OOPSE/libmdtools/DumpReader.cpp

#define _LARGEFILE_SOURCE64
#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


DumpReader :: DumpReader(const 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();
  }
  
  inFileName = 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
  vector<fpos_t*>::iterator i;

  int error;
  error = fclose( inFile );
  if( error ){
    sprintf( painCave.errMsg,
             "Error closing %s\n", inFileName.c_str());
    simError();
  }

  for(i = framePos.begin(); i != framePos.end(); ++i)
    delete *i;
  framePos.clear();
  
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Dump file closed successfully." );
  MPIcheckPoint();
#endif

  return;
}

int DumpReader::getNframes( void ){

  if( !isScanned )
    scanFile();
  return framePos.size();
}

void DumpReader::scanFile( void ){

  int i, j;
  int lineNum = 0;
  char readBuffer[2000];
  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 ), inFile );
    lineNum++;
    if( feof( inFile ) ){
      sprintf( painCave.errMsg,
               "File \"%s\" ended unexpectedly at line %d\n", 
               inFileName.c_str(),
               lineNum );
      painCave.isFatal = 1;
      simError();
    }

    while( !feof( inFile ) ){
      
      framePos.push_back(currPos);

      i = atoi(readBuffer);
      
      fgets( readBuffer, sizeof( readBuffer ), inFile );
      lineNum++;    
      if( feof( inFile ) ){
        sprintf( painCave.errMsg,
                 "File \"%s\" ended unexpectedly at line %d\n",
                 inFileName.c_str(),
                 lineNum );
        painCave.isFatal = 1;
        simError();
      }
            
      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", 
                   inFileName.c_str(),
                   lineNum, 
                   j );
          painCave.isFatal = 1;
          simError();
        }
        
      }
      
      currPos = new fpos_t;
      fgetpos( inFile, currPos );
      fgets( readBuffer, sizeof( readBuffer ), inFile );
      lineNum++;
    }
    
    delete currPos;
    rewind( inFile );
     
    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;
  unsigned int j;

#ifdef IS_MPI
  int done, which_node, which_atom; // loop counter
#endif //is_mpi

  const int BUFFERSIZE = 2000; // size of the read buffer
  int nTotObjs; // the number of atoms
  char read_buffer[BUFFERSIZE]; //the line buffer for reading

  char *eof_test; // ptr to see when we reach the end of the file
  char *parseErr;

  vector<StuntDouble*> integrableObjects;


#ifndef IS_MPI

  fsetpos(inFile, framePos[whichFrame]);
  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",
             inFileName.c_str() );
    painCave.isFatal = 1;
    simError();
  }

  nTotObjs = atoi( read_buffer );

  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
    sprintf( painCave.errMsg,
             "DumpReader error. %s n_atoms, %d, "
             "does not match the BASS file's n_atoms, %d.\n",
             inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
    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", inFileName.c_str());
    painCave.isFatal = 1;
    simError();
  }

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

  //parse dump lines

  for( i=0; i < simnfo->n_mol; i++){

    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();

    for(j = 0; j < integrableObjects.size(); j++){

      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",
              inFileName.c_str(), nTotObjs, i );
        painCave.isFatal = 1;
        simError();
      }
      
      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
      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 *MolToProcMap = mpiSim->getMolToProcMap();
  int localIndex;
  int nCurObj;
  int nitems;

  nTotObjs = simnfo->getTotIntegrableObjects();
  haveError = 0;
  if (worldRank == 0) {
     fsetpos(inFile,  framePos[whichFrame]);

    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
    if( eof_test == NULL ){
      sprintf( painCave.errMsg,
               "Error reading 1st line of %s \n ",inFileName.c_str());
      haveError = 1;
      simError();
    }

    nitems = atoi( read_buffer );

    // Check to see that the number of integrable objects  in the intial configuration file is the
    // same as declared in simBass.

    if( nTotObjs != nitems){
      sprintf( painCave.errMsg,
               "DumpReadererror. %s n_atoms, %d, "
               "does not match the BASS file's n_atoms, %d.\n",
               inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
      haveError= 1;
      simError();
    }

    //read the 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", inFileName.c_str());
      haveError = 1;
      simError();
    }

    //Every single processor will parse the comment line by itself
    //By using this way, we might lose some efficiency, but if we want to add
    //more parameters into comment line, we only need to modify function
    //parseCommentLine

