src/io/DumpReader.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]  Vardeman & Gezelter, in progress (2009).                        
 */
  
#define _LARGEFILE_SOURCE64 
#define _FILE_OFFSET_BITS 64 
 
#include <sys/types.h> 
#include <sys/stat.h> 
 
#include <iostream> 
#include <math.h> 
 
#include <stdio.h> 
#include <stdlib.h> 
#include <string.h> 
 
#include "io/DumpReader.hpp" 
#include "primitives/Molecule.hpp" 
#include "utils/simError.h" 
#include "utils/MemoryUtils.hpp" 
#include "utils/StringTokenizer.hpp" 
 
#ifdef IS_MPI 
 
#include <mpi.h> 
#define TAKE_THIS_TAG_CHAR 0 
#define TAKE_THIS_TAG_INT 1 
 
#endif // is_mpi 
 
 
namespace OpenMD { 
   
  DumpReader::DumpReader(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) { 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif 
      
      inFile_ = new std::ifstream(filename_.c_str()); 
      
      if (inFile_->fail()) { 
        sprintf(painCave.errMsg, 
                "DumpReader: Cannot open file: %s\n", 
                filename_.c_str()); 
        painCave.isFatal = 1; 
        simError(); 
      } 
      
#ifdef IS_MPI 
      
    } 
    
    strcpy(checkPointMsg, "Dump file opened for reading successfully."); 
    errorCheckPoint(); 
    
#endif 
    
    return; 
  } 
  
  DumpReader::~DumpReader() { 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif 
      
      delete inFile_; 
      
#ifdef IS_MPI 
      
    } 
    
    strcpy(checkPointMsg, "Dump file closed successfully."); 
    errorCheckPoint(); 
    
#endif 
    
    return; 
  } 
  
  int DumpReader::getNFrames(void) { 
     
    if (!isScanned_) 
      scanFile(); 
     
    return nframes_; 
  } 
   
  void DumpReader::scanFile(void) { 
    int lineNo = 0; 
    std::streampos prevPos;
    std::streampos  currPos; 
    
#ifdef IS_MPI 
    
    if (worldRank == 0) { 
#endif // is_mpi 
      
      currPos = inFile_->tellg();
      prevPos = currPos;
      bool foundOpenSnapshotTag = false;
      bool foundClosedSnapshotTag = false;
      while(inFile_->getline(buffer, bufferSize)) {
        ++lineNo;
        
        std::string line = buffer;
        currPos = inFile_->tellg(); 
        if (line.find("<Snapshot>")!= std::string::npos) {
          if (foundOpenSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError();           
          }
          foundOpenSnapshotTag = true;
          foundClosedSnapshotTag = false;
          framePos_.push_back(prevPos);
          
        } else if (line.find("</Snapshot>") != std::string::npos){
          if (!foundOpenSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError(); 
          }
          
          if (foundClosedSnapshotTag) {
            sprintf(painCave.errMsg, 
                    "DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo, 
                    filename_.c_str()); 
            painCave.isFatal = 1; 
            simError(); 
          }
          foundClosedSnapshotTag = true;
          foundOpenSnapshotTag = false;
        }
        prevPos = currPos;
      }
      
      // only found <Snapshot> for the last frame means the file is corrupted, we should discard
      // it and give a warning message
      if (foundOpenSnapshotTag) {
        sprintf(painCave.errMsg, 
                "DumpReader: last frame in %s is invalid\n", filename_.c_str()); 
        painCave.isFatal = 0; 
        simError();       
        framePos_.pop_back();
      }
      
      nframes_ = framePos_.size(); 
      
      if (nframes_ == 0) {
        sprintf(painCave.errMsg, 
                "DumpReader: %s does not contain a valid frame\n", filename_.c_str()); 
        painCave.isFatal = 1; 
        simError();      
      }
#ifdef IS_MPI 
    } 
     
    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); 
    
#endif // is_mpi 
    
    isScanned_ = true; 
  } 
   
  void DumpReader::readFrame(int whichFrame) { 
    if (!isScanned_) 
      scanFile(); 
         
    int storageLayout = info_->getSnapshotManager()->getStorageLayout(); 
     
    if (storageLayout & DataStorage::dslPosition) { 
      needPos_ = true; 
    } else { 
      needPos_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslVelocity) { 
      needVel_ = true; 
    } else { 
      needVel_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { 
      needQuaternion_ = true; 
    } else { 
      needQuaternion_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslAngularMomentum) { 
      needAngMom_ = true; 
    } else { 
      needAngMom_ = false;     
    } 
     
    readSet(whichFrame); 

    if (needCOMprops_) {
      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
      Vector3d com;
      Vector3d comvel;
      Vector3d comw;
      if (needPos_ && needVel_){
        info_->getComAll(com, comvel);
        comw = info_->getAngularMomentum();
      }else{
        com = info_->getCom();
        comvel = 0.0;
        comw   = 0.0;
      }
      s->setCOMprops(com, comvel, comw);      
    }

