OOPSE/libmdtools/DumpReader.cpp

#define _FILE_OFFSET_BITS 64

#include <iostream>
#include <cmath>
#include <vector>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.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
  
  class FilePos{
    
  public:
    FilePos(){ myPos = NULL; }
    FilePos( fpos_t* thePos ) { myPos = thePos; }
    ~FilePos(){ if( myPos != NULL ) delete myPos; }

    FilePos &operator=(fpos_t *thePos){ myPos = thePos; return *this; }

    void setPos( fpos_t *thePos ){ myPos = thePos; }
    fpos_t *getPos( void ){ return myPos; }
   
  private:
    
    fpos_t *myPos

  };

  bool operator<(FilePos a, FilePos b){
    return (a.getPos())->__pos < (b.getPos())->__pos; }

  bool operator==(FilePos a, FilePos b){
    return (a.getPos())->__pos == (b.getPos())->__pos; }

  vector<FilePos> frameStart;
}

using namespace dumpRead;


DumpReader :: DumpReader( char *in_name ){

  isScanned = false;

#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;

#ifdef IS_MPI
  if( worldRank == 0 ){
#endif // is_mpi
    
    rewind( inFile );
    
    currPos = new fpos_t;
    fgetpos( inFile, currPos );
    fgets( readBuffer, sizeof( readBuffer ), in_file );
    lineNum++;
    if( feof( in_file ) ){
      sprintf( painCave.errMsg,
               "File \"%s\" ended unexpectedly at line %d\n", 
               inName,
               lineNum );
      painCave.isFatal = 1;
      simError();
    }
    
    while( !feof( in_file ) ){
      
      frameStart.push_back( FilePos( currPos ) );
      i = atoi(readBuffer);
      
      fgets( readBuffer, sizeof( readBuffer ), in_file );
      lineNum++;    
      if( feof( in_file ) ){
        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 ), in_file );
        lineNum++;    
        if( feof( in_file ) ){
          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 ), in_file );
      lineNum++;
    }
    
    delete currPos;
    vectorSize = frameStart.size();
    rewind( inFile );
    
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
  MPIcheckPoint();
#endif // is_mpi

  nFrames = vectorSize;
  isScanned = true;
}

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];
  
  fpos_t *framePos;
  
#ifndef IS_MPI
  
  framePos = startFrame[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 rx, ry, rz; // position place holders
  double vx, vy, vz; // 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 );
  }
  rx = 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 );
  }
  ry = 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 );
  }
  rz = 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 );
  }
  vx = 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 );
  }
  vy = 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 );
  }
  vz = 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]->setX( rx );
  atoms[atomIndex]->setY( ry );
  atoms[atomIndex]->setZ( rz );
    
  atoms[atomIndex]->set_vx( vx );
  atoms[atomIndex]->set_vy( vy );
  atoms[atomIndex]->set_vz( vz );

  return NULL;
}


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

  char *foo; // the pointer to the current string token 
  int j;

