OOPSE/libmdtools/DumpReader.cpp

#define _FILE_OFFSET_BITS 64

#include <sys/types.h>
#include <sys/stat.h>

#include <iostream>
#include <cmath>

#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;

  // 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 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:	804
Committed:	Thu Oct 16 19:16:24 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	18815 byte(s)
Log Message:	Changed DumpReader to use linked lists instead of a vector. Fixed the makefile to build DumpReader.cpp Removed a comment output in Exclude.cpp Modified DumpWriter and Integrator to write an eor file every time a frame is written. This lets the .eor file represent the last written frame of a simulation.
#	User	Rev	Content
1	mmeineke	643	#define _FILE_OFFSET_BITS 64
2
3	mmeineke	804	#include <sys/types.h>
4			#include <sys/stat.h>
5
6	gezelter	637	#include <iostream>
7			#include <cmath>
8
9			#include <stdio.h>
10			#include <stdlib.h>
11			#include <string.h>
12
13	mmeineke	804
14	gezelter	637	#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	gezelter	637	}
32
33			using namespace dumpRead;
34
35
36			DumpReader :: DumpReader( char *in_name ){
37	mmeineke	647
38			isScanned = false;
39	mmeineke	804	headFP = new FilePos;
40	mmeineke	647
41	gezelter	637	#ifdef IS_MPI
42			if (worldRank == 0) {
43			#endif
44
45	mmeineke	647	inFile = fopen(in_name, "r");
46			if(inFile == NULL){
47	gezelter	637	sprintf(painCave.errMsg,
48			"Cannot open file: %s\n", in_name);
49			painCave.isFatal = 1;
50			simError();
51			}
52
53	mmeineke	647	strcpy( inName, in_name);
54	gezelter	637	#ifdef IS_MPI
55			}
56			strcpy( checkPointMsg, "Dump file opened for reading successfully." );
57			MPIcheckPoint();
58			#endif
59			return;
60			}
61
62			DumpReader :: ~DumpReader( ){
63			#ifdef IS_MPI
64			if (worldRank == 0) {
65			#endif
66			int error;
67	mmeineke	647	error = fclose( inFile );
68	gezelter	637	if( error ){
69			sprintf( painCave.errMsg,
70	mmeineke	647	"Error closing %s\n", inName );
71	gezelter	637	simError();
72			}
73			#ifdef IS_MPI
74			}
75			strcpy( checkPointMsg, "Dump file closed successfully." );
76			MPIcheckPoint();
77			#endif
78
79			return;
80			}
81
82	mmeineke	647	int DumpReader::getNframes( void ){
83	gezelter	637
84	mmeineke	647	if( !isScanned ) scanFile();
85			return nFrames;
86			}
87	mmeineke	643
88	mmeineke	647	void DumpReader::scanFile( void ){
89
90			int vectorSize;
91			int i, j, k;
92			int lineNum = 0;
93			char readBuffer[2000];
94			char* foo;
95			fpos_t *currPos;
96	mmeineke	804	double time;
97	mmeineke	647
98	mmeineke	804	FilePos *currFP;
99
100
101	mmeineke	647	#ifdef IS_MPI
102			if( worldRank == 0 ){
103			#endif // is_mpi
104
105			rewind( inFile );
106
107			currPos = new fpos_t;
108			fgetpos( inFile, currPos );
109	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
110	mmeineke	647	lineNum++;
111	mmeineke	804	if( feof( inFile ) ){
112	mmeineke	647	sprintf( painCave.errMsg,
113			"File \"%s\" ended unexpectedly at line %d\n",
114			inName,
115			lineNum );
116			painCave.isFatal = 1;
117			simError();
118			}
119
120	mmeineke	804	nFrames = 0;
121			while( !feof( inFile ) ){
122
123			headFP->add( currPos );
124			nFrames++;
125
126	mmeineke	647	i = atoi(readBuffer);
127
128	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
129	mmeineke	647	lineNum++;
130	mmeineke	804	if( feof( inFile ) ){
131	mmeineke	647	sprintf( painCave.errMsg,
132			"File \"%s\" ended unexpectedly at line %d\n",
133			inName,
134			lineNum );
135			painCave.isFatal = 1;
136			simError();
137			}
138
139	mmeineke	804	// if(outTime){
140			// foo = strtok( readBuffer, " ,;\t" );
141			// time = atof( foo );
142			// }
143	mmeineke	647
144			for(j=0; j<i; j++){
145
146	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
147	mmeineke	647	lineNum++;
148	mmeineke	804	if( feof( inFile ) ){
149	mmeineke	647	sprintf( painCave.errMsg,
150			"File \"%s\" ended unexpectedly at line %d,"
