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.
#	User	Rev	Content
1	gezelter	1390	/*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1390	*/
42	chrisfen	721
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	gezelter	1390	namespace OpenMD {
72	chrisfen	721
73			DumpReader::DumpReader(SimInfo* info, const std::string& filename)
74	gezelter	1104	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
75	chrisfen	996
76	chrisfen	721	#ifdef IS_MPI
77	chrisfen	996
78			if (worldRank == 0) {
79	chrisfen	721	#endif
80	chrisfen	996
81	chrisfen	721	inFile_ = new std::ifstream(filename_.c_str());
82	chrisfen	996
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	chrisfen	721	#ifdef IS_MPI
92	chrisfen	996
93			}
94
95			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
96	gezelter	1241	errorCheckPoint();
97	chrisfen	996
98	chrisfen	721	#endif
99	chrisfen	996
100			return;
101			}
102
103	chrisfen	721	DumpReader::~DumpReader() {
104	chrisfen	996
105	chrisfen	721	#ifdef IS_MPI
106	chrisfen	996
107	chrisfen	721	if (worldRank == 0) {
108			#endif
109	chrisfen	996
110	chrisfen	721	delete inFile_;
111	chrisfen	996
112	chrisfen	721	#ifdef IS_MPI
113	chrisfen	996
114	chrisfen	721	}
115	chrisfen	996
116	chrisfen	721	strcpy(checkPointMsg, "Dump file closed successfully.");
117	gezelter	1241	errorCheckPoint();
118	chrisfen	996
119	chrisfen	721	#endif
120	chrisfen	996
121	chrisfen	721	return;
122			}
123	chrisfen	996
124	chrisfen	721	int DumpReader::getNFrames(void) {
125
126			if (!isScanned_)
127			scanFile();
128
129			return nframes_;
130			}
131
132			void DumpReader::scanFile(void) {
133	tim	1024	int lineNo = 0;
134			std::streampos prevPos;
135	chrisfen	721	std::streampos currPos;
136	tim	1024
137	chrisfen	721	#ifdef IS_MPI
138	tim	1024
139	chrisfen	721	if (worldRank == 0) {
140			#endif // is_mpi
141	tim	1024
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	chrisfen	721	sprintf(painCave.errMsg,
154	tim	1024	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155			filename_.c_str());
156	chrisfen	721	painCave.isFatal = 1;
157	tim	1024	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	chrisfen	721	simError();
170	tim	1024	}
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	chrisfen	721	nframes_ = framePos_.size();
196	tim	1024
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	chrisfen	721	#ifdef IS_MPI
204			}
205
206			MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207	tim	1024
208	chrisfen	721	#endif // is_mpi
209	tim	1024
210	chrisfen	721	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	gezelter	1104
245			if (needCOMprops_) {
246			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
247			Vector3d com;
248			Vector3d comvel;
249			Vector3d comw;
250	chuckv	1112	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	gezelter	1104	s->setCOMprops(com, comvel, comw);
259			}
260
261	chrisfen	721	}
262
263	tim	1024	void DumpReader::readSet(int whichFrame) {
264			std::string line;
265
266	chrisfen	721	#ifndef IS_MPI
267			inFile_->clear();
268			inFile_->seekg(framePos_[whichFrame]);
269	tim	1024
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	gezelter	1313	assert(recvBuffer);
301			recvBuffer[sendBufferSize] = '\0';
302	tim	1024	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303			sstream.str(recvBuffer);
304	gezelter	1313	delete [] recvBuffer;
305	tim	1024	}
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	chrisfen	721	sprintf(painCave.errMsg,
315	tim	1024	"DumpReader Error: can not find <Snapshot>\n");
316	chrisfen	721	painCave.isFatal = 1;
317			simError();
318			}
319	tim	1024
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	chrisfen	721	sprintf(painCave.errMsg,
330	tim	1024	"DumpReader Error: can not find </Snapshot>\n");
331	chrisfen	721	painCave.isFatal = 1;
332			simError();
333	tim	1024	}
334
335	chrisfen	721	}
336
337	tim	1024	void DumpReader::parseDumpLine(const std::string& line) {
338
339
340	chrisfen	721	StringTokenizer tokenizer(line);
341			int nTokens;
342
343			nTokens = tokenizer.countTokens();
344
345	gezelter	1450	if (nTokens < 2) {
346	chrisfen	721	sprintf(painCave.errMsg,
347	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
348	chrisfen	721	painCave.isFatal = 1;
349			simError();
350			}
351	tim	1024
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	gezelter	1037
362	gezelter	1450	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	tim	1024	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	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
425	tim	1024
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	gezelter	1037	break;
451	tim	1024	}
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	gezelter	1629	case 'u' : {
471
472			RealType particlePot;
473			particlePot = tokenizer.nextTokenAsDouble();
474			integrableObject->setParticlePot(particlePot);
475			break;
476			}
477	gezelter	1714	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	tim	1024	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	chrisfen	721
518	tim	1024	}
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	chrisfen	721	sprintf(painCave.errMsg,
528	tim	1024	"DumpReader Error: Missing <StuntDoubles>\n");
529	chrisfen	721	painCave.isFatal = 1;
530	tim	1024	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	chrisfen	721	sprintf(painCave.errMsg,
568	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
569	chrisfen	721	painCave.isFatal = 1;
570	tim	1024	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	chrisfen	721
618	gezelter	1390	}//end namespace OpenMD