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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */ 

 
#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::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
#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::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize, 
                            MPI::CHAR, masterNode);
      
      sstream.str(sendBuffer);
    } else {
      int sendBufferSize;
      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
      char * recvBuffer = new char[sendBufferSize+1];
      assert(recvBuffer);
      recvBuffer[sendBufferSize] = '\0';
      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
      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");
      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 (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:	1796
Committed:	Mon Sep 10 18:38:44 2012 UTC (13 years, 1 month ago) by gezelter
File size:	13497 byte(s)
Log Message:	Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft
#	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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43
44	#include <sys/types.h>
45	#include <sys/stat.h>
46
47	#include <math.h>
48	#include <string>
49	#include <sstream>
50	#include <iostream>
51	#include <stdio.h>
52	#include <stdlib.h>
53	#include <string.h>
54
55	#include "io/RestReader.hpp"
56	#include "primitives/Molecule.hpp"
57	#include "utils/simError.h"
58	#include "utils/MemoryUtils.hpp"
59	#include "utils/StringTokenizer.hpp"
60	#include "restraints/ObjectRestraint.hpp"
61	#include "restraints/MolecularRestraint.hpp"
62
63	#ifdef IS_MPI
64
65	#include <mpi.h>
66	#endif
67
68	namespace OpenMD {
69
70	void RestReader::scanFile(){
71	int lineNo = 0;
72	std::streampos prevPos;
73	std::streampos currPos;
74
75	#ifdef IS_MPI
76
77	if (worldRank == 0) {
78	#endif // is_mpi
79
80	inFile_->clear();
81	currPos = inFile_->tellg();
82	prevPos = currPos;
83
84	bool foundOpenSnapshotTag = false;
85
86	while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
87	++lineNo;
88
89	std::string line = buffer;
90	currPos = inFile_->tellg();
91	if (line.find("<Snapshot>")!= std::string::npos) {
92	foundOpenSnapshotTag = true;
93	framePos_ = prevPos;
94	}
95	prevPos = currPos;
96	}
97
98	#ifdef IS_MPI
99	}
100	MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
101	#endif // is_mpi
102	}
103
104
105	void RestReader::readSet(){
106	std::string line;
107
108	#ifndef IS_MPI
109
110	inFile_->clear();
111	inFile_->seekg(framePos_);
112
113	std::istream& inputStream = *inFile_;
114	#else
115
116	int masterNode = 0;
117	std::stringstream sstream;
118	if (worldRank == masterNode) {
119	std::string sendBuffer;
120
121	inFile_->clear();
122	inFile_->seekg(framePos_);
123
124	while (inFile_->getline(buffer, bufferSize)) {
125
126	line = buffer;
127	sendBuffer += line;
128	sendBuffer += '\n';
129	if (line.find("</Snapshot>") != std::string::npos) {
130	break;
131	}
132	}
133
134	int sendBufferSize = sendBuffer.size();
135	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
136	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
137	MPI::CHAR, masterNode);
138
139	sstream.str(sendBuffer);
140	} else {
141	int sendBufferSize;
142	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
143	char * recvBuffer = new char[sendBufferSize+1];
144	assert(recvBuffer);
145	recvBuffer[sendBufferSize] = '\0';
146	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
147	sstream.str(recvBuffer);
148	delete [] recvBuffer;
149	}
150
151	std::istream& inputStream = sstream;
152	#endif
153
154	inputStream.getline(buffer, bufferSize);
155
156	line = buffer;
157	if (line.find("<Snapshot>") == std::string::npos) {
158	sprintf(painCave.errMsg,
159	"RestReader Error: can not find <Snapshot>\n");
160	painCave.isFatal = 1;
161	simError();
162	}
163
164	//read frameData
165	readFrameProperties(inputStream);
166
167	//read StuntDoubles
168	readStuntDoubles(inputStream);
169
170	inputStream.getline(buffer, bufferSize);
171	line = buffer;
172	if (line.find("</Snapshot>") == std::string::npos) {
173	sprintf(painCave.errMsg,
174	"RestReader Error: can not find </Snapshot>\n");
175	painCave.isFatal = 1;
176	simError();
177	}
178	}
179
180	void RestReader::readReferenceStructure() {
181
182	// We need temporary storage to keep track of all StuntDouble positions
183	// in case some of the restraints are molecular (i.e. if they use
184	// multiple SD positions to determine restrained orientations or positions:
185
186	all_pos_.clear();
187	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
188
189	// Restraint files are just standard dump files, but with the reference
190	// structure stored in the first frame (frame 0).
