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;

      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::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0); 
    
#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();
      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::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);     
      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize, 
                            MPI::CHAR, masterNode);     
      
      sstream.str(sendBuffer);
    } else {
      int sendBufferSize;
      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
      char * recvBuffer = new char[sendBufferSize+1];
      assert(recvBuffer);
      recvBuffer[sendBufferSize] = '\0';
      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
      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:	1796
Committed:	Mon Sep 10 18:38:44 2012 UTC (12 years, 7 months ago) by gezelter
File size:	21345 byte(s)
Log Message:	Updating MPI calls to C++, fixing a DumpWriter bug, cleaning cruft
#	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	1782	* [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	1782	#include "brains/Thermo.hpp"
62	chrisfen	721
63			#ifdef IS_MPI
64			#include <mpi.h>
65	gezelter	1782	#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	1790	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	1793
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	gezelter	1796	MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
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			if (storageLayout & DataStorage::dslAmat \|\| storageLayout & DataStorage::dslElectroFrame) {
231			needQuaternion_ = true;
232			} else {
233			needQuaternion_ = false;
234			}
235
236			if (storageLayout & DataStorage::dslAngularMomentum) {
237			needAngMom_ = true;
238			} else {
239			needAngMom_ = false;
240			}
241
242			readSet(whichFrame);
243	gezelter	1104
244			if (needCOMprops_) {
245			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	gezelter	1782	Thermo thermo(info_);
247	gezelter	1104	Vector3d com;
248	gezelter	1782
249			if (needPos_ && needVel_) {
250			Vector3d comvel;
251			Vector3d comw;
252			thermo.getComAll(com, comvel);
253			comw = thermo.getAngularMomentum();
254			} else {
255			com = thermo.getCom();
256			}
257	gezelter	1104	}
258	chrisfen	721	}
259
260	tim	1024	void DumpReader::readSet(int whichFrame) {
261			std::string line;
262
263	chrisfen	721	#ifndef IS_MPI
264			inFile_->clear();
265			inFile_->seekg(framePos_[whichFrame]);
266	tim	1024
267			std::istream& inputStream = *inFile_;
268
269			#else
270			int masterNode = 0;
271			std::stringstream sstream;
272			if (worldRank == masterNode) {
273			std::string sendBuffer;
274
275			inFile_->clear();
276			inFile_->seekg(framePos_[whichFrame]);
277
278			while (inFile_->getline(buffer, bufferSize)) {
279
280			line = buffer;
281			sendBuffer += line;
282			sendBuffer += '\n';
283			if (line.find("</Snapshot>") != std::string::npos) {
284			break;
285			}
286			}
287
288			int sendBufferSize = sendBuffer.size();
289	gezelter	1796	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
290			MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
291			MPI::CHAR, masterNode);
292	tim	1024
293			sstream.str(sendBuffer);
294			} else {
295			int sendBufferSize;
296	gezelter	1796	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
297	tim	1024	char * recvBuffer = new char[sendBufferSize+1];
298	gezelter	1313	assert(recvBuffer);
299			recvBuffer[sendBufferSize] = '\0';
300	gezelter	1796	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
301	tim	1024	sstream.str(recvBuffer);
302	gezelter	1313	delete [] recvBuffer;
303	tim	1024	}
304
305			std::istream& inputStream = sstream;
306			#endif
307
308			inputStream.getline(buffer, bufferSize);
309
310			line = buffer;
311			if (line.find("<Snapshot>") == std::string::npos) {
