src/io/DumpWriter.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).
 */
 
#include "io/DumpWriter.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "io/basic_teebuf.hpp"
#include "io/gzstream.hpp"
#include "io/Globals.hpp"


#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

using namespace std;
namespace OpenMD {

  DumpWriter::DumpWriter(SimInfo* info) 
    : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){

    Globals* simParams = info->getSimParams();
    needCompression_   = simParams->getCompressDumpFile();
    needForceVector_   = simParams->getOutputForceVector();
    needParticlePot_   = simParams->getOutputParticlePotential();
    needFlucQ_         = simParams->getOutputFluctuatingCharges();
    needElectricField_ = simParams->getOutputElectricField();

    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
      doSiteData_ = true;
    } else {
      doSiteData_ = false;
    }

    createDumpFile_ = true;
#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi
        
      dumpFile_ = createOStream(filename_);

      if (!dumpFile_) {
        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }

#ifdef IS_MPI

    }

#endif // is_mpi

  }


  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) 
    : info_(info), filename_(filename){

    Globals* simParams = info->getSimParams();
    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    

    needCompression_   = simParams->getCompressDumpFile();
    needForceVector_   = simParams->getOutputForceVector();
    needParticlePot_   = simParams->getOutputParticlePotential();
    needFlucQ_         = simParams->getOutputFluctuatingCharges();
    needElectricField_ = simParams->getOutputElectricField();

    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
      doSiteData_ = true;
    } else {
      doSiteData_ = false;
    }

    createDumpFile_ = true;
#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

      
      dumpFile_ = createOStream(filename_);

      if (!dumpFile_) {
        sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                filename_.c_str());
        painCave.isFatal = 1;
        simError();
      }

#ifdef IS_MPI

    }

#endif // is_mpi

  }
  
  DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) 
    : info_(info), filename_(filename){
    
    Globals* simParams = info->getSimParams();
    eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
    
    needCompression_   = simParams->getCompressDumpFile();
    needForceVector_   = simParams->getOutputForceVector();
    needParticlePot_   = simParams->getOutputParticlePotential();
    needFlucQ_         = simParams->getOutputFluctuatingCharges();
    needElectricField_ = simParams->getOutputElectricField();

    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
      doSiteData_ = true;
    } else {
      doSiteData_ = false;
    }

#ifdef HAVE_LIBZ
    if (needCompression_) {
      filename_ += ".gz";
      eorFilename_ += ".gz";
    }
#endif
    
#ifdef IS_MPI
    
    if (worldRank == 0) {
#endif // is_mpi
      
      createDumpFile_ = writeDumpFile;
      if (createDumpFile_) {
        dumpFile_ = createOStream(filename_);
      
        if (!dumpFile_) {
          sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                  filename_.c_str());
          painCave.isFatal = 1;
          simError();
        }
      }
#ifdef IS_MPI
      
    }

    
#endif // is_mpi
    
  }

  DumpWriter::~DumpWriter() {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi
      if (createDumpFile_){
        writeClosing(*dumpFile_);
        delete dumpFile_;
      }
#ifdef IS_MPI

    }

#endif // is_mpi

  }

  void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {

    char buffer[1024];

    os << "    <FrameData>\n";

    RealType currentTime = s->getTime();

    if (isinf(currentTime) || isnan(currentTime)) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the time");      
      painCave.isFatal = 1;
      simError();
    }
    
    sprintf(buffer, "        Time: %.10g\n", currentTime);
    os << buffer;

    Mat3x3d hmat;
    hmat = s->getHmat();

    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the box");
          painCave.isFatal = 1;
          simError();
        }        
      }
    }
    
    sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", 
            hmat(0, 0), hmat(1, 0), hmat(2, 0), 
            hmat(0, 1), hmat(1, 1), hmat(2, 1),
            hmat(0, 2), hmat(1, 2), hmat(2, 2));
    os << buffer;

    RealType chi = s->getChi();
    RealType integralOfChiDt = s->getIntegralOfChiDt();
    if (isinf(chi) || isnan(chi) || 
        isinf(integralOfChiDt) || isnan(integralOfChiDt)) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the thermostat");
      painCave.isFatal = 1;
      simError();
    }
    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
    os << buffer;

    Mat3x3d eta;
    eta = s->getEta();

    for (unsigned int i = 0; i < 3; i++) {
      for (unsigned int j = 0; j < 3; j++) {
        if (isinf(eta(i,j)) || isnan(eta(i,j))) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the barostat");
          painCave.isFatal = 1;
          simError();
        }        
      }
    }

    sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
            eta(0, 0), eta(1, 0), eta(2, 0), 
            eta(0, 1), eta(1, 1), eta(2, 1),
            eta(0, 2), eta(1, 2), eta(2, 2));
    os << buffer;

    os << "    </FrameData>\n";
  }

  void DumpWriter::writeFrame(std::ostream& os) {

#ifdef IS_MPI
    MPI_Status istatus;
#endif

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;
    RigidBody::AtomIterator ai;
    Atom* atom;

