src/io/RestReader.cpp

/* 
 * Copyright (c) 2005 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 "io/DumpReader.hpp" 
#include "io/RestReader.hpp"
#include "primitives/Molecule.hpp"
#include "restraints/ObjectRestraint.hpp"
#include "restraints/MolecularRestraint.hpp"

namespace OpenMD { 
      
  void RestReader::readReferenceStructure() {

    // some of this comes directly from DumpReader.

    if (!isScanned_) 
      scanFile(); 
         
    int storageLayout = info_->getSnapshotManager()->getStorageLayout(); 
     
    if (storageLayout & DataStorage::dslPosition) { 
      needPos_ = true; 
    } else {
      needPos_ = false; 
    } 
     
    needVel_ = false;
     
    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { 
      needQuaternion_ = true; 
    } else { 
      needQuaternion_ = false; 
    } 

    needAngMom_ = false;

    // 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:

    readSet(0); 
    
    // 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->getGlobalIndex()] );
              
              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, 
              "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); 
      painCave.isFatal = 1; 
      simError(); 
    } 

    int index = tokenizer.nextTokenAsInt();
 
    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);

    if (integrableObject == NULL) {
      return;
    }   

    std::string type = tokenizer.nextToken(); 
    int size = type.size();
    Vector3d pos;
    Vector3d vel;
    Quat4d q;
    Vector3d ji;
    Vector3d force;
    Vector3d torque;
          
    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' : {
            vel[0] = tokenizer.nextTokenAsDouble(); 
            vel[1] = tokenizer.nextTokenAsDouble(); 
            vel[2] = tokenizer.nextTokenAsDouble(); 
            break;
        }

        case 'q' : {
           if (integrableObject->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, 
                       "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); 
               painCave.isFatal = 1; 
               simError(); 
                
             }  
              
             q.normalize(); 
           }            
           break;
        }  
        case 'j' : {
          if (integrableObject->isDirectional()) {
             ji[0] = tokenizer.nextTokenAsDouble(); 
             ji[1] = tokenizer.nextTokenAsDouble(); 
             ji[2] = tokenizer.nextTokenAsDouble(); 
          }
          break;
        }  
        case 'f': {
          force[0] = tokenizer.nextTokenAsDouble(); 
          force[1] = tokenizer.nextTokenAsDouble(); 
          force[2] = tokenizer.nextTokenAsDouble();           

          break;
        }
        case 't' : {
           torque[0] = tokenizer.nextTokenAsDouble(); 
           torque[1] = tokenizer.nextTokenAsDouble(); 
           torque[2] = tokenizer.nextTokenAsDouble();           

           break;
        }
        default: {
               sprintf(painCave.errMsg, 
                       "DumpReader 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 = 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::readFrameProperties(std::istream& inputStream) {
    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);

