str(sendBuffer);
    } else {
      int sendBufferSize;
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      char * recvBuffer = new char[sendBufferSize+1];
      assert(recvBuffer);
      recvBuffer[sendBufferSize] = '\0';
      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      sstream.str(recvBuffer);
      delete [] recvBuffer;
    }      
    
    std::istream& inputStream = sstream;  
#endif
    
    inputStream.getline(buffer, bufferSize);

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

    // We need temporary storage to keep track of all StuntDouble positions
    // in case some of the restraints are molecular (i.e. if they use
    // multiple SD positions to determine restrained orientations or positions:

    all_pos_.clear();
    all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
    
    // Restraint files are just standard dump files, but with the reference
    // structure stored in the first frame (frame 0).
    // RestReader overloads readSet and explicitly handles all of the
    // ObjectRestraints in that method:

    scanFile();


    readSet();


    // all ObjectRestraints have been handled, now we have to worry about
    // molecular restraints:

    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule* mol;
    StuntDouble* sd;
    
    // no need to worry about parallel molecules, as molecules are not
    // split across processor boundaries.  Just loop over all molecules
    // we know about:
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {          
      
      // is this molecule restrained?    
      GenericData* data = mol->getPropertyByName("Restraint");
      
      if (data != NULL) {
        
        // make sure we can reinterpret the generic data as restraint data:
        
        RestraintData* restData= dynamic_cast<RestraintData*>(data);        
        
        if (restData != NULL) {
          
          // make sure we can reinterpet the restraint data as a
          // pointer to a MolecularRestraint:
          
          MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
          
          if (mRest != NULL) {          
            
            // now we need to pack the stunt doubles for the reference
            // structure:
            
            std::vector<Vector3d> ref;
            int count = 0;
            RealType mass, mTot;
            Vector3d COM(0.0);
            
            mTot = 0.0;
            
            // loop over the stunt doubles in this molecule in the order we
            // will be looping them in the restraint code:
            
            for (sd = mol->beginIntegrableObject(j); sd != NULL; 
                 sd = mol->nextIntegrableObject(j)) {
              
              // push back the reference positions of the stunt
              // doubles from the *globally* sorted array of
              // positions:
              
              ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
              mass = sd->getMass();              
              COM = COM + mass * ref[count];
              mTot = mTot + mass;
              count = count + 1;
            }
            COM /= mTot;
            mRest->setReferenceStructure(ref, COM);         
          }
        }
      }
    }
  }

   
  void RestReader::parseDumpLine(const std::string& line) {        

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

    int index = tokenizer.nextTokenAsInt();

  
    if (index < 1116){
      std::string type = tokenizer.nextToken(); 
      
      Vector3d pos;
      
      pos[0] = tokenizer.nextTokenAsDouble(); 
      pos[1] = tokenizer.nextTokenAsDouble(); 
      pos[2] = tokenizer.nextTokenAsDouble();
      
      all_pos_[index] = pos;
    }else{
      
      bool exist = false;
      int indexCount = 0;
      
      while ( (!exist) && (indexCount < stuntDoubleIndex_.size())){
        if (index == stuntDoubleIndex_[indexCount])
          exist = true;
        indexCount++;
      }
      
      StuntDouble* integrableObject;
      
      if (exist){
        
        integrableObject = info_->getIOIndexToIntegrableObject(index);
        
        int compareindex = integrableObject->getGlobalIntegrableObjectIndex();
        
        if (integrableObject == NULL) {
          return;
        }   
        
        std::string type = tokenizer.nextToken(); 
        
        Vector3d pos;
        
        pos[0] = tokenizer.nextTokenAsDouble(); 
        pos[1] = tokenizer.nextTokenAsDouble(); 
        pos[2] = tokenizer.nextTokenAsDouble(); 
        
        Vector3d vel;
        vel[0] = tokenizer.nextTokenAsDouble(); 
        vel[1] = tokenizer.nextTokenAsDouble(); 
        vel[2] = tokenizer.nextTokenAsDouble(); 
        