    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);

    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      if(which_node == 0){
       //molecules belong to master node

      localIndex = mpiSim->getGlobalToLocalMol(i);

      if(localIndex == -1) {
        strcpy(painCave.errMsg, "Molecule not found on node 0!");
        haveError = 1;
        simError();
      }

       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
       for(j=0; j < integrableObjects.size(); j++){
        
          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",
                    inFileName.c_str(), nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

          parseDumpLine(read_buffer, integrableObjects[j]);
           
       }


      }
      else{
      //molecule belongs to slave nodes

        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
       for(j=0; j < nCurObj; j++){
        
          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",
                    inFileName.c_str(), nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
           
       }

      }
      
    }
    
  }
  else{
  //actions taken at slave nodes
    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);

    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }
  
    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      
      if(which_node == worldRank){
      //molecule with global index i belongs to this processor
      
        localIndex = mpiSim->getGlobalToLocalMol(i);

        if(localIndex == -1) {
          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
          haveError = 1;
          simError();
        }

        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        

        nCurObj = integrableObjects.size();
        
        MPI_Send(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);

        for(j = 0; j < integrableObjects.size(); j++){

          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);

          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);

          if( parseErr != NULL ){
                strcpy( painCave.errMsg, parseErr );
                simError();
          }

        }
          
      }
      
    }

  }

#endif
}

char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){

  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 ji[3]; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.


  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");

  // check the atom name to the current atom

  if( strcmp( foo, sd->getType() ) ){
    sprintf( painCave.errMsg,
             "DumpReader error.  Does not"
             " match the BASS atom %s.\n",
             sd->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",
             inFileName.c_str());
    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",
             inFileName.c_str());
    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",
             inFileName.c_str());
    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",
             inFileName.c_str() );
    return strdup( painCave.errMsg );
  }
  vel[0] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             inFileName.c_str() );
    return strdup( painCave.errMsg );
  }
  vel[1] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             inFileName.c_str() );
    return strdup( painCave.errMsg );
  }
  vel[2] = atof( foo );


  // add the positions and velocities to the atom

  sd->setPos( pos );
  sd->setVel( vel );

  if (!sd->isDirectional())
    return NULL;

  // get the quaternions

  if( sd->isDirectional() ){

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      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 velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    ji[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    ji[1] = atof(foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    ji[2] = atof( foo );


    // 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;

    // add quaternion and angular velocities

    sd->setQ( q );
    sd->setJ( ji );
  }


  return NULL;
}


char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){

  double currTime;
  double boxMat[9];
  double theBoxMat3[3][3];
  double chi;
  double integralOfChidt;
  double eta[9];

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

  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");
  // set the timeToken.

  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Time from %s\n",
             inFileName.c_str() );
    return strdup( painCave.errMsg );
  }

  currTime = atof( foo );
  entry_plug->setTime( currTime );

  //get H-Matrix

  for(int i = 0 ; i < 9; i++){
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading H[%d] from %s\n", i, inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    boxMat[i] = atof( foo );
  }

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

  //set H-Matrix
  entry_plug->setBoxM( theBoxMat3 );

  //get chi and integralOfChidt, they should appear by pair

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

  return NULL;
}

#ifdef IS_MPI
void DumpReader::nodeZeroError( void ){
  int j, myStatus;

  myStatus = 0;
  for (j = 0; j < mpiSim->getNProcessors(); j++) {
    MPI_Send( &myStatus, 1, MPI_INT, j,
              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
  }


  MPI_Finalize();
  exit (0);