312	chrisfen	721	sprintf(painCave.errMsg,
313	tim	1024	"DumpReader Error: can not find <Snapshot>\n");
314	chrisfen	721	painCave.isFatal = 1;
315			simError();
316			}
317	tim	1024
318			//read frameData
319			readFrameProperties(inputStream);
320
321			//read StuntDoubles
322			readStuntDoubles(inputStream);
323
324			inputStream.getline(buffer, bufferSize);
325			line = buffer;
326	gezelter	1782
327			if (line.find("<SiteData>") != std::string::npos) {
328			//read SiteData
329			readSiteData(inputStream);
330			} else {
331			if (line.find("</Snapshot>") == std::string::npos) {
332			sprintf(painCave.errMsg,
333			"DumpReader Error: can not find </Snapshot>\n");
334			painCave.isFatal = 1;
335			simError();
336			}
337			}
338	chrisfen	721	}
339
340	tim	1024	void DumpReader::parseDumpLine(const std::string& line) {
341
342
343	chrisfen	721	StringTokenizer tokenizer(line);
344			int nTokens;
345
346			nTokens = tokenizer.countTokens();
347
348	gezelter	1450	if (nTokens < 2) {
349	chrisfen	721	sprintf(painCave.errMsg,
350	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351	chrisfen	721	painCave.isFatal = 1;
352			simError();
353			}
354	tim	1024
355			int index = tokenizer.nextTokenAsInt();
356
357	gezelter	1782	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358	tim	1024
359	gezelter	1782	if (sd == NULL) {
360	tim	1024	return;
361			}
362			std::string type = tokenizer.nextToken();
363			int size = type.size();
364	gezelter	1037
365	gezelter	1450	size_t found;
366
367			if (needPos_) {
368			found = type.find("p");
369			if (found == std::string::npos) {
370			sprintf(painCave.errMsg,
371			"DumpReader Error: StuntDouble %d has no Position\n"
372			"\tField (\"p\") specified.\n%s\n", index,
373			line.c_str());
374			painCave.isFatal = 1;
375			simError();
376			}
377			}
378
379	gezelter	1782	if (sd->isDirectional()) {
380	gezelter	1450	if (needQuaternion_) {
381			found = type.find("q");
382			if (found == std::string::npos) {
383			sprintf(painCave.errMsg,
384			"DumpReader Error: Directional StuntDouble %d has no\n"
385			"\tQuaternion Field (\"q\") specified.\n%s\n", index,
386			line.c_str());
387			painCave.isFatal = 1;
388			simError();
389			}
390			}
391			}
392
393	tim	1024	for(int i = 0; i < size; ++i) {
394			switch(type[i]) {
395
396			case 'p': {
397			Vector3d pos;
398			pos[0] = tokenizer.nextTokenAsDouble();
399			pos[1] = tokenizer.nextTokenAsDouble();
400			pos[2] = tokenizer.nextTokenAsDouble();
401			if (needPos_) {
402	gezelter	1782	sd->setPos(pos);
403	tim	1024	}
404			break;
405			}
406			case 'v' : {
407			Vector3d vel;
408			vel[0] = tokenizer.nextTokenAsDouble();
409			vel[1] = tokenizer.nextTokenAsDouble();
410			vel[2] = tokenizer.nextTokenAsDouble();
411			if (needVel_) {
412	gezelter	1782	sd->setVel(vel);
413	tim	1024	}
414			break;
415			}
416
417			case 'q' : {
418			Quat4d q;
419	gezelter	1782	if (sd->isDirectional()) {
420	tim	1024
421			q[0] = tokenizer.nextTokenAsDouble();
422			q[1] = tokenizer.nextTokenAsDouble();
423			q[2] = tokenizer.nextTokenAsDouble();
424			q[3] = tokenizer.nextTokenAsDouble();
425
426			RealType qlen = q.length();
427	gezelter	1390	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428	tim	1024
429			sprintf(painCave.errMsg,
430			"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
431			painCave.isFatal = 1;
432			simError();
433
434			}
435
436			q.normalize();
437			if (needQuaternion_) {
438	gezelter	1782	sd->setQ(q);
439	tim	1024	}
440			}
441			break;
442			}
443			case 'j' : {
444			Vector3d ji;
445	gezelter	1782	if (sd->isDirectional()) {
446	tim	1024	ji[0] = tokenizer.nextTokenAsDouble();
447			ji[1] = tokenizer.nextTokenAsDouble();
448			ji[2] = tokenizer.nextTokenAsDouble();
449			if (needAngMom_) {
450	gezelter	1782	sd->setJ(ji);
451	tim	1024	}
452			}
453	gezelter	1037	break;
454	tim	1024	}
455			case 'f': {
456
457			Vector3d force;
458			force[0] = tokenizer.nextTokenAsDouble();
