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" 
#include "brains/Thermo.hpp"
 
#ifdef IS_MPI 
#include <mpi.h> 
#endif
 
 
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(),   
                                  ifstream::in | ifstream::binary); 
      
      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;
      bool foundOpenSiteDataTag = 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::dslDipole || 
        storageLayout & DataStorage::dslQuadrupole) { 
      needQuaternion_ = true; 
    } else { 
      needQuaternion_ = false; 
    } 
     
    if (storageLayout & DataStorage::dslAngularMomentum) { 
      needAngMom_ = true; 
    } else { 
      needAngMom_ = false;     
    } 
     
    readSet(whichFrame); 

    if (needCOMprops_) {
      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
      Thermo thermo(info_);
      Vector3d com;

      if (needPos_ && needVel_) {
        Vector3d comvel;
        Vector3d comw;
        thermo.getComAll(com, comvel);
        comw = thermo.getAngularMomentum();
      } else {
        com = thermo.getCom();
      }                    
    }
  } 
   
  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("<SiteData>") != std::string::npos) {
      //read SiteData
      readSiteData(inputStream);         
    } else {
      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* sd = info_->getIOIndexToIntegrableObject(index);

    if (sd == 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 (sd->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_) { 
              sd->setPos(pos); 
            }             
            break;
        }
        case 'v' : {
            Vector3d vel;
            vel[0] = tokenizer.nextTokenAsDouble(); 
            vel[1] = tokenizer.nextTokenAsDouble(); 
            vel[2] = tokenizer.nextTokenAsDouble(); 
            if (needVel_) { 
              sd->setVel(vel); 
            } 
            break;
        }

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

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

           Vector3d torque;
           torque[0] = tokenizer.nextTokenAsDouble(); 
           torque[1] = tokenizer.nextTokenAsDouble(); 
           torque[2] = tokenizer.nextTokenAsDouble();           
           sd->setTrq(torque);          
           break;
        }
        case 'u' : {

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

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

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

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

           Vector3d eField;
           eField[0] = tokenizer.nextTokenAsDouble(); 
           eField[1] = tokenizer.nextTokenAsDouble(); 
           eField[2] = tokenizer.nextTokenAsDouble();           
           sd->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::parseSiteLine(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(); 
    } 

    /**
     * The first token is the global integrable object index.
     */

    int index = tokenizer.nextTokenAsInt();
    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
    if (sd == NULL) {
      return;
    }

    /**
     * Test to see if the next token is an integer or not.  If not,
     * we've got data on the integrable object itself.  If there is an
     * integer, we're parsing data for a site on a rigid body.
     */

    std::string indexTest = tokenizer.peekNextToken();
    std::istringstream i(indexTest);
    int siteIndex;
    if (i >> siteIndex) {
      // chew up this token and parse as an int:
      siteIndex = tokenizer.nextTokenAsInt();
      RigidBody* rb = static_cast<RigidBody*>(sd);
      sd = rb->getAtoms()[siteIndex];
    }

    /**
     * The next token contains information on what follows.
     */
    std::string type = tokenizer.nextToken(); 
    int size = type.size();
    
    for(int i = 0; i < size; ++i) {
      switch(type[i]) {
        
      case 'u' : {
        
        RealType particlePot;
        particlePot = tokenizer.nextTokenAsDouble(); 
        sd->setParticlePot(particlePot);
        break;
      }
      case 'c' : {
        
        RealType flucQPos;
        flucQPos = tokenizer.nextTokenAsDouble(); 
        sd->setFlucQPos(flucQPos);
        break;
      }
      case 'w' : {
        
        RealType flucQVel;
        flucQVel = tokenizer.nextTokenAsDouble(); 
        sd->setFlucQVel(flucQVel);
        break;
      }
      case 'g' : {
        
        RealType flucQFrc;
        flucQFrc = tokenizer.nextTokenAsDouble(); 
        sd->setFlucQFrc(flucQFrc);
        break;
      }
      case 'e' : {
        