191	// RestReader overloads readSet and explicitly handles all of the
192	// ObjectRestraints in that method:
193
194	scanFile();
195
196	readSet();
197
198
199	// all ObjectRestraints have been handled, now we have to worry about
200	// molecular restraints:
201
202	SimInfo::MoleculeIterator i;
203	Molecule::IntegrableObjectIterator j;
204	Molecule* mol;
205	StuntDouble* sd;
206
207	// no need to worry about parallel molecules, as molecules are not
208	// split across processor boundaries. Just loop over all molecules
209	// we know about:
210
211	for (mol = info_->beginMolecule(i); mol != NULL;
212	mol = info_->nextMolecule(i)) {
213
214	// is this molecule restrained?
215	GenericData* data = mol->getPropertyByName("Restraint");
216
217	if (data != NULL) {
218
219	// make sure we can reinterpret the generic data as restraint data:
220
221	RestraintData* restData= dynamic_cast<RestraintData*>(data);
222
223	if (restData != NULL) {
224
225	// make sure we can reinterpet the restraint data as a
226	// pointer to a MolecularRestraint:
227
228	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
229
230	if (mRest != NULL) {
231
232	// now we need to pack the stunt doubles for the reference
233	// structure:
234
235	std::vector<Vector3d> ref;
236	int count = 0;
237	RealType mass, mTot;
238	Vector3d COM(0.0);
239
240	mTot = 0.0;
241
242	// loop over the stunt doubles in this molecule in the order we
243	// will be looping them in the restraint code:
244
245	for (sd = mol->beginIntegrableObject(j); sd != NULL;
246	sd = mol->nextIntegrableObject(j)) {
247
248	// push back the reference positions of the stunt
249	// doubles from the globally sorted array of
250	// positions:
251
252	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
253	mass = sd->getMass();
254	COM = COM + mass * ref[count];
255	mTot = mTot + mass;
256	count = count + 1;
257	}
258	COM /= mTot;
259	mRest->setReferenceStructure(ref, COM);
260	}
261	}
262	}
263	}
264	}
265
266
267
268	void RestReader::parseDumpLine(const std::string& line) {
269
270	StringTokenizer tokenizer(line);
271	int nTokens;
272
273	nTokens = tokenizer.countTokens();
274
275	if (nTokens < 2) {
276	sprintf(painCave.errMsg,
277	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
278	painCave.isFatal = 1;
279	simError();
280	}
281
282	int index = tokenizer.nextTokenAsInt();
283
284	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
285
286	if (sd == NULL) {
287	return;
288	}
289
290	std::string type = tokenizer.nextToken();
291	int size = type.size();
292
293	Vector3d pos;
294	Quat4d q;
295
296	for(int i = 0; i < size; ++i) {
297	switch(type[i]) {
298
299	case 'p': {
300	pos[0] = tokenizer.nextTokenAsDouble();
301	pos[1] = tokenizer.nextTokenAsDouble();
302	pos[2] = tokenizer.nextTokenAsDouble();
303	break;
304	}
305	case 'v' : {
306	Vector3d vel;
307	vel[0] = tokenizer.nextTokenAsDouble();
308	vel[1] = tokenizer.nextTokenAsDouble();
309	vel[2] = tokenizer.nextTokenAsDouble();
310	break;
311	}
312
313	case 'q' : {
314	if (sd->isDirectional()) {
315
316	q[0] = tokenizer.nextTokenAsDouble();
317	q[1] = tokenizer.nextTokenAsDouble();
318	q[2] = tokenizer.nextTokenAsDouble();