  // 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;
}


#ifdef IS_MPI

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

void initFile::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 initFile::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	656
Committed:	Tue Jul 29 16:32:37 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	19190 byte(s)
Log Message:	working on the props code
#	User	Rev	Content
1	mmeineke	643	#define _FILE_OFFSET_BITS 64
2
3	gezelter	637	#include <iostream>
4			#include <cmath>
5	mmeineke	646	#include <vector>
6	gezelter	637
7			#include <stdio.h>
8			#include <stdlib.h>
9			#include <string.h>
10			#include <unistd.h>
11			#include <sys/types.h>
12			#include <sys/stat.h>
13
14			#include "ReadWrite.hpp"
15			#include "simError.h"
16
17			#ifdef IS_MPI
18			#include <mpi.h>
19			#include "mpiSimulation.hpp"
20			#define TAKE_THIS_TAG_CHAR 0
21			#define TAKE_THIS_TAG_INT 1
22	mmeineke	647	#endif // is_mpi
23	gezelter	637
24			namespace dumpRead{
25	mmeineke	647
26			#ifdef IS_MPI
27	gezelter	637	void nodeZeroError( void );
28			void anonymousNodeDie( void );
29	mmeineke	647	#endif // is_mpi
30	mmeineke	646
31			class FilePos{
32	mmeineke	647
33	mmeineke	646	public:
34	mmeineke	647	FilePos(){ myPos = NULL; }
35			FilePos( fpos_t* thePos ) { myPos = thePos; }
36			~FilePos(){ if( myPos != NULL ) delete myPos; }
37	mmeineke	646
38	mmeineke	647	FilePos &operator=(fpos_t thePos){ myPos = thePos; return this; }
39
40			void setPos( fpos_t *thePos ){ myPos = thePos; }
41			fpos_t *getPos( void ){ return myPos; }
42
43	mmeineke	646	private:
44
45	mmeineke	647	fpos_t *myPos
46	mmeineke	646
47			};
48
49	mmeineke	647	bool operator<(FilePos a, FilePos b){
50			return (a.getPos())->__pos < (b.getPos())->__pos; }
51
52			bool operator==(FilePos a, FilePos b){
53			return (a.getPos())->__pos == (b.getPos())->__pos; }
54
55	mmeineke	646	vector<FilePos> frameStart;
56	gezelter	637	}
57
58			using namespace dumpRead;
59
60
61			DumpReader :: DumpReader( char *in_name ){
62	mmeineke	647
63			isScanned = false;
64
65	gezelter	637	#ifdef IS_MPI
66			if (worldRank == 0) {
67			#endif
68
69	mmeineke	647	inFile = fopen(in_name, "r");
70			if(inFile == NULL){
71	gezelter	637	sprintf(painCave.errMsg,
72			"Cannot open file: %s\n", in_name);
73			painCave.isFatal = 1;
74			simError();
75			}
76
77	mmeineke	647	strcpy( inName, in_name);
78	gezelter	637	#ifdef IS_MPI
79			}
80			strcpy( checkPointMsg, "Dump file opened for reading successfully." );
81			MPIcheckPoint();
82			#endif
83			return;
84			}
85
86			DumpReader :: ~DumpReader( ){
87			#ifdef IS_MPI
88			if (worldRank == 0) {
89			#endif
90			int error;
91	mmeineke	647	error = fclose( inFile );
92	gezelter	637	if( error ){
93			sprintf( painCave.errMsg,
94	mmeineke	647	"Error closing %s\n", inName );
95	gezelter	637	simError();
96			}
97			#ifdef IS_MPI
98			}
99			strcpy( checkPointMsg, "Dump file closed successfully." );
100			MPIcheckPoint();
101			#endif
102
103			return;
104			}
105
106	mmeineke	647	int DumpReader::getNframes( void ){
107	gezelter	637
108	mmeineke	647	if( !isScanned ) scanFile();
109			return nFrames;
110			}
111	mmeineke	643
112	mmeineke	647	void DumpReader::scanFile( void ){
113
114			int vectorSize;
115			int i, j, k;
116			int lineNum = 0;
117			char readBuffer[2000];
118			char* foo;
119			fpos_t *currPos;
120
121			#ifdef IS_MPI
122			if( worldRank == 0 ){
123			#endif // is_mpi
124
125			rewind( inFile );
126
127			currPos = new fpos_t;
128			fgetpos( inFile, currPos );
129			fgets( readBuffer, sizeof( readBuffer ), in_file );
130			lineNum++;
131			if( feof( in_file ) ){
132			sprintf( painCave.errMsg,
133			"File \"%s\" ended unexpectedly at line %d\n",
134			inName,
135			lineNum );
