OOPSE/libmdtools/DumpReader.cpp

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

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 0
#define TAKE_THIS_TAG_INT 1
#endif // is_mpi

namespace dumpRead{

#ifdef IS_MPI
  void nodeZeroError( void );
  void anonymousNodeDie( void );
#endif // is_mpi
  
}

using namespace dumpRead;


DumpReader :: DumpReader( char *in_name ){

  isScanned = false;
  headFP = new FilePos;

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

  inFile = fopen(in_name, "r");
  if(inFile == NULL){
    sprintf(painCave.errMsg,
            "Cannot open file: %s\n", in_name);
    painCave.isFatal = 1;
    simError();
  }
  
  strcpy( inName, in_name);
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Dump file opened for reading successfully." );
  MPIcheckPoint();
#endif
  return;  
}

DumpReader :: ~DumpReader( ){
#ifdef IS_MPI
  if (worldRank == 0) {
#endif
  int error;
  error = fclose( inFile );
  if( error ){
    sprintf( painCave.errMsg,
             "Error closing %s\n", inName );
    simError();
  }
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Dump file closed successfully." );
  MPIcheckPoint();
#endif

  return;
}

int DumpReader::getNframes( void ){

  if( !isScanned ) scanFile();
  return nFrames;
}

void DumpReader::scanFile( void ){

  int vectorSize;
  int i, j, k;
  int lineNum = 0;
  char readBuffer[2000];
  char* foo;
  fpos_t *currPos;
  double time;

  FilePos *currFP;


#ifdef IS_MPI
  if( worldRank == 0 ){
#endif // is_mpi
    
    rewind( inFile );
    
    currPos = new fpos_t;
    fgetpos( inFile, currPos );
    fgets( readBuffer, sizeof( readBuffer ), inFile );
    lineNum++;
    if( feof( inFile ) ){
      sprintf( painCave.errMsg,
               "File \"%s\" ended unexpectedly at line %d\n", 
               inName,
               lineNum );
      painCave.isFatal = 1;
      simError();
    }
    
    nFrames = 0;
    while( !feof( inFile ) ){

      headFP->add( currPos );
      nFrames++;

      i = atoi(readBuffer);
      
      fgets( readBuffer, sizeof( readBuffer ), inFile );
      lineNum++;    
      if( feof( inFile ) ){
        sprintf( painCave.errMsg,
                 "File \"%s\" ended unexpectedly at line %d\n",
                 inName,
                 lineNum );
        painCave.isFatal = 1;
        simError();
      }
      
//       if(outTime){
//      foo = strtok( readBuffer, " ,;\t" );
//      time = atof( foo );
//       }
      
      for(j=0; j<i; j++){
        
        fgets( readBuffer, sizeof( readBuffer ), inFile );
        lineNum++;    
        if( feof( inFile ) ){
          sprintf( painCave.errMsg,
                   "File \"%s\" ended unexpectedly at line %d,"
                   " with atom %d\n", 
                   inName,
                   lineNum, 
                   j );
          painCave.isFatal = 1;
          simError();
        }
        
      }
      
      currPos = new fpos_t;
      fgetpos( inFile, currPos );
      fgets( readBuffer, sizeof( readBuffer ), inFile );
      lineNum++;
    }
    
    delete currPos;
    rewind( inFile );
    
    frameStart = new FilePos*[nFrames];
    currFP = headFP;
    for(i=0; i<nFrames; i++){
      
      currFP = currFP->getNext();
      if( currFP == NULL ){
        sprintf( painCave.errMsg,
                 "DumpReader error: scanFile FilePos mismatch at "
                 "nFrames = %d\n",
                 i );
        painCave.isFatal = 1;
        simError();
      }
      
      frameStart[i] = currFP;
    }

    isScanned = true;

#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
  MPIcheckPoint();
#endif // is_mpi
}

void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){

  simnfo = the_simnfo;

  this->readSet( whichFrame );
}


void DumpReader :: readSet( int whichFrame ){

  int i, j, done, which_node, which_atom; // loop counter

  const int BUFFERSIZE = 2000; // size of the read buffer
  int n_atoms; // the number of atoms
  char read_buffer[BUFFERSIZE]; //the line buffer for reading 
#ifdef IS_MPI
  char send_buffer[BUFFERSIZE];
#endif

  char *eof_test; // ptr to see when we reach the end of the file 
  char *parseErr;
  int procIndex;
  double boxMat[9];
  double theBoxMat3[3][3];
  double time;

  fpos_t *framePos;
  
#ifndef IS_MPI
  
  framePos = frameStart[whichFrame]->getPos();

  
  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
  if( eof_test == NULL ){
    sprintf( painCave.errMsg,
             "DumpReader error: error reading 1st line of \"%s\"\n",
             inName );
    painCave.isFatal = 1;
    simError();
  }
  
  n_atoms = atoi( read_buffer );