319	q[3] = tokenizer.nextTokenAsDouble();
320
321	RealType qlen = q.length();
322	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
323
324	sprintf(painCave.errMsg,
325	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
326	painCave.isFatal = 1;
327	simError();
328	}
329
330	q.normalize();
331	}
332	break;
333	}
334	case 'j' : {
335	Vector3d ji;
336	if (sd->isDirectional()) {
337	ji[0] = tokenizer.nextTokenAsDouble();
338	ji[1] = tokenizer.nextTokenAsDouble();
339	ji[2] = tokenizer.nextTokenAsDouble();
340	}
341	break;
342	}
343	case 'f': {
344	Vector3d force;
345	force[0] = tokenizer.nextTokenAsDouble();
346	force[1] = tokenizer.nextTokenAsDouble();
347	force[2] = tokenizer.nextTokenAsDouble();
348	break;
349	}
350	case 't' : {
351	Vector3d torque;
352	torque[0] = tokenizer.nextTokenAsDouble();
353	torque[1] = tokenizer.nextTokenAsDouble();
354	torque[2] = tokenizer.nextTokenAsDouble();
355	break;
356	}
357	default: {
358	sprintf(painCave.errMsg,
359	"RestReader Error: %s is an unrecognized type\n", type.c_str());
360	painCave.isFatal = 1;
361	simError();
362	break;
363	}
364	}
365	// keep the position in case we need it for a molecular restraint:
366
367	all_pos_[index] = pos;
368
369	// is this io restrained?
370	GenericData* data = sd->getPropertyByName("Restraint");
371	ObjectRestraint* oRest;
372
373	if (data != NULL) {
374	// make sure we can reinterpret the generic data as restraint data:
375	RestraintData* restData= dynamic_cast<RestraintData*>(data);
376	if (restData != NULL) {
377	// make sure we can reinterpet the restraint data as a pointer to
378	// an ObjectRestraint:
379	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
380	if (oRest != NULL) {
381	if (sd->isDirectional()) {
382	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
383	} else {
384	oRest->setReferenceStructure(pos);
385	}
386	}
387	}
388	}
389	}
390	}
391
392	void RestReader::readStuntDoubles(std::istream& inputStream) {
393
394	inputStream.getline(buffer, bufferSize);
395	std::string line(buffer);
396
397	if (line.find("<StuntDoubles>") == std::string::npos) {
398	sprintf(painCave.errMsg,
399	"RestReader Error: Missing <StuntDoubles>\n");
400	painCave.isFatal = 1;
401	simError();
402	}
403
404	while(inputStream.getline(buffer, bufferSize)) {
405	line = buffer;
406
407	if(line.find("</StuntDoubles>") != std::string::npos) {
408	break;
409	}
410
411	parseDumpLine(line);
412	}
413
414	}
415
416
417	void RestReader::readFrameProperties(std::istream& inputStream) {
418	inputStream.getline(buffer, bufferSize);
419	std::string line(buffer);
420
421	if (line.find("<FrameData>") == std::string::npos) {
422	sprintf(painCave.errMsg,
423	"RestReader Error: Missing <FrameData>\n");
424	painCave.isFatal = 1;
425	simError();
426	}
427
428	// restraints don't care about frame data (unless we need to wrap
429	// coordinates, but we'll worry about that later), so
430	// we'll just scan ahead until the end of the frame data:
431
432	while(inputStream.getline(buffer, bufferSize)) {
433	line = buffer;
434
435	if(line.find("</FrameData>") != std::string::npos) {
436	break;
437	}
438
439	}
440
441	}
442
443
444	}//end namespace OpenMD