459			force[1] = tokenizer.nextTokenAsDouble();
460			force[2] = tokenizer.nextTokenAsDouble();
461	gezelter	1782	sd->setFrc(force);
462	tim	1024	break;
463			}
464			case 't' : {
465
466			Vector3d torque;
467			torque[0] = tokenizer.nextTokenAsDouble();
468			torque[1] = tokenizer.nextTokenAsDouble();
469			torque[2] = tokenizer.nextTokenAsDouble();
470	gezelter	1782	sd->setTrq(torque);
471	tim	1024	break;
472			}
473	gezelter	1610	case 'u' : {
474
475			RealType particlePot;
476			particlePot = tokenizer.nextTokenAsDouble();
477	gezelter	1782	sd->setParticlePot(particlePot);
478	gezelter	1610	break;
479			}
480	gezelter	1782	case 'c' : {
481
482			RealType flucQPos;
483			flucQPos = tokenizer.nextTokenAsDouble();
484			sd->setFlucQPos(flucQPos);
485			break;
486			}
487			case 'w' : {
488
489			RealType flucQVel;
490			flucQVel = tokenizer.nextTokenAsDouble();
491			sd->setFlucQVel(flucQVel);
492			break;
493			}
494			case 'g' : {
495
496			RealType flucQFrc;
497			flucQFrc = tokenizer.nextTokenAsDouble();
498			sd->setFlucQFrc(flucQFrc);
499			break;
500			}
501			case 'e' : {
502
503			Vector3d eField;
504			eField[0] = tokenizer.nextTokenAsDouble();
505			eField[1] = tokenizer.nextTokenAsDouble();
506			eField[2] = tokenizer.nextTokenAsDouble();
507			sd->setElectricField(eField);
508			break;
509			}
510	tim	1024	default: {
511			sprintf(painCave.errMsg,
512			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
513			painCave.isFatal = 1;
514			simError();
515			break;
516			}
517
518			}
519			}
520	chrisfen	721
521	tim	1024	}
522
523
524	gezelter	1782	void DumpReader::parseSiteLine(const std::string& line) {
525
526			StringTokenizer tokenizer(line);
527			int nTokens;
528
529			nTokens = tokenizer.countTokens();
530
531			if (nTokens < 2) {
532			sprintf(painCave.errMsg,
533			"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
534			painCave.isFatal = 1;
535			simError();
536			}
537
538			/**
539			* The first token is the global integrable object index.
540			*/
541
542			int index = tokenizer.nextTokenAsInt();
543			StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
544			if (sd == NULL) {
545			return;
546			}
547
548			/**
549			* Test to see if the next token is an integer or not. If not,
550			* we've got data on the integrable object itself. If there is an
551			* integer, we're parsing data for a site on a rigid body.
552			*/
553
554			std::string indexTest = tokenizer.peekNextToken();
555			std::istringstream i(indexTest);
556			int siteIndex;
557			if (i >> siteIndex) {
558			// chew up this token and parse as an int:
559			siteIndex = tokenizer.nextTokenAsInt();
560			RigidBody* rb = static_cast<RigidBody*>(sd);
561			sd = rb->getAtoms()[siteIndex];
562			}
563
564			/**
565			* The next token contains information on what follows.
566			*/
567			std::string type = tokenizer.nextToken();
568			int size = type.size();
569
570			for(int i = 0; i < size; ++i) {
571			switch(type[i]) {
572
573			case 'u' : {
574
575			RealType particlePot;
576			particlePot = tokenizer.nextTokenAsDouble();
577			sd->setParticlePot(particlePot);
578			break;
579			}
580			case 'c' : {
581
582			RealType flucQPos;
583			flucQPos = tokenizer.nextTokenAsDouble();
584			sd->setFlucQPos(flucQPos);
585			break;
586			}
587			case 'w' : {
588
589			RealType flucQVel;
590			flucQVel = tokenizer.nextTokenAsDouble();
591			sd->setFlucQVel(flucQVel);
592			break;
593			}
594			case 'g' : {
595
596			RealType flucQFrc;
597			flucQFrc = tokenizer.nextTokenAsDouble();
598			sd->setFlucQFrc(flucQFrc);
599			break;
600			}
601			case 'e' : {
602
603			Vector3d eField;
604			eField[0] = tokenizer.nextTokenAsDouble();
605			eField[1] = tokenizer.nextTokenAsDouble();
606			eField[2] = tokenizer.nextTokenAsDouble();
607			sd->setElectricField(eField);
608			break;
609			}
610			default: {
611			sprintf(painCave.errMsg,
612			"DumpReader Error: %s is an unrecognized type\n", type.c_str());
