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, 234107 (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 
 
#ifdef IS_MPI 
#include <mpi.h> 
#endif
 
#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"
 
 
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) { 

    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;

      int lineNo = 0; 
      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_) {
      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;
        }
        case 's' : {

           RealType sPot;
           sPot = tokenizer.nextTokenAsDouble(); 
           sd->setSitePotential(sPot);          
           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();

      if (sd->isRigidBody()) {
        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;
      }
      case 's' : {
        
        RealType sPot;
        sPot = tokenizer.nextTokenAsDouble(); 
        sd->setSitePotential(sPot);          
        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) {

    std::string line(buffer);

    // We already found the starting <SiteData> tag or we wouldn't be
    // here, so just start parsing until we get to the ending
    // </SiteData> tag:
    
    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:	2069
Committed:	Thu Mar 5 16:30:23 2015 UTC (10 years, 1 month ago) by gezelter
File size:	21693 byte(s)
Log Message:	More g++ warning fixes
#	Content
1	/*
2	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#define _LARGEFILE_SOURCE64
44	#define _FILE_OFFSET_BITS 64
45
46	#ifdef IS_MPI
47	#include <mpi.h>
48	#endif
49
50	#include <sys/types.h>
51	#include <sys/stat.h>
52
53	#include <iostream>
54	#include <math.h>
55
56	#include <stdio.h>
57	#include <stdlib.h>
58	#include <string.h>
59
60	#include "io/DumpReader.hpp"
61	#include "primitives/Molecule.hpp"
62	#include "utils/simError.h"
63	#include "utils/MemoryUtils.hpp"
64	#include "utils/StringTokenizer.hpp"
65	#include "brains/Thermo.hpp"
66
67
68	namespace OpenMD {
69
70	DumpReader::DumpReader(SimInfo* info, const std::string& filename)
71	: info_(info), filename_(filename), isScanned_(false), nframes_(0), needCOMprops_(false) {
72
73	#ifdef IS_MPI
74
75	if (worldRank == 0) {
76	#endif
77
78	inFile_ = new std::ifstream(filename_.c_str(),
79	ifstream::in \| ifstream::binary);
80
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	#ifdef IS_MPI
90
91	}
92
93	strcpy(checkPointMsg, "Dump file opened for reading successfully.");
94	errorCheckPoint();
95
96	#endif
97
98	return;
99	}
100
101	DumpReader::~DumpReader() {
102
103	#ifdef IS_MPI
104
105	if (worldRank == 0) {
106	#endif
107
108	delete inFile_;
109
110	#ifdef IS_MPI
111
112	}
113
114	strcpy(checkPointMsg, "Dump file closed successfully.");
115	errorCheckPoint();
116
117	#endif
118
119	return;
120	}
121
122	int DumpReader::getNFrames(void) {
123
124	if (!isScanned_)
125	scanFile();
126
127	return nframes_;
128	}
129
130	void DumpReader::scanFile(void) {
131
132	std::streampos prevPos;
133	std::streampos currPos;
134
135	#ifdef IS_MPI
136
137	if (worldRank == 0) {
138	#endif // is_mpi
139
140	currPos = inFile_->tellg();
141	prevPos = currPos;
142	bool foundOpenSnapshotTag = false;
143	bool foundClosedSnapshotTag = false;
144
145	int lineNo = 0;
146	while(inFile_->getline(buffer, bufferSize)) {
147	++lineNo;
148
149	std::string line = buffer;
150	currPos = inFile_->tellg();
151	if (line.find("<Snapshot>")!= std::string::npos) {
152	if (foundOpenSnapshotTag) {