        Vector3d eField;
        eField[0] = tokenizer.nextTokenAsDouble(); 
        eField[1] = tokenizer.nextTokenAsDouble(); 
        eField[2] = tokenizer.nextTokenAsDouble();  
        sd->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::readSiteData(std::istream& inputStream) {

    inputStream.getline(buffer, bufferSize);
    std::string line(buffer);
    
    if (line.find("<SiteData>") == std::string::npos) {
      // site data isn't required for a simulation, so skip
      return;
    }

    while(inputStream.getline(buffer, bufferSize)) {
      line = buffer;
      
      if(line.find("</SiteData>") != std::string::npos) {
        break;
      }

      parseSiteLine(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") {
        pair<RealType, RealType> thermostat;
        thermostat.first = tokenizer.nextTokenAsDouble();
        thermostat.second = tokenizer.nextTokenAsDouble();
        s->setThermostat(thermostat); 
     } 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->setBarostat(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:	1794
Committed:	Thu Sep 6 19:44:06 2012 UTC (12 years, 7 months ago) by gezelter
File size:	21439 byte(s)
Log Message:	Merging some of the trunk changes back to the development branch, cleaning up a datastorage bug
#	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	gezelter	1764	#include "brains/Thermo.hpp"
62	chrisfen	721
63			#ifdef IS_MPI
64			#include <mpi.h>
65	gezelter	1764	#endif
66	chrisfen	721
67
68	gezelter	1390	namespace OpenMD {
69	chrisfen	721
70			DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	gezelter	1104	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72	chrisfen	996
73	chrisfen	721	#ifdef IS_MPI
74	chrisfen	996
75			if (worldRank == 0) {
76	chrisfen	721	#endif
77	chrisfen	996
78	gezelter	1794	inFile_ = new std::ifstream(filename_.c_str(),
79			ifstream::in \| ifstream::binary);
80	chrisfen	996
81			if (inFile_->fail()) {
82			sprintf(painCave.errMsg,
83			"DumpReader: Cannot open file: %s\n",
84			filename_.c_str());
85			painCave.isFatal = 1;
86			simError();
87			}
88
89	chrisfen	721	#ifdef IS_MPI
90	chrisfen	996
91			}
92
93			strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	gezelter	1241	errorCheckPoint();
95	chrisfen	996
96	chrisfen	721	#endif
97	chrisfen	996
98			return;
99			}
100
101	chrisfen	721	DumpReader::~DumpReader() {
102	chrisfen	996
103	chrisfen	721	#ifdef IS_MPI
104	chrisfen	996
105	chrisfen	721	if (worldRank == 0) {
106			#endif
107	chrisfen	996
108	chrisfen	721	delete inFile_;
109	chrisfen	996
110	chrisfen	721	#ifdef IS_MPI
111	chrisfen	996
112	chrisfen	721	}
113	chrisfen	996
114	chrisfen	721	strcpy(checkPointMsg, "Dump file closed successfully.");
115	gezelter	1241	errorCheckPoint();
116	chrisfen	996
117	chrisfen	721	#endif
118	chrisfen	996
119	chrisfen	721	return;
120			}
121	chrisfen	996
122	chrisfen	721	int DumpReader::getNFrames(void) {
123
124			if (!isScanned_)
125			scanFile();
126
127			return nframes_;
128			}
129
130			void DumpReader::scanFile(void) {
131	tim	1024	int lineNo = 0;
132			std::streampos prevPos;
133	chrisfen	721	std::streampos currPos;
134	tim	1024
135	chrisfen	721	#ifdef IS_MPI
136	tim	1024
137	chrisfen	721	if (worldRank == 0) {
138			#endif // is_mpi
139	tim	1024
140			currPos = inFile_->tellg();
141			prevPos = currPos;
142			bool foundOpenSnapshotTag = false;
143			bool foundClosedSnapshotTag = false;
144	gezelter	1752	bool foundOpenSiteDataTag = false;