151			" with atom %d\n",
152			inName,
153			lineNum,
154			j );
155			painCave.isFatal = 1;
156			simError();
157			}
158
159			}
160
161			currPos = new fpos_t;
162			fgetpos( inFile, currPos );
163	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
164	mmeineke	647	lineNum++;
165			}
166
167			delete currPos;
168			rewind( inFile );
169
170	mmeineke	804	frameStart = new FilePos*[nFrames];
171			currFP = headFP;
172			for(i=0; i<nFrames; i++){
173
174			currFP = currFP->getNext();
175			if( currFP == NULL ){
176			sprintf( painCave.errMsg,
177			"DumpReader error: scanFile FilePos mismatch at "
178			"nFrames = %d\n",
179			i );
180			painCave.isFatal = 1;
181			simError();
182			}
183
184			frameStart[i] = currFP;
185			}
186
187			isScanned = true;
188
189	mmeineke	647	#ifdef IS_MPI
190			}
191			strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
192			MPIcheckPoint();
193			#endif // is_mpi
194			}
195
196	mmeineke	656	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
197	mmeineke	647
198	mmeineke	656	simnfo = the_simnfo;
199	mmeineke	647
200	mmeineke	656	this->readSet( whichFrame );
201			}
202	gezelter	637
203	mmeineke	656
204
205			void DumpReader :: readSet( int whichFrame ){
206
207	gezelter	637	int i, j, done, which_node, which_atom; // loop counter
208
209			const int BUFFERSIZE = 2000; // size of the read buffer
210			int n_atoms; // the number of atoms
211			char read_buffer[BUFFERSIZE]; //the line buffer for reading
212			#ifdef IS_MPI
213			char send_buffer[BUFFERSIZE];
214			#endif
215
216			char *eof_test; // ptr to see when we reach the end of the file
217			char *parseErr;
218			int procIndex;
219			double boxMat[9];
220			double theBoxMat3[3][3];
221	mmeineke	804	double time;
222
223	mmeineke	656	fpos_t *framePos;
224
225			#ifndef IS_MPI
226
227	mmeineke	804	framePos = frameStart[whichFrame]->getPos();
228	gezelter	637
229	mmeineke	656
230	gezelter	637
231	mmeineke	656
232	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
233	gezelter	637	if( eof_test == NULL ){
234			sprintf( painCave.errMsg,
235			"DumpReader error: error reading 1st line of \"%s\"\n",
236	mmeineke	647	inName );
237	gezelter	637	painCave.isFatal = 1;
238			simError();
239			}
240
241			n_atoms = atoi( read_buffer );
242
243			Atom **atoms = simnfo->atoms;
244			DirectionalAtom* dAtom;
245
246			if( n_atoms != simnfo->n_atoms ){
247			sprintf( painCave.errMsg,
248			"DumpReader error. %s n_atoms, %d, "
249			"does not match the BASS file's n_atoms, %d.\n",
250	mmeineke	647	inName, n_atoms, simnfo->n_atoms );
251	gezelter	637	painCave.isFatal = 1;
252			simError();
253			}
254
255			//read the box mat from the comment line
256
257	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
258	gezelter	637	if(eof_test == NULL){
259			sprintf( painCave.errMsg,
260	mmeineke	647	"error in reading commment in %s\n", inName);
261	gezelter	637	painCave.isFatal = 1;
262			simError();
263			}
264
265			parseErr = parseCommentLine( read_buffer, time, boxMat );
266			if( parseErr != NULL ){
267			strcpy( painCave.errMsg, parseErr );
268			painCave.isFatal = 1;
269			simError();
270			}
271
272			simnfo->setTime( time );
273
274			for(i=0;i<3;i++)
275			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
276
277
278			simnfo->setBoxM( theBoxMat3 );
279
280
281			for( i=0; i < n_atoms; i++){
282
283	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
284	gezelter	637	if(eof_test == NULL){
285			sprintf(painCave.errMsg,
286			"error in reading file %s\n"
287			"natoms = %d; index = %d\n"
288			"error reading the line from the file.\n",
289	mmeineke	647	inName, n_atoms, i );
290	gezelter	637	painCave.isFatal = 1;
291			simError();
292			}
293
294
295			parseErr = parseDumpLine( read_buffer, i );
296			if( parseErr != NULL ){
297			strcpy( painCave.errMsg, parseErr );
298			painCave.isFatal = 1;
299			simError();
300			}
301			}
302
303
304			// MPI Section of code..........