}

void DumpReader::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}
#endif
Revision:	1252
Committed:	Mon Jun 7 14:26:33 2004 UTC (20 years, 1 month ago) by gezelter
File size:	17927 byte(s)
Log Message:	Fixes from gcc -Wall
#	User	Rev	Content
1	tim	1078	#define _LARGEFILE_SOURCE64
2	mmeineke	643	#define _FILE_OFFSET_BITS 64
3
4	mmeineke	804	#include <sys/types.h>
5			#include <sys/stat.h>
6
7	gezelter	637	#include <iostream>
8	gezelter	829	#include <math.h>
9	gezelter	637
10			#include <stdio.h>
11			#include <stdlib.h>
12			#include <string.h>
13
14	mmeineke	804
15	gezelter	637	#include "ReadWrite.hpp"
16			#include "simError.h"
17
18			#ifdef IS_MPI
19			#include <mpi.h>
20			#include "mpiSimulation.hpp"
21			#define TAKE_THIS_TAG_CHAR 0
22			#define TAKE_THIS_TAG_INT 1
23	mmeineke	647	#endif // is_mpi
24	gezelter	637
25	mmeineke	647
26	tim	1074	DumpReader :: DumpReader(const char *in_name ){
27	mmeineke	647
28			isScanned = false;
29
30	gezelter	637	#ifdef IS_MPI
31			if (worldRank == 0) {
32			#endif
33
34	mmeineke	647	inFile = fopen(in_name, "r");
35			if(inFile == NULL){
36	gezelter	637	sprintf(painCave.errMsg,
37			"Cannot open file: %s\n", in_name);
38			painCave.isFatal = 1;
39			simError();
40			}
41
42	tim	1118	inFileName = in_name;
43	gezelter	637	#ifdef IS_MPI
44			}
45			strcpy( checkPointMsg, "Dump file opened for reading successfully." );
46			MPIcheckPoint();
47			#endif
48			return;
49			}
50
51			DumpReader :: ~DumpReader( ){
52			#ifdef IS_MPI
53			if (worldRank == 0) {
54			#endif
55	tim	1118	vector<fpos_t*>::iterator i;
56
57	gezelter	637	int error;
58	mmeineke	647	error = fclose( inFile );
59	gezelter	637	if( error ){
60			sprintf( painCave.errMsg,
61	tim	1118	"Error closing %s\n", inFileName.c_str());
62	gezelter	637	simError();
63			}
64	tim	1118
65			for(i = framePos.begin(); i != framePos.end(); ++i)
66			delete *i;
67			framePos.clear();
68
69	gezelter	637	#ifdef IS_MPI
70			}
71			strcpy( checkPointMsg, "Dump file closed successfully." );
72			MPIcheckPoint();
73			#endif
74
75			return;
76			}
77
78	mmeineke	647	int DumpReader::getNframes( void ){
79	gezelter	637
80	tim	1118	if( !isScanned )
81			scanFile();
82			return framePos.size();
83	mmeineke	647	}
84	mmeineke	643
85	mmeineke	647	void DumpReader::scanFile( void ){
86
87	gezelter	1252	int i, j;
88	mmeineke	647	int lineNum = 0;
89			char readBuffer[2000];
90			fpos_t *currPos;
91
92			#ifdef IS_MPI
93			if( worldRank == 0 ){
94			#endif // is_mpi
95
96			rewind( inFile );
97
98			currPos = new fpos_t;
99			fgetpos( inFile, currPos );
100	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
101	mmeineke	647	lineNum++;
102	mmeineke	804	if( feof( inFile ) ){
103	mmeineke	647	sprintf( painCave.errMsg,
104			"File \"%s\" ended unexpectedly at line %d\n",
105	tim	1118	inFileName.c_str(),
106	mmeineke	647	lineNum );
107			painCave.isFatal = 1;
108			simError();
109			}
110	tim	1118
111	mmeineke	804	while( !feof( inFile ) ){
112	tim	1119
113			framePos.push_back(currPos);
114	mmeineke	804
115	mmeineke	647	i = atoi(readBuffer);
116
117	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
118	mmeineke	647	lineNum++;
119	mmeineke	804	if( feof( inFile ) ){
120	mmeineke	647	sprintf( painCave.errMsg,
121			"File \"%s\" ended unexpectedly at line %d\n",
122	tim	1118	inFileName.c_str(),
123	mmeineke	647	lineNum );
124			painCave.isFatal = 1;
125			simError();
126			}
127	tim	1118
128	mmeineke	647	for(j=0; j<i; j++){
129
130	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
131	mmeineke	647	lineNum++;
132	mmeineke	804	if( feof( inFile ) ){
133	mmeineke	647	sprintf( painCave.errMsg,
134			"File \"%s\" ended unexpectedly at line %d,"
135			" with atom %d\n",
136	tim	1118	inFileName.c_str(),
137	mmeineke	647	lineNum,
138			j );
139			painCave.isFatal = 1;
140			simError();
141			}
142
143			}
144
145			currPos = new fpos_t;
146			fgetpos( inFile, currPos );
147	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
