OOPSE/libmdtools/DumpWriter.cpp

#define _FILE_OFFSET_BITS 64

#include <string.h>
#include <iostream>
#include <fstream>

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"

namespace dWrite{
  void DieDieDie( void );
}

using namespace dWrite;
#endif //is_mpi

#include "ReadWrite.hpp"
#include "simError.h"

DumpWriter::DumpWriter( SimInfo* the_entry_plug ){

  entry_plug = the_entry_plug;

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

    strcpy( outName, entry_plug->sampleName );

    outFile.open(outName, ios::out | ios::trunc );

    if( !outFile ){

      sprintf( painCave.errMsg,
               "Could not open \"%s\" for dump output.\n",
               outName);
      painCave.isFatal = 1;
      simError();
    }

    //outFile.setf( ios::scientific );

#ifdef IS_MPI
  }

  sprintf( checkPointMsg,
           "Sucessfully opened output file for dumping.\n");
  MPIcheckPoint();
#endif // is_mpi
}

DumpWriter::~DumpWriter( ){

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

    outFile.close();

#ifdef IS_MPI
  }
#endif // is_mpi
}

void DumpWriter::writeDump( double currentTime ){

  const int BUFFERSIZE = 2000;
  const int MINIBUFFERSIZE = 100;

  char tempBuffer[BUFFERSIZE];
  char writeLine[BUFFERSIZE];

  int i;
#ifdef IS_MPI
  int j, which_node, done, which_atom, local_index;
  double atomTransData[6];
  double atomOrientData[7];
  int isDirectional;
  char* atomTypeString;
  char MPIatomTypeString[MINIBUFFERSIZE];
  int me;
  int atomTypeTag;
  int atomIsDirectionalTag;
  int atomTransDataTag;
  int atomOrientDataTag;
#else //is_mpi
  int nAtoms = entry_plug->n_atoms;
#endif //is_mpi

  double q[4];
  DirectionalAtom* dAtom;
  Atom** atoms = entry_plug->atoms;
  double pos[3], vel[3];

  // write current frame to the eor file

  this->writeFinal( currentTime );

#ifndef IS_MPI

  outFile << nAtoms << "\n";

  outFile << currentTime << ";\t"
          << entry_plug->Hmat[0][0] << "\t"
          << entry_plug->Hmat[1][0] << "\t"
          << entry_plug->Hmat[2][0] << ";\t"

          << entry_plug->Hmat[0][1] << "\t"
          << entry_plug->Hmat[1][1] << "\t"
          << entry_plug->Hmat[2][1] << ";\t"

          << entry_plug->Hmat[0][2] << "\t"
          << entry_plug->Hmat[1][2] << "\t"
          << entry_plug->Hmat[2][2] << ";";
  //write out additional parameters, such as chi and eta
  outFile << entry_plug->the_integrator->getAdditionalParameters();
  outFile << endl;

  for( i=0; i<nAtoms; i++ ){

    atoms[i]->getPos(pos);
    atoms[i]->getVel(vel);

    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
    strcpy( writeLine, tempBuffer );

    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );

      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );

    outFile << writeLine;
  }
  outFile.flush();

#else // is_mpi

  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

  MPI_Status istatus;
  int *AtomToProcMap = mpiSim->getAtomToProcMap();

  // write out header and node 0's coordinates

  if( worldRank == 0 ){
    outFile << mpiSim->getTotAtoms() << "\n";

    outFile << currentTime << ";\t"
            << entry_plug->Hmat[0][0] << "\t"
            << entry_plug->Hmat[1][0] << "\t"
            << entry_plug->Hmat[2][0] << ";\t"

            << entry_plug->Hmat[0][1] << "\t"
            << entry_plug->Hmat[1][1] << "\t"
            << entry_plug->Hmat[2][1] << ";\t"

            << entry_plug->Hmat[0][2] << "\t"
            << entry_plug->Hmat[1][2] << "\t"
            << entry_plug->Hmat[2][2] << ";";

    outFile << entry_plug->the_integrator->getAdditionalParameters();
    outFile << endl;
    outFile.flush();
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      // Get the Node number which has this atom;

      which_node = AtomToProcMap[i];

      if (which_node != 0) {
        
        atomTypeTag          = 4*i;
        atomIsDirectionalTag = 4*i + 1;
        atomTransDataTag     = 4*i + 2;
        atomOrientDataTag    = 4*i + 3;