  } 
   
  void DumpReader::readSet(int whichFrame) {     
    std::string line;

#ifndef IS_MPI 
    inFile_->clear();  
    inFile_->seekg(framePos_[whichFrame]); 

    std::istream& inputStream = *inFile_;     

#else 
    int masterNode = 0;
    std::stringstream sstream;
    if (worldRank == masterNode) {
      std::string sendBuffer;

      inFile_->clear();  
      inFile_->seekg(framePos_[whichFrame]); 
      
      while (inFile_->getline(buffer, bufferSize)) {

        line = buffer;
        sendBuffer += line;
        sendBuffer += '\n';
        if (line.find("</Snapshot>") != std::string::npos) {
          break;
        }        
      }

      int sendBufferSize = sendBuffer.size();
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      
      sstream.str(sendBuffer);
    } else {
      int sendBufferSize;
      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
      char * recvBuffer = new char[sendBufferSize+1];
      assert(recvBuffer);
      recvBuffer[sendBufferSize] = '\0';
      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
      sstream.str(recvBuffer);
      delete [] recvBuffer;
    }      

    std::istream& inputStream = sstream;  
#endif

    inputStream.getline(buffer, bufferSize);

    line = buffer;
    if (line.find("<Snapshot>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader 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, 
              "DumpReader Error: can not find </Snapshot>\n"); 
      painCave.isFatal = 1; 
      simError(); 
    }        
   
  } 
   
  void DumpReader::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();

    size_t found;
    
    if (needPos_) {
      found = type.find("p");      
      if (found == std::string::npos) {
        sprintf(painCave.errMsg, 
                "DumpReader Error: StuntDouble %d has no Position\n"
                "\tField (\"p\") specified.\n%s\n", index, 
                line.c_str());  
        painCave.isFatal = 1; 
        simError(); 
      }
    }
    
    if (integrableObject->isDirectional()) {
      if (needQuaternion_) {
        found = type.find("q");      
        if (found == std::string::npos) {
          sprintf(painCave.errMsg, 
                  "DumpReader Error: Directional StuntDouble %d has no\n"
                  "\tQuaternion Field (\"q\") specified.\n%s\n", index, 
                  line.c_str());  
          painCave.isFatal = 1; 
          simError(); 
        }
      }      
    }

    for(int i = 0; i < size; ++i) {
      switch(type[i]) {
        
        case 'p': {
            Vector3d pos;
            pos[0] = tokenizer.nextTokenAsDouble(); 
            pos[1] = tokenizer.nextTokenAsDouble(); 
            pos[2] = tokenizer.nextTokenAsDouble(); 
            if (needPos_) { 
              integrableObject->setPos(pos); 
            }             
            break;
        }
        case 'v' : {
            Vector3d vel;
            vel[0] = tokenizer.nextTokenAsDouble(); 
            vel[1] = tokenizer.nextTokenAsDouble(); 
            vel[2] = tokenizer.nextTokenAsDouble(); 
            if (needVel_) { 
              integrableObject->setVel(vel); 
            } 
            break;
        }

        case 'q' : {
           Quat4d 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(); 
             if (needQuaternion_) {            
               integrableObject->setQ(q); 
             }               
           }            
           break;
        }  
        case 'j' : {
          Vector3d ji;
          if (integrableObject->isDirectional()) {
             ji[0] = tokenizer.nextTokenAsDouble(); 
             ji[1] = tokenizer.nextTokenAsDouble(); 
             ji[2] = tokenizer.nextTokenAsDouble(); 
             if (needAngMom_) { 
               integrableObject->setJ(ji); 
             } 
          }
          break;
        }  
        case 'f': {

          Vector3d force;
          force[0] = tokenizer.nextTokenAsDouble(); 
          force[1] = tokenizer.nextTokenAsDouble(); 
          force[2] = tokenizer.nextTokenAsDouble();           
          integrableObject->setFrc(force); 
          break;
        }
        case 't' : {

