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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
#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;
        }
        case 'u' : {

           RealType particlePot;
           particlePot = tokenizer.nextTokenAsDouble(); 
           integrableObject->setParticlePot(particlePot);          
           break;
        }
        case 'c' : {

           RealType flucQPos;
           flucQPos = tokenizer.nextTokenAsDouble(); 
           integrableObject->setFlucQPos(flucQPos);          
           break;
        }
        case 'w' : {

           RealType flucQVel;
           flucQVel = tokenizer.nextTokenAsDouble(); 
           integrableObject->setFlucQVel(flucQVel);          
           break;
        }
        case 'g' : {

           RealType flucQFrc;
           flucQFrc = tokenizer.nextTokenAsDouble(); 
           integrableObject->setFlucQFrc(flucQFrc);          
           break;
        }
        case 'e' : {

           Vector3d eField;
           eField[0] = tokenizer.nextTokenAsDouble(); 
           eField[1] = tokenizer.nextTokenAsDouble(); 
           eField[2] = tokenizer.nextTokenAsDouble();           
           integrableObject->setElectricField(eField);          
           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:	1714
Committed:	Sat May 19 18:12:46 2012 UTC (12 years, 11 months ago) by gezelter
File size:	18347 byte(s)
Log Message:	Added ability to read / write dump files with fluctuating charges and electric fields.
#	Content
1	/*
2	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#define _LARGEFILE_SOURCE64
44	#define _FILE_OFFSET_BITS 64
45
46	#include <sys/types.h>
47	#include <sys/stat.h>
48
49	#include <iostream>
50	#include <math.h>
51
52	#include <stdio.h>
53	#include <stdlib.h>
54	#include <string.h>
55
56	#include "io/DumpReader.hpp"
57	#include "primitives/Molecule.hpp"
58	#include "utils/simError.h"
59	#include "utils/MemoryUtils.hpp"
60	#include "utils/StringTokenizer.hpp"
61
62	#ifdef IS_MPI
63
64	#include <mpi.h>
65	#define TAKE_THIS_TAG_CHAR 0
66	#define TAKE_THIS_TAG_INT 1
67
68	#endif // is_mpi
69
70
71	namespace OpenMD {
72
73	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75
76	#ifdef IS_MPI
77
78	if (worldRank == 0) {
79	#endif
80
81	inFile_ = new std::ifstream(filename_.c_str());
82
83	if (inFile_->fail()) {
84	sprintf(painCave.errMsg,
85	"DumpReader: Cannot open file: %s\n",
86	filename_.c_str());
87	painCave.isFatal = 1;
88	simError();
89	}
90
91	#ifdef IS_MPI
92
93	}
94
95	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	errorCheckPoint();
97
98	#endif
99
100	return;
101	}
102
103	DumpReader::~DumpReader() {
104
105	#ifdef IS_MPI
106
107	if (worldRank == 0) {
108	#endif
109
110	delete inFile_;
111
112	#ifdef IS_MPI
113
114	}
115
116	strcpy(checkPointMsg, "Dump file closed successfully.");
117	errorCheckPoint();
118
119	#endif
120
121	return;
122	}
123
124	int DumpReader::getNFrames(void) {
125
126	if (!isScanned_)
127	scanFile();
128
129	return nframes_;
130	}
131
132	void DumpReader::scanFile(void) {
133	int lineNo = 0;
134	std::streampos prevPos;
135	std::streampos currPos;
136
137	#ifdef IS_MPI
138
139	if (worldRank == 0) {
140	#endif // is_mpi
141
142	currPos = inFile_->tellg();
143	prevPos = currPos;
144	bool foundOpenSnapshotTag = false;
145	bool foundClosedSnapshotTag = false;
146	while(inFile_->getline(buffer, bufferSize)) {
147	++lineNo;
148
149	std::string line = buffer;
150	currPos = inFile_->tellg();
151	if (line.find("<Snapshot>")!= std::string::npos) {
152	if (foundOpenSnapshotTag) {
153	sprintf(painCave.errMsg,
154	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155	filename_.c_str());
156	painCave.isFatal = 1;
157	simError();
158	}
159	foundOpenSnapshotTag = true;