613			painCave.isFatal = 1;
614			simError();
615			break;
616			}
617			}
618			}
619			}
620
621
622	tim	1024	void DumpReader::readStuntDoubles(std::istream& inputStream) {
623	gezelter	1782
624	tim	1024	inputStream.getline(buffer, bufferSize);
625			std::string line(buffer);
626
627			if (line.find("<StuntDoubles>") == std::string::npos) {
628	chrisfen	721	sprintf(painCave.errMsg,
629	tim	1024	"DumpReader Error: Missing <StuntDoubles>\n");
630	chrisfen	721	painCave.isFatal = 1;
631	tim	1024	simError();
632			}
633
634			while(inputStream.getline(buffer, bufferSize)) {
635			line = buffer;
636
637			if(line.find("</StuntDoubles>") != std::string::npos) {
638			break;
639			}
640
641			parseDumpLine(line);
642			}
643
644			}
645
646	gezelter	1782	void DumpReader::readSiteData(std::istream& inputStream) {
647
648			inputStream.getline(buffer, bufferSize);
649			std::string line(buffer);
650
651			if (line.find("<SiteData>") == std::string::npos) {
652			// site data isn't required for a simulation, so skip
653			return;
654			}
655
656			while(inputStream.getline(buffer, bufferSize)) {
657			line = buffer;
658
659			if(line.find("</SiteData>") != std::string::npos) {
660			break;
661			}
662
663			parseSiteLine(line);
664			}
665
666			}
667
668	tim	1024	void DumpReader::readFrameProperties(std::istream& inputStream) {
669
670			Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
671			inputStream.getline(buffer, bufferSize);
672			std::string line(buffer);
673
674			if (line.find("<FrameData>") == std::string::npos) {
675			sprintf(painCave.errMsg,
676			"DumpReader Error: Missing <FrameData>\n");
677			painCave.isFatal = 1;
678			simError();
679			}
680
681			while(inputStream.getline(buffer, bufferSize)) {
682			line = buffer;
683
684			if(line.find("</FrameData>") != std::string::npos) {
685			break;
686			}
687
688			StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
689			if (!tokenizer.hasMoreTokens()) {
690	chrisfen	721	sprintf(painCave.errMsg,
691	tim	1024	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
692	chrisfen	721	painCave.isFatal = 1;
693	tim	1024	simError();
694			}
695
696			std::string propertyName = tokenizer.nextToken();
697			if (propertyName == "Time") {
698			RealType currTime = tokenizer.nextTokenAsDouble();
699			s->setTime(currTime);
700			} else if (propertyName == "Hmat"){
701			Mat3x3d hmat;
702			hmat(0, 0) = tokenizer.nextTokenAsDouble();
703			hmat(0, 1) = tokenizer.nextTokenAsDouble();
704			hmat(0, 2) = tokenizer.nextTokenAsDouble();
705			hmat(1, 0) = tokenizer.nextTokenAsDouble();
706			hmat(1, 1) = tokenizer.nextTokenAsDouble();
707			hmat(1, 2) = tokenizer.nextTokenAsDouble();
708			hmat(2, 0) = tokenizer.nextTokenAsDouble();
709			hmat(2, 1) = tokenizer.nextTokenAsDouble();
710			hmat(2, 2) = tokenizer.nextTokenAsDouble();
711			s->setHmat(hmat);
712			} else if (propertyName == "Thermostat") {
713	gezelter	1782	pair<RealType, RealType> thermostat;
714			thermostat.first = tokenizer.nextTokenAsDouble();
715			thermostat.second = tokenizer.nextTokenAsDouble();
716			s->setThermostat(thermostat);
717	tim	1024	} else if (propertyName == "Barostat") {
718			Mat3x3d eta;
719			eta(0, 0) = tokenizer.nextTokenAsDouble();
720			eta(0, 1) = tokenizer.nextTokenAsDouble();
721			eta(0, 2) = tokenizer.nextTokenAsDouble();
722			eta(1, 0) = tokenizer.nextTokenAsDouble();
723			eta(1, 1) = tokenizer.nextTokenAsDouble();
724			eta(1, 2) = tokenizer.nextTokenAsDouble();
725			eta(2, 0) = tokenizer.nextTokenAsDouble();
726			eta(2, 1) = tokenizer.nextTokenAsDouble();
727			eta(2, 2) = tokenizer.nextTokenAsDouble();
728	gezelter	1782	s->setBarostat(eta);
729	tim	1024	} else {
730			sprintf(painCave.errMsg,
731			"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
732			painCave.isFatal = 0;
733			simError();
734			}
735
736			}
737
738			}
739
740	chrisfen	721
741	gezelter	1390	}//end namespace OpenMD