        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
                 atomTypeTag, MPI_COMM_WORLD, &istatus);
        
        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);
        
        // Null terminate the atomTypeString just in case:

        atomTypeString[strlen(atomTypeString) - 1] = '\0';

        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
        
        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
                 atomTransDataTag, MPI_COMM_WORLD, &istatus);

        if (isDirectional) {

          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);

        }

      } else {
        
        haveError = 0;
        which_atom = i;
        local_index=-1;

        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }

        if (local_index != -1) {

          atomTypeString = atoms[local_index]->getType();

          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);

          atomTransData[0] = pos[0];
          atomTransData[1] = pos[1];
          atomTransData[2] = pos[2];

          atomTransData[3] = vel[0];
          atomTransData[4] = vel[1];
          atomTransData[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            atomOrientData[0] = q[0];
            atomOrientData[1] = q[1];
            atomOrientData[2] = q[2];
            atomOrientData[3] = q[3];

            atomOrientData[4] = dAtom->getJx();
            atomOrientData[5] = dAtom->getJy();
            atomOrientData[6] = dAtom->getJz();
          }

        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        }

        if(haveError) DieDieDie();
                              
        // If we've survived to here, format the line:
        
        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atomTypeString,
                 atomTransData[0],
                 atomTransData[1],
                 atomTransData[2],
                 atomTransData[3],
                 atomTransData[4],
                 atomTransData[5]);

        strcpy( writeLine, tempBuffer );

        if (isDirectional) {

          sprintf( tempBuffer,
                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                   atomOrientData[0],
                   atomOrientData[1],
                   atomOrientData[2],
                   atomOrientData[3],
                   atomOrientData[4],
                   atomOrientData[5],
                   atomOrientData[6]);
          strcat( writeLine, tempBuffer );

        } else {
          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
        }

        outFile << writeLine;
        outFile.flush();
      }
    }

    outFile.flush();
    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    MPIcheckPoint();        
    
  } else {

    // worldRank != 0, so I'm a remote node.  
    
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Am I the node which has this atom?
      
      if (AtomToProcMap[i] == worldRank) {

        local_index=-1;
        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }
        if (local_index != -1) {
         
          atomTypeString = atoms[local_index]->getType();

          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);

          atomTransData[0] = pos[0];
          atomTransData[1] = pos[1];
          atomTransData[2] = pos[2];

          atomTransData[3] = vel[0];
          atomTransData[4] = vel[1];
          atomTransData[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            atomOrientData[0] = q[0];
            atomOrientData[1] = q[1];
            atomOrientData[2] = q[2];
            atomOrientData[3] = q[3];

            atomOrientData[4] = dAtom->getJx();
            atomOrientData[5] = dAtom->getJy();
            atomOrientData[6] = dAtom->getJz();
          }

        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        }

        // I've survived this far, so send off the data!

        atomTypeTag          = 4*i;
        atomIsDirectionalTag = 4*i + 1;
        atomTransDataTag     = 4*i + 2;
        atomOrientDataTag    = 4*i + 3;


        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);

        // null terminate the string before sending (just in case):
        MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';

        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                 atomTypeTag, MPI_COMM_WORLD);
        
        MPI_Send(&isDirectional, 1, MPI_INT, 0,
                 atomIsDirectionalTag, MPI_COMM_WORLD);
        
        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
                 atomTransDataTag, MPI_COMM_WORLD);

        if (isDirectional) {

          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
                   atomOrientDataTag, MPI_COMM_WORLD);
          
        }
      
      }
    }

    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    MPIcheckPoint();        
    
  }
  
  painCave.isEventLoop = 0;

#endif // is_mpi
}

void DumpWriter::writeFinal(double finalTime){

  char finalName[500];
  ofstream finalOut;

  const int BUFFERSIZE = 2000;
  const int MINIBUFFERSIZE = 100;
  char tempBuffer[BUFFERSIZE];
  char writeLine[BUFFERSIZE];

  double q[4];
  DirectionalAtom* dAtom;
  Atom** atoms = entry_plug->atoms;
  int i;
#ifdef IS_MPI
  int j, which_node, done, which_atom, local_index;
  double atomTransData[6];
  double atomOrientData[7];
  int isDirectional;
  char* atomTypeString;
  char MPIatomTypeString[MINIBUFFERSIZE];
  int atomTypeTag;
  int atomIsDirectionalTag;
  int atomTransDataTag;
  int atomOrientDataTag;
#else //is_mpi
  int nAtoms = entry_plug->n_atoms;
#endif //is_mpi

  double pos[3], vel[3];