305			#else //IS_MPI
306
307			// first thing first, suspend fatalities.
308			painCave.isEventLoop = 1;
309
310			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
311			int haveError;
312
313			MPI_Status istatus;
314			int *AtomToProcMap = mpiSim->getAtomToProcMap();
315
316
317			haveError = 0;
318			if (worldRank == 0) {
319
320	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
321	gezelter	637	if( eof_test == NULL ){
322			sprintf( painCave.errMsg,
323	mmeineke	647	"Error reading 1st line of %d \n ",inName);
324	gezelter	637	haveError = 1;
325			simError();
326			}
327
328			n_atoms = atoi( read_buffer );
329
330			Atom **atoms = simnfo->atoms;
331			DirectionalAtom* dAtom;
332
333			// Check to see that the number of atoms in the intial configuration file is the
334			// same as declared in simBass.
335
336			if( n_atoms != mpiSim->getTotAtoms() ){
337			sprintf( painCave.errMsg,
338			"Initialize from File error. %s n_atoms, %d, "
339			"does not match the BASS file's n_atoms, %d.\n",
340	mmeineke	647	inName, n_atoms, simnfo->n_atoms );
341	gezelter	637	haveError= 1;
342			simError();
343			}
344
345			//read the time and boxMat from the comment line
346
347	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
348	gezelter	637	if(eof_test == NULL){
349			sprintf( painCave.errMsg,
350	mmeineke	647	"error in reading commment in %s\n", inName);
351	gezelter	637	haveError = 1;
352			simError();
353			}
354
355			parseErr = parseCommentLine( read_buffer, time, boxMat );
356			if( parseErr != NULL ){
357			strcpy( painCave.errMsg, parseErr );
358			haveError = 1;
359			simError();
360			}
361
362	mmeineke	804	MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
363	gezelter	637
364			MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
365
366			if(haveError) nodeZeroError();
367
368			for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
369
370	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
371	gezelter	637	if(eof_test == NULL){
372			sprintf(painCave.errMsg,
373			"error in reading file %s\n"
374			"natoms = %d; index = %d\n"
375			"error reading the line from the file.\n",
376	mmeineke	647	inName, n_atoms, i );
377	gezelter	637	haveError= 1;
378			simError();
379			}
380
381			if(haveError) nodeZeroError();
382
383			// Get the Node number which wants this atom:
384			which_node = AtomToProcMap[i];
385			if (which_node == 0) {
386			parseErr = parseDumpLine( read_buffer, i );
387			if( parseErr != NULL ){
388			strcpy( painCave.errMsg, parseErr );
389			haveError = 1;
390			simError();
391			}
392			if(haveError) nodeZeroError();
393			}
394
395			else {
396
397			myStatus = 1;
398			MPI_Send(&myStatus, 1, MPI_INT, which_node,
399			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
400			MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
401			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
402			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
403			MPI_COMM_WORLD);
404			MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
405			MPI_COMM_WORLD, &istatus);
406
407			if(!myStatus) nodeZeroError();
408			}
409			}
410			myStatus = -1;
411			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
412			MPI_Send( &myStatus, 1, MPI_INT, j,
413			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
414			}
415
416			} else {
417
418	mmeineke	804	MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
419	gezelter	637	MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
420
421			done = 0;
422			while (!done) {
423
424			MPI_Recv(&myStatus, 1, MPI_INT, 0,
425			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
426
427			if(!myStatus) anonymousNodeDie();
428
429			if(myStatus < 0) break;
430
431			MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
432			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
433			MPI_Recv(&which_atom, 1, MPI_INT, 0,
434			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
435
436			myStatus = 1;
437			parseErr = parseDumpLine( read_buffer, which_atom );
438			if( parseErr != NULL ){
439			strcpy( painCave.errMsg, parseErr );
440			myStatus = 0;;
441			simError();
442			}
443
444			MPI_Send( &myStatus, 1, MPI_INT, 0,
445			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
446
447			}
448			}
449
450			// last thing last, enable fatalities.