153	sprintf(painCave.errMsg,
154	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
155	filename_.c_str());
156	painCave.isFatal = 1;
157	simError();
158	}
159	foundOpenSnapshotTag = true;
160	foundClosedSnapshotTag = false;
161	framePos_.push_back(prevPos);
162
163	} else if (line.find("</Snapshot>") != std::string::npos){
164	if (!foundOpenSnapshotTag) {
165	sprintf(painCave.errMsg,
166	"DumpReader:</Snapshot> appears before <Snapshot> at line %d in %s \n", lineNo,
167	filename_.c_str());
168	painCave.isFatal = 1;
169	simError();
170	}
171
172	if (foundClosedSnapshotTag) {
173	sprintf(painCave.errMsg,
174	"DumpReader:</Snapshot> appears multiply nested at line %d in %s \n", lineNo,
175	filename_.c_str());
176	painCave.isFatal = 1;
177	simError();
178	}
179	foundClosedSnapshotTag = true;
180	foundOpenSnapshotTag = false;
181	}
182	prevPos = currPos;
183	}
184
185	// only found <Snapshot> for the last frame means the file is corrupted, we should discard
186	// it and give a warning message
187	if (foundOpenSnapshotTag) {
188	sprintf(painCave.errMsg,
189	"DumpReader: last frame in %s is invalid\n", filename_.c_str());
190	painCave.isFatal = 0;
191	simError();
192	framePos_.pop_back();
193	}
194
195	nframes_ = framePos_.size();
196
197	if (nframes_ == 0) {
198	sprintf(painCave.errMsg,
199	"DumpReader: %s does not contain a valid frame\n", filename_.c_str());
200	painCave.isFatal = 1;
201	simError();
202	}
203	#ifdef IS_MPI
204	}
205
206	MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD);
207
208	#endif // is_mpi
209
210	isScanned_ = true;
211	}
212
213	void DumpReader::readFrame(int whichFrame) {
214	if (!isScanned_)
215	scanFile();
216
217	int storageLayout = info_->getSnapshotManager()->getStorageLayout();
218
219	if (storageLayout & DataStorage::dslPosition) {
220	needPos_ = true;
221	} else {
222	needPos_ = false;
223	}
224
225	if (storageLayout & DataStorage::dslVelocity) {
226	needVel_ = true;
227	} else {
228	needVel_ = false;
229	}
230
231	if (storageLayout & DataStorage::dslAmat \|\|
232	storageLayout & DataStorage::dslDipole \|\|
233	storageLayout & DataStorage::dslQuadrupole) {
234	needQuaternion_ = true;
235	} else {
236	needQuaternion_ = false;
237	}
238
239	if (storageLayout & DataStorage::dslAngularMomentum) {
240	needAngMom_ = true;
241	} else {
242	needAngMom_ = false;
243	}
244
245	readSet(whichFrame);
246
247	if (needCOMprops_) {
248	Thermo thermo(info_);
249	Vector3d com;
250
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	}
260	}
261
262	void DumpReader::readSet(int whichFrame) {
263	std::string line;
264
265	#ifndef IS_MPI
266	inFile_->clear();
267	inFile_->seekg(framePos_[whichFrame]);
268
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,
293	MPI_CHAR, masterNode, MPI_COMM_WORLD);
294
295	sstream.str(sendBuffer);
296	} else {
297	int sendBufferSize;
298	MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
299	char * recvBuffer = new char[sendBufferSize+1];
300	assert(recvBuffer);
301	recvBuffer[sendBufferSize] = '\0';
302	MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
303	sstream.str(recvBuffer);
304	delete [] recvBuffer;
305	}
306
307	std::istream& inputStream = sstream;
308	#endif
309
310	inputStream.getline(buffer, bufferSize);
311
312	line = buffer;
313	if (line.find("<Snapshot>") == std::string::npos) {
314	sprintf(painCave.errMsg,
315	"DumpReader Error: can not find <Snapshot>\n");
316	painCave.isFatal = 1;
317	simError();
318	}
319
320	//read frameData
321	readFrameProperties(inputStream);
322