  Atom **atoms = simnfo->atoms;
  DirectionalAtom* dAtom;

  if( n_atoms != simnfo->n_atoms ){
    sprintf( painCave.errMsg,
             "DumpReader error. %s n_atoms, %d, "
             "does not match the BASS file's n_atoms, %d.\n",
             inName, n_atoms, simnfo->n_atoms );
    painCave.isFatal = 1;
    simError();
  }
  
  //read the box mat from the comment line 
  
  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
  if(eof_test == NULL){
    sprintf( painCave.errMsg,
             "error in reading commment in %s\n", inName);
    painCave.isFatal = 1;
    simError();
  }

  parseErr = parseCommentLine( read_buffer, time, boxMat );
  if( parseErr != NULL ){
    strcpy( painCave.errMsg, parseErr );
    painCave.isFatal = 1;
    simError();
  }

  simnfo->setTime( time );
  
  for(i=0;i<3;i++)
    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
  

  simnfo->setBoxM( theBoxMat3 );
  

  for( i=0; i < n_atoms; i++){
    
    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
    if(eof_test == NULL){
      sprintf(painCave.errMsg,
              "error in reading file %s\n"
              "natoms  = %d; index = %d\n"
              "error reading the line from the file.\n",
              inName, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }

    
    parseErr = parseDumpLine( read_buffer, i );
    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      painCave.isFatal = 1;
      simError();
    }
  }


  // MPI Section of code..........
#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();

  
  haveError = 0;
  if (worldRank == 0) {

    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
    if( eof_test == NULL ){
      sprintf( painCave.errMsg,
               "Error reading 1st line of %d \n ",inName);
      haveError = 1;
      simError();
    }
    
    n_atoms = atoi( read_buffer );
    
    Atom **atoms = simnfo->atoms;
    DirectionalAtom* dAtom;
 
    // Check to see that the number of atoms in the intial configuration file is the
    // same as declared in simBass.
    
    if( n_atoms != mpiSim->getTotAtoms() ){
      sprintf( painCave.errMsg,
               "Initialize from File error. %s n_atoms, %d, "
               "does not match the BASS file's n_atoms, %d.\n",
               inName, n_atoms, simnfo->n_atoms );
      haveError= 1;
      simError();
    }
    
    //read the time and boxMat from the comment line 
    
    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
    if(eof_test == NULL){
      sprintf( painCave.errMsg,
               "error in reading commment in %s\n", inName);
      haveError = 1;
      simError();
    }
    
    parseErr = parseCommentLine( read_buffer, time, boxMat );
    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
    
    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
    
    if(haveError) nodeZeroError();
    
    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
      
      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
      if(eof_test == NULL){
        sprintf(painCave.errMsg,
                "error in reading file %s\n"
                "natoms  = %d; index = %d\n"
                "error reading the line from the file.\n",
                inName, n_atoms, i );
        haveError= 1;
        simError();
      }
    
      if(haveError) nodeZeroError();

      // Get the Node number which wants this atom:
      which_node = AtomToProcMap[i];     
      if (which_node == 0) {
        parseErr = parseDumpLine( read_buffer, i );
        if( parseErr != NULL ){
          strcpy( painCave.errMsg, parseErr );
          haveError = 1;
          simError();
        }    
        if(haveError) nodeZeroError();
      } 
      
      else {
       
        myStatus = 1;
        MPI_Send(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, 
                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
                 MPI_COMM_WORLD);
        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, 
                 MPI_COMM_WORLD, &istatus);
        
        if(!myStatus) nodeZeroError();
      }
    }
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI_Send( &myStatus, 1, MPI_INT, j, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }
    
  } else {
    
    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);

    done = 0;
    while (!done) {

      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;

      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, 
               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      myStatus = 1;
      parseErr = parseDumpLine( read_buffer, which_atom );
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        myStatus = 0;;
        simError();
      }
      
      MPI_Send( &myStatus, 1, MPI_INT, 0, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
      
    }
  }
     
 // last  thing last, enable  fatalities.
  painCave.isEventLoop = 0;

  simnfo->setTime( time );

  for(i=0;i<3;i++)
    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];

  simnfo->setBoxM( theBoxMat3 );

   
#endif
}

char* DumpReader::parseDumpLine(char* readLine, int globalIndex){

  char *foo; // the pointer to the current string token 
  
  double pos[3]; // position place holders
  double vel[3]; // velocity placeholders
  double q[4]; // the quaternions
  double jx, jy, jz; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.
  