160	foundClosedSnapshotTag = false;
161	framePos_.push_back(prevPos);
162
163	} else if (line.find("</Snapshot>") != std::string::npos){
164	if (!foundOpenSnapshotTag) {
165	sprintf(painCave.errMsg,
166	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
167	filename_.c_str());
168	painCave.isFatal = 1;
169	simError();
170	}
171
172	if (foundClosedSnapshotTag) {
173	sprintf(painCave.errMsg,
174	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
175	filename_.c_str());
176	painCave.isFatal = 1;
177	simError();
178	}
179	foundClosedSnapshotTag = true;
180	foundOpenSnapshotTag = false;
181	}
182	prevPos = currPos;
183	}
184
185	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
186	// it and give a warning message
187	if (foundOpenSnapshotTag) {
188	sprintf(painCave.errMsg,
189	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
190	painCave.isFatal = 0;
191	simError();
192	framePos_.pop_back();
193	}
194
195	nframes_ = framePos_.size();
196
197	if (nframes_ == 0) {
198	sprintf(painCave.errMsg,
199	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
200	painCave.isFatal = 1;
201	simError();
202	}
203	#ifdef IS_MPI
204	}
205
206	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207
208	#endif // is_mpi
209
210	isScanned_ = true;
211	}
212
213	void DumpReader::readFrame(int whichFrame) {
214	if (!isScanned_)
215	scanFile();
216
217	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
218
219	if (storageLayout & DataStorage::dslPosition) {
220	needPos_ = true;
221	} else {
222	needPos_ = false;
223	}
224
225	if (storageLayout & DataStorage::dslVelocity) {
226	needVel_ = true;
227	} else {
228	needVel_ = false;
229	}
230
231	if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
232	needQuaternion_ = true;
233	} else {
234	needQuaternion_ = false;
235	}
236
237	if (storageLayout & DataStorage::dslAngularMomentum) {
238	needAngMom_ = true;
239	} else {
240	needAngMom_ = false;
241	}
242
243	readSet(whichFrame);
244
245	if (needCOMprops_) {
246	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247	Vector3d com;
248	Vector3d comvel;
249	Vector3d comw;
250	if (needPos_ && needVel_){
251	info_->getComAll(com, comvel);
252	comw = info_->getAngularMomentum();
253	}else{
254	com = info_->getCom();
255	comvel = 0.0;
256	comw = 0.0;
257	}
258	s->setCOMprops(com, comvel, comw);
259	}
260
261	}
262
263	void DumpReader::readSet(int whichFrame) {
264	std::string line;
265
266	#ifndef IS_MPI
267	inFile_->clear();
268	inFile_->seekg(framePos_[whichFrame]);
269
270	std::istream& inputStream = *inFile_;
271
272	#else
273	int masterNode = 0;
274	std::stringstream sstream;
275	if (worldRank == masterNode) {
276	std::string sendBuffer;
277
278	inFile_->clear();
279	inFile_->seekg(framePos_[whichFrame]);
280
281	while (inFile_->getline(buffer, bufferSize)) {
282
283	line = buffer;
284	sendBuffer += line;
285	sendBuffer += '\n';
286	if (line.find("</Snapshot>") != std::string::npos) {
287	break;
288	}
289	}
290
291	int sendBufferSize = sendBuffer.size();
292	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
293	MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
294
295	sstream.str(sendBuffer);
296	} else {
297	int sendBufferSize;
298	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	char * recvBuffer = new char[sendBufferSize+1];
300	assert(recvBuffer);
301	recvBuffer[sendBufferSize] = '\0';
302	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	sstream.str(recvBuffer);
304	delete [] recvBuffer;
305	}
306
307	std::istream& inputStream = sstream;
308	#endif
309
310	inputStream.getline(buffer, bufferSize);
311
312	line = buffer;
313	if (line.find("<Snapshot>") == std::string::npos) {
314	sprintf(painCave.errMsg,
315	"DumpReader Error: can not find <Snapshot>\n");
316	painCave.isFatal = 1;
317	simError();
318	}