    if (line.find("<FrameData>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader 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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	10389 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	cli2	1360	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
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			* [4] Vardeman & Gezelter, in progress (2009).
40	cli2	1360	*/
41
42			#include "io/DumpReader.hpp"
43			#include "io/RestReader.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "restraints/ObjectRestraint.hpp"
46			#include "restraints/MolecularRestraint.hpp"
47	chrisfen	417
48	gezelter	1390	namespace OpenMD {
49	cli2	1360
50			void RestReader::readReferenceStructure() {
51	chrisfen	417
52	cli2	1360	// some of this comes directly from DumpReader.
53	chrisfen	417
54	cli2	1360	if (!isScanned_)
55			scanFile();
56
57			int storageLayout = info_->getSnapshotManager()->getStorageLayout();
58
59			if (storageLayout & DataStorage::dslPosition) {
60			needPos_ = true;
61			} else {
62			needPos_ = false;
63			}
64
65			needVel_ = false;
66
67			if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
68			needQuaternion_ = true;
69			} else {
70			needQuaternion_ = false;
71			}
72	chrisfen	417
73	cli2	1360	needAngMom_ = false;
74	chrisfen	417
75	cli2	1360	// We need temporary storage to keep track of all StuntDouble positions
76			// in case some of the restraints are molecular (i.e. if they use
77			// multiple SD positions to determine restrained orientations or positions:
78	chrisfen	417
79	cli2	1360	all_pos_.clear();
80			all_pos_.resize(info_->getNGlobalIntegrableObjects() );
81	chrisfen	417
82	chrisfen	996
83	cli2	1360	// Restraint files are just standard dump files, but with the reference
84			// structure stored in the first frame (frame 0).
85			// RestReader overloads readSet and explicitly handles all of the
86			// ObjectRestraints in that method:
87	chrisfen	996
88	cli2	1360	readSet(0);
89
90			// all ObjectRestraints have been handled, now we have to worry about
91			// molecular restraints:
92	chrisfen	431
93	cli2	1360	SimInfo::MoleculeIterator i;
94			Molecule::IntegrableObjectIterator j;
95			Molecule* mol;
96			StuntDouble* sd;
97	chrisfen	996
98	cli2	1360	// no need to worry about parallel molecules, as molecules are not
99			// split across processor boundaries. Just loop over all molecules
100			// we know about:
101	chrisfen	996
102	cli2	1360	for (mol = info_->beginMolecule(i); mol != NULL;
103			mol = info_->nextMolecule(i)) {
104	chrisfen	996
105	cli2	1360	// is this molecule restrained?
106			GenericData* data = mol->getPropertyByName("Restraint");
107	chrisfen	417
108	cli2	1360	if (data != NULL) {
109	chrisfen	996
110	cli2	1360	// make sure we can reinterpret the generic data as restraint data:
111	chrisfen	996
112	cli2	1360	RestraintData* restData= dynamic_cast<RestraintData*>(data);
113	chrisfen	423
114	cli2	1360	if (restData != NULL) {
115	chrisfen	431
116	cli2	1360	// make sure we can reinterpet the restraint data as a
117			// pointer to a MolecularRestraint:
118	chrisfen	996
119	cli2	1360	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
120	chrisfen	996
121	cli2	1360	if (mRest != NULL) {
122	chrisfen	431
123	cli2	1360	// now we need to pack the stunt doubles for the reference
124			// structure:
125	chrisfen	990
126	cli2	1360	std::vector<Vector3d> ref;
127			int count = 0;
128			RealType mass, mTot;
129			Vector3d COM(0.0);
130	chrisfen	417
131	cli2	1360	mTot = 0.0;
132	chrisfen	417
133	cli2	1360	// loop over the stunt doubles in this molecule in the order we
134			// will be looping them in the restraint code:
135
136			for (sd = mol->beginIntegrableObject(j); sd != NULL;
137			sd = mol->nextIntegrableObject(j)) {
138
139			// push back the reference positions of the stunt
140			// doubles from the globally sorted array of
141			// positions:
142
143			ref.push_back( all_pos_[sd->getGlobalIndex()] );
144
145			mass = sd->getMass();
146
147			COM = COM + mass * ref[count];
148			mTot = mTot + mass;
149			count = count + 1;
150	chrisfen	417	}
151
152	cli2	1360	COM /= mTot;
153	chrisfen	990
154	cli2	1360	mRest->setReferenceStructure(ref, COM);
155	chrisfen	990
156	chrisfen	417	}
157			}
158			}
159			}
160			}
161	chrisfen	431
162	cli2	1360
163
164			void RestReader::parseDumpLine(const std::string& line) {
165			StringTokenizer tokenizer(line);
166			int nTokens;