           Vector3d torque;
           torque[0] = tokenizer.nextTokenAsDouble(); 
           torque[1] = tokenizer.nextTokenAsDouble(); 
           torque[2] = tokenizer.nextTokenAsDouble();           
           integrableObject->setTrq(torque);          
           break;
        }
        default: {
               sprintf(painCave.errMsg, 
                       "DumpReader Error: %s is an unrecognized type\n", type.c_str()); 
               painCave.isFatal = 1; 
               simError(); 
          break;   
        }

      }
    }
     
  } 
   

  void  DumpReader::readStuntDoubles(std::istream& inputStream) {

    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);
    
    if (line.find("<StuntDoubles>") == std::string::npos) {
      sprintf(painCave.errMsg, 
              "DumpReader 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 DumpReader::readFrameProperties(std::istream& inputStream) {

    Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
    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(); 
    }

    while(inputStream.getline(buffer, bufferSize)) {
      line = buffer;
      
      if(line.find("</FrameData>") != std::string::npos) {
        break;
      }
      
      StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
      if (!tokenizer.hasMoreTokens()) {
        sprintf(painCave.errMsg, 
                "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); 
        painCave.isFatal = 1; 
        simError();      
      }

      std::string propertyName = tokenizer.nextToken();
      if (propertyName == "Time") {
        RealType currTime = tokenizer.nextTokenAsDouble(); 
        s->setTime(currTime); 
      } else if (propertyName == "Hmat"){
        Mat3x3d hmat;
        hmat(0, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(0, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(0, 2) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(1, 2) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 0) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 1) = tokenizer.nextTokenAsDouble(); 
        hmat(2, 2) = tokenizer.nextTokenAsDouble(); 
        s->setHmat(hmat);      
      } else if (propertyName == "Thermostat") {
        RealType chi = tokenizer.nextTokenAsDouble();
        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
        s->setChi(chi); 
        s->setIntegralOfChiDt(integralOfChiDt);        
     } else if (propertyName == "Barostat") {
        Mat3x3d eta;
        eta(0, 0) = tokenizer.nextTokenAsDouble(); 
        eta(0, 1) = tokenizer.nextTokenAsDouble(); 
        eta(0, 2) = tokenizer.nextTokenAsDouble(); 
        eta(1, 0) = tokenizer.nextTokenAsDouble(); 
        eta(1, 1) = tokenizer.nextTokenAsDouble(); 
        eta(1, 2) = tokenizer.nextTokenAsDouble(); 
        eta(2, 0) = tokenizer.nextTokenAsDouble(); 
        eta(2, 1) = tokenizer.nextTokenAsDouble(); 
        eta(2, 2) = tokenizer.nextTokenAsDouble(); 
        s->setEta(eta); 
      } else {
        sprintf(painCave.errMsg, 
                "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); 
        painCave.isFatal = 0; 
        simError();         
      }
      