145	tim	1024	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	chrisfen	721	sprintf(painCave.errMsg,
153	tim	1024	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154			filename_.c_str());
155	chrisfen	721	painCave.isFatal = 1;
156	tim	1024	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	chrisfen	721	simError();
169	tim	1024	}
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	chrisfen	721	nframes_ = framePos_.size();
195	tim	1024
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	chrisfen	721	#ifdef IS_MPI
203			}
204
205			MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
206	tim	1024
207	chrisfen	721	#endif // is_mpi
208	tim	1024
209	chrisfen	721	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	gezelter	1787	if (storageLayout & DataStorage::dslAmat \|\|
231			storageLayout & DataStorage::dslDipole \|\|
232			storageLayout & DataStorage::dslQuadrupole) {
233	chrisfen	721	needQuaternion_ = true;
234			} else {
235			needQuaternion_ = false;
236			}
237
238			if (storageLayout & DataStorage::dslAngularMomentum) {
239			needAngMom_ = true;
240			} else {
241			needAngMom_ = false;
242			}
243
244			readSet(whichFrame);
245	gezelter	1104
246			if (needCOMprops_) {
247			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
248	gezelter	1764	Thermo thermo(info_);
249	gezelter	1104	Vector3d com;
250	gezelter	1764
251			if (needPos_ && needVel_) {
252			Vector3d comvel;
253			Vector3d comw;
254			thermo.getComAll(com, comvel);
255			comw = thermo.getAngularMomentum();
256			} else {
257			com = thermo.getCom();
258			}
259	gezelter	1104	}
260	chrisfen	721	}
261
262	tim	1024	void DumpReader::readSet(int whichFrame) {
263			std::string line;
264
265	chrisfen	721	#ifndef IS_MPI
266			inFile_->clear();
267			inFile_->seekg(framePos_[whichFrame]);
268	tim	1024
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	gezelter	1313	assert(recvBuffer);
300			recvBuffer[sendBufferSize] = '\0';
301	tim	1024	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
302			sstream.str(recvBuffer);
303	gezelter	1313	delete [] recvBuffer;
304	tim	1024	}
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	chrisfen	721	sprintf(painCave.errMsg,
314	tim	1024	"DumpReader Error: can not find <Snapshot>\n");
315	chrisfen	721	painCave.isFatal = 1;
316			simError();
317			}
318	tim	1024
319			//read frameData
320			readFrameProperties(inputStream);
321
322			//read StuntDoubles
323			readStuntDoubles(inputStream);
324
325			inputStream.getline(buffer, bufferSize);
326			line = buffer;
327	gezelter	1752
328			if (line.find("<SiteData>") != std::string::npos) {
329			//read SiteData
330			readSiteData(inputStream);
331			} else {
332			if (line.find("</Snapshot>") == std::string::npos) {
333			sprintf(painCave.errMsg,
334			"DumpReader Error: can not find </Snapshot>\n");
335			painCave.isFatal = 1;
336			simError();
337			}
338			}
339	chrisfen	721	}
340
341	tim	1024	void DumpReader::parseDumpLine(const std::string& line) {
342
343
344	chrisfen	721	StringTokenizer tokenizer(line);
345			int nTokens;
346
347			nTokens = tokenizer.countTokens();
348
349	gezelter	1450	if (nTokens < 2) {
350	chrisfen	721	sprintf(painCave.errMsg,
351	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
352	chrisfen	721	painCave.isFatal = 1;
353			simError();
354			}
355	tim	1024
356			int index = tokenizer.nextTokenAsInt();
357
358	gezelter	1769	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
359	tim	1024
360	gezelter	1769	if (sd == NULL) {
361	tim	1024	return;
362			}
363			std::string type = tokenizer.nextToken();