148	mmeineke	647	lineNum++;
149			}
150
151			delete currPos;
152			rewind( inFile );
153	tim	1118
154	mmeineke	804	isScanned = true;
155
156	mmeineke	647	#ifdef IS_MPI
157			}
158			strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
159			MPIcheckPoint();
160			#endif // is_mpi
161			}
162
163	mmeineke	656	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
164	mmeineke	647
165	mmeineke	656	simnfo = the_simnfo;
166	mmeineke	647
167	mmeineke	656	this->readSet( whichFrame );
168			}
169	gezelter	637
170	mmeineke	656
171
172			void DumpReader :: readSet( int whichFrame ){
173
174	gezelter	1252	int i;
175			unsigned int j;
176	gezelter	637
177			#ifdef IS_MPI
178	tim	1118	int done, which_node, which_atom; // loop counter
179			#endif //is_mpi
180	gezelter	637
181	tim	1118	const int BUFFERSIZE = 2000; // size of the read buffer
182			int nTotObjs; // the number of atoms
183			char read_buffer[BUFFERSIZE]; //the line buffer for reading
184
185			char *eof_test; // ptr to see when we reach the end of the file
186	gezelter	637	char *parseErr;
187	mmeineke	804
188	tim	1118	vector<StuntDouble*> integrableObjects;
189
190
191	mmeineke	656	#ifndef IS_MPI
192	gezelter	637
193	tim	1118	fsetpos(inFile, framePos[whichFrame]);
194	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
195	gezelter	637	if( eof_test == NULL ){
196			sprintf( painCave.errMsg,
197	tim	1119	"DumpReader error: error reading 1st line of \"%s\"\n",
198	tim	1118	inFileName.c_str() );
199	gezelter	637	painCave.isFatal = 1;
200			simError();
201			}
202
203	tim	1118	nTotObjs = atoi( read_buffer );
204	gezelter	637
205	tim	1118	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
206	gezelter	637	sprintf( painCave.errMsg,
207	tim	1119	"DumpReader error. %s n_atoms, %d, "
208	gezelter	637	"does not match the BASS file's n_atoms, %d.\n",
209	tim	1118	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
210	gezelter	637	painCave.isFatal = 1;
211			simError();
212			}
213	tim	1118
214			//read the box mat from the comment line
215
216	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
217	gezelter	637	if(eof_test == NULL){
218			sprintf( painCave.errMsg,
219	tim	1118	"error in reading commment in %s\n", inFileName.c_str());
220	gezelter	637	painCave.isFatal = 1;
221			simError();
222			}
223
224	tim	1118	parseErr = parseCommentLine( read_buffer, simnfo);
225	gezelter	637	if( parseErr != NULL ){
226			strcpy( painCave.errMsg, parseErr );
227			painCave.isFatal = 1;
228			simError();
229			}
230
231	tim	1118	//parse dump lines
232	gezelter	637
233	tim	1118	for( i=0; i < simnfo->n_mol; i++){
234	gezelter	637
235	tim	1118	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
236	gezelter	637
237	tim	1118	for(j = 0; j < integrableObjects.size(); j++){
238
239			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
240			if(eof_test == NULL){
241			sprintf(painCave.errMsg,
242			"error in reading file %s\n"
243			"natoms = %d; index = %d\n"
244			"error reading the line from the file.\n",
245			inFileName.c_str(), nTotObjs, i );
246			painCave.isFatal = 1;
247			simError();
248			}
249
250			parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
251			if( parseErr != NULL ){
252			strcpy( painCave.errMsg, parseErr );
253			painCave.isFatal = 1;
254			simError();
255			}
256	gezelter	637	}
257			}
258
259			// MPI Section of code..........
260			#else //IS_MPI
261
262			// first thing first, suspend fatalities.
263			painCave.isEventLoop = 1;
264
265			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
266			int haveError;
267	tim	1118
268	gezelter	637	MPI_Status istatus;
269	tim	1118	int *MolToProcMap = mpiSim->getMolToProcMap();
270			int localIndex;
271			int nCurObj;
272	tim	1129	int nitems;
273	gezelter	637
274	tim	1129	nTotObjs = simnfo->getTotIntegrableObjects();
275	gezelter	637	haveError = 0;
276			if (worldRank == 0) {
277	tim	1118	fsetpos(inFile, framePos[whichFrame]);
278
279	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