    }

  }

   
}//end namespace OpenMD 
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	17167 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#define _LARGEFILE_SOURCE64
43	#define _FILE_OFFSET_BITS 64
44
45	#include <sys/types.h>
46	#include <sys/stat.h>
47
48	#include <iostream>
49	#include <math.h>
50
51	#include <stdio.h>
52	#include <stdlib.h>
53	#include <string.h>
54
55	#include "io/DumpReader.hpp"
56	#include "primitives/Molecule.hpp"
57	#include "utils/simError.h"
58	#include "utils/MemoryUtils.hpp"
59	#include "utils/StringTokenizer.hpp"
60
61	#ifdef IS_MPI
62
63	#include <mpi.h>
64	#define TAKE_THIS_TAG_CHAR 0
65	#define TAKE_THIS_TAG_INT 1
66
67	#endif // is_mpi
68
69
70	namespace OpenMD {
71
72	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
73	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
74
75	#ifdef IS_MPI
76
77	if (worldRank == 0) {
78	#endif
79
80	inFile_ = new std::ifstream(filename_.c_str());
81
82	if (inFile_->fail()) {
83	sprintf(painCave.errMsg,
84	"DumpReader: Cannot open file: %s\n",
85	filename_.c_str());
86	painCave.isFatal = 1;
87	simError();
88	}
89
90	#ifdef IS_MPI
91
92	}
93
94	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
95	errorCheckPoint();
96
97	#endif
98
99	return;
100	}
101
102	DumpReader::~DumpReader() {
103
104	#ifdef IS_MPI
105
106	if (worldRank == 0) {
107	#endif
108
109	delete inFile_;
110
111	#ifdef IS_MPI
112
113	}
114
115	strcpy(checkPointMsg, "Dump file closed successfully.");
116	errorCheckPoint();
117
118	#endif
119
120	return;
121	}
122
123	int DumpReader::getNFrames(void) {
124
125	if (!isScanned_)
126	scanFile();
127
128	return nframes_;
129	}
130
131	void DumpReader::scanFile(void) {
132	int lineNo = 0;
133	std::streampos prevPos;
134	std::streampos currPos;
135
136	#ifdef IS_MPI
137
138	if (worldRank == 0) {
139	#endif // is_mpi
140
141	currPos = inFile_->tellg();
142	prevPos = currPos;
143	bool foundOpenSnapshotTag = false;
144	bool foundClosedSnapshotTag = false;
145	while(inFile_->getline(buffer, bufferSize)) {
146	++lineNo;
147
148	std::string line = buffer;
149	currPos = inFile_->tellg();
150	if (line.find("<Snapshot>")!= std::string::npos) {
151	if (foundOpenSnapshotTag) {
152	sprintf(painCave.errMsg,
153	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	filename_.c_str());
155	painCave.isFatal = 1;
156	simError();
157	}
158	foundOpenSnapshotTag = true;
159	foundClosedSnapshotTag = false;
160	framePos_.push_back(prevPos);
161
162	} else if (line.find("</Snapshot>") != std::string::npos){
163	if (!foundOpenSnapshotTag) {
164	sprintf(painCave.errMsg,
165	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
166	filename_.c_str());
167	painCave.isFatal = 1;
168	simError();
169	}
170
171	if (foundClosedSnapshotTag) {
172	sprintf(painCave.errMsg,
173	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
174	filename_.c_str());
175	painCave.isFatal = 1;
176	simError();
177	}
178	foundClosedSnapshotTag = true;
179	foundOpenSnapshotTag = false;
180	}
181	prevPos = currPos;
182	}
183
184	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
185	// it and give a warning message
186	if (foundOpenSnapshotTag) {
187	sprintf(painCave.errMsg,
188	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
189	painCave.isFatal = 0;
190	simError();
191	framePos_.pop_back();
192	}
193
194	nframes_ = framePos_.size();
195
196	if (nframes_ == 0) {
197	sprintf(painCave.errMsg,
198	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
199	painCave.isFatal = 1;
200	simError();
201	}
202	#ifdef IS_MPI
203	}
204
205	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206
207	#endif // is_mpi
208
209	isScanned_ = true;
210	}
211
212	void DumpReader::readFrame(int whichFrame) {
213	if (!isScanned_)
214	scanFile();
215
216	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
217
218	if (storageLayout & DataStorage::dslPosition) {
219	needPos_ = true;
220	} else {
221	needPos_ = false;
222	}
223
224	if (storageLayout & DataStorage::dslVelocity) {
225	needVel_ = true;
226	} else {
227	needVel_ = false;
228	}
229
230	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
231	needQuaternion_ = true;
232	} else {
233	needQuaternion_ = false;
234	}
235
236	if (storageLayout & DataStorage::dslAngularMomentum) {
237	needAngMom_ = true;
238	} else {