364			int size = type.size();
365	gezelter	1037
366	gezelter	1450	size_t found;
367
368			if (needPos_) {
369			found = type.find("p");
370			if (found == std::string::npos) {
371			sprintf(painCave.errMsg,
372			"DumpReader Error: StuntDouble %d has no Position\n"
373			"\tField (\"p\") specified.\n%s\n", index,
374			line.c_str());
375			painCave.isFatal = 1;
376			simError();
377			}
378			}
379
380	gezelter	1769	if (sd->isDirectional()) {
381	gezelter	1450	if (needQuaternion_) {
382			found = type.find("q");
383			if (found == std::string::npos) {
384			sprintf(painCave.errMsg,
385			"DumpReader Error: Directional StuntDouble %d has no\n"
386			"\tQuaternion Field (\"q\") specified.\n%s\n", index,
387			line.c_str());
388			painCave.isFatal = 1;
389			simError();
390			}
391			}
392			}
393
394	tim	1024	for(int i = 0; i < size; ++i) {
395			switch(type[i]) {
396
397			case 'p': {
398			Vector3d pos;
399			pos[0] = tokenizer.nextTokenAsDouble();
400			pos[1] = tokenizer.nextTokenAsDouble();
401			pos[2] = tokenizer.nextTokenAsDouble();
402			if (needPos_) {
403	gezelter	1769	sd->setPos(pos);
404	tim	1024	}
405			break;
406			}
407			case 'v' : {
408			Vector3d vel;
409			vel[0] = tokenizer.nextTokenAsDouble();
410			vel[1] = tokenizer.nextTokenAsDouble();
411			vel[2] = tokenizer.nextTokenAsDouble();
412			if (needVel_) {
413	gezelter	1769	sd->setVel(vel);
414	tim	1024	}
415			break;
416			}
417
418			case 'q' : {
419			Quat4d q;
420	gezelter	1769	if (sd->isDirectional()) {
421	tim	1024
422			q[0] = tokenizer.nextTokenAsDouble();
423			q[1] = tokenizer.nextTokenAsDouble();
424			q[2] = tokenizer.nextTokenAsDouble();
425			q[3] = tokenizer.nextTokenAsDouble();
426
427			RealType qlen = q.length();
428	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
429	tim	1024
430			sprintf(painCave.errMsg,
431			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
432			painCave.isFatal = 1;
433			simError();
434
435			}
436
437			q.normalize();
438			if (needQuaternion_) {
439	gezelter	1769	sd->setQ(q);
440	tim	1024	}
441			}
442			break;
443			}
444			case 'j' : {
445			Vector3d ji;
446	gezelter	1769	if (sd->isDirectional()) {
447	tim	1024	ji[0] = tokenizer.nextTokenAsDouble();
448			ji[1] = tokenizer.nextTokenAsDouble();
449			ji[2] = tokenizer.nextTokenAsDouble();
450			if (needAngMom_) {
451	gezelter	1769	sd->setJ(ji);
452	tim	1024	}
453			}
454	gezelter	1037	break;
455	tim	1024	}
456			case 'f': {
457
458			Vector3d force;
459			force[0] = tokenizer.nextTokenAsDouble();
460			force[1] = tokenizer.nextTokenAsDouble();
461			force[2] = tokenizer.nextTokenAsDouble();
462	gezelter	1769	sd->setFrc(force);
463	tim	1024	break;
464			}
465			case 't' : {
466
467			Vector3d torque;
468			torque[0] = tokenizer.nextTokenAsDouble();
469			torque[1] = tokenizer.nextTokenAsDouble();
470			torque[2] = tokenizer.nextTokenAsDouble();
471	gezelter	1769	sd->setTrq(torque);
472	tim	1024	break;
473			}
474	gezelter	1629	case 'u' : {
475
476			RealType particlePot;
477			particlePot = tokenizer.nextTokenAsDouble();
478	gezelter	1769	sd->setParticlePot(particlePot);
479	gezelter	1629	break;
480			}
481	gezelter	1714	case 'c' : {
482
483			RealType flucQPos;
484			flucQPos = tokenizer.nextTokenAsDouble();
485	gezelter	1769	sd->setFlucQPos(flucQPos);
486	gezelter	1714	break;
487			}
488			case 'w' : {
489
490			RealType flucQVel;
491			flucQVel = tokenizer.nextTokenAsDouble();
492	gezelter	1769	sd->setFlucQVel(flucQVel);
493	gezelter	1714	break;
494			}