280	gezelter	637	if( eof_test == NULL ){
281			sprintf( painCave.errMsg,
282	tim	1118	"Error reading 1st line of %s \n ",inFileName.c_str());
283	gezelter	637	haveError = 1;
284			simError();
285			}
286	tim	1118
287	tim	1129	nitems = atoi( read_buffer );
288	tim	1118
289			// Check to see that the number of integrable objects in the intial configuration file is the
290	gezelter	637	// same as declared in simBass.
291	tim	1118
292	tim	1129	if( nTotObjs != nitems){
293	gezelter	637	sprintf( painCave.errMsg,
294	tim	1119	"DumpReadererror. %s n_atoms, %d, "
295	gezelter	637	"does not match the BASS file's n_atoms, %d.\n",
296	tim	1118	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
297	gezelter	637	haveError= 1;
298			simError();
299			}
300	tim	1118
301			//read the boxMat from the comment line
302
303	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
304	gezelter	637	if(eof_test == NULL){
305			sprintf( painCave.errMsg,
306	tim	1118	"error in reading commment in %s\n", inFileName.c_str());
307	gezelter	637	haveError = 1;
308			simError();
309			}
310	tim	1118
311			//Every single processor will parse the comment line by itself
312			//By using this way, we might lose some efficiency, but if we want to add
313			//more parameters into comment line, we only need to modify function
314			//parseCommentLine
315
316			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
317
318			parseErr = parseCommentLine( read_buffer, simnfo);
319
320	gezelter	637	if( parseErr != NULL ){
321			strcpy( painCave.errMsg, parseErr );
322			haveError = 1;
323			simError();
324			}
325
326	gezelter	1203	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
327	tim	1118	which_node = MolToProcMap[i];
328			if(which_node == 0){
329			//molecules belong to master node
330
331			localIndex = mpiSim->getGlobalToLocalMol(i);
332
333			if(localIndex == -1) {
334			strcpy(painCave.errMsg, "Molecule not found on node 0!");
335			haveError = 1;
336			simError();
337	gezelter	637	}
338
339	tim	1118	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
340			for(j=0; j < integrableObjects.size(); j++){
341
342			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
343			if(eof_test == NULL){
344			sprintf(painCave.errMsg,
345			"error in reading file %s\n"
346			"natoms = %d; index = %d\n"
347			"error reading the line from the file.\n",
348			inFileName.c_str(), nTotObjs, i );
349			haveError= 1;
350			simError();
351			}
352
353			if(haveError) nodeZeroError();
354
355	tim	1129	parseDumpLine(read_buffer, integrableObjects[j]);
356	tim	1118
357			}
358
359
360	gezelter	637	}
361	tim	1118	else{
362			//molecule belongs to slave nodes
363	gezelter	637
364	tim	1129	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
365	gezelter	637	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
366
367	tim	1130	for(j=0; j < nCurObj; j++){
368	tim	1118
369			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
370			if(eof_test == NULL){
371			sprintf(painCave.errMsg,
372			"error in reading file %s\n"
373			"natoms = %d; index = %d\n"
374			"error reading the line from the file.\n",
375			inFileName.c_str(), nTotObjs, i );
376			haveError= 1;
377			simError();
378			}
379
380			if(haveError) nodeZeroError();
381	gezelter	637
382	tim	1118	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
383			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
384
385			}
386
387	gezelter	637	}
388
389			}
390	tim	1118
391	gezelter	637	}
392	tim	1118	else{
393			//actions taken at slave nodes
394	tim	1129	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
395
396			parseErr = parseCommentLine( read_buffer, simnfo);
397
398			if( parseErr != NULL ){
399			strcpy( painCave.errMsg, parseErr );
400			haveError = 1;
401			simError();
402			}
403
404	gezelter	1203	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
405	tim	1118	which_node = MolToProcMap[i];
406
407			if(which_node == worldRank){