239	needAngMom_ = false;
240	}
241
242	readSet(whichFrame);
243
244	if (needCOMprops_) {
245	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	Vector3d com;
247	Vector3d comvel;
248	Vector3d comw;
249	if (needPos_ && needVel_){
250	info_->getComAll(com, comvel);
251	comw = info_->getAngularMomentum();
252	}else{
253	com = info_->getCom();
254	comvel = 0.0;
255	comw = 0.0;
256	}
257	s->setCOMprops(com, comvel, comw);
258	}
259
260	}
261
262	void DumpReader::readSet(int whichFrame) {
263	std::string line;
264
265	#ifndef IS_MPI
266	inFile_->clear();
267	inFile_->seekg(framePos_[whichFrame]);
268
269	std::istream& inputStream = *inFile_;
270
271	#else
272	int masterNode = 0;
273	std::stringstream sstream;
274	if (worldRank == masterNode) {
275	std::string sendBuffer;
276
277	inFile_->clear();
278	inFile_->seekg(framePos_[whichFrame]);
279
280	while (inFile_->getline(buffer, bufferSize)) {
281
282	line = buffer;
283	sendBuffer += line;
284	sendBuffer += '\n';
285	if (line.find("</Snapshot>") != std::string::npos) {
286	break;
287	}
288	}
289
290	int sendBufferSize = sendBuffer.size();
291	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
292	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
293
294	sstream.str(sendBuffer);
295	} else {
296	int sendBufferSize;
297	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
298	char * recvBuffer = new char[sendBufferSize+1];
299	assert(recvBuffer);
300	recvBuffer[sendBufferSize] = '\0';
301	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302	sstream.str(recvBuffer);
303	delete [] recvBuffer;
304	}
305
306	std::istream& inputStream = sstream;
307	#endif
308
309	inputStream.getline(buffer, bufferSize);
310
311	line = buffer;
312	if (line.find("<Snapshot>") == std::string::npos) {
313	sprintf(painCave.errMsg,
314	"DumpReader Error: can not find <Snapshot>\n");
315	painCave.isFatal = 1;
316	simError();
317	}
318
319	//read frameData
320	readFrameProperties(inputStream);
321
322	//read StuntDoubles
323	readStuntDoubles(inputStream);
324
325	inputStream.getline(buffer, bufferSize);
326	line = buffer;
327	if (line.find("</Snapshot>") == std::string::npos) {
328	sprintf(painCave.errMsg,
329	"DumpReader Error: can not find </Snapshot>\n");
330	painCave.isFatal = 1;
331	simError();
332	}
333
334	}
335
336	void DumpReader::parseDumpLine(const std::string& line) {
337
338
339	StringTokenizer tokenizer(line);
340	int nTokens;
341
342	nTokens = tokenizer.countTokens();
343
344	if (nTokens < 2) {
345	sprintf(painCave.errMsg,
346	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
347	painCave.isFatal = 1;
348	simError();
349	}
350
351	int index = tokenizer.nextTokenAsInt();
352
353	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
354
355	if (integrableObject == NULL) {
356	return;
357	}
358	std::string type = tokenizer.nextToken();
359	int size = type.size();
360
361	size_t found;
362
363	if (needPos_) {
364	found = type.find("p");
365	if (found == std::string::npos) {
366	sprintf(painCave.errMsg,
367	"DumpReader Error: StuntDouble %d has no Position\n"
368	"\tField (\"p\") specified.\n%s\n", index,
369	line.c_str());
370	painCave.isFatal = 1;
371	simError();
372	}
373	}
374
375	if (integrableObject->isDirectional()) {
376	if (needQuaternion_) {
377	found = type.find("q");
378	if (found == std::string::npos) {
379	sprintf(painCave.errMsg,
380	"DumpReader Error: Directional StuntDouble %d has no\n"
381	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
382	line.c_str());
383	painCave.isFatal = 1;
384	simError();
385	}
386	}
387	}
388
389	for(int i = 0; i < size; ++i) {
390	switch(type[i]) {
391
392	case 'p': {
393	Vector3d pos;
394	pos[0] = tokenizer.nextTokenAsDouble();
395	pos[1] = tokenizer.nextTokenAsDouble();
396	pos[2] = tokenizer.nextTokenAsDouble();
397	if (needPos_) {
398	integrableObject->setPos(pos);
399	}
400	break;
401	}
402	case 'v' : {
403	Vector3d vel;
404	vel[0] = tokenizer.nextTokenAsDouble();
405	vel[1] = tokenizer.nextTokenAsDouble();
406	vel[2] = tokenizer.nextTokenAsDouble();
407	if (needVel_) {
408	integrableObject->setVel(vel);
409	}
410	break;
411	}
412
413	case 'q' : {
414	Quat4d q;
415	if (integrableObject->isDirectional()) {
416
417	q[0] = tokenizer.nextTokenAsDouble();
418	q[1] = tokenizer.nextTokenAsDouble();
419	q[2] = tokenizer.nextTokenAsDouble();