        
        Quat4d q;
        if (integrableObject->isDirectional()) { 
          
          q[0] = tokenizer.nextTokenAsDouble(); 
          q[1] = tokenizer.nextTokenAsDouble(); 
          q[2] = tokenizer.nextTokenAsDouble(); 
          q[3] = tokenizer.nextTokenAsDouble(); 
        }  
        // keep the position in case we need it for a molecular restraint:
        
        all_pos_[index] = pos;
        
        // is this io restrained?
        GenericData* data = integrableObject->getPropertyByName("Restraint");
        ObjectRestraint* oRest;
        
        if (data != NULL) {
          // make sure we can reinterpret the generic data as restraint data:
          RestraintData* restData= dynamic_cast<RestraintData*>(data);        
          if (restData != NULL) {
            // make sure we can reinterpet the restraint data as a pointer to
            // an ObjectRestraint:
            oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
            if (oRest != NULL) {          
              if (integrableObject->isDirectional()) {
                oRest->setReferenceStructure(pos, q.toRotationMatrix3());
              } else {                           
                oRest->setReferenceStructure(pos);
              }
            }
          }
        }
      }
    }
  }
  
  void  RestReader::readStuntDoubles(std::istream& inputStream) {
    
    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);
    
    if (line.find("<StuntDoubles>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "RestReader 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 RestReader::readFrameProperties(std::istream& inputStream) {
    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);

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

    // restraints don't care about frame data (unless we need to wrap
    // coordinates, but we'll worry about that later), so 
    // we'll just scan ahead until the end of the frame data:

