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;
      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::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("<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* 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::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* integrableObject = info_->getIOIndexToIntegrableObject(index);
    if (integrableObject == NULL) {
      return;
    }
    StuntDouble* sd = integrableObject;

    /**
     * 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*>(integrableObject);
      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") {
        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:	1752
Committed:	Sun Jun 10 14:05:02 2012 UTC (12 years, 10 months ago) by gezelter
File size:	21658 byte(s)
Log Message:	Added SiteData parsing and writing.
#	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	gezelter	1752	bool foundOpenSiteDataTag = false;
147	tim	1024	while(inFile_->getline(buffer, bufferSize)) {
148			++lineNo;
149
150			std::string line = buffer;
151			currPos = inFile_->tellg();
152			if (line.find("<Snapshot>")!= std::string::npos) {
153			if (foundOpenSnapshotTag) {
154	chrisfen	721	sprintf(painCave.errMsg,
155	tim	1024	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
156			filename_.c_str());
157	chrisfen	721	painCave.isFatal = 1;
158	tim	1024	simError();
159			}
160			foundOpenSnapshotTag = true;
161			foundClosedSnapshotTag = false;
162			framePos_.push_back(prevPos);
163
164			} else if (line.find("</Snapshot>") != std::string::npos){
165			if (!foundOpenSnapshotTag) {
166			sprintf(painCave.errMsg,
167			"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
168			filename_.c_str());
169			painCave.isFatal = 1;
170	chrisfen	721	simError();
171	tim	1024	}
172
173			if (foundClosedSnapshotTag) {
174			sprintf(painCave.errMsg,
175			"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
176			filename_.c_str());
177			painCave.isFatal = 1;
178			simError();
179			}
180			foundClosedSnapshotTag = true;
181			foundOpenSnapshotTag = false;
182			}
183			prevPos = currPos;
184			}
185
186			// only found <Snapshot> for the last frame means the file is corrupted, we should discard
187			// it and give a warning message
188			if (foundOpenSnapshotTag) {
189			sprintf(painCave.errMsg,
190			"DumpReader: last frame in %s is invalid\n", filename_.c_str());
191			painCave.isFatal = 0;
192			simError();
193			framePos_.pop_back();
194			}
195
196	chrisfen	721	nframes_ = framePos_.size();
197	tim	1024
198			if (nframes_ == 0) {
199			sprintf(painCave.errMsg,
200			"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
201			painCave.isFatal = 1;
202			simError();
203			}
204	chrisfen	721	#ifdef IS_MPI
205			}
206
207			MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
208	tim	1024
209	chrisfen	721	#endif // is_mpi
210	tim	1024
211	chrisfen	721	isScanned_ = true;
212			}
213
214			void DumpReader::readFrame(int whichFrame) {
215			if (!isScanned_)
216			scanFile();
217
218			int storageLayout = info_->getSnapshotManager()->getStorageLayout();
219
220			if (storageLayout & DataStorage::dslPosition) {
221			needPos_ = true;
222			} else {
223			needPos_ = false;
224			}
225
226			if (storageLayout & DataStorage::dslVelocity) {
227			needVel_ = true;
228			} else {
229			needVel_ = false;
230			}
231
232			if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
233			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			Vector3d com;
249			Vector3d comvel;
250			Vector3d comw;
251	chuckv	1112	if (needPos_ && needVel_){
252			info_->getComAll(com, comvel);
253			comw = info_->getAngularMomentum();
254			}else{
255			com = info_->getCom();
256			comvel = 0.0;
257			comw = 0.0;
258			}
259	gezelter	1104	s->setCOMprops(com, comvel, comw);
260			}
261
262	chrisfen	721	}
263
264	tim	1024	void DumpReader::readSet(int whichFrame) {
265			std::string line;
266
267	chrisfen	721	#ifndef IS_MPI
268			inFile_->clear();
269			inFile_->seekg(framePos_[whichFrame]);