  Atom **atoms = simnfo->atoms;
  DirectionalAtom* dAtom;
  
  int j, n_atoms, atomIndex;

#ifdef IS_MPI
  n_atoms = mpiSim->getTotAtoms();
  atomIndex=-1;        
  for (j=0; j < mpiSim->getMyNlocal(); j++) {
    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
  }
  if (atomIndex == -1) {
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom at index %d "
             "in file %s does not exist on processor %d .\n",
             globalIndex, inName, mpiSim->getMyNode() );
    return strdup( painCave.errMsg );
  }  
#else
  n_atoms = simnfo->n_atoms;
  atomIndex = globalIndex;
#endif // is_mpi

  // set the string tokenizer
  
  foo = strtok(readLine, " ,;\t");
  
  // check the atom name to the current atom
  
  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom %s at index %d "
             "in file %s does not"
             " match the BASS atom %s.\n",
             foo, atomIndex, inName, atoms[atomIndex]->getType() );
    return strdup( painCave.errMsg );
  }
    
  // get the positions

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition x from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  pos[0] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition y from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  pos[1] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition z from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  pos[2] = atof( foo );    


  // get the velocities

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[0] = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity y from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[1] = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity z from %s\n"
             "natoms  = %d, index = %d\n",
             inName, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vel[2] = atof( foo );
    
    
  // get the quaternions
    
  if( atoms[atomIndex]->isDirectional() ){
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf(painCave.errMsg,
              "error in reading quaternion 0 from %s\n"
              "natoms  = %d, index = %d\n",
              inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 1 from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 2 from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 3 from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[3] = atof( foo );
      
    // get the angular velocities
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jx from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jx = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jy from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jy = atof(foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jz from %s\n"
               "natoms  = %d, index = %d\n",
               inName, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jz = atof( foo );
      
    dAtom = ( DirectionalAtom* )atoms[atomIndex];

    // check that the quaternion vector is normalized

    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
      
    qLength = sqrt( qSqr );
    q[0] = q[0] / qLength;
    q[1] = q[1] / qLength;
    q[2] = q[2] / qLength;
    q[3] = q[3] / qLength;
      
    dAtom->setQ( q );
      
    // add the angular velocities

    dAtom->setJx( jx );
    dAtom->setJy( jy );
    dAtom->setJz( jz );
  }
    
  // add the positions and velocities to the atom

  atoms[atomIndex]->setPos( pos );
  atoms[atomIndex]->setVel( vel );

  return NULL;
}


char* DumpReader::parseCommentLine(char* readLine, double &time, 
                                   double boxMat[9]){

  char *foo; // the pointer to the current string token 
  int j;
  double chi, integralOfChidt;
  double eta[9];

  // set the string tokenizer
  
  foo = strtok(readLine, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading time from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  time = atof( foo );

  // get the Hx vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[0] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[0] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[1] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[1] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hx[2] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[2] = atof( foo );    

  // get the Hy vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[0] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[3] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[1] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[4] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hy[2] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[5] = atof( foo );    

  // get the Hz vector

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[0] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[6] = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[1] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[7] = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Hz[2] from %s\n",
             inName );
    return strdup( painCave.errMsg );
  }
  boxMat[8] = atof( foo );    

  return NULL;

  //get chi and integralOfChidt, they should appear by pair
  foo = strtok(NULL, " ,;\t\n");
  if(foo != NULL){
    chi = atof(foo);
    
    foo = strtok(NULL, " ,;\t\n");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "chi and integralOfChidt should appear by pair in %s\n", inName );
      return strdup( painCave.errMsg );
    }
    integralOfChidt = atof( foo );
    
    //push chi and integralOfChidt into SimInfo::properties which can be
    //retrieved by integrator later
    DoubleData* chiValue = new DoubleData();
    chiValue->setID(CHIVALUE_ID);
    chiValue->setData(chi);
    simnfo->addProperty(chiValue);
    
    DoubleData* integralOfChidtValue = new DoubleData();
    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
    integralOfChidtValue->setData(integralOfChidt);
    simnfo->addProperty(integralOfChidtValue);
    
  }
  else
    return NULL;
  
  //get eta
  for(int i = 0 ; i < 9; i++){
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading eta[%d] from %s\n", i, inName );
      return strdup( painCave.errMsg );
    }
    eta[i] = atof( foo );
  }
  
  //push eta into SimInfo::properties which can be
  //retrieved by integrator later
  //simnfo->setBoxM( theBoxMat3 );
  DoubleArrayData* etaValue = new DoubleArrayData();
  etaValue->setID(ETAVALUE_ID);
  etaValue->setData(eta, 9);
  simnfo->addProperty(etaValue);
  
  
  return NULL;
  
  
}


#ifdef IS_MPI

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

void dumpRead::nodeZeroError( void ){
  int j, myStatus;
  
  myStatus = 0;
  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
    MPI_Send( &myStatus, 1, MPI_INT, j, 
              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
  }  
  

  MPI_Finalize();
  exit (0);
  
}

void dumpRead::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	847
Committed:	Fri Oct 31 18:28:52 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	20329 byte(s)
Log Message:	added template stuff to the Maikefile template little changes to some printf format statements