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
#	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, 24107 (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	#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	#include "brains/Thermo.hpp"
62
63	#ifdef IS_MPI
64	#include <mpi.h>
65	#endif
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	int lineNo = 0;
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	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	sprintf(painCave.errMsg,
153	"DumpReader:<Snapshot> is multiply nested at line %d in %s \n", lineNo,
154	filename_.c_str());
155	painCave.isFatal = 1;
156	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	simError();
169	}
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	nframes_ = framePos_.size();
195
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	#ifdef IS_MPI
203	}
204
205	MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0);
206
207	#endif // is_mpi
208
209	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
244	if (needCOMprops_) {
245	Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
246	Thermo thermo(info_);
247	Vector3d com;
248
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	}
258	}
259
260	void DumpReader::readSet(int whichFrame) {
261	std::string line;
262
263	#ifndef IS_MPI
264	inFile_->clear();
265	inFile_->seekg(framePos_[whichFrame]);
266
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	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
290	MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize,
291	MPI::CHAR, masterNode);
292
293	sstream.str(sendBuffer);
294	} else {
295	int sendBufferSize;
296	MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
297	char * recvBuffer = new char[sendBufferSize+1];
298	assert(recvBuffer);
299	recvBuffer[sendBufferSize] = '\0';
300	MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
301	sstream.str(recvBuffer);
302	delete [] recvBuffer;
303	}
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	sprintf(painCave.errMsg,
313	"DumpReader Error: can not find <Snapshot>\n");
314	painCave.isFatal = 1;
315	simError();
316	}
317
318	//read frameData
319	readFrameProperties(inputStream);
320
321	//read StuntDoubles
322	readStuntDoubles(inputStream);
323
324	inputStream.getline(buffer, bufferSize);
325	line = buffer;
326
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	}
339
340	void DumpReader::parseDumpLine(const std::string& line) {
341
342
343	StringTokenizer tokenizer(line);
344	int nTokens;
345
346	nTokens = tokenizer.countTokens();
347
348	if (nTokens < 2) {
349	sprintf(painCave.errMsg,
350	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
351	painCave.isFatal = 1;
352	simError();
353	}
354
355	int index = tokenizer.nextTokenAsInt();
356
357	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
358
359	if (sd == NULL) {
360	return;
361	}
362	std::string type = tokenizer.nextToken();
363	int size = type.size();
364
365	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	if (sd->isDirectional()) {
380	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	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	sd->setPos(pos);
403	}
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	sd->setVel(vel);
413	}
414	break;
415	}
416
417	case 'q' : {
418	Quat4d q;
419	if (sd->isDirectional()) {
420
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	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
428
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	sd->setQ(q);
439	}
440	}
441	break;
442	}
443	case 'j' : {
444	Vector3d ji;
445	if (sd->isDirectional()) {
446	ji[0] = tokenizer.nextTokenAsDouble();
447	ji[1] = tokenizer.nextTokenAsDouble();
448	ji[2] = tokenizer.nextTokenAsDouble();
449	if (needAngMom_) {
450	sd->setJ(ji);
451	}
452	}
453	break;
454	}
455	case 'f': {
456
457	Vector3d force;
458	force[0] = tokenizer.nextTokenAsDouble();
459	force[1] = tokenizer.nextTokenAsDouble();
460	force[2] = tokenizer.nextTokenAsDouble();
461	sd->setFrc(force);
462	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	sd->setTrq(torque);
471	break;
472	}
473	case 'u' : {
474
475	RealType particlePot;
476	particlePot = tokenizer.nextTokenAsDouble();
477	sd->setParticlePot(particlePot);
478	break;
479	}
480	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	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
521	}
522
523
524	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	void DumpReader::readStuntDoubles(std::istream& inputStream) {
623
624	inputStream.getline(buffer, bufferSize);
625	std::string line(buffer);
626
627	if (line.find("<StuntDoubles>") == std::string::npos) {
628	sprintf(painCave.errMsg,
629	"DumpReader Error: Missing <StuntDoubles>\n");
630	painCave.isFatal = 1;
631	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	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	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	sprintf(painCave.errMsg,
691	"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
692	painCave.isFatal = 1;
693	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	pair<RealType, RealType> thermostat;
714	thermostat.first = tokenizer.nextTokenAsDouble();
715	thermostat.second = tokenizer.nextTokenAsDouble();
716	s->setThermostat(thermostat);
717	} 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	s->setBarostat(eta);
729	} 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
741	}//end namespace OpenMD