270	tim	1024
271			std::istream& inputStream = *inFile_;
272
273			#else
274			int masterNode = 0;
275			std::stringstream sstream;
276			if (worldRank == masterNode) {
277			std::string sendBuffer;
278
279			inFile_->clear();
280			inFile_->seekg(framePos_[whichFrame]);
281
282			while (inFile_->getline(buffer, bufferSize)) {
283
284			line = buffer;
285			sendBuffer += line;
286			sendBuffer += '\n';
287			if (line.find("</Snapshot>") != std::string::npos) {
288			break;
289			}
290			}
291
292			int sendBufferSize = sendBuffer.size();
293			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
294			MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
295
296			sstream.str(sendBuffer);
297			} else {
298			int sendBufferSize;
299			MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
300			char * recvBuffer = new char[sendBufferSize+1];
301	gezelter	1313	assert(recvBuffer);
302			recvBuffer[sendBufferSize] = '\0';
303	tim	1024	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
304			sstream.str(recvBuffer);
305	gezelter	1313	delete [] recvBuffer;
306	tim	1024	}
307
308			std::istream& inputStream = sstream;
309			#endif
310
311			inputStream.getline(buffer, bufferSize);
312
313			line = buffer;
314			if (line.find("<Snapshot>") == std::string::npos) {
315	chrisfen	721	sprintf(painCave.errMsg,
316	tim	1024	"DumpReader Error: can not find <Snapshot>\n");
317	chrisfen	721	painCave.isFatal = 1;
318			simError();
319			}
320	tim	1024
321			//read frameData
322			readFrameProperties(inputStream);
323
324			//read StuntDoubles
325			readStuntDoubles(inputStream);
326
327			inputStream.getline(buffer, bufferSize);
328			line = buffer;
329	gezelter	1752
330			if (line.find("<SiteData>") != std::string::npos) {
331			//read SiteData
332			readSiteData(inputStream);
333			} else {
334			if (line.find("</Snapshot>") == std::string::npos) {
335			sprintf(painCave.errMsg,
336			"DumpReader Error: can not find </Snapshot>\n");
337			painCave.isFatal = 1;
338			simError();
339			}
340			}
341	chrisfen	721	}
342
343	tim	1024	void DumpReader::parseDumpLine(const std::string& line) {
344
345
346	chrisfen	721	StringTokenizer tokenizer(line);
347			int nTokens;
348
349			nTokens = tokenizer.countTokens();
350
351	gezelter	1450	if (nTokens < 2) {
352	chrisfen	721	sprintf(painCave.errMsg,
353	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
354	chrisfen	721	painCave.isFatal = 1;
355			simError();
356			}
357	tim	1024
358			int index = tokenizer.nextTokenAsInt();
359
360			StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
361
362			if (integrableObject == NULL) {
363			return;
364			}
365			std::string type = tokenizer.nextToken();
366			int size = type.size();
367	gezelter	1037
368	gezelter	1450	size_t found;
369
370			if (needPos_) {
371			found = type.find("p");
372			if (found == std::string::npos) {
373			sprintf(painCave.errMsg,
374			"DumpReader Error: StuntDouble %d has no Position\n"
375			"\tField (\"p\") specified.\n%s\n", index,
376			line.c_str());
377			painCave.isFatal = 1;
378			simError();
379			}
380			}
381
382			if (integrableObject->isDirectional()) {
383			if (needQuaternion_) {
384			found = type.find("q");
385			if (found == std::string::npos) {
386			sprintf(painCave.errMsg,
387			"DumpReader Error: Directional StuntDouble %d has no\n"
388			"\tQuaternion Field (\"q\") specified.\n%s\n", index,
389			line.c_str());
390			painCave.isFatal = 1;
391			simError();
392			}
393			}
394			}
395
396	tim	1024	for(int i = 0; i < size; ++i) {
397			switch(type[i]) {
398
399			case 'p': {
400			Vector3d pos;
401			pos[0] = tokenizer.nextTokenAsDouble();
402			pos[1] = tokenizer.nextTokenAsDouble();
403			pos[2] = tokenizer.nextTokenAsDouble();
404			if (needPos_) {
405			integrableObject->setPos(pos);
406			}
407			break;
408			}
409			case 'v' : {
410			Vector3d vel;
411			vel[0] = tokenizer.nextTokenAsDouble();
412			vel[1] = tokenizer.nextTokenAsDouble();
413			vel[2] = tokenizer.nextTokenAsDouble();
414			if (needVel_) {
415			integrableObject->setVel(vel);