495			case 'g' : {
496
497			RealType flucQFrc;
498			flucQFrc = tokenizer.nextTokenAsDouble();
499	gezelter	1769	sd->setFlucQFrc(flucQFrc);
500	gezelter	1714	break;
501			}
502			case 'e' : {
503
504			Vector3d eField;
505			eField[0] = tokenizer.nextTokenAsDouble();
506			eField[1] = tokenizer.nextTokenAsDouble();
507			eField[2] = tokenizer.nextTokenAsDouble();
508	gezelter	1769	sd->setElectricField(eField);
509	gezelter	1714	break;
510			}
511	tim	1024	default: {
512			sprintf(painCave.errMsg,
513			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
514			painCave.isFatal = 1;
515			simError();
516			break;
517			}
518
519			}
520			}
521	chrisfen	721
522	tim	1024	}
523
524
525	gezelter	1752	void DumpReader::parseSiteLine(const std::string& line) {
526
527			StringTokenizer tokenizer(line);
528			int nTokens;
529
530			nTokens = tokenizer.countTokens();
531
532			if (nTokens < 2) {
533			sprintf(painCave.errMsg,
534			"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
535			painCave.isFatal = 1;
536			simError();
537			}
538
539			/**
540			* The first token is the global integrable object index.
541			*/
542
543			int index = tokenizer.nextTokenAsInt();
544	gezelter	1769	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
545			if (sd == NULL) {
546	gezelter	1752	return;
547			}
548
549			/**
550			* Test to see if the next token is an integer or not. If not,
551			* we've got data on the integrable object itself. If there is an
552			* integer, we're parsing data for a site on a rigid body.
553			*/
554
555			std::string indexTest = tokenizer.peekNextToken();
556			std::istringstream i(indexTest);
557			int siteIndex;
558			if (i >> siteIndex) {
559			// chew up this token and parse as an int:
560			siteIndex = tokenizer.nextTokenAsInt();
561	gezelter	1769	RigidBody* rb = static_cast<RigidBody*>(sd);
562	gezelter	1752	sd = rb->getAtoms()[siteIndex];
563			}
564
565			/**
566			* The next token contains information on what follows.
567			*/
568			std::string type = tokenizer.nextToken();
569			int size = type.size();
570
571			for(int i = 0; i < size; ++i) {
572			switch(type[i]) {
573
574			case 'u' : {
575
576			RealType particlePot;
577			particlePot = tokenizer.nextTokenAsDouble();
578			sd->setParticlePot(particlePot);
579			break;
580			}
581			case 'c' : {
582
583			RealType flucQPos;
584			flucQPos = tokenizer.nextTokenAsDouble();
585			sd->setFlucQPos(flucQPos);
586			break;
587			}
588			case 'w' : {
589
590			RealType flucQVel;
591			flucQVel = tokenizer.nextTokenAsDouble();
592			sd->setFlucQVel(flucQVel);
593			break;
594			}
595			case 'g' : {
596
597			RealType flucQFrc;
598			flucQFrc = tokenizer.nextTokenAsDouble();
599			sd->setFlucQFrc(flucQFrc);
600			break;
601			}
602			case 'e' : {
603
604			Vector3d eField;
605			eField[0] = tokenizer.nextTokenAsDouble();
606			eField[1] = tokenizer.nextTokenAsDouble();
607			eField[2] = tokenizer.nextTokenAsDouble();
608			sd->setElectricField(eField);
609			break;
610			}
611			default: {
612			sprintf(painCave.errMsg,
613			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
614			painCave.isFatal = 1;
615			simError();
616			break;
617			}
618			}
619			}
620			}
621
622
623	tim	1024	void DumpReader::readStuntDoubles(std::istream& inputStream) {
624	gezelter	1752
625	tim	1024	inputStream.getline(buffer, bufferSize);
626			std::string line(buffer);
627
628			if (line.find("<StuntDoubles>") == std::string::npos) {
629	chrisfen	721	sprintf(painCave.errMsg,