136			painCave.isFatal = 1;
137			simError();
138			}
139
140			while( !feof( in_file ) ){
141
142			frameStart.push_back( FilePos( currPos ) );
143			i = atoi(readBuffer);
144
145			fgets( readBuffer, sizeof( readBuffer ), in_file );
146			lineNum++;
147			if( feof( in_file ) ){
148			sprintf( painCave.errMsg,
149			"File \"%s\" ended unexpectedly at line %d\n",
150			inName,
151			lineNum );
152			painCave.isFatal = 1;
153			simError();
154			}
155
156			if(outTime){
157			foo = strtok( readBuffer, " ,;\t" );
158			time = atof( foo );
159			}
160
161			for(j=0; j<i; j++){
162
163			fgets( readBuffer, sizeof( readBuffer ), in_file );
164			lineNum++;
165			if( feof( in_file ) ){
166			sprintf( painCave.errMsg,
167			"File \"%s\" ended unexpectedly at line %d,"
168			" with atom %d\n",
169			inName,
170			lineNum,
171			j );
172			painCave.isFatal = 1;
173			simError();
174			}
175
176			}
177
178			currPos = new fpos_t;
179			fgetpos( inFile, currPos );
180			fgets( readBuffer, sizeof( readBuffer ), in_file );
181			lineNum++;
182			}
183
184			delete currPos;
185			vectorSize = frameStart.size();
186			rewind( inFile );
187
188			#ifdef IS_MPI
189			}
190			strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
191			MPIcheckPoint();
192			#endif // is_mpi
193
194			nFrames = vectorSize;
195			isScanned = true;
196			}
197
198	mmeineke	656	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
199	mmeineke	647
200	mmeineke	656	simnfo = the_simnfo;
201	mmeineke	647
202	mmeineke	656	this->readSet( whichFrame );
203			}
204	gezelter	637
205	mmeineke	656
206
207			void DumpReader :: readSet( int whichFrame ){
208
209	gezelter	637	int i, j, done, which_node, which_atom; // loop counter
210
211			const int BUFFERSIZE = 2000; // size of the read buffer
212			int n_atoms; // the number of atoms
213			char read_buffer[BUFFERSIZE]; //the line buffer for reading
214			#ifdef IS_MPI
215			char send_buffer[BUFFERSIZE];
216			#endif
217
218			char *eof_test; // ptr to see when we reach the end of the file
219			char *parseErr;
220			int procIndex;
221			double boxMat[9];
222			double theBoxMat3[3][3];
223	mmeineke	656
224			fpos_t *framePos;
225
226			#ifndef IS_MPI
227
228			framePos = startFrame[whichFrame].getPos();
229	gezelter	637
230	mmeineke	656
231	gezelter	637
232	mmeineke	656
233	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
234	gezelter	637	if( eof_test == NULL ){
235			sprintf( painCave.errMsg,
236			"DumpReader error: error reading 1st line of \"%s\"\n",
237	mmeineke	647	inName );
238	gezelter	637	painCave.isFatal = 1;
239			simError();
240			}
241
242			n_atoms = atoi( read_buffer );
243
244			Atom **atoms = simnfo->atoms;
245			DirectionalAtom* dAtom;
246
247			if( n_atoms != simnfo->n_atoms ){
248			sprintf( painCave.errMsg,
249			"DumpReader error. %s n_atoms, %d, "
250			"does not match the BASS file's n_atoms, %d.\n",
251	mmeineke	647	inName, n_atoms, simnfo->n_atoms );
252	gezelter	637	painCave.isFatal = 1;
253			simError();
254			}
255
256			//read the box mat from the comment line
257
258	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
259	gezelter	637	if(eof_test == NULL){
260			sprintf( painCave.errMsg,
261	mmeineke	647	"error in reading commment in %s\n", inName);
262	gezelter	637	painCave.isFatal = 1;
263			simError();
264			}
265
266			parseErr = parseCommentLine( read_buffer, time, boxMat );
267			if( parseErr != NULL ){
268			strcpy( painCave.errMsg, parseErr );
269			painCave.isFatal = 1;
270			simError();
271			}
272
273			simnfo->setTime( time );
274
275			for(i=0;i<3;i++)
276			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
277
278
279			simnfo->setBoxM( theBoxMat3 );
280
281
282			for( i=0; i < n_atoms; i++){
283
284	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