420	q[3] = tokenizer.nextTokenAsDouble();
421
422	RealType qlen = q.length();
423	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
424
425	sprintf(painCave.errMsg,
426	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
427	painCave.isFatal = 1;
428	simError();
429
430	}
431
432	q.normalize();
433	if (needQuaternion_) {
434	integrableObject->setQ(q);
435	}
436	}
437	break;
438	}
439	case 'j' : {
440	Vector3d ji;
441	if (integrableObject->isDirectional()) {
442	ji[0] = tokenizer.nextTokenAsDouble();
443	ji[1] = tokenizer.nextTokenAsDouble();
444	ji[2] = tokenizer.nextTokenAsDouble();
445	if (needAngMom_) {
446	integrableObject->setJ(ji);
447	}
448	}
449	break;
450	}
451	case 'f': {
452
453	Vector3d force;
454	force[0] = tokenizer.nextTokenAsDouble();
455	force[1] = tokenizer.nextTokenAsDouble();
456	force[2] = tokenizer.nextTokenAsDouble();
457	integrableObject->setFrc(force);
458	break;
459	}
460	case 't' : {
461
462	Vector3d torque;
463	torque[0] = tokenizer.nextTokenAsDouble();
464	torque[1] = tokenizer.nextTokenAsDouble();
465	torque[2] = tokenizer.nextTokenAsDouble();
466	integrableObject->setTrq(torque);
467	break;
468	}
469	default: {
470	sprintf(painCave.errMsg,
471	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
472	painCave.isFatal = 1;
473	simError();
474	break;
475	}
476
477	}
478	}
479
480	}
481
482
483	void DumpReader::readStuntDoubles(std::istream& inputStream) {
484
485	inputStream.getline(buffer, bufferSize);
486	std::string line(buffer);
487
488	if (line.find("<StuntDoubles>") == std::string::npos) {
489	sprintf(painCave.errMsg,
490	"DumpReader Error: Missing <StuntDoubles>\n");
491	painCave.isFatal = 1;
492	simError();
493	}
494
495	while(inputStream.getline(buffer, bufferSize)) {
496	line = buffer;
497
498	if(line.find("</StuntDoubles>") != std::string::npos) {
499	break;
500	}
501
502	parseDumpLine(line);
503	}
504
505	}
506
507	void DumpReader::readFrameProperties(std::istream& inputStream) {
508
509	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
510	inputStream.getline(buffer, bufferSize);
511	std::string line(buffer);
512
513	if (line.find("<FrameData>") == std::string::npos) {
514	sprintf(painCave.errMsg,
515	"DumpReader Error: Missing <FrameData>\n");
516	painCave.isFatal = 1;
517	simError();
518	}
519
520	while(inputStream.getline(buffer, bufferSize)) {
521	line = buffer;
522
523	if(line.find("</FrameData>") != std::string::npos) {
524	break;
525	}
526
527	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
528	if (!tokenizer.hasMoreTokens()) {
529	sprintf(painCave.errMsg,
530	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
531	painCave.isFatal = 1;
532	simError();
533	}
534
535	std::string propertyName = tokenizer.nextToken();
536	if (propertyName == "Time") {
537	RealType currTime = tokenizer.nextTokenAsDouble();
538	s->setTime(currTime);
539	} else if (propertyName == "Hmat"){
540	Mat3x3d hmat;
541	hmat(0, 0) = tokenizer.nextTokenAsDouble();
542	hmat(0, 1) = tokenizer.nextTokenAsDouble();
543	hmat(0, 2) = tokenizer.nextTokenAsDouble();
544	hmat(1, 0) = tokenizer.nextTokenAsDouble();
545	hmat(1, 1) = tokenizer.nextTokenAsDouble();
546	hmat(1, 2) = tokenizer.nextTokenAsDouble();
547	hmat(2, 0) = tokenizer.nextTokenAsDouble();
548	hmat(2, 1) = tokenizer.nextTokenAsDouble();
549	hmat(2, 2) = tokenizer.nextTokenAsDouble();
550	s->setHmat(hmat);
551	} else if (propertyName == "Thermostat") {
552	RealType chi = tokenizer.nextTokenAsDouble();
553	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
554	s->setChi(chi);
555	s->setIntegralOfChiDt(integralOfChiDt);
556	} else if (propertyName == "Barostat") {
557	Mat3x3d eta;
558	eta(0, 0) = tokenizer.nextTokenAsDouble();
559	eta(0, 1) = tokenizer.nextTokenAsDouble();
560	eta(0, 2) = tokenizer.nextTokenAsDouble();
561	eta(1, 0) = tokenizer.nextTokenAsDouble();
562	eta(1, 1) = tokenizer.nextTokenAsDouble();
563	eta(1, 2) = tokenizer.nextTokenAsDouble();
564	eta(2, 0) = tokenizer.nextTokenAsDouble();
565	eta(2, 1) = tokenizer.nextTokenAsDouble();
566	eta(2, 2) = tokenizer.nextTokenAsDouble();
567	s->setEta(eta);
568	} else {
569	sprintf(painCave.errMsg,
570	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
571	painCave.isFatal = 0;
572	simError();
573	}
574
575	}
576
577	}
578
579
580	}//end namespace OpenMD