416			}
417			break;
418			}
419
420			case 'q' : {
421			Quat4d q;
422			if (integrableObject->isDirectional()) {
423
424			q[0] = tokenizer.nextTokenAsDouble();
425			q[1] = tokenizer.nextTokenAsDouble();
426			q[2] = tokenizer.nextTokenAsDouble();
427			q[3] = tokenizer.nextTokenAsDouble();
428
429			RealType qlen = q.length();
430	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
431	tim	1024
432			sprintf(painCave.errMsg,
433			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
434			painCave.isFatal = 1;
435			simError();
436
437			}
438
439			q.normalize();
440			if (needQuaternion_) {
441			integrableObject->setQ(q);
442			}
443			}
444			break;
445			}
446			case 'j' : {
447			Vector3d ji;
448			if (integrableObject->isDirectional()) {
449			ji[0] = tokenizer.nextTokenAsDouble();
450			ji[1] = tokenizer.nextTokenAsDouble();
451			ji[2] = tokenizer.nextTokenAsDouble();
452			if (needAngMom_) {
453			integrableObject->setJ(ji);
454			}
455			}
456	gezelter	1037	break;
457	tim	1024	}
458			case 'f': {
459
460			Vector3d force;
461			force[0] = tokenizer.nextTokenAsDouble();
462			force[1] = tokenizer.nextTokenAsDouble();
463			force[2] = tokenizer.nextTokenAsDouble();
464			integrableObject->setFrc(force);
465			break;
466			}
467			case 't' : {
468
469			Vector3d torque;
470			torque[0] = tokenizer.nextTokenAsDouble();
471			torque[1] = tokenizer.nextTokenAsDouble();
472			torque[2] = tokenizer.nextTokenAsDouble();
473			integrableObject->setTrq(torque);
474			break;
475			}
476	gezelter	1629	case 'u' : {
477
478			RealType particlePot;
479			particlePot = tokenizer.nextTokenAsDouble();
480			integrableObject->setParticlePot(particlePot);
481			break;
482			}
483	gezelter	1714	case 'c' : {
484
485			RealType flucQPos;
486			flucQPos = tokenizer.nextTokenAsDouble();
487			integrableObject->setFlucQPos(flucQPos);
488			break;
489			}
490			case 'w' : {
491
492			RealType flucQVel;
493			flucQVel = tokenizer.nextTokenAsDouble();
494			integrableObject->setFlucQVel(flucQVel);
495			break;
496			}
497			case 'g' : {
498
499			RealType flucQFrc;
500			flucQFrc = tokenizer.nextTokenAsDouble();
501			integrableObject->setFlucQFrc(flucQFrc);
502			break;
503			}
504			case 'e' : {
505
506			Vector3d eField;
507			eField[0] = tokenizer.nextTokenAsDouble();
508			eField[1] = tokenizer.nextTokenAsDouble();
509			eField[2] = tokenizer.nextTokenAsDouble();
510			integrableObject->setElectricField(eField);
511			break;
512			}
513	tim	1024	default: {
514			sprintf(painCave.errMsg,
515			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
516			painCave.isFatal = 1;
517			simError();
518			break;
519			}
520
521			}
522			}
523	chrisfen	721
524	tim	1024	}
525
526
527	gezelter	1752	void DumpReader::parseSiteLine(const std::string& line) {
528
529			StringTokenizer tokenizer(line);
530			int nTokens;
531
532			nTokens = tokenizer.countTokens();
533
534			if (nTokens < 2) {
535			sprintf(painCave.errMsg,
536			"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
537			painCave.isFatal = 1;
538			simError();
539			}
540
541			/**
542			* The first token is the global integrable object index.
543			*/
544
545			int index = tokenizer.nextTokenAsInt();
546			StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
547			if (integrableObject == NULL) {
548			return;
549			}
550			StuntDouble* sd = integrableObject;
551
552			/**
553			* Test to see if the next token is an integer or not. If not,
554			* we've got data on the integrable object itself. If there is an
555			* integer, we're parsing data for a site on a rigid body.
556			*/
557
558			std::string indexTest = tokenizer.peekNextToken();
559			std::istringstream i(indexTest);
560			int siteIndex;
561			if (i >> siteIndex) {
562			// chew up this token and parse as an int:
563			siteIndex = tokenizer.nextTokenAsInt();
564			RigidBody* rb = static_cast<RigidBody*>(integrableObject);
565			sd = rb->getAtoms()[siteIndex];
566			}
567
568			/**
569			* The next token contains information on what follows.