#ifndef IS_MPI
    os << "  <Snapshot>\n";
 
    writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());

    os << "    <StuntDoubles>\n";
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

      
      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
           integrableObject = mol->nextIntegrableObject(ii)) {  
          os << prepareDumpLine(integrableObject);
          
      }
    }    
    os << "    </StuntDoubles>\n";

    if (doSiteData_) {
      os << "    <SiteData>\n";
      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
               
        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
           integrableObject = mol->nextIntegrableObject(ii)) {  

          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
          // do one for the IO itself
          os << prepareSiteLine(integrableObject, ioIndex, 0);

          if (integrableObject->isRigidBody()) {
            
            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
            int siteIndex = 0;
            for (atom = rb->beginAtom(ai); atom != NULL;  
                 atom = rb->nextAtom(ai)) {                                             
              os << prepareSiteLine(atom, ioIndex, siteIndex);
              siteIndex++;
            }
          }
        }
      }    
      os << "    </SiteData>\n";
    }
    os << "  </Snapshot>\n";

    os.flush();
#else
    //every node prepares the dump lines for integrable objects belong to itself
    std::string buffer;
    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {


      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) {  
          buffer += prepareDumpLine(integrableObject);
      }
    }
    
    const int masterNode = 0;
    int nProc;
    MPI_Comm_size(MPI_COMM_WORLD, &nProc);
    if (worldRank == masterNode) {      
      os << "  <Snapshot>\n";   
      writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
      os << "    <StuntDoubles>\n";
        
      os << buffer;

      for (int i = 1; i < nProc; ++i) {

        // receive the length of the string buffer that was
        // prepared by processor i

        MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
        int recvLength;
        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
        char* recvBuffer = new char[recvLength];
        if (recvBuffer == NULL) {
        } else {
          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
          os << recvBuffer;
          delete [] recvBuffer;
        }
      } 
      os << "    </StuntDoubles>\n";
      
      os << "  </Snapshot>\n";
      os.flush();
    } else {
      int sendBufferLength = buffer.size() + 1;
      int myturn = 0;
      for (int i = 1; i < nProc; ++i){
        MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
        if (myturn == worldRank){
          MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
          MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
        }
      }
    }

#endif // is_mpi

  }

  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
        
    int index = integrableObject->getGlobalIntegrableObjectIndex();
    std::string type("pv");
    std::string line;
    char tempBuffer[4096];

    Vector3d pos;
    Vector3d vel;
    pos = integrableObject->getPos();

    if (isinf(pos[0]) || isnan(pos[0]) || 
        isinf(pos[1]) || isnan(pos[1]) || 
        isinf(pos[2]) || isnan(pos[2]) ) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the position"
               " for object %d", index);      
      painCave.isFatal = 1;
      simError();
    }

    vel = integrableObject->getVel();           

    if (isinf(vel[0]) || isnan(vel[0]) || 
        isinf(vel[1]) || isnan(vel[1]) || 
        isinf(vel[2]) || isnan(vel[2]) ) {      
      sprintf( painCave.errMsg,
               "DumpWriter detected a numerical error writing the velocity"
               " for object %d", index);      
      painCave.isFatal = 1;
      simError();
    }

    sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", 
            pos[0], pos[1], pos[2],
            vel[0], vel[1], vel[2]);                    
    line += tempBuffer;

    if (integrableObject->isDirectional()) {
      type += "qj";
      Quat4d q;
      Vector3d ji;
      q = integrableObject->getQ();

      if (isinf(q[0]) || isnan(q[0]) || 
          isinf(q[1]) || isnan(q[1]) || 
          isinf(q[2]) || isnan(q[2]) || 
          isinf(q[3]) || isnan(q[3]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the quaternion"
                 " for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }

      ji = integrableObject->getJ();

      if (isinf(ji[0]) || isnan(ji[0]) || 
          isinf(ji[1]) || isnan(ji[1]) || 
          isinf(ji[2]) || isnan(ji[2]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the angular"
                 " momentum for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }

      sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
              q[0], q[1], q[2], q[3],
              ji[0], ji[1], ji[2]);
      line += tempBuffer;
    }

    if (needForceVector_) {
      type += "f";
      Vector3d frc = integrableObject->getFrc();
      if (isinf(frc[0]) || isnan(frc[0]) || 
          isinf(frc[1]) || isnan(frc[1]) || 
          isinf(frc[2]) || isnan(frc[2]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the force"
                 " for object %d", index);      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e %13e %13e",
              frc[0], frc[1], frc[2]);
      line += tempBuffer;
      
      if (integrableObject->isDirectional()) {
        type += "t";
        Vector3d trq = integrableObject->getTrq();        
        if (isinf(trq[0]) || isnan(trq[0]) || 
            isinf(trq[1]) || isnan(trq[1]) || 
            isinf(trq[2]) || isnan(trq[2]) ) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the torque"
                   " for object %d", index);      
          painCave.isFatal = 1;
          simError();
        }        
        sprintf(tempBuffer, " %13e %13e %13e",
                trq[0], trq[1], trq[2]);
        line += tempBuffer;
      }      
    }