451			painCave.isEventLoop = 0;
452
453			simnfo->setTime( time );
454
455			for(i=0;i<3;i++)
456			for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
457
458			simnfo->setBoxM( theBoxMat3 );
459
460
461			#endif
462			}
463
464			char* DumpReader::parseDumpLine(char* readLine, int globalIndex){
465
466			char *foo; // the pointer to the current string token
467
468	mmeineke	804	double pos[3]; // position place holders
469			double vel[3]; // velocity placeholders
470	gezelter	637	double q[4]; // the quaternions
471			double jx, jy, jz; // angular velocity placeholders;
472			double qSqr, qLength; // needed to normalize the quaternion vector.
473
474			Atom **atoms = simnfo->atoms;
475			DirectionalAtom* dAtom;
476
477			int j, n_atoms, atomIndex;
478
479			#ifdef IS_MPI
480			n_atoms = mpiSim->getTotAtoms();
481			atomIndex=-1;
482			for (j=0; j < mpiSim->getMyNlocal(); j++) {
483			if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
484			}
485			if (atomIndex == -1) {
486			sprintf( painCave.errMsg,
487			"Initialize from file error. Atom at index %d "
488			"in file %s does not exist on processor %d .\n",
489	mmeineke	647	globalIndex, inName, mpiSim->getMyNode() );
490	gezelter	637	return strdup( painCave.errMsg );
491			}
492			#else
493			n_atoms = simnfo->n_atoms;
494			atomIndex = globalIndex;
495			#endif // is_mpi
496
497			// set the string tokenizer
498
499			foo = strtok(readLine, " ,;\t");
500
501			// check the atom name to the current atom
502
503			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
504			sprintf( painCave.errMsg,
505			"Initialize from file error. Atom %s at index %d "
506			"in file %s does not"
507			" match the BASS atom %s.\n",
508	mmeineke	647	foo, atomIndex, inName, atoms[atomIndex]->getType() );
509	gezelter	637	return strdup( painCave.errMsg );
510			}
511
512			// get the positions
513
514			foo = strtok(NULL, " ,;\t");
515			if(foo == NULL){
516			sprintf( painCave.errMsg,
517			"error in reading postition x from %s\n"
518			"natoms = %d, index = %d\n",
519	mmeineke	647	inName, n_atoms, atomIndex );
520	gezelter	637	return strdup( painCave.errMsg );
521			}
522	mmeineke	804	pos[0] = atof( foo );
523	gezelter	637
524			foo = strtok(NULL, " ,;\t");
525			if(foo == NULL){
526			sprintf( painCave.errMsg,
527			"error in reading postition y from %s\n"
528			"natoms = %d, index = %d\n",
529	mmeineke	647	inName, n_atoms, atomIndex );
530	gezelter	637	return strdup( painCave.errMsg );
531			}
532	mmeineke	804	pos[1] = atof( foo );
533	gezelter	637
534			foo = strtok(NULL, " ,;\t");
535			if(foo == NULL){
536			sprintf( painCave.errMsg,
537			"error in reading postition z from %s\n"
538			"natoms = %d, index = %d\n",
539	mmeineke	647	inName, n_atoms, atomIndex );
540	gezelter	637	return strdup( painCave.errMsg );
541			}
542	mmeineke	804	pos[2] = atof( foo );
543	gezelter	637
544
545			// get the velocities
546
547			foo = strtok(NULL, " ,;\t");
548			if(foo == NULL){
549			sprintf( painCave.errMsg,
550			"error in reading velocity x from %s\n"
551			"natoms = %d, index = %d\n",
552	mmeineke	647	inName, n_atoms, atomIndex );
553	gezelter	637	return strdup( painCave.errMsg );
554			}
555	mmeineke	804	vel[0] = atof( foo );
556	gezelter	637
557			foo = strtok(NULL, " ,;\t");
558			if(foo == NULL){
559			sprintf( painCave.errMsg,
560			"error in reading velocity y from %s\n"
561			"natoms = %d, index = %d\n",
562	mmeineke	647	inName, n_atoms, atomIndex );