285	gezelter	637	if(eof_test == NULL){
286			sprintf(painCave.errMsg,
287			"error in reading file %s\n"
288			"natoms = %d; index = %d\n"
289			"error reading the line from the file.\n",
290	mmeineke	647	inName, n_atoms, i );
291	gezelter	637	painCave.isFatal = 1;
292			simError();
293			}
294
295
296			parseErr = parseDumpLine( read_buffer, i );
297			if( parseErr != NULL ){
298			strcpy( painCave.errMsg, parseErr );
299			painCave.isFatal = 1;
300			simError();
301			}
302			}
303
304
305			// MPI Section of code..........
306			#else //IS_MPI
307
308			// first thing first, suspend fatalities.
309			painCave.isEventLoop = 1;
310
311			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
312			int haveError;
313
314			MPI_Status istatus;
315			int *AtomToProcMap = mpiSim->getAtomToProcMap();
316
317
318			haveError = 0;
319			if (worldRank == 0) {
320
321	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
322	gezelter	637	if( eof_test == NULL ){
323			sprintf( painCave.errMsg,
324	mmeineke	647	"Error reading 1st line of %d \n ",inName);
325	gezelter	637	haveError = 1;
326			simError();
327			}
328
329			n_atoms = atoi( read_buffer );
330
331			Atom **atoms = simnfo->atoms;
332			DirectionalAtom* dAtom;
333
334			// Check to see that the number of atoms in the intial configuration file is the
335			// same as declared in simBass.
336
337			if( n_atoms != mpiSim->getTotAtoms() ){
338			sprintf( painCave.errMsg,
339			"Initialize from File error. %s n_atoms, %d, "
340			"does not match the BASS file's n_atoms, %d.\n",
341	mmeineke	647	inName, n_atoms, simnfo->n_atoms );
342	gezelter	637	haveError= 1;
343			simError();
344			}
345
346			//read the time and boxMat from the comment line
347
348	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
349	gezelter	637	if(eof_test == NULL){
350			sprintf( painCave.errMsg,
351	mmeineke	647	"error in reading commment in %s\n", inName);
352	gezelter	637	haveError = 1;
353			simError();
354			}
355
356			parseErr = parseCommentLine( read_buffer, time, boxMat );
357			if( parseErr != NULL ){
358			strcpy( painCave.errMsg, parseErr );
359			haveError = 1;
360			simError();
361			}
362
363			MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
364
365			MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
366
367			if(haveError) nodeZeroError();
368
369			for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
370
371	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
372	gezelter	637	if(eof_test == NULL){
373			sprintf(painCave.errMsg,
374			"error in reading file %s\n"
375			"natoms = %d; index = %d\n"
376			"error reading the line from the file.\n",
377	mmeineke	647	inName, n_atoms, i );
378	gezelter	637	haveError= 1;
379			simError();
380			}
381
382			if(haveError) nodeZeroError();
383
384			// Get the Node number which wants this atom:
385			which_node = AtomToProcMap[i];
386			if (which_node == 0) {
387			parseErr = parseDumpLine( read_buffer, i );
388			if( parseErr != NULL ){
389			strcpy( painCave.errMsg, parseErr );
390			haveError = 1;
391			simError();
392			}
393			if(haveError) nodeZeroError();
394			}
395
396			else {
397
398			myStatus = 1;
399			MPI_Send(&myStatus, 1, MPI_INT, which_node,
400			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
401			MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
402			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
403			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
404			MPI_COMM_WORLD);
405			MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
406			MPI_COMM_WORLD, &istatus);
407
408			if(!myStatus) nodeZeroError();
409			}
410			}
411			myStatus = -1;
412			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
413			MPI_Send( &myStatus, 1, MPI_INT, j,