570			*/
571			std::string type = tokenizer.nextToken();
572			int size = type.size();
573
574			for(int i = 0; i < size; ++i) {
575			switch(type[i]) {
576
577			case 'u' : {
578
579			RealType particlePot;
580			particlePot = tokenizer.nextTokenAsDouble();
581			sd->setParticlePot(particlePot);
582			break;
583			}
584			case 'c' : {
585
586			RealType flucQPos;
587			flucQPos = tokenizer.nextTokenAsDouble();
588			sd->setFlucQPos(flucQPos);
589			break;
590			}
591			case 'w' : {
592
593			RealType flucQVel;
594			flucQVel = tokenizer.nextTokenAsDouble();
595			sd->setFlucQVel(flucQVel);
596			break;
597			}
598			case 'g' : {
599
600			RealType flucQFrc;
601			flucQFrc = tokenizer.nextTokenAsDouble();
602			sd->setFlucQFrc(flucQFrc);
603			break;
604			}
605			case 'e' : {
606
607			Vector3d eField;
608			eField[0] = tokenizer.nextTokenAsDouble();
609			eField[1] = tokenizer.nextTokenAsDouble();
610			eField[2] = tokenizer.nextTokenAsDouble();
611			sd->setElectricField(eField);
612			break;
613			}
614			default: {
615			sprintf(painCave.errMsg,
616			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
617			painCave.isFatal = 1;
618			simError();
619			break;
620			}
621			}
622			}
623			}
624
625
626	tim	1024	void DumpReader::readStuntDoubles(std::istream& inputStream) {
627	gezelter	1752
628	tim	1024	inputStream.getline(buffer, bufferSize);
629			std::string line(buffer);
630
631			if (line.find("<StuntDoubles>") == std::string::npos) {
632	chrisfen	721	sprintf(painCave.errMsg,
633	tim	1024	"DumpReader Error: Missing <StuntDoubles>\n");
634	chrisfen	721	painCave.isFatal = 1;
635	tim	1024	simError();
636			}
637
638			while(inputStream.getline(buffer, bufferSize)) {
639			line = buffer;
640
641			if(line.find("</StuntDoubles>") != std::string::npos) {
642			break;
643			}
644
645			parseDumpLine(line);
646			}
647
648			}
649
650	gezelter	1752	void DumpReader::readSiteData(std::istream& inputStream) {
651
652			inputStream.getline(buffer, bufferSize);
653			std::string line(buffer);
654
655			if (line.find("<SiteData>") == std::string::npos) {
656			// site data isn't required for a simulation, so skip
657			return;
658			}
659
660			while(inputStream.getline(buffer, bufferSize)) {
661			line = buffer;
662
663			if(line.find("</SiteData>") != std::string::npos) {
664			break;
665			}
666
667			parseSiteLine(line);
668			}
669
670			}
671
672	tim	1024	void DumpReader::readFrameProperties(std::istream& inputStream) {
673
674			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
675			inputStream.getline(buffer, bufferSize);
676			std::string line(buffer);
677
678			if (line.find("<FrameData>") == std::string::npos) {
679			sprintf(painCave.errMsg,
680			"DumpReader Error: Missing <FrameData>\n");
681			painCave.isFatal = 1;
682			simError();
683			}
684
685			while(inputStream.getline(buffer, bufferSize)) {
686			line = buffer;
687
688			if(line.find("</FrameData>") != std::string::npos) {
689			break;
690			}
691
692			StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
693			if (!tokenizer.hasMoreTokens()) {
694	chrisfen	721	sprintf(painCave.errMsg,
695	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
696	chrisfen	721	painCave.isFatal = 1;
697	tim	1024	simError();
698			}
699
700			std::string propertyName = tokenizer.nextToken();
701			if (propertyName == "Time") {
702			RealType currTime = tokenizer.nextTokenAsDouble();
703			s->setTime(currTime);
704			} else if (propertyName == "Hmat"){
705			Mat3x3d hmat;
706			hmat(0, 0) = tokenizer.nextTokenAsDouble();
707			hmat(0, 1) = tokenizer.nextTokenAsDouble();
708			hmat(0, 2) = tokenizer.nextTokenAsDouble();
709			hmat(1, 0) = tokenizer.nextTokenAsDouble();
710			hmat(1, 1) = tokenizer.nextTokenAsDouble();
711			hmat(1, 2) = tokenizer.nextTokenAsDouble();
712			hmat(2, 0) = tokenizer.nextTokenAsDouble();
713			hmat(2, 1) = tokenizer.nextTokenAsDouble();
714			hmat(2, 2) = tokenizer.nextTokenAsDouble();
715			s->setHmat(hmat);
716			} else if (propertyName == "Thermostat") {
717			RealType chi = tokenizer.nextTokenAsDouble();
718			RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
719			s->setChi(chi);
720			s->setIntegralOfChiDt(integralOfChiDt);
721			} else if (propertyName == "Barostat") {
722			Mat3x3d eta;
723			eta(0, 0) = tokenizer.nextTokenAsDouble();
724			eta(0, 1) = tokenizer.nextTokenAsDouble();
725			eta(0, 2) = tokenizer.nextTokenAsDouble();
726			eta(1, 0) = tokenizer.nextTokenAsDouble();
727			eta(1, 1) = tokenizer.nextTokenAsDouble();
728			eta(1, 2) = tokenizer.nextTokenAsDouble();
729			eta(2, 0) = tokenizer.nextTokenAsDouble();
730			eta(2, 1) = tokenizer.nextTokenAsDouble();
731			eta(2, 2) = tokenizer.nextTokenAsDouble();
732			s->setEta(eta);
733			} else {
734			sprintf(painCave.errMsg,
735			"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
736			painCave.isFatal = 0;
737			simError();
738			}
739
740			}
741
742			}
743
744	chrisfen	721
745	gezelter	1390	}//end namespace OpenMD