563	gezelter	637	return strdup( painCave.errMsg );
564			}
565	mmeineke	804	vel[1] = atof( foo );
566	gezelter	637
567			foo = strtok(NULL, " ,;\t");
568			if(foo == NULL){
569			sprintf( painCave.errMsg,
570			"error in reading velocity z from %s\n"
571			"natoms = %d, index = %d\n",
572	mmeineke	647	inName, n_atoms, atomIndex );
573	gezelter	637	return strdup( painCave.errMsg );
574			}
575	mmeineke	804	vel[2] = atof( foo );
576	gezelter	637
577
578			// get the quaternions
579
580			if( atoms[atomIndex]->isDirectional() ){
581
582			foo = strtok(NULL, " ,;\t");
583			if(foo == NULL){
584			sprintf(painCave.errMsg,
585			"error in reading quaternion 0 from %s\n"
586			"natoms = %d, index = %d\n",
587	mmeineke	647	inName, n_atoms, atomIndex );
588	gezelter	637	return strdup( painCave.errMsg );
589			}
590			q[0] = atof( foo );
591
592			foo = strtok(NULL, " ,;\t");
593			if(foo == NULL){
594			sprintf( painCave.errMsg,
595			"error in reading quaternion 1 from %s\n"
596			"natoms = %d, index = %d\n",
597	mmeineke	647	inName, n_atoms, atomIndex );
598	gezelter	637	return strdup( painCave.errMsg );
599			}
600			q[1] = atof( foo );
601
602			foo = strtok(NULL, " ,;\t");
603			if(foo == NULL){
604			sprintf( painCave.errMsg,
605			"error in reading quaternion 2 from %s\n"
606			"natoms = %d, index = %d\n",
607	mmeineke	647	inName, n_atoms, atomIndex );
608	gezelter	637	return strdup( painCave.errMsg );
609			}
610			q[2] = atof( foo );
611
612			foo = strtok(NULL, " ,;\t");
613			if(foo == NULL){
614			sprintf( painCave.errMsg,
615			"error in reading quaternion 3 from %s\n"
616			"natoms = %d, index = %d\n",
617	mmeineke	647	inName, n_atoms, atomIndex );
618	gezelter	637	return strdup( painCave.errMsg );
619			}
620			q[3] = atof( foo );
621
622			// get the angular velocities
623
624			foo = strtok(NULL, " ,;\t");
625			if(foo == NULL){
626			sprintf( painCave.errMsg,
627			"error in reading angular momentum jx from %s\n"
628			"natoms = %d, index = %d\n",
629	mmeineke	647	inName, n_atoms, atomIndex );
630	gezelter	637	return strdup( painCave.errMsg );
631			}
632			jx = atof( foo );
633
634			foo = strtok(NULL, " ,;\t");
635			if(foo == NULL){
636			sprintf( painCave.errMsg,
637			"error in reading angular momentum jy from %s\n"
638			"natoms = %d, index = %d\n",
639	mmeineke	647	inName, n_atoms, atomIndex );
640	gezelter	637	return strdup( painCave.errMsg );
641			}
642			jy = atof(foo );
643
644			foo = strtok(NULL, " ,;\t");
645			if(foo == NULL){
646			sprintf( painCave.errMsg,
647			"error in reading angular momentum jz from %s\n"
648			"natoms = %d, index = %d\n",
649	mmeineke	647	inName, n_atoms, atomIndex );
650	gezelter	637	return strdup( painCave.errMsg );
651			}
652			jz = atof( foo );
653
654			dAtom = ( DirectionalAtom* )atoms[atomIndex];
655
656			// check that the quaternion vector is normalized
657
658			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
659
660			qLength = sqrt( qSqr );
661			q[0] = q[0] / qLength;
662			q[1] = q[1] / qLength;
663			q[2] = q[2] / qLength;
664			q[3] = q[3] / qLength;
665
666			dAtom->setQ( q );
667
668			// add the angular velocities
669
670			dAtom->setJx( jx );
671			dAtom->setJy( jy );
672			dAtom->setJz( jz );
673			}
674
675			// add the positions and velocities to the atom
676
677	mmeineke	804	atoms[atomIndex]->setPos( pos );
678			atoms[atomIndex]->setVel( vel );
679
680	gezelter	637	return NULL;
681			}
682
683