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

   
}//end namespace OpenMD 
Revision:	1407
Committed:	Wed Jan 20 16:04:40 2010 UTC (15 years, 3 months ago) by cli2
File size:	12741 byte(s)
Log Message:	Fixed bugs in Restraint, refactored RestReader and RestWriter
#	Content
1	/*
2	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42
43	#include <sys/types.h>
44	#include <sys/stat.h>
45
46	#include <math.h>
47	#include <string>
48	#include <sstream>
49	#include <iostream>
50	#include <stdio.h>
51	#include <stdlib.h>
52	#include <string.h>
53
54	#include "io/RestReader.hpp"
55	#include "primitives/Molecule.hpp"
56	#include "utils/simError.h"
57	#include "utils/MemoryUtils.hpp"
58	#include "utils/StringTokenizer.hpp"
59	#include "restraints/ObjectRestraint.hpp"
60	#include "restraints/MolecularRestraint.hpp"
61
62	#ifdef IS_MPI
63
64	#include <mpi.h>
65	#endif
66
67	namespace OpenMD {
68
69	void RestReader::scanFile(){
70	int lineNo = 0;
71	std::streampos prevPos;
72	std::streampos currPos;
73
74	#ifdef IS_MPI
75
76	if (worldRank == 0) {
77	#endif // is_mpi
78
79	inFile_->clear();
80	currPos = inFile_->tellg();
81	prevPos = currPos;
82
83	bool foundOpenSnapshotTag = false;
84
85	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
86	++lineNo;
87
88	std::string line = buffer;
89	currPos = inFile_->tellg();
90	if (line.find("<Snapshot>")!= std::string::npos) {
91	foundOpenSnapshotTag = true;
92	framePos_ = prevPos;
93	}
94	prevPos = currPos;
95	}
96
97	#ifdef IS_MPI
98	}
99	MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
100	#endif // is_mpi
101	}
102
103
104	void RestReader::readSet(){
105	std::string line;
106
107	#ifndef IS_MPI
108
109	inFile_->clear();
110	inFile_->seekg(framePos_);
111
112	std::istream& inputStream = *inFile_;
113	#else
114
115	int masterNode = 0;
116	std::stringstream sstream;
117	if (worldRank == masterNode) {
118	std::string sendBuffer;
119
120	inFile_->clear();
121	inFile_->seekg(framePos_);
122
123	while (inFile_->getline(buffer, bufferSize)) {
124
125	line = buffer;
126	sendBuffer += line;
127	sendBuffer += '\n';
128	if (line.find("</Snapshot>") != std::string::npos) {
129	break;
130	}
131	}
132
133	int sendBufferSize = sendBuffer.size();
134	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
135	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
136
137	sstream.str(sendBuffer);
138	} else {
139	int sendBufferSize;
140	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
141	char * recvBuffer = new char[sendBufferSize+1];
142	assert(recvBuffer);
143	recvBuffer[sendBufferSize] = '\0';
144	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
145	sstream.str(recvBuffer);
146	delete [] recvBuffer;
147	}
148
149	std::istream& inputStream = sstream;
150	#endif
151
152	inputStream.getline(buffer, bufferSize);
153
154	line = buffer;
155	if (line.find("<Snapshot>") == std::string::npos) {
156	sprintf(painCave.errMsg,
157	"RestReader Error: can not find <Snapshot>\n");
158	painCave.isFatal = 1;
159	simError();
160	}
161
162	//read frameData
163	readFrameProperties(inputStream);
164
165	//read StuntDoubles
166	readStuntDoubles(inputStream);
167
168	inputStream.getline(buffer, bufferSize);
169	line = buffer;
170	if (line.find("</Snapshot>") == std::string::npos) {
171	sprintf(painCave.errMsg,
172	"RestReader Error: can not find </Snapshot>\n");
173	painCave.isFatal = 1;
174	simError();
175	}
176	}
177
178	void RestReader::readReferenceStructure() {
179
180	// We need temporary storage to keep track of all StuntDouble positions
181	// in case some of the restraints are molecular (i.e. if they use
182	// multiple SD positions to determine restrained orientations or positions:
183
184	all_pos_.clear();
185	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
186
187	// Restraint files are just standard dump files, but with the reference
188	// structure stored in the first frame (frame 0).
189	// RestReader overloads readSet and explicitly handles all of the
190	// ObjectRestraints in that method:
191
192	scanFile();
193
194
195	readSet();
196
197
198	// all ObjectRestraints have been handled, now we have to worry about
199	// molecular restraints:
200
201	SimInfo::MoleculeIterator i;
202	Molecule::IntegrableObjectIterator j;
203	Molecule* mol;
204	StuntDouble* sd;
205
206	// no need to worry about parallel molecules, as molecules are not
207	// split across processor boundaries. Just loop over all molecules
208	// we know about:
209
210	for (mol = info_->beginMolecule(i); mol != NULL;
211	mol = info_->nextMolecule(i)) {
212
213	// is this molecule restrained?
214	GenericData* data = mol->getPropertyByName("Restraint");
215
216	if (data != NULL) {
217
218	// make sure we can reinterpret the generic data as restraint data:
219
220	RestraintData* restData= dynamic_cast<RestraintData*>(data);
221
222	if (restData != NULL) {
223