414			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
415			}
416
417			} else {
418
419			MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
420			MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
421
422			done = 0;
423			while (!done) {
424
425			MPI_Recv(&myStatus, 1, MPI_INT, 0,
426			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
427
428			if(!myStatus) anonymousNodeDie();
429
430			if(myStatus < 0) break;
431
432			MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
433			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
434			MPI_Recv(&which_atom, 1, MPI_INT, 0,
435			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
436
437			myStatus = 1;
438			parseErr = parseDumpLine( read_buffer, which_atom );
439			if( parseErr != NULL ){
440			strcpy( painCave.errMsg, parseErr );
441			myStatus = 0;;
442			simError();
443			}
444
445			MPI_Send( &myStatus, 1, MPI_INT, 0,
446			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
447
448			}
449			}
450
451			// last thing last, enable fatalities.
452			painCave.isEventLoop = 0;
453
454			simnfo->setTime( time );
455
456			for(i=0;i<3;i++)
457			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
458
459			simnfo->setBoxM( theBoxMat3 );
460
461
462			#endif
463			}
464
465			char* DumpReader::parseDumpLine(char* readLine, int globalIndex){
466
467			char *foo; // the pointer to the current string token
468
469			double rx, ry, rz; // position place holders
470			double vx, vy, vz; // velocity placeholders
471			double q[4]; // the quaternions
472			double jx, jy, jz; // angular velocity placeholders;
473			double qSqr, qLength; // needed to normalize the quaternion vector.
474
475			Atom **atoms = simnfo->atoms;
476			DirectionalAtom* dAtom;
477
478			int j, n_atoms, atomIndex;
479
480			#ifdef IS_MPI
481			n_atoms = mpiSim->getTotAtoms();
482			atomIndex=-1;
483			for (j=0; j < mpiSim->getMyNlocal(); j++) {
484			if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
485			}
486			if (atomIndex == -1) {
487			sprintf( painCave.errMsg,
488			"Initialize from file error. Atom at index %d "
489			"in file %s does not exist on processor %d .\n",
490	mmeineke	647	globalIndex, inName, mpiSim->getMyNode() );
491	gezelter	637	return strdup( painCave.errMsg );
492			}
493			#else
494			n_atoms = simnfo->n_atoms;
495			atomIndex = globalIndex;
496			#endif // is_mpi
497
498			// set the string tokenizer
499
500			foo = strtok(readLine, " ,;\t");
501
502			// check the atom name to the current atom
503
504			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
505			sprintf( painCave.errMsg,
506			"Initialize from file error. Atom %s at index %d "
507			"in file %s does not"
508			" match the BASS atom %s.\n",
509	mmeineke	647	foo, atomIndex, inName, atoms[atomIndex]->getType() );
510	gezelter	637	return strdup( painCave.errMsg );
511			}
512
513			// get the positions
514
515			foo = strtok(NULL, " ,;\t");
516			if(foo == NULL){
517			sprintf( painCave.errMsg,
518			"error in reading postition x from %s\n"
519			"natoms = %d, index = %d\n",
520	mmeineke	647	inName, n_atoms, atomIndex );
521	gezelter	637	return strdup( painCave.errMsg );
522			}
523			rx = atof( foo );
524
525			foo = strtok(NULL, " ,;\t");
526			if(foo == NULL){
527			sprintf( painCave.errMsg,
528			"error in reading postition y from %s\n"
529			"natoms = %d, index = %d\n",
530	mmeineke	647	inName, n_atoms, atomIndex );
531	gezelter	637	return strdup( painCave.errMsg );
532			}
533			ry = atof( foo );
534
535			foo = strtok(NULL, " ,;\t");
536			if(foo == NULL){
537			sprintf( painCave.errMsg,
538			"error in reading postition z from %s\n"
539			"natoms = %d, index = %d\n",
540	mmeineke	647	inName, n_atoms, atomIndex );
541	gezelter	637	return strdup( painCave.errMsg );