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

    strcpy( finalName, entry_plug->finalName );

    finalOut.open( finalName, ios::out | ios::trunc );
    if( !finalOut ){
      sprintf( painCave.errMsg,
               "Could not open \"%s\" for final dump output.\n",
               finalName );
      painCave.isFatal = 1;
      simError();
    }

    // finalOut.setf( ios::scientific );

#ifdef IS_MPI
  }

  sprintf(checkPointMsg,"Opened file for final configuration\n");
  MPIcheckPoint();

#endif //is_mpi


#ifndef IS_MPI

  finalOut << nAtoms << "\n";

  finalOut << finalTime << ";\t"
           << entry_plug->Hmat[0][0] << "\t"
           << entry_plug->Hmat[1][0] << "\t"
           << entry_plug->Hmat[2][0] << ";\t"

           << entry_plug->Hmat[0][1] << "\t"
           << entry_plug->Hmat[1][1] << "\t"
           << entry_plug->Hmat[2][1] << ";\t"

           << entry_plug->Hmat[0][2] << "\t"
           << entry_plug->Hmat[1][2] << "\t"
           << entry_plug->Hmat[2][2] << ";";

  //write out additional parameters, such as chi and eta
  finalOut << entry_plug->the_integrator->getAdditionalParameters();
  finalOut << endl;

  for( i=0; i<nAtoms; i++ ){

    atoms[i]->getPos(pos);
    atoms[i]->getVel(vel);

    sprintf( tempBuffer,
             "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
             atoms[i]->getType(),
             pos[0],
             pos[1],
             pos[2],
             vel[0],
             vel[1],
             vel[2]);
    strcpy( writeLine, tempBuffer );

    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];
      dAtom->getQ( q );

      sprintf( tempBuffer,
               "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
               q[0],
               q[1],
               q[2],
               q[3],
               dAtom->getJx(),
               dAtom->getJy(),
               dAtom->getJz());
      strcat( writeLine, tempBuffer );
    }
    else
      strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );

    finalOut << writeLine;
  }
  finalOut.flush();
  finalOut.close();

#else // is_mpi

  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

  MPI_Status istatus;
  int *AtomToProcMap = mpiSim->getAtomToProcMap();

  // write out header and node 0's coordinates

  if( worldRank == 0 ){
    finalOut << mpiSim->getTotAtoms() << "\n";

    finalOut << finalTime << ";\t"
            << entry_plug->Hmat[0][0] << "\t"
            << entry_plug->Hmat[1][0] << "\t"
            << entry_plug->Hmat[2][0] << ";\t"

            << entry_plug->Hmat[0][1] << "\t"
            << entry_plug->Hmat[1][1] << "\t"
            << entry_plug->Hmat[2][1] << ";\t"

            << entry_plug->Hmat[0][2] << "\t"
            << entry_plug->Hmat[1][2] << "\t"
            << entry_plug->Hmat[2][2] << ";";

    finalOut << entry_plug->the_integrator->getAdditionalParameters();
    finalOut << endl;
    finalOut.flush();
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      // Get the Node number which has this atom;

      which_node = AtomToProcMap[i];

      if (which_node != 0) {
        
        atomTypeTag          = 4*i;
        atomIsDirectionalTag = 4*i + 1;
        atomTransDataTag     = 4*i + 2;
        atomOrientDataTag    = 4*i + 3;

        MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
                 atomTypeTag, MPI_COMM_WORLD, &istatus);
        
        strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE);

        MPI_Recv(&isDirectional, 1, MPI_INT, which_node,
                 atomIsDirectionalTag, MPI_COMM_WORLD, &istatus);
        
        MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node,
                 atomTransDataTag, MPI_COMM_WORLD, &istatus);

        if (isDirectional) {

          MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node,
                   atomOrientDataTag, MPI_COMM_WORLD, &istatus);

        }

      } else {
        
        haveError = 0;
        which_atom = i;
        local_index=-1;

