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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */ 
 
#ifdef IS_MPI 
#include <mpi.h> 
#endif
 
#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" 

namespace OpenMD { 

  void RestReader::scanFile(){

    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;
      int lineNo = 0;       
      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();

    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);

    if (sd == NULL) {
      return;
    }
  
    std::string type = tokenizer.nextToken(); 
    int size = type.size();
    
    Vector3d pos;
    Quat4d q;

    for(int i = 0; i < size; ++i) {
      switch(type[i]) {

      case 'p': {
        pos[0] = tokenizer.nextTokenAsDouble(); 
        pos[1] = tokenizer.nextTokenAsDouble(); 
        pos[2] = tokenizer.nextTokenAsDouble(); 
        break;
      }
      case 'v' : {
        Vector3d vel;
        vel[0] = tokenizer.nextTokenAsDouble(); 
        vel[1] = tokenizer.nextTokenAsDouble(); 
        vel[2] = tokenizer.nextTokenAsDouble(); 
        break;
      }

      case 'q' : {
        if (sd->isDirectional()) { 
          
          q[0] = tokenizer.nextTokenAsDouble(); 
          q[1] = tokenizer.nextTokenAsDouble(); 
          q[2] = tokenizer.nextTokenAsDouble(); 
          q[3] = tokenizer.nextTokenAsDouble(); 
          
          RealType qlen = q.length(); 
          if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 
            
            sprintf(painCave.errMsg, 
                    "RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); 
            painCave.isFatal = 1; 
            simError();             
          }  
              
          q.normalize(); 
        }          
        break;
      }  
      case 'j' : {
        Vector3d ji;
        if (sd->isDirectional()) {
          ji[0] = tokenizer.nextTokenAsDouble(); 
          ji[1] = tokenizer.nextTokenAsDouble(); 
          ji[2] = tokenizer.nextTokenAsDouble(); 
        }
        break;
      }  
      case 'f': {        
        Vector3d force;
        force[0] = tokenizer.nextTokenAsDouble(); 
        force[1] = tokenizer.nextTokenAsDouble(); 
        force[2] = tokenizer.nextTokenAsDouble();           
        break;
      }
      case 't' : {        
        Vector3d torque;
        torque[0] = tokenizer.nextTokenAsDouble(); 
        torque[1] = tokenizer.nextTokenAsDouble(); 
        torque[2] = tokenizer.nextTokenAsDouble();           
        break;
      }
      default: {
        sprintf(painCave.errMsg, 
                "RestReader Error: %s is an unrecognized type\n", type.c_str()); 
        painCave.isFatal = 1; 
        simError();     
        break;   
      }
      }
      // keep the position in case we need it for a molecular restraint:

      all_pos_[index] = pos;      
        