408			//molecule with global index i belongs to this processor
409
410			localIndex = mpiSim->getGlobalToLocalMol(i);
411	gezelter	637
412	tim	1118	if(localIndex == -1) {
413			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
414			haveError = 1;
415			simError();
416			}
417	gezelter	637
418	tim	1118	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
419	gezelter	637
420	tim	1118	nCurObj = integrableObjects.size();
421
422	tim	1129	MPI_Send(&nCurObj, 1, MPI_INT, 0,
423			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
424	gezelter	637
425	tim	1118	for(j = 0; j < integrableObjects.size(); j++){
426
427			MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
428			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
429
430			parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
431
432			if( parseErr != NULL ){
433			strcpy( painCave.errMsg, parseErr );
434			simError();
435			}
436
437			}
438
439			}
440
441			}
442
443			}
444
445	gezelter	637	#endif
446			}
447
448	tim	1118	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
449	gezelter	637
450	tim	1118	char *foo; // the pointer to the current string token
451
452			double pos[3]; // position place holders
453			double vel[3]; // velocity placeholders
454			double q[4]; // the quaternions
455			double ji[3]; // angular velocity placeholders;
456	gezelter	637	double qSqr, qLength; // needed to normalize the quaternion vector.
457
458
459			// set the string tokenizer
460	tim	1118
461	gezelter	637	foo = strtok(readLine, " ,;\t");
462	tim	1118
463	gezelter	637	// check the atom name to the current atom
464	tim	1118
465			if( strcmp( foo, sd->getType() ) ){
466			sprintf( painCave.errMsg,
467	tim	1119	"DumpReader error. Does not"
468	tim	1118	" match the BASS atom %s.\n",
469			sd->getType() );
470			return strdup( painCave.errMsg );
471			}
472
473	gezelter	637	// get the positions
474
475			foo = strtok(NULL, " ,;\t");
476			if(foo == NULL){
477			sprintf( painCave.errMsg,
478	tim	1118	"error in reading postition x from %s\n",
479			inFileName.c_str());
480	gezelter	637	return strdup( painCave.errMsg );
481			}
482	mmeineke	804	pos[0] = atof( foo );
483	tim	1118
484	gezelter	637	foo = strtok(NULL, " ,;\t");
485			if(foo == NULL){
486			sprintf( painCave.errMsg,
487	tim	1118	"error in reading postition y from %s\n",
488			inFileName.c_str());
489	gezelter	637	return strdup( painCave.errMsg );
490			}
491	mmeineke	804	pos[1] = atof( foo );
492	tim	1118
493	gezelter	637	foo = strtok(NULL, " ,;\t");
494			if(foo == NULL){
495			sprintf( painCave.errMsg,
496	tim	1118	"error in reading postition z from %s\n",
497			inFileName.c_str());
498	gezelter	637	return strdup( painCave.errMsg );
499			}
500	tim	1118	pos[2] = atof( foo );
501	gezelter	637
502
503			// get the velocities
504
505			foo = strtok(NULL, " ,;\t");
506			if(foo == NULL){
507			sprintf( painCave.errMsg,
508	tim	1118	"error in reading velocity x from %s\n",
509			inFileName.c_str() );
510	gezelter	637	return strdup( painCave.errMsg );
511			}
512	mmeineke	804	vel[0] = atof( foo );
513	tim	1118
514	gezelter	637	foo = strtok(NULL, " ,;\t");
515			if(foo == NULL){
516			sprintf( painCave.errMsg,
517	tim	1118	"error in reading velocity x from %s\n",
518			inFileName.c_str() );
519	gezelter	637	return strdup( painCave.errMsg );
520			}
521	mmeineke	804	vel[1] = atof( foo );
522	tim	1118
523	gezelter	637	foo = strtok(NULL, " ,;\t");
524			if(foo == NULL){
525			sprintf( painCave.errMsg,
526	tim	1118	"error in reading velocity x from %s\n",
527			inFileName.c_str() );
528	gezelter	637	return strdup( painCave.errMsg );
529			}
530	mmeineke	804	vel[2] = atof( foo );
531	tim	1118
532
533			// add the positions and velocities to the atom
534
535			sd->setPos( pos );
536			sd->setVel( vel );
537
538			if (!sd->isDirectional())
539			return NULL;
540
541	gezelter	637	// get the quaternions
542	tim	1118
543			if( sd->isDirectional() ){
544
545	gezelter	637	foo = strtok(NULL, " ,;\t");
546			if(foo == NULL){