684	mmeineke	804	char* DumpReader::parseCommentLine(char* readLine, double &time,
685	gezelter	637	double boxMat[9]){
686
687			char *foo; // the pointer to the current string token
688			int j;
689
690			// set the string tokenizer
691
692			foo = strtok(readLine, " ,;\t");
693			if(foo == NULL){
694			sprintf( painCave.errMsg,
695			"error in reading time from %s\n",
696	mmeineke	647	inName );
697	gezelter	637	return strdup( painCave.errMsg );
698			}
699			time = atof( foo );
700
701			// get the Hx vector
702
703			foo = strtok(NULL, " ,;\t");
704			if(foo == NULL){
705			sprintf( painCave.errMsg,
706			"error in reading Hx[0] from %s\n",
707	mmeineke	647	inName );
708	gezelter	637	return strdup( painCave.errMsg );
709			}
710			boxMat[0] = atof( foo );
711
712			foo = strtok(NULL, " ,;\t");
713			if(foo == NULL){
714			sprintf( painCave.errMsg,
715			"error in reading Hx[1] from %s\n",
716	mmeineke	647	inName );
717	gezelter	637	return strdup( painCave.errMsg );
718			}
719			boxMat[1] = atof( foo );
720
721			foo = strtok(NULL, " ,;\t");
722			if(foo == NULL){
723			sprintf( painCave.errMsg,
724			"error in reading Hx[2] from %s\n",
725	mmeineke	647	inName );
726	gezelter	637	return strdup( painCave.errMsg );
727			}
728			boxMat[2] = atof( foo );
729
730			// get the Hy vector
731
732			foo = strtok(NULL, " ,;\t");
733			if(foo == NULL){
734			sprintf( painCave.errMsg,
735			"error in reading Hy[0] from %s\n",
736	mmeineke	647	inName );
737	gezelter	637	return strdup( painCave.errMsg );
738			}
739			boxMat[3] = atof( foo );
740
741			foo = strtok(NULL, " ,;\t");
742			if(foo == NULL){
743			sprintf( painCave.errMsg,
744			"error in reading Hy[1] from %s\n",
745	mmeineke	647	inName );
746	gezelter	637	return strdup( painCave.errMsg );
747			}
748			boxMat[4] = atof( foo );
749
750			foo = strtok(NULL, " ,;\t");
751			if(foo == NULL){
752			sprintf( painCave.errMsg,
753			"error in reading Hy[2] from %s\n",
754	mmeineke	647	inName );
755	gezelter	637	return strdup( painCave.errMsg );
756			}
757			boxMat[5] = atof( foo );
758
759			// get the Hz vector
760
761			foo = strtok(NULL, " ,;\t");
762			if(foo == NULL){
763			sprintf( painCave.errMsg,
764			"error in reading Hz[0] from %s\n",
765	mmeineke	647	inName );
766	gezelter	637	return strdup( painCave.errMsg );
767			}
768			boxMat[6] = atof( foo );
769
770			foo = strtok(NULL, " ,;\t");
771			if(foo == NULL){
772			sprintf( painCave.errMsg,
773			"error in reading Hz[1] from %s\n",
774	mmeineke	647	inName );
775	gezelter	637	return strdup( painCave.errMsg );
776			}
777			boxMat[7] = atof( foo );
778
779			foo = strtok(NULL, " ,;\t");
780			if(foo == NULL){
781			sprintf( painCave.errMsg,
782			"error in reading Hz[2] from %s\n",
783	mmeineke	647	inName );
784	gezelter	637	return strdup( painCave.errMsg );
785			}
786			boxMat[8] = atof( foo );
787
788			return NULL;
789			}
790
791
792			#ifdef IS_MPI
793
794			// a couple of functions to let us escape the read loop
795
796	mmeineke	804	void dumpRead::nodeZeroError( void ){
797	gezelter	637	int j, myStatus;
798
799			myStatus = 0;
800			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
801			MPI_Send( &myStatus, 1, MPI_INT, j,
802			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
803			}
804
805
806			MPI_Finalize();
807			exit (0);
808
809			}
810
811	mmeineke	804	void dumpRead::anonymousNodeDie( void ){
812	gezelter	637
813			MPI_Finalize();
814			exit (0);
815			}
816
817			#endif //is_mpi