542			}
543			rz = atof( foo );
544
545
546			// get the velocities
547
548			foo = strtok(NULL, " ,;\t");
549			if(foo == NULL){
550			sprintf( painCave.errMsg,
551			"error in reading velocity x from %s\n"
552			"natoms = %d, index = %d\n",
553	mmeineke	647	inName, n_atoms, atomIndex );
554	gezelter	637	return strdup( painCave.errMsg );
555			}
556			vx = atof( foo );
557
558			foo = strtok(NULL, " ,;\t");
559			if(foo == NULL){
560			sprintf( painCave.errMsg,
561			"error in reading velocity y from %s\n"
562			"natoms = %d, index = %d\n",
563	mmeineke	647	inName, n_atoms, atomIndex );
564	gezelter	637	return strdup( painCave.errMsg );
565			}
566			vy = atof( foo );
567
568			foo = strtok(NULL, " ,;\t");
569			if(foo == NULL){
570			sprintf( painCave.errMsg,
571			"error in reading velocity z from %s\n"
572			"natoms = %d, index = %d\n",
573	mmeineke	647	inName, n_atoms, atomIndex );
574	gezelter	637	return strdup( painCave.errMsg );
575			}
576			vz = atof( foo );
577
578
579			// get the quaternions
580
581			if( atoms[atomIndex]->isDirectional() ){
582
583			foo = strtok(NULL, " ,;\t");
584			if(foo == NULL){
585			sprintf(painCave.errMsg,
586			"error in reading quaternion 0 from %s\n"
587			"natoms = %d, index = %d\n",
588	mmeineke	647	inName, n_atoms, atomIndex );
589	gezelter	637	return strdup( painCave.errMsg );
590			}
591			q[0] = atof( foo );
592
593			foo = strtok(NULL, " ,;\t");
594			if(foo == NULL){
595			sprintf( painCave.errMsg,
596			"error in reading quaternion 1 from %s\n"
597			"natoms = %d, index = %d\n",
598	mmeineke	647	inName, n_atoms, atomIndex );
599	gezelter	637	return strdup( painCave.errMsg );
600			}
601			q[1] = atof( foo );
602
603			foo = strtok(NULL, " ,;\t");
604			if(foo == NULL){
605			sprintf( painCave.errMsg,
606			"error in reading quaternion 2 from %s\n"
607			"natoms = %d, index = %d\n",
608	mmeineke	647	inName, n_atoms, atomIndex );
609	gezelter	637	return strdup( painCave.errMsg );
610			}
611			q[2] = atof( foo );
612
613			foo = strtok(NULL, " ,;\t");
614			if(foo == NULL){
615			sprintf( painCave.errMsg,
616			"error in reading quaternion 3 from %s\n"
617			"natoms = %d, index = %d\n",
618	mmeineke	647	inName, n_atoms, atomIndex );
619	gezelter	637	return strdup( painCave.errMsg );
620			}
621			q[3] = atof( foo );
622
623			// get the angular velocities
624
625			foo = strtok(NULL, " ,;\t");
626			if(foo == NULL){
627			sprintf( painCave.errMsg,
628			"error in reading angular momentum jx from %s\n"
629			"natoms = %d, index = %d\n",
630	mmeineke	647	inName, n_atoms, atomIndex );
631	gezelter	637	return strdup( painCave.errMsg );
632			}
633			jx = atof( foo );
634
635			foo = strtok(NULL, " ,;\t");
636			if(foo == NULL){
637			sprintf( painCave.errMsg,
638			"error in reading angular momentum jy from %s\n"
639			"natoms = %d, index = %d\n",
640	mmeineke	647	inName, n_atoms, atomIndex );
641	gezelter	637	return strdup( painCave.errMsg );
642			}
643			jy = atof(foo );
644
645			foo = strtok(NULL, " ,;\t");
646			if(foo == NULL){
647			sprintf( painCave.errMsg,
648			"error in reading angular momentum jz from %s\n"
649			"natoms = %d, index = %d\n",
650	mmeineke	647	inName, n_atoms, atomIndex );
651	gezelter	637	return strdup( painCave.errMsg );
652			}
653			jz = atof( foo );
654
655			dAtom = ( DirectionalAtom* )atoms[atomIndex];
656
657			// check that the quaternion vector is normalized
658
659			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
660
661			qLength = sqrt( qSqr );
662			q[0] = q[0] / qLength;
663			q[1] = q[1] / qLength;
664			q[2] = q[2] / qLength;
665			q[3] = q[3] / qLength;
666
667			dAtom->setQ( q );
668
669			// add the angular velocities
670
671			dAtom->setJx( jx );
672			dAtom->setJy( jy );