323	//read StuntDoubles
324	readStuntDoubles(inputStream);
325
326	inputStream.getline(buffer, bufferSize);
327	line = buffer;
328
329	if (line.find("<SiteData>") != std::string::npos) {
330	//read SiteData
331	readSiteData(inputStream);
332	} else {
333	if (line.find("</Snapshot>") == std::string::npos) {
334	sprintf(painCave.errMsg,
335	"DumpReader Error: can not find </Snapshot>\n");
336	painCave.isFatal = 1;
337	simError();
338	}
339	}
340	}
341
342	void DumpReader::parseDumpLine(const std::string& line) {
343
344
345	StringTokenizer tokenizer(line);
346	int nTokens;
347
348	nTokens = tokenizer.countTokens();
349
350	if (nTokens < 2) {
351	sprintf(painCave.errMsg,
352	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
353	painCave.isFatal = 1;
354	simError();
355	}
356
357	int index = tokenizer.nextTokenAsInt();
358
359	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
360
361	if (sd == NULL) {
362	return;
363	}
364	std::string type = tokenizer.nextToken();
365	int size = type.size();
366
367	size_t found;
368
369	if (needPos_) {
370	found = type.find("p");
371	if (found == std::string::npos) {
372	sprintf(painCave.errMsg,
373	"DumpReader Error: StuntDouble %d has no Position\n"
374	"\tField (\"p\") specified.\n%s\n", index,
375	line.c_str());
376	painCave.isFatal = 1;
377	simError();
378	}
379	}
380
381	if (sd->isDirectional()) {
382	if (needQuaternion_) {
383	found = type.find("q");
384	if (found == std::string::npos) {
385	sprintf(painCave.errMsg,
386	"DumpReader Error: Directional StuntDouble %d has no\n"
387	"\tQuaternion Field (\"q\") specified.\n%s\n", index,
388	line.c_str());
389	painCave.isFatal = 1;
390	simError();
391	}
392	}
393	}
394
395	for(int i = 0; i < size; ++i) {
396	switch(type[i]) {
397
398	case 'p': {
399	Vector3d pos;
400	pos[0] = tokenizer.nextTokenAsDouble();
401	pos[1] = tokenizer.nextTokenAsDouble();
402	pos[2] = tokenizer.nextTokenAsDouble();
403	if (needPos_) {
404	sd->setPos(pos);
405	}
406	break;
407	}
408	case 'v' : {
409	Vector3d vel;
410	vel[0] = tokenizer.nextTokenAsDouble();
411	vel[1] = tokenizer.nextTokenAsDouble();
412	vel[2] = tokenizer.nextTokenAsDouble();
413	if (needVel_) {
414	sd->setVel(vel);
415	}
416	break;
417	}
418
419	case 'q' : {
420	Quat4d q;
421	if (sd->isDirectional()) {
422
423	q[0] = tokenizer.nextTokenAsDouble();
424	q[1] = tokenizer.nextTokenAsDouble();
425	q[2] = tokenizer.nextTokenAsDouble();
426	q[3] = tokenizer.nextTokenAsDouble();
427
428	RealType qlen = q.length();
429	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
430
431	sprintf(painCave.errMsg,
432	"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
433	painCave.isFatal = 1;
434	simError();
435
436	}
437
438	q.normalize();
439	if (needQuaternion_) {
440	sd->setQ(q);
441	}
442	}
443	break;
444	}
445	case 'j' : {
446	Vector3d ji;
447	if (sd->isDirectional()) {
448	ji[0] = tokenizer.nextTokenAsDouble();
449	ji[1] = tokenizer.nextTokenAsDouble();
450	ji[2] = tokenizer.nextTokenAsDouble();
451	if (needAngMom_) {
452	sd->setJ(ji);
453	}
454	}
455	break;
456	}
457	case 'f': {
458
459	Vector3d force;
460	force[0] = tokenizer.nextTokenAsDouble();
461	force[1] = tokenizer.nextTokenAsDouble();
462	force[2] = tokenizer.nextTokenAsDouble();
463	sd->setFrc(force);
464	break;
465	}
466	case 't' : {
467
468	Vector3d torque;
469	torque[0] = tokenizer.nextTokenAsDouble();
470	torque[1] = tokenizer.nextTokenAsDouble();
471	torque[2] = tokenizer.nextTokenAsDouble();
472	sd->setTrq(torque);
473	break;
474	}
475	case 'u' : {