319
320	//read frameData
321	readFrameProperties(inputStream);
322
323	//read StuntDoubles
324	readStuntDoubles(inputStream);
325
326	inputStream.getline(buffer, bufferSize);
327	line = buffer;
328	if (line.find("</Snapshot>") == std::string::npos) {
329	sprintf(painCave.errMsg,
330	"DumpReader Error: can not find </Snapshot>\n");
331	painCave.isFatal = 1;
332	simError();
333	}
334
335	}
336
337	void DumpReader::parseDumpLine(const std::string& line) {
338
339
340	StringTokenizer tokenizer(line);
341	int nTokens;
342
343	nTokens = tokenizer.countTokens();
344
345	if (nTokens < 2) {
346	sprintf(painCave.errMsg,
347	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348	painCave.isFatal = 1;
349	simError();
350	}
351
352	int index = tokenizer.nextTokenAsInt();
353
354	StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
355
356	if (integrableObject == NULL) {
357	return;
358	}
359	std::string type = tokenizer.nextToken();
360	int size = type.size();
361
362	size_t found;
363
364	if (needPos_) {
365	found = type.find("p");
366	if (found == std::string::npos) {
367	sprintf(painCave.errMsg,
368	"DumpReader Error: StuntDouble %d has no Position\n"
369	"\tField (\"p\") specified.\n%s\n", index,
370	line.c_str());
371	painCave.isFatal = 1;
372	simError();
373	}
374	}
375
376	if (integrableObject->isDirectional()) {
377	if (needQuaternion_) {
378	found = type.find("q");
379	if (found == std::string::npos) {
380	sprintf(painCave.errMsg,
381	"DumpReader Error: Directional StuntDouble %d has no\n"
382	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
383	line.c_str());
384	painCave.isFatal = 1;
385	simError();
386	}
387	}
388	}
389
390	for(int i = 0; i < size; ++i) {
391	switch(type[i]) {
392
393	case 'p': {
394	Vector3d pos;
395	pos[0] = tokenizer.nextTokenAsDouble();
396	pos[1] = tokenizer.nextTokenAsDouble();
397	pos[2] = tokenizer.nextTokenAsDouble();
398	if (needPos_) {
399	integrableObject->setPos(pos);
400	}
401	break;
402	}
403	case 'v' : {
404	Vector3d vel;
405	vel[0] = tokenizer.nextTokenAsDouble();
406	vel[1] = tokenizer.nextTokenAsDouble();
407	vel[2] = tokenizer.nextTokenAsDouble();
408	if (needVel_) {
409	integrableObject->setVel(vel);
410	}
411	break;
412	}
413
414	case 'q' : {
415	Quat4d q;
416	if (integrableObject->isDirectional()) {
417
418	q[0] = tokenizer.nextTokenAsDouble();
419	q[1] = tokenizer.nextTokenAsDouble();
420	q[2] = tokenizer.nextTokenAsDouble();
421	q[3] = tokenizer.nextTokenAsDouble();
422
423	RealType qlen = q.length();
424	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425
426	sprintf(painCave.errMsg,
427	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
428	painCave.isFatal = 1;
429	simError();
430
431	}
432
433	q.normalize();
434	if (needQuaternion_) {
435	integrableObject->setQ(q);
436	}
437	}
438	break;
439	}
440	case 'j' : {
441	Vector3d ji;
442	if (integrableObject->isDirectional()) {
443	ji[0] = tokenizer.nextTokenAsDouble();
444	ji[1] = tokenizer.nextTokenAsDouble();
445	ji[2] = tokenizer.nextTokenAsDouble();
446	if (needAngMom_) {
447	integrableObject->setJ(ji);
448	}
449	}
450	break;
451	}
452	case 'f': {
453
454	Vector3d force;
455	force[0] = tokenizer.nextTokenAsDouble();
456	force[1] = tokenizer.nextTokenAsDouble();
457	force[2] = tokenizer.nextTokenAsDouble();
458	integrableObject->setFrc(force);
459	break;
460	}
461	case 't' : {
462
463	Vector3d torque;
464	torque[0] = tokenizer.nextTokenAsDouble();
465	torque[1] = tokenizer.nextTokenAsDouble();
466	torque[2] = tokenizer.nextTokenAsDouble();
467	integrableObject->setTrq(torque);
468	break;
469	}
470	case 'u' : {
471
472	RealType particlePot;
473	particlePot = tokenizer.nextTokenAsDouble();
474	integrableObject->setParticlePot(particlePot);
475	break;
476	}
477	case 'c' : {
478
479	RealType flucQPos;