630	tim	1024	"DumpReader Error: Missing <StuntDoubles>\n");
631	chrisfen	721	painCave.isFatal = 1;
632	tim	1024	simError();
633			}
634
635			while(inputStream.getline(buffer, bufferSize)) {
636			line = buffer;
637
638			if(line.find("</StuntDoubles>") != std::string::npos) {
639			break;
640			}
641
642			parseDumpLine(line);
643			}
644
645			}
646
647	gezelter	1752	void DumpReader::readSiteData(std::istream& inputStream) {
648
649			inputStream.getline(buffer, bufferSize);
650			std::string line(buffer);
651
652			if (line.find("<SiteData>") == std::string::npos) {
653			// site data isn't required for a simulation, so skip
654			return;
655			}
656
657			while(inputStream.getline(buffer, bufferSize)) {
658			line = buffer;
659
660			if(line.find("</SiteData>") != std::string::npos) {
661			break;
662			}
663
664			parseSiteLine(line);
665			}
666
667			}
668
669	tim	1024	void DumpReader::readFrameProperties(std::istream& inputStream) {
670
671			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
672			inputStream.getline(buffer, bufferSize);
673			std::string line(buffer);
674
675			if (line.find("<FrameData>") == std::string::npos) {
676			sprintf(painCave.errMsg,
677			"DumpReader Error: Missing <FrameData>\n");
678			painCave.isFatal = 1;
679			simError();
680			}
681
682			while(inputStream.getline(buffer, bufferSize)) {
683			line = buffer;
684
685			if(line.find("</FrameData>") != std::string::npos) {
686			break;
687			}
688
689			StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
690			if (!tokenizer.hasMoreTokens()) {
691	chrisfen	721	sprintf(painCave.errMsg,
692	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
693	chrisfen	721	painCave.isFatal = 1;
694	tim	1024	simError();
695			}
696
697			std::string propertyName = tokenizer.nextToken();
698			if (propertyName == "Time") {
699			RealType currTime = tokenizer.nextTokenAsDouble();
700			s->setTime(currTime);
701			} else if (propertyName == "Hmat"){
702			Mat3x3d hmat;
703			hmat(0, 0) = tokenizer.nextTokenAsDouble();
704			hmat(0, 1) = tokenizer.nextTokenAsDouble();
705			hmat(0, 2) = tokenizer.nextTokenAsDouble();
706			hmat(1, 0) = tokenizer.nextTokenAsDouble();
707			hmat(1, 1) = tokenizer.nextTokenAsDouble();
708			hmat(1, 2) = tokenizer.nextTokenAsDouble();
709			hmat(2, 0) = tokenizer.nextTokenAsDouble();
710			hmat(2, 1) = tokenizer.nextTokenAsDouble();
711			hmat(2, 2) = tokenizer.nextTokenAsDouble();
712			s->setHmat(hmat);
713			} else if (propertyName == "Thermostat") {
714	gezelter	1764	pair<RealType, RealType> thermostat;
715			thermostat.first = tokenizer.nextTokenAsDouble();
716			thermostat.second = tokenizer.nextTokenAsDouble();
717			s->setThermostat(thermostat);
718	tim	1024	} else if (propertyName == "Barostat") {
719			Mat3x3d eta;
720			eta(0, 0) = tokenizer.nextTokenAsDouble();
721			eta(0, 1) = tokenizer.nextTokenAsDouble();
722			eta(0, 2) = tokenizer.nextTokenAsDouble();
723			eta(1, 0) = tokenizer.nextTokenAsDouble();
724			eta(1, 1) = tokenizer.nextTokenAsDouble();
725			eta(1, 2) = tokenizer.nextTokenAsDouble();
726			eta(2, 0) = tokenizer.nextTokenAsDouble();
727			eta(2, 1) = tokenizer.nextTokenAsDouble();
728			eta(2, 2) = tokenizer.nextTokenAsDouble();
729	gezelter	1764	s->setBarostat(eta);
730	tim	1024	} else {
731			sprintf(painCave.errMsg,
732			"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
733			painCave.isFatal = 0;
734			simError();
735			}
736
737			}
738
739			}
740
741	chrisfen	721
742	gezelter	1390	}//end namespace OpenMD