167
168			nTokens = tokenizer.countTokens();
169
170			if (nTokens < 2) {
171			sprintf(painCave.errMsg,
172			"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
173			painCave.isFatal = 1;
174			simError();
175			}
176	chrisfen	431
177	cli2	1360	int index = tokenizer.nextTokenAsInt();
178
179			StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
180	chrisfen	431
181	cli2	1360	if (integrableObject == NULL) {
182			return;
183			}
184	chrisfen	431
185	cli2	1360	std::string type = tokenizer.nextToken();
186			int size = type.size();
187			Vector3d pos;
188			Vector3d vel;
189			Quat4d q;
190			Vector3d ji;
191			Vector3d force;
192			Vector3d torque;
193
194			for(int i = 0; i < size; ++i) {
195			switch(type[i]) {
196
197			case 'p': {
198			pos[0] = tokenizer.nextTokenAsDouble();
199			pos[1] = tokenizer.nextTokenAsDouble();
200			pos[2] = tokenizer.nextTokenAsDouble();
201			break;
202			}
203			case 'v' : {
204			vel[0] = tokenizer.nextTokenAsDouble();
205			vel[1] = tokenizer.nextTokenAsDouble();
206			vel[2] = tokenizer.nextTokenAsDouble();
207			break;
208			}
209	chrisfen	431
210	cli2	1360	case 'q' : {
211			if (integrableObject->isDirectional()) {
212
213			q[0] = tokenizer.nextTokenAsDouble();
214			q[1] = tokenizer.nextTokenAsDouble();
215			q[2] = tokenizer.nextTokenAsDouble();
216			q[3] = tokenizer.nextTokenAsDouble();
217
218			RealType qlen = q.length();
219	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
220	cli2	1360
221			sprintf(painCave.errMsg,
222			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
223			painCave.isFatal = 1;
224			simError();
225
226			}
227
228			q.normalize();
229			}
230			break;
231			}
232			case 'j' : {
233			if (integrableObject->isDirectional()) {
234			ji[0] = tokenizer.nextTokenAsDouble();
235			ji[1] = tokenizer.nextTokenAsDouble();
236			ji[2] = tokenizer.nextTokenAsDouble();
237			}
238			break;
239			}
240			case 'f': {
241			force[0] = tokenizer.nextTokenAsDouble();
242			force[1] = tokenizer.nextTokenAsDouble();
243			force[2] = tokenizer.nextTokenAsDouble();
244	chrisfen	996
245	cli2	1360	break;
246			}
247			case 't' : {
248			torque[0] = tokenizer.nextTokenAsDouble();
249			torque[1] = tokenizer.nextTokenAsDouble();
250			torque[2] = tokenizer.nextTokenAsDouble();
251
252			break;
253			}
254			default: {
255			sprintf(painCave.errMsg,
256			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
257			painCave.isFatal = 1;
258			simError();
259			break;
260			}
261
262	chrisfen	417	}
263			}
264	cli2	1360
265			// keep the position in case we need it for a molecular restraint:
266	chrisfen	417
267	cli2	1360	all_pos_[index] = pos;
268	chrisfen	996
269	cli2	1360	// is this io restrained?
270			GenericData* data = integrableObject->getPropertyByName("Restraint");
271			ObjectRestraint* oRest;
272	chrisfen	996
273	cli2	1360	if (data != NULL) {
274			// make sure we can reinterpret the generic data as restraint data:
275			RestraintData* restData= dynamic_cast<RestraintData*>(data);
276			if (restData != NULL) {
277			// make sure we can reinterpet the restraint data as a pointer to
278			// an ObjectRestraint:
279			oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
280			if (oRest != NULL) {
281			if (integrableObject->isDirectional()) {
282			oRest->setReferenceStructure(pos, q.toRotationMatrix3());
283			} else {
284			oRest->setReferenceStructure(pos);
285			}
286			}
287	chrisfen	417	}
288			}
289	chrisfen	423
290	cli2	1360	}
291
292	chrisfen	996
293	chrisfen	423
294	cli2	1360	void RestReader::readFrameProperties(std::istream& inputStream) {
295			inputStream.getline(buffer, bufferSize);
296			std::string line(buffer);
297	chrisfen	423
298	cli2	1360	if (line.find("<FrameData>") == std::string::npos) {
299			sprintf(painCave.errMsg,
300			"DumpReader Error: Missing <FrameData>\n");
301			painCave.isFatal = 1;
302			simError();
303			}
304	chrisfen	996
305	cli2	1360	// restraints don't care about frame data (unless we need to wrap
306			// coordinates, but we'll worry about that later), so
307			// we'll just scan ahead until the end of the frame data:
308
309			while(inputStream.getline(buffer, bufferSize)) {
310			line = buffer;
311	chrisfen	417
312	cli2	1360	if(line.find("</FrameData>") != std::string::npos) {
313			break;
314	chrisfen	417	}
315
316	cli2	1360	}
317	chrisfen	985
318	chrisfen	417	}
319	chrisfen	1030
320	cli2	1360
321	gezelter	1390	}//end namespace OpenMD