    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
    return std::string(tempBuffer);
  }

  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
        

    std::string id;
    std::string type;
    std::string line;
    char tempBuffer[4096];

    if (integrableObject->isRigidBody()) {
      sprintf(tempBuffer, "%10d           ", ioIndex);
      id = std::string(tempBuffer);
    } else {
      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
      id = std::string(tempBuffer);
    }
              
    if (needFlucQ_) {
      type += "cw";
      RealType fqPos = integrableObject->getFlucQPos();
      if (isinf(fqPos) || isnan(fqPos) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the"
                 " fluctuating charge for object %s", id.c_str());      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e ", fqPos);
      line += tempBuffer;
    
      RealType fqVel = integrableObject->getFlucQVel();
      if (isinf(fqVel) || isnan(fqVel) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the"
                 " fluctuating charge velocity for object %s", id.c_str());      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e ", fqVel);
      line += tempBuffer;

      if (needForceVector_) {
        type += "g";
        RealType fqFrc = integrableObject->getFlucQFrc();        
        if (isinf(fqFrc) || isnan(fqFrc) ) {      
          sprintf( painCave.errMsg,
                   "DumpWriter detected a numerical error writing the"
                   " fluctuating charge force for object %s", id.c_str());      
          painCave.isFatal = 1;
          simError();
        }
        sprintf(tempBuffer, " %13e ", fqFrc);        
        line += tempBuffer;
      }
    }

    if (needElectricField_) {
      type += "e";
      Vector3d eField= integrableObject->getElectricField();
      if (isinf(eField[0]) || isnan(eField[0]) || 
          isinf(eField[1]) || isnan(eField[1]) || 
          isinf(eField[2]) || isnan(eField[2]) ) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the electric"
                 " field for object %s", id.c_str());      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e %13e %13e",
              eField[0], eField[1], eField[2]);
      line += tempBuffer;
    }


    if (needParticlePot_) {
      type += "u";
      RealType particlePot = integrableObject->getParticlePot();
      if (isinf(particlePot) || isnan(particlePot)) {      
        sprintf( painCave.errMsg,
                 "DumpWriter detected a numerical error writing the particle "
                 " potential for object %s", id.c_str());      
        painCave.isFatal = 1;
        simError();
      }
      sprintf(tempBuffer, " %13e", particlePot);
      line += tempBuffer;
    }
    

    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
    return std::string(tempBuffer);
  }

  void DumpWriter::writeDump() {
    writeFrame(*dumpFile_);
  }

  void DumpWriter::writeEor() {
    std::ostream* eorStream;
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      eorStream = createOStream(eorFilename_);

#ifdef IS_MPI
    }
#endif // is_mpi    

    writeFrame(*eorStream);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      writeClosing(*eorStream);
      delete eorStream;
#ifdef IS_MPI
    }
#endif // is_mpi  

  }


  void DumpWriter::writeDumpAndEor() {
    std::vector<std::streambuf*> buffers;
    std::ostream* eorStream;
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      buffers.push_back(dumpFile_->rdbuf());

      eorStream = createOStream(eorFilename_);

      buffers.push_back(eorStream->rdbuf());
        
#ifdef IS_MPI
    }
#endif // is_mpi    

    TeeBuf tbuf(buffers.begin(), buffers.end());
    std::ostream os(&tbuf);

    writeFrame(os);

#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      writeClosing(*eorStream);
      delete eorStream;
#ifdef IS_MPI
    }
#endif // is_mpi  
    
  }

  std::ostream* DumpWriter::createOStream(const std::string& filename) {

    std::ostream* newOStream;
#ifdef HAVE_LIBZ 
    if (needCompression_) {
      newOStream = new ogzstream(filename.c_str());
    } else {
      newOStream = new std::ofstream(filename.c_str());
    }
#else
    newOStream = new std::ofstream(filename.c_str());
#endif
    //write out MetaData first
    (*newOStream) << "<OpenMD version=2>" << std::endl;
    (*newOStream) << "  <MetaData>" << std::endl;
    (*newOStream) << info_->getRawMetaData();
    (*newOStream) << "  </MetaData>" << std::endl;
    return newOStream;
  }

  void DumpWriter::writeClosing(std::ostream& os) {

    os << "</OpenMD>\n";
    os.flush();
  }

}//end namespace OpenMD
Revision:	1752
Committed:	Sun Jun 10 14:05:02 2012 UTC (12 years, 10 months ago) by gezelter
File size:	20820 byte(s)
Log Message:	Added SiteData parsing and writing.