        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }

        if (local_index != -1) {

          atomTypeString = atoms[local_index]->getType();

          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);

          atomTransData[0] = pos[0];
          atomTransData[1] = pos[1];
          atomTransData[2] = pos[2];

          atomTransData[3] = vel[0];
          atomTransData[4] = vel[1];
          atomTransData[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            atomOrientData[0] = q[0];
            atomOrientData[1] = q[1];
            atomOrientData[2] = q[2];
            atomOrientData[3] = q[3];

            atomOrientData[4] = dAtom->getJx();
            atomOrientData[5] = dAtom->getJy();
            atomOrientData[6] = dAtom->getJz();
          }

        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        }

        if(haveError) DieDieDie();
                              
        // If we've survived to here, format the line:
        
        sprintf( tempBuffer,
                 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                 atomTypeString,
                 atomTransData[0],
                 atomTransData[1],
                 atomTransData[2],
                 atomTransData[3],
                 atomTransData[4],
                 atomTransData[5]);

        strcpy( writeLine, tempBuffer );

        if (isDirectional) {

          sprintf( tempBuffer,
                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                   atomOrientData[0],
                   atomOrientData[1],
                   atomOrientData[2],
                   atomOrientData[3],
                   atomOrientData[4],
                   atomOrientData[5],
                   atomOrientData[6]);
          strcat( writeLine, tempBuffer );

        } else {
          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
        }

        finalOut << writeLine;
        finalOut.flush();
      }
    }

    finalOut.flush();
    sprintf( checkPointMsg,
             "Sucessfully took a dump.\n");
    MPIcheckPoint();        
    
  } else {

    // worldRank != 0, so I'm a remote node.  
    
    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
      
      // Am I the node which has this atom?
      
      if (AtomToProcMap[i] == worldRank) {

        local_index=-1;
        for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
          if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
        }
        if (local_index != -1) {
         
          atomTypeString = atoms[local_index]->getType();

          atoms[local_index]->getPos(pos);
          atoms[local_index]->getVel(vel);

          atomTransData[0] = pos[0];
          atomTransData[1] = pos[1];
          atomTransData[2] = pos[2];

          atomTransData[3] = vel[0];
          atomTransData[4] = vel[1];
          atomTransData[5] = vel[2];
          
          isDirectional = 0;

          if( atoms[local_index]->isDirectional() ){

            isDirectional = 1;
            
            dAtom = (DirectionalAtom *)atoms[local_index];
            dAtom->getQ( q );
            
            atomOrientData[0] = q[0];
            atomOrientData[1] = q[1];
            atomOrientData[2] = q[2];
            atomOrientData[3] = q[3];

            atomOrientData[4] = dAtom->getJx();
            atomOrientData[5] = dAtom->getJy();
            atomOrientData[6] = dAtom->getJz();
          }

        } else {
          sprintf(painCave.errMsg,
                  "Atom %d not found on processor %d\n",
                  i, worldRank );
          haveError= 1;
          simError();
        }

        // I've survived this far, so send off the data!

        atomTypeTag          = 4*i;
        atomIsDirectionalTag = 4*i + 1;
        atomTransDataTag     = 4*i + 2;
        atomOrientDataTag    = 4*i + 3;

        strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);

        MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                 atomTypeTag, MPI_COMM_WORLD);
        
        MPI_Send(&isDirectional, 1, MPI_INT, 0,
                 atomIsDirectionalTag, MPI_COMM_WORLD);
        
        MPI_Send(atomTransData, 6, MPI_DOUBLE, 0,
                 atomTransDataTag, MPI_COMM_WORLD);

        if (isDirectional) {

          MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0,
                   atomOrientDataTag, MPI_COMM_WORLD);
          
        }
      
      }
    }

    sprintf( checkPointMsg,
             "Sucessfully wrote final file.\n");
    MPIcheckPoint();        
    
  }
  
  painCave.isEventLoop = 0;

  if( worldRank == 0 ) finalOut.close();
#endif // is_mpi
}


#ifdef IS_MPI

// a couple of functions to let us escape the write loop

void dWrite::DieDieDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	912
Committed:	Thu Jan 8 18:59:36 2004 UTC (20 years, 6 months ago) by gezelter
File size:	19717 byte(s)
Log Message:	null terminate some strings just in case