224	// make sure we can reinterpet the restraint data as a
225	// pointer to a MolecularRestraint:
226
227	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
228
229	if (mRest != NULL) {
230
231	// now we need to pack the stunt doubles for the reference
232	// structure:
233
234	std::vector<Vector3d> ref;
235	int count = 0;
236	RealType mass, mTot;
237	Vector3d COM(0.0);
238
239	mTot = 0.0;
240
241	// loop over the stunt doubles in this molecule in the order we
242	// will be looping them in the restraint code:
243
244	for (sd = mol->beginIntegrableObject(j); sd != NULL;
245	sd = mol->nextIntegrableObject(j)) {
246
247	// push back the reference positions of the stunt
248	// doubles from the globally sorted array of
249	// positions:
250
251	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
252	mass = sd->getMass();
253	COM = COM + mass * ref[count];
254	mTot = mTot + mass;
255	count = count + 1;
256	}
257	COM /= mTot;
258	mRest->setReferenceStructure(ref, COM);
259	}
260	}
261	}
262	}
263	}
264
265
266
267	void RestReader::parseDumpLine(const std::string& line) {
268
269	StringTokenizer tokenizer(line);
270	int nTokens;
271
272	nTokens = tokenizer.countTokens();
273
274	if (nTokens < 2) {
275	sprintf(painCave.errMsg,
276	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
277	painCave.isFatal = 1;
278	simError();
279	}
280
281	int index = tokenizer.nextTokenAsInt();
282
283
284	if (index < 1116){
285	std::string type = tokenizer.nextToken();
286
287	Vector3d pos;
288
289	pos[0] = tokenizer.nextTokenAsDouble();
290	pos[1] = tokenizer.nextTokenAsDouble();
291	pos[2] = tokenizer.nextTokenAsDouble();
292
293	all_pos_[index] = pos;
294	}else{
295
296	bool exist = false;
297	int indexCount = 0;
298
299	while ( (!exist) && (indexCount < stuntDoubleIndex_.size())){
300	if (index == stuntDoubleIndex_[indexCount])
301	exist = true;
302	indexCount++;
303	}
304
305	StuntDouble* integrableObject;
306
307	if (exist){
308
309	integrableObject = info_->getIOIndexToIntegrableObject(index);
310
311	int compareindex = integrableObject->getGlobalIntegrableObjectIndex();
312
313	if (integrableObject == NULL) {
314	return;
315	}
316
317	std::string type = tokenizer.nextToken();
318
319	Vector3d pos;
320
321	pos[0] = tokenizer.nextTokenAsDouble();
322	pos[1] = tokenizer.nextTokenAsDouble();
323	pos[2] = tokenizer.nextTokenAsDouble();
324
325	Vector3d vel;
326	vel[0] = tokenizer.nextTokenAsDouble();
327	vel[1] = tokenizer.nextTokenAsDouble();
328	vel[2] = tokenizer.nextTokenAsDouble();
329
330
331	Quat4d q;
332	if (integrableObject->isDirectional()) {
333
334	q[0] = tokenizer.nextTokenAsDouble();
335	q[1] = tokenizer.nextTokenAsDouble();
336	q[2] = tokenizer.nextTokenAsDouble();
337	q[3] = tokenizer.nextTokenAsDouble();
338	}
339	// keep the position in case we need it for a molecular restraint:
340
341	all_pos_[index] = pos;
342
343	// is this io restrained?
344	GenericData* data = integrableObject->getPropertyByName("Restraint");
345	ObjectRestraint* oRest;
346
347	if (data != NULL) {
348	// make sure we can reinterpret the generic data as restraint data:
349	RestraintData* restData= dynamic_cast<RestraintData*>(data);
350	if (restData != NULL) {
351	// make sure we can reinterpet the restraint data as a pointer to
352	// an ObjectRestraint:
353	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
354	if (oRest != NULL) {
355	if (integrableObject->isDirectional()) {
356	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
357	} else {
358	oRest->setReferenceStructure(pos);
359	}
360	}
361	}
362	}
363	}
364	}
365	}
366
367	void RestReader::readStuntDoubles(std::istream& inputStream) {
368
369	inputStream.getline(buffer, bufferSize);
370	std::string line(buffer);
371
372	if (line.find("<StuntDoubles>") == std::string::npos) {
373	sprintf(painCave.errMsg,
374	"RestReader Error: Missing <StuntDoubles>\n");
375	painCave.isFatal = 1;
376	simError();
377	}
378
379	while(inputStream.getline(buffer, bufferSize)) {
380	line = buffer;
381
382	if(line.find("</StuntDoubles>") != std::string::npos) {
383	break;
384	}
385
386	parseDumpLine(line);
387	}
388
389	}
390
391
392	void RestReader::readFrameProperties(std::istream& inputStream) {
393	inputStream.getline(buffer, bufferSize);
394	std::string line(buffer);
395
396	if (line.find("<FrameData>") == std::string::npos) {
397	sprintf(painCave.errMsg,
398	"RestReader Error: Missing <FrameData>\n");
399	painCave.isFatal = 1;
400	simError();
401	}
402
403	// restraints don't care about frame data (unless we need to wrap
404	// coordinates, but we'll worry about that later), so
405	// we'll just scan ahead until the end of the frame data:
406
407	while(inputStream.getline(buffer, bufferSize)) {
408	line = buffer;
409
410	if(line.find("</FrameData>") != std::string::npos) {
411	break;
412	}
413
414	}
415
416	}
417
418
419	}//end namespace OpenMD