480	flucQPos = tokenizer.nextTokenAsDouble();
481	integrableObject->setFlucQPos(flucQPos);
482	break;
483	}
484	case 'w' : {
485
486	RealType flucQVel;
487	flucQVel = tokenizer.nextTokenAsDouble();
488	integrableObject->setFlucQVel(flucQVel);
489	break;
490	}
491	case 'g' : {
492
493	RealType flucQFrc;
494	flucQFrc = tokenizer.nextTokenAsDouble();
495	integrableObject->setFlucQFrc(flucQFrc);
496	break;
497	}
498	case 'e' : {
499
500	Vector3d eField;
501	eField[0] = tokenizer.nextTokenAsDouble();
502	eField[1] = tokenizer.nextTokenAsDouble();
503	eField[2] = tokenizer.nextTokenAsDouble();
504	integrableObject->setElectricField(eField);
505	break;
506	}
507	default: {
508	sprintf(painCave.errMsg,
509	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
510	painCave.isFatal = 1;
511	simError();
512	break;
513	}
514
515	}
516	}
517
518	}
519
520
521	void DumpReader::readStuntDoubles(std::istream& inputStream) {
522
523	inputStream.getline(buffer, bufferSize);
524	std::string line(buffer);
525
526	if (line.find("<StuntDoubles>") == std::string::npos) {
527	sprintf(painCave.errMsg,
528	"DumpReader Error: Missing <StuntDoubles>\n");
529	painCave.isFatal = 1;
530	simError();
531	}
532
533	while(inputStream.getline(buffer, bufferSize)) {
534	line = buffer;
535
536	if(line.find("</StuntDoubles>") != std::string::npos) {
537	break;
538	}
539
540	parseDumpLine(line);
541	}
542
543	}
544
545	void DumpReader::readFrameProperties(std::istream& inputStream) {
546
547	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
548	inputStream.getline(buffer, bufferSize);
549	std::string line(buffer);
550
551	if (line.find("<FrameData>") == std::string::npos) {
552	sprintf(painCave.errMsg,
553	"DumpReader Error: Missing <FrameData>\n");
554	painCave.isFatal = 1;
555	simError();
556	}
557
558	while(inputStream.getline(buffer, bufferSize)) {
559	line = buffer;
560
561	if(line.find("</FrameData>") != std::string::npos) {
562	break;
563	}
564
565	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
566	if (!tokenizer.hasMoreTokens()) {
567	sprintf(painCave.errMsg,
568	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
569	painCave.isFatal = 1;
570	simError();
571	}
572
573	std::string propertyName = tokenizer.nextToken();
574	if (propertyName == "Time") {
575	RealType currTime = tokenizer.nextTokenAsDouble();
576	s->setTime(currTime);
577	} else if (propertyName == "Hmat"){
578	Mat3x3d hmat;
579	hmat(0, 0) = tokenizer.nextTokenAsDouble();
580	hmat(0, 1) = tokenizer.nextTokenAsDouble();
581	hmat(0, 2) = tokenizer.nextTokenAsDouble();
582	hmat(1, 0) = tokenizer.nextTokenAsDouble();
583	hmat(1, 1) = tokenizer.nextTokenAsDouble();
584	hmat(1, 2) = tokenizer.nextTokenAsDouble();
585	hmat(2, 0) = tokenizer.nextTokenAsDouble();
586	hmat(2, 1) = tokenizer.nextTokenAsDouble();
587	hmat(2, 2) = tokenizer.nextTokenAsDouble();
588	s->setHmat(hmat);
589	} else if (propertyName == "Thermostat") {
590	RealType chi = tokenizer.nextTokenAsDouble();
591	RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
592	s->setChi(chi);
593	s->setIntegralOfChiDt(integralOfChiDt);
594	} else if (propertyName == "Barostat") {
595	Mat3x3d eta;
596	eta(0, 0) = tokenizer.nextTokenAsDouble();
597	eta(0, 1) = tokenizer.nextTokenAsDouble();
598	eta(0, 2) = tokenizer.nextTokenAsDouble();
599	eta(1, 0) = tokenizer.nextTokenAsDouble();
600	eta(1, 1) = tokenizer.nextTokenAsDouble();
601	eta(1, 2) = tokenizer.nextTokenAsDouble();
602	eta(2, 0) = tokenizer.nextTokenAsDouble();
603	eta(2, 1) = tokenizer.nextTokenAsDouble();
604	eta(2, 2) = tokenizer.nextTokenAsDouble();
605	s->setEta(eta);
606	} else {
607	sprintf(painCave.errMsg,
608	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
609	painCave.isFatal = 0;
610	simError();
611	}
612
613	}
614
615	}
616
617
618	}//end namespace OpenMD