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, 5 months ago) by gezelter
Original Path:	*trunk/src/io/RestReader.cpp*
File size:	10389 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#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
48	namespace OpenMD {
49
50	void RestReader::readReferenceStructure() {
51
52	// some of this comes directly from DumpReader.
53
54	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
73	needAngMom_ = false;
74
75	// 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
79	all_pos_.clear();
80	all_pos_.resize(info_->getNGlobalIntegrableObjects() );
81
82
83	// 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
88	readSet(0);
89
90	// all ObjectRestraints have been handled, now we have to worry about
91	// molecular restraints:
92
93	SimInfo::MoleculeIterator i;
94	Molecule::IntegrableObjectIterator j;
95	Molecule* mol;
96	StuntDouble* sd;
97
98	// 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
102	for (mol = info_->beginMolecule(i); mol != NULL;
103	mol = info_->nextMolecule(i)) {
104
105	// is this molecule restrained?
106	GenericData* data = mol->getPropertyByName("Restraint");
107
108	if (data != NULL) {
109
110	// make sure we can reinterpret the generic data as restraint data:
111
112	RestraintData* restData= dynamic_cast<RestraintData*>(data);
113
114	if (restData != NULL) {
115
116	// make sure we can reinterpet the restraint data as a
117	// pointer to a MolecularRestraint:
118
119	MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
120
121	if (mRest != NULL) {
122
123	// now we need to pack the stunt doubles for the reference
124	// structure:
125
126	std::vector<Vector3d> ref;
127	int count = 0;
128	RealType mass, mTot;
129	Vector3d COM(0.0);
130
131	mTot = 0.0;
132
133	// 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	}
151
152	COM /= mTot;
153
154	mRest->setReferenceStructure(ref, COM);
155
156	}
157	}
158	}
159	}
160	}
161
162
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
177	int index = tokenizer.nextTokenAsInt();
178
179	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
180
181	if (integrableObject == NULL) {
182	return;
183	}
184
185	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
210	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	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
220
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
245	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	}
263	}
264
265	// keep the position in case we need it for a molecular restraint:
266
267	all_pos_[index] = pos;
268
269	// is this io restrained?
270	GenericData* data = integrableObject->getPropertyByName("Restraint");
271	ObjectRestraint* oRest;
272
273	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	}
288	}
289
290	}
291
292
293
294	void RestReader::readFrameProperties(std::istream& inputStream) {
295	inputStream.getline(buffer, bufferSize);
296	std::string line(buffer);
297
298	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
305	// 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
312	if(line.find("</FrameData>") != std::string::npos) {
313	break;
314	}
315
316	}
317
318	}
319
320
321	}//end namespace OpenMD