      // is this io restrained?
      GenericData* data = sd->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
            // an ObjectRestraint:
          ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
          if (oRest != NULL) {          
            if (sd->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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 2 months ago) by gezelter
File size:	13503 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include <sys/types.h>
48	#include <sys/stat.h>
49
50	#include <math.h>
51	#include <string>
52	#include <sstream>
53	#include <iostream>
54	#include <stdio.h>
55	#include <stdlib.h>
56	#include <string.h>
57
58	#include "io/RestReader.hpp"
59	#include "primitives/Molecule.hpp"
60	#include "utils/simError.h"
61	#include "utils/MemoryUtils.hpp"
62	#include "utils/StringTokenizer.hpp"
63	#include "restraints/ObjectRestraint.hpp"
64	#include "restraints/MolecularRestraint.hpp"
65
66	namespace OpenMD {
67
68	void RestReader::scanFile(){
69
70	std::streampos prevPos;
71	std::streampos currPos;
72
73	#ifdef IS_MPI
74
75	if (worldRank == 0) {
76	#endif // is_mpi
77
78	inFile_->clear();
79	currPos = inFile_->tellg();
80	prevPos = currPos;
81
82	bool foundOpenSnapshotTag = false;
83	int lineNo = 0;
84	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
85	++lineNo;
86
87	std::string line = buffer;
88	currPos = inFile_->tellg();
89	if (line.find("<Snapshot>")!= std::string::npos) {
90	foundOpenSnapshotTag = true;
91	framePos_ = prevPos;
92	}
93	prevPos = currPos;
94	}
95
96	#ifdef IS_MPI
97	}
98	MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD);
99	#endif // is_mpi
100	}
101
102
103	void RestReader::readSet(){
104	std::string line;
105
106	#ifndef IS_MPI
107
108	inFile_->clear();
109	inFile_->seekg(framePos_);
110
111	std::istream& inputStream = *inFile_;
112	#else
113
114	int masterNode = 0;
115	std::stringstream sstream;
116	if (worldRank == masterNode) {
117	std::string sendBuffer;
118
119	inFile_->clear();
120	inFile_->seekg(framePos_);
121
122	while (inFile_->getline(buffer, bufferSize)) {
123
124	line = buffer;
125	sendBuffer += line;
126	sendBuffer += '\n';
127	if (line.find("</Snapshot>") != std::string::npos) {
128	break;
129	}
130	}
131
132	int sendBufferSize = sendBuffer.size();
133	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
134	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize,
135	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,
145	MPI_COMM_WORLD);
146	sstream.str(recvBuffer);
147	delete [] recvBuffer;
148	}
149
150	std::istream& inputStream = sstream;
151	#endif
152
153	inputStream.getline(buffer, bufferSize);
154
155	line = buffer;
156	if (line.find("<Snapshot>") == std::string::npos) {
157	sprintf(painCave.errMsg,
158	"RestReader Error: can not find <Snapshot>\n");
159	painCave.isFatal = 1;
160	simError();
161	}
162
163	//read frameData
164	readFrameProperties(inputStream);
165
166	//read StuntDoubles
167	readStuntDoubles(inputStream);
168
169	inputStream.getline(buffer, bufferSize);
170	line = buffer;
171	if (line.find("</Snapshot>") == std::string::npos) {
172	sprintf(painCave.errMsg,
173	"RestReader Error: can not find </Snapshot>\n");
174	painCave.isFatal = 1;
175	simError();
176	}
177	}
178
179	void RestReader::readReferenceStructure() {
180
181	// We need temporary storage to keep track of all StuntDouble positions
182	// in case some of the restraints are molecular (i.e. if they use
183	// multiple SD positions to determine restrained orientations or positions:
184
185	all_pos_.clear();
186	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
187
188	// Restraint files are just standard dump files, but with the reference
189	// structure stored in the first frame (frame 0).
190	// RestReader overloads readSet and explicitly handles all of the
191	// ObjectRestraints in that method:
192
193	scanFile();
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	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284
285	if (sd == NULL) {
286	return;
287	}
288
289	std::string type = tokenizer.nextToken();
290	int size = type.size();
291
292	Vector3d pos;
293	Quat4d q;
294
295	for(int i = 0; i < size; ++i) {
296	switch(type[i]) {
297
298	case 'p': {
299	pos[0] = tokenizer.nextTokenAsDouble();
300	pos[1] = tokenizer.nextTokenAsDouble();
301	pos[2] = tokenizer.nextTokenAsDouble();
302	break;
303	}
304	case 'v' : {
305	Vector3d vel;
306	vel[0] = tokenizer.nextTokenAsDouble();
307	vel[1] = tokenizer.nextTokenAsDouble();
308	vel[2] = tokenizer.nextTokenAsDouble();
309	break;
310	}
311
312	case 'q' : {
313	if (sd->isDirectional()) {
314
315	q[0] = tokenizer.nextTokenAsDouble();
316	q[1] = tokenizer.nextTokenAsDouble();
317	q[2] = tokenizer.nextTokenAsDouble();
318	q[3] = tokenizer.nextTokenAsDouble();
319
320	RealType qlen = q.length();
321	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
322
323	sprintf(painCave.errMsg,
324	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
325	painCave.isFatal = 1;
326	simError();
327	}
328
329	q.normalize();
330	}
331	break;
332	}
333	case 'j' : {
334	Vector3d ji;
335	if (sd->isDirectional()) {
336	ji[0] = tokenizer.nextTokenAsDouble();
337	ji[1] = tokenizer.nextTokenAsDouble();
338	ji[2] = tokenizer.nextTokenAsDouble();
339	}
340	break;
341	}
342	case 'f': {
343	Vector3d force;
344	force[0] = tokenizer.nextTokenAsDouble();
345	force[1] = tokenizer.nextTokenAsDouble();
346	force[2] = tokenizer.nextTokenAsDouble();
347	break;
348	}
349	case 't' : {
350	Vector3d torque;
351	torque[0] = tokenizer.nextTokenAsDouble();
352	torque[1] = tokenizer.nextTokenAsDouble();
353	torque[2] = tokenizer.nextTokenAsDouble();
354	break;
355	}
356	default: {
357	sprintf(painCave.errMsg,
358	"RestReader Error: %s is an unrecognized type\n", type.c_str());
359	painCave.isFatal = 1;
360	simError();
361	break;
362	}
363	}
364	// keep the position in case we need it for a molecular restraint:
365
366	all_pos_[index] = pos;
367
368	// is this io restrained?
369	GenericData* data = sd->getPropertyByName("Restraint");
370
371	if (data != NULL) {
372	// make sure we can reinterpret the generic data as restraint data:
373	RestraintData* restData= dynamic_cast<RestraintData*>(data);
374	if (restData != NULL) {
375	// make sure we can reinterpet the restraint data as a pointer to
376	// an ObjectRestraint:
377	ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
378	if (oRest != NULL) {
379	if (sd->isDirectional()) {
380	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
381	} else {
382	oRest->setReferenceStructure(pos);
383	}
384	}
385	}
386	}
387	}
388	}
389
390	void RestReader::readStuntDoubles(std::istream& inputStream) {
391
392	inputStream.getline(buffer, bufferSize);
393	std::string line(buffer);
394
395	if (line.find("<StuntDoubles>") == std::string::npos) {
396	sprintf(painCave.errMsg,
397	"RestReader Error: Missing <StuntDoubles>\n");
398	painCave.isFatal = 1;
399	simError();
400	}
401
402	while(inputStream.getline(buffer, bufferSize)) {
403	line = buffer;
404
405	if(line.find("</StuntDoubles>") != std::string::npos) {
406	break;
407	}
408
409	parseDumpLine(line);
410	}
411
412	}
413
414
415	void RestReader::readFrameProperties(std::istream& inputStream) {
416	inputStream.getline(buffer, bufferSize);
417	std::string line(buffer);
418
419	if (line.find("<FrameData>") == std::string::npos) {
420	sprintf(painCave.errMsg,
421	"RestReader Error: Missing <FrameData>\n");
422	painCave.isFatal = 1;
423	simError();
424	}
425
426	// restraints don't care about frame data (unless we need to wrap
427	// coordinates, but we'll worry about that later), so
428	// we'll just scan ahead until the end of the frame data:
429
430	while(inputStream.getline(buffer, bufferSize)) {
431	line = buffer;
432
433	if(line.find("</FrameData>") != std::string::npos) {
434	break;
435	}
436
437	}
438
439	}
440
441
442	}//end namespace OpenMD