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:	1798
Committed:	Thu Sep 13 14:10:11 2012 UTC (12 years, 7 months ago) by gezelter
File size:	13497 byte(s)
Log Message:	Merged trunk changes into the development branch
#	User	Rev	Content
1	cli2	1360	/*
2	cli2	1407	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	cli2	1360	*
4	gezelter	1390	* 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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	cli2	1360	*/
42	cli2	1407
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	gezelter	1409	#include "utils/StringTokenizer.hpp"
60	cli2	1360	#include "restraints/ObjectRestraint.hpp"
61	cli2	1407	#include "restraints/MolecularRestraint.hpp"
62
63			#ifdef IS_MPI
64
65			#include <mpi.h>
66			#endif
67	chrisfen	417
68	gezelter	1390	namespace OpenMD {
69	cli2	1407
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	cli2	1360
84	cli2	1407	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	gezelter	1798	MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
101	cli2	1407	#endif // is_mpi
102			}
103	chrisfen	417
104
105	cli2	1407	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	gezelter	1798	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
136			MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
137			MPI::CHAR, masterNode);
138	cli2	1407
139			sstream.str(sendBuffer);
140	cli2	1360	} else {
141	cli2	1407	int sendBufferSize;
142	gezelter	1798	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
143	cli2	1407	char * recvBuffer = new char[sendBufferSize+1];
144			assert(recvBuffer);
145			recvBuffer[sendBufferSize] = '\0';
146	gezelter	1798	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
147	cli2	1407	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	cli2	1360	}
163	cli2	1407
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	chrisfen	417
182	cli2	1360	// 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	chrisfen	417
186	cli2	1360	all_pos_.clear();
187	cli2	1407	all_pos_.resize(info_->getNGlobalIntegrableObjects()) ;
188
189	cli2	1360	// 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	chrisfen	996
194	cli2	1407	scanFile();
195
196			readSet();
197
198
199	cli2	1360	// all ObjectRestraints have been handled, now we have to worry about
200			// molecular restraints:
201	chrisfen	431
202	cli2	1360	SimInfo::MoleculeIterator i;
203			Molecule::IntegrableObjectIterator j;
204			Molecule* mol;
205			StuntDouble* sd;
206	cli2	1407
207	cli2	1360	// 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	cli2	1407
211	cli2	1360	for (mol = info_->beginMolecule(i); mol != NULL;
212			mol = info_->nextMolecule(i)) {
213	cli2	1407
214	cli2	1360	// is this molecule restrained?
215			GenericData* data = mol->getPropertyByName("Restraint");
216	chrisfen	417
217	cli2	1360	if (data != NULL) {
218	cli2	1407
219	cli2	1360	// make sure we can reinterpret the generic data as restraint data:
220	cli2	1407
221	cli2	1360	RestraintData* restData= dynamic_cast<RestraintData*>(data);
222	cli2	1407
223	cli2	1360	if (restData != NULL) {
224	cli2	1407
225	cli2	1360	// make sure we can reinterpet the restraint data as a
226			// pointer to a MolecularRestraint:
227	cli2	1407
228	cli2	1360	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
229	cli2	1407
230	cli2	1360	if (mRest != NULL) {
231	cli2	1407
232	cli2	1360	// now we need to pack the stunt doubles for the reference
233			// structure:
234	cli2	1407
235	cli2	1360	std::vector<Vector3d> ref;
236			int count = 0;
237			RealType mass, mTot;
238			Vector3d COM(0.0);
239	chrisfen	417
240	cli2	1360	mTot = 0.0;
241	chrisfen	417
242	cli2	1360	// 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	cli2	1407	ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] );
253			mass = sd->getMass();
254	cli2	1360	COM = COM + mass * ref[count];
255			mTot = mTot + mass;
256			count = count + 1;
257	chrisfen	417	}
258	cli2	1360	COM /= mTot;
259			mRest->setReferenceStructure(ref, COM);
260	chrisfen	417	}
261			}
262			}
263			}
264			}
265	chrisfen	431
266	cli2	1360
267
268			void RestReader::parseDumpLine(const std::string& line) {
269	cli2	1407
270	cli2	1360	StringTokenizer tokenizer(line);
271			int nTokens;
272
273			nTokens = tokenizer.countTokens();
274
275			if (nTokens < 2) {
276			sprintf(painCave.errMsg,
277	cli2	1407	"RestReader Error: Not enough Tokens.\n%s\n", line.c_str());
278	cli2	1360	painCave.isFatal = 1;
279			simError();
280			}
281	chrisfen	431
282	cli2	1360	int index = tokenizer.nextTokenAsInt();
283	chrisfen	431
284	gezelter	1769	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
285	gezelter	1408
286	gezelter	1769	if (sd == NULL) {
287	gezelter	1408	return;
288			}
289	cli2	1407
290	gezelter	1408	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	cli2	1407	pos[0] = tokenizer.nextTokenAsDouble();
301			pos[1] = tokenizer.nextTokenAsDouble();
302			pos[2] = tokenizer.nextTokenAsDouble();
303	gezelter	1408	break;
304			}
305			case 'v' : {
306	cli2	1407	Vector3d vel;
307			vel[0] = tokenizer.nextTokenAsDouble();
308			vel[1] = tokenizer.nextTokenAsDouble();
309			vel[2] = tokenizer.nextTokenAsDouble();
310	gezelter	1408	break;
311			}
312
313			case 'q' : {
314	gezelter	1769	if (sd->isDirectional()) {
315	cli2	1360
316	cli2	1407	q[0] = tokenizer.nextTokenAsDouble();
317			q[1] = tokenizer.nextTokenAsDouble();
318			q[2] = tokenizer.nextTokenAsDouble();
319			q[3] = tokenizer.nextTokenAsDouble();
320	gezelter	1408
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	gezelter	1769	if (sd->isDirectional()) {
337	gezelter	1408	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	cli2	1360
369	gezelter	1408	// is this io restrained?
370	gezelter	1769	GenericData* data = sd->getPropertyByName("Restraint");
371	gezelter	1408	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	cli2	1407	// an ObjectRestraint:
379	gezelter	1408	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
380			if (oRest != NULL) {
381	gezelter	1769	if (sd->isDirectional()) {
382	gezelter	1408	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
383			} else {
384			oRest->setReferenceStructure(pos);
385	cli2	1407	}
386	cli2	1360	}
387			}
388	chrisfen	417	}
389			}
390	cli2	1407	}
391
392			void RestReader::readStuntDoubles(std::istream& inputStream) {
393	chrisfen	417
394	cli2	1407	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	chrisfen	417	}
410	cli2	1407
411			parseDumpLine(line);
412	chrisfen	417	}
413	cli2	1407
414	cli2	1360	}
415	chrisfen	996
416	cli2	1407
417	cli2	1360	void RestReader::readFrameProperties(std::istream& inputStream) {
418			inputStream.getline(buffer, bufferSize);
419			std::string line(buffer);
420	chrisfen	423
421	cli2	1360	if (line.find("<FrameData>") == std::string::npos) {
422			sprintf(painCave.errMsg,
423	cli2	1407	"RestReader Error: Missing <FrameData>\n");
424	cli2	1360	painCave.isFatal = 1;
425			simError();
426			}
427	chrisfen	996
428	cli2	1360	// 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	chrisfen	417
435	cli2	1360	if(line.find("</FrameData>") != std::string::npos) {
436			break;
437	chrisfen	417	}
438
439	cli2	1360	}
440	cli2	1407
441	chrisfen	417	}
442	chrisfen	1030
443	cli2	1360
444	gezelter	1390	}//end namespace OpenMD