476
477	RealType particlePot;
478	particlePot = tokenizer.nextTokenAsDouble();
479	sd->setParticlePot(particlePot);
480	break;
481	}
482	case 'c' : {
483
484	RealType flucQPos;
485	flucQPos = tokenizer.nextTokenAsDouble();
486	sd->setFlucQPos(flucQPos);
487	break;
488	}
489	case 'w' : {
490
491	RealType flucQVel;
492	flucQVel = tokenizer.nextTokenAsDouble();
493	sd->setFlucQVel(flucQVel);
494	break;
495	}
496	case 'g' : {
497
498	RealType flucQFrc;
499	flucQFrc = tokenizer.nextTokenAsDouble();
500	sd->setFlucQFrc(flucQFrc);
501	break;
502	}
503	case 'e' : {
504
505	Vector3d eField;
506	eField[0] = tokenizer.nextTokenAsDouble();
507	eField[1] = tokenizer.nextTokenAsDouble();
508	eField[2] = tokenizer.nextTokenAsDouble();
509	sd->setElectricField(eField);
510	break;
511	}
512	case 's' : {
513
514	RealType sPot;
515	sPot = tokenizer.nextTokenAsDouble();
516	sd->setSitePotential(sPot);
517	break;
518	}
519	default: {
520	sprintf(painCave.errMsg,
521	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
522	painCave.isFatal = 1;
523	simError();
524	break;
525	}
526
527	}
528	}
529	}
530
531
532	void DumpReader::parseSiteLine(const std::string& line) {
533
534	StringTokenizer tokenizer(line);
535	int nTokens;
536
537	nTokens = tokenizer.countTokens();
538
539	if (nTokens < 2) {
540	sprintf(painCave.errMsg,
541	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
542	painCave.isFatal = 1;
543	simError();
544	}
545
546	/**
547	* The first token is the global integrable object index.
548	*/
549
550	int index = tokenizer.nextTokenAsInt();
551	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
552	if (sd == NULL) {
553	return;
554	}
555
556	/**
557	* Test to see if the next token is an integer or not. If not,
558	* we've got data on the integrable object itself. If there is an
559	* integer, we're parsing data for a site on a rigid body.
560	*/
561
562	std::string indexTest = tokenizer.peekNextToken();
563	std::istringstream i(indexTest);
564	int siteIndex;
565	if (i >> siteIndex) {
566	// chew up this token and parse as an int:
567	siteIndex = tokenizer.nextTokenAsInt();
568
569	if (sd->isRigidBody()) {
570	RigidBody* rb = static_cast<RigidBody*>(sd);
571	sd = rb->getAtoms()[siteIndex];
572	}
573	}
574
575	/**
576	* The next token contains information on what follows.
577	*/
578	std::string type = tokenizer.nextToken();
579	int size = type.size();
580
581	for(int i = 0; i < size; ++i) {
582	switch(type[i]) {
583
584	case 'u' : {
585
586	RealType particlePot;
587	particlePot = tokenizer.nextTokenAsDouble();
588	sd->setParticlePot(particlePot);
589	break;
590	}
591	case 'c' : {
592
593	RealType flucQPos;
594	flucQPos = tokenizer.nextTokenAsDouble();
595	sd->setFlucQPos(flucQPos);
596	break;
597	}
598	case 'w' : {
599
600	RealType flucQVel;
601	flucQVel = tokenizer.nextTokenAsDouble();
602	sd->setFlucQVel(flucQVel);
603	break;
604	}
605	case 'g' : {
606
607	RealType flucQFrc;
608	flucQFrc = tokenizer.nextTokenAsDouble();
609	sd->setFlucQFrc(flucQFrc);
610	break;
611	}
612	case 'e' : {
613
614	Vector3d eField;
615	eField[0] = tokenizer.nextTokenAsDouble();
616	eField[1] = tokenizer.nextTokenAsDouble();
617	eField[2] = tokenizer.nextTokenAsDouble();
618	sd->setElectricField(eField);
619	break;
620	}
621	case 's' : {
622
623	RealType sPot;
624	sPot = tokenizer.nextTokenAsDouble();
625	sd->setSitePotential(sPot);
626	break;
627	}
628	default: {
629	sprintf(painCave.errMsg,
630	"DumpReader Error: %s is an unrecognized type\n", type.c_str());