673			dAtom->setJz( jz );
674			}
675
676			// add the positions and velocities to the atom
677
678			atoms[atomIndex]->setX( rx );
679			atoms[atomIndex]->setY( ry );
680			atoms[atomIndex]->setZ( rz );
681
682			atoms[atomIndex]->set_vx( vx );
683			atoms[atomIndex]->set_vy( vy );
684			atoms[atomIndex]->set_vz( vz );
685
686			return NULL;
687			}
688
689
690			char* DumpReader::parseCommentLine(char* readLine, double time,
691			double boxMat[9]){
692
693			char *foo; // the pointer to the current string token
694			int j;
695
696			// set the string tokenizer
697
698			foo = strtok(readLine, " ,;\t");
699			if(foo == NULL){
700			sprintf( painCave.errMsg,
701			"error in reading time from %s\n",
702	mmeineke	647	inName );
703	gezelter	637	return strdup( painCave.errMsg );
704			}
705			time = atof( foo );
706
707			// get the Hx vector
708
709			foo = strtok(NULL, " ,;\t");
710			if(foo == NULL){
711			sprintf( painCave.errMsg,
712			"error in reading Hx[0] from %s\n",
713	mmeineke	647	inName );
714	gezelter	637	return strdup( painCave.errMsg );
715			}
716			boxMat[0] = atof( foo );
717
718			foo = strtok(NULL, " ,;\t");
719			if(foo == NULL){
720			sprintf( painCave.errMsg,
721			"error in reading Hx[1] from %s\n",
722	mmeineke	647	inName );
723	gezelter	637	return strdup( painCave.errMsg );
724			}
725			boxMat[1] = atof( foo );
726
727			foo = strtok(NULL, " ,;\t");
728			if(foo == NULL){
729			sprintf( painCave.errMsg,
730			"error in reading Hx[2] from %s\n",
731	mmeineke	647	inName );
732	gezelter	637	return strdup( painCave.errMsg );
733			}
734			boxMat[2] = atof( foo );
735
736			// get the Hy vector
737
738			foo = strtok(NULL, " ,;\t");
739			if(foo == NULL){
740			sprintf( painCave.errMsg,
741			"error in reading Hy[0] from %s\n",
742	mmeineke	647	inName );
743	gezelter	637	return strdup( painCave.errMsg );
744			}
745			boxMat[3] = atof( foo );
746
747			foo = strtok(NULL, " ,;\t");
748			if(foo == NULL){
749			sprintf( painCave.errMsg,
750			"error in reading Hy[1] from %s\n",
751	mmeineke	647	inName );
752	gezelter	637	return strdup( painCave.errMsg );
753			}
754			boxMat[4] = atof( foo );
755
756			foo = strtok(NULL, " ,;\t");
757			if(foo == NULL){
758			sprintf( painCave.errMsg,
759			"error in reading Hy[2] from %s\n",
760	mmeineke	647	inName );
761	gezelter	637	return strdup( painCave.errMsg );
762			}
763			boxMat[5] = atof( foo );
764
765			// get the Hz vector
766
767			foo = strtok(NULL, " ,;\t");
768			if(foo == NULL){
769			sprintf( painCave.errMsg,
770			"error in reading Hz[0] from %s\n",
771	mmeineke	647	inName );
772	gezelter	637	return strdup( painCave.errMsg );
773			}
774			boxMat[6] = atof( foo );
775
776			foo = strtok(NULL, " ,;\t");
777			if(foo == NULL){
778			sprintf( painCave.errMsg,
779			"error in reading Hz[1] from %s\n",
780	mmeineke	647	inName );
781	gezelter	637	return strdup( painCave.errMsg );
782			}
783			boxMat[7] = atof( foo );
784
785			foo = strtok(NULL, " ,;\t");
786			if(foo == NULL){
787			sprintf( painCave.errMsg,
788			"error in reading Hz[2] from %s\n",
789	mmeineke	647	inName );
790	gezelter	637	return strdup( painCave.errMsg );
791			}
792			boxMat[8] = atof( foo );
793
794			return NULL;
795			}
796
797
798			#ifdef IS_MPI
799
800			// a couple of functions to let us escape the read loop
801
802			void initFile::nodeZeroError( void ){
803			int j, myStatus;
804
805			myStatus = 0;
806			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
807			MPI_Send( &myStatus, 1, MPI_INT, j,
808			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
809			}
810
811
812			MPI_Finalize();
813			exit (0);
814
815			}
816
817			void initFile::anonymousNodeDie( void ){
818
819			MPI_Finalize();
820			exit (0);
821			}
822
823			#endif //is_mpi