631	painCave.isFatal = 1;
632	simError();
633	break;
634	}
635	}
636	}
637	}
638
639
640	void DumpReader::readStuntDoubles(std::istream& inputStream) {
641
642	inputStream.getline(buffer, bufferSize);
643	std::string line(buffer);
644
645	if (line.find("<StuntDoubles>") == std::string::npos) {
646	sprintf(painCave.errMsg,
647	"DumpReader Error: Missing <StuntDoubles>\n");
648	painCave.isFatal = 1;
649	simError();
650	}
651
652	while(inputStream.getline(buffer, bufferSize)) {
653	line = buffer;
654
655	if(line.find("</StuntDoubles>") != std::string::npos) {
656	break;
657	}
658
659	parseDumpLine(line);
660	}
661
662	}
663
664	void DumpReader::readSiteData(std::istream& inputStream) {
665
666	std::string line(buffer);
667
668	// We already found the starting <SiteData> tag or we wouldn't be
669	// here, so just start parsing until we get to the ending
670	// </SiteData> tag:
671
672	while(inputStream.getline(buffer, bufferSize)) {
673	line = buffer;
674
675	if(line.find("</SiteData>") != std::string::npos) {
676	break;
677	}
678
679	parseSiteLine(line);
680	}
681
682	}
683
684	void DumpReader::readFrameProperties(std::istream& inputStream) {
685
686	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
687	inputStream.getline(buffer, bufferSize);
688	std::string line(buffer);
689
690	if (line.find("<FrameData>") == std::string::npos) {
691	sprintf(painCave.errMsg,
692	"DumpReader Error: Missing <FrameData>\n");
693	painCave.isFatal = 1;
694	simError();
695	}
696
697	while(inputStream.getline(buffer, bufferSize)) {
698	line = buffer;
699
700	if(line.find("</FrameData>") != std::string::npos) {
701	break;
702	}
703
704	StringTokenizer tokenizer(line, " ;\t\n\r{}:,");
705	if (!tokenizer.hasMoreTokens()) {
706	sprintf(painCave.errMsg,
707	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
708	painCave.isFatal = 1;
709	simError();
710	}
711
712	std::string propertyName = tokenizer.nextToken();
713	if (propertyName == "Time") {
714	RealType currTime = tokenizer.nextTokenAsDouble();
715	s->setTime(currTime);
716	} else if (propertyName == "Hmat"){
717	Mat3x3d hmat;
718	hmat(0, 0) = tokenizer.nextTokenAsDouble();
719	hmat(0, 1) = tokenizer.nextTokenAsDouble();
720	hmat(0, 2) = tokenizer.nextTokenAsDouble();
721	hmat(1, 0) = tokenizer.nextTokenAsDouble();
722	hmat(1, 1) = tokenizer.nextTokenAsDouble();
723	hmat(1, 2) = tokenizer.nextTokenAsDouble();
724	hmat(2, 0) = tokenizer.nextTokenAsDouble();
725	hmat(2, 1) = tokenizer.nextTokenAsDouble();
726	hmat(2, 2) = tokenizer.nextTokenAsDouble();
727	s->setHmat(hmat);
728	} else if (propertyName == "Thermostat") {
729	pair<RealType, RealType> thermostat;
730	thermostat.first = tokenizer.nextTokenAsDouble();
731	thermostat.second = tokenizer.nextTokenAsDouble();
732	s->setThermostat(thermostat);
733	} else if (propertyName == "Barostat") {
734	Mat3x3d eta;
735	eta(0, 0) = tokenizer.nextTokenAsDouble();
736	eta(0, 1) = tokenizer.nextTokenAsDouble();
737	eta(0, 2) = tokenizer.nextTokenAsDouble();
738	eta(1, 0) = tokenizer.nextTokenAsDouble();
739	eta(1, 1) = tokenizer.nextTokenAsDouble();
740	eta(1, 2) = tokenizer.nextTokenAsDouble();
741	eta(2, 0) = tokenizer.nextTokenAsDouble();
742	eta(2, 1) = tokenizer.nextTokenAsDouble();
743	eta(2, 2) = tokenizer.nextTokenAsDouble();
744	s->setBarostat(eta);
745	} else {
746	sprintf(painCave.errMsg,
747	"DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());
748	painCave.isFatal = 0;
749	simError();
750	}
751
752	}
753
754	}
755
756
757	}//end namespace OpenMD