547	tim	1118	sprintf( painCave.errMsg,
548			"error in reading velocity x from %s\n",
549			inFileName.c_str() );
550	gezelter	637	return strdup( painCave.errMsg );
551			}
552			q[0] = atof( foo );
553	tim	1118
554	gezelter	637	foo = strtok(NULL, " ,;\t");
555			if(foo == NULL){
556			sprintf( painCave.errMsg,
557	tim	1118	"error in reading velocity x from %s\n",
558			inFileName.c_str() );
559	gezelter	637	return strdup( painCave.errMsg );
560			}
561			q[1] = atof( foo );
562	tim	1118
563	gezelter	637	foo = strtok(NULL, " ,;\t");
564			if(foo == NULL){
565			sprintf( painCave.errMsg,
566	tim	1118	"error in reading velocity x from %s\n",
567			inFileName.c_str() );
568	gezelter	637	return strdup( painCave.errMsg );
569			}
570			q[2] = atof( foo );
571	tim	1118
572	gezelter	637	foo = strtok(NULL, " ,;\t");
573			if(foo == NULL){
574			sprintf( painCave.errMsg,
575	tim	1118	"error in reading velocity x from %s\n",
576			inFileName.c_str() );
577	gezelter	637	return strdup( painCave.errMsg );
578			}
579			q[3] = atof( foo );
580	tim	1118
581	gezelter	637	// get the angular velocities
582	tim	1118
583	gezelter	637	foo = strtok(NULL, " ,;\t");
584			if(foo == NULL){
585			sprintf( painCave.errMsg,
586	tim	1118	"error in reading velocity x from %s\n",
587			inFileName.c_str() );
588	gezelter	637	return strdup( painCave.errMsg );
589			}
590	gezelter	1097	ji[0] = atof( foo );
591	tim	1118
592	gezelter	637	foo = strtok(NULL, " ,;\t");
593			if(foo == NULL){
594			sprintf( painCave.errMsg,
595	tim	1118	"error in reading velocity x from %s\n",
596			inFileName.c_str() );
597	gezelter	637	return strdup( painCave.errMsg );
598			}
599	gezelter	1097	ji[1] = atof(foo );
600	tim	1118
601	gezelter	637	foo = strtok(NULL, " ,;\t");
602			if(foo == NULL){
603			sprintf( painCave.errMsg,
604	tim	1118	"error in reading velocity x from %s\n",
605			inFileName.c_str() );
606	gezelter	637	return strdup( painCave.errMsg );
607			}
608	gezelter	1097	ji[2] = atof( foo );
609	gezelter	637
610	tim	1118
611	gezelter	637	// check that the quaternion vector is normalized
612
613			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
614	tim	1118
615	gezelter	637	qLength = sqrt( qSqr );
616			q[0] = q[0] / qLength;
617			q[1] = q[1] / qLength;
618			q[2] = q[2] / qLength;
619			q[3] = q[3] / qLength;
620
621	tim	1118	// add quaternion and angular velocities
622
623			sd->setQ( q );
624			sd->setJ( ji );
625	gezelter	637	}
626
627	mmeineke	804
628	tim	1118
629	gezelter	637	return NULL;
630			}
631
632
633	tim	1118	char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
634	gezelter	637
635	tim	1118	double currTime;
636			double boxMat[9];
637			double theBoxMat3[3][3];
638			double chi;
639			double integralOfChidt;
640	mmeineke	847	double eta[9];
641	gezelter	637
642	tim	1118	char *foo; // the pointer to the current string token
643
644	gezelter	637	// set the string tokenizer
645	tim	1118
646	gezelter	637	foo = strtok(readLine, " ,;\t");
647	tim	1118	// set the timeToken.
648
649	gezelter	637	if(foo == NULL){
650			sprintf( painCave.errMsg,
651	tim	1118	"error in reading Time from %s\n",
652			inFileName.c_str() );
653	gezelter	637	return strdup( painCave.errMsg );
654			}
655
656	tim	1118	currTime = atof( foo );
657			entry_plug->setTime( currTime );
658	gezelter	637
659	tim	1118	//get H-Matrix
660	gezelter	637
661	tim	1118	for(int i = 0 ; i < 9; i++){
662			foo = strtok(NULL, " ,;\t");
663			if(foo == NULL){
664			sprintf( painCave.errMsg,
665			"error in reading H[%d] from %s\n", i, inFileName.c_str() );
666			return strdup( painCave.errMsg );
667			}
668			boxMat[i] = atof( foo );
669	gezelter	637	}
670
671	tim	1118	for(int i=0;i<3;i++)
672			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
673	gezelter	637
674	tim	1118	//set H-Matrix
675			entry_plug->setBoxM( theBoxMat3 );
676	gezelter	637
677	tim	1118	//get chi and integralOfChidt, they should appear by pair
678	mmeineke	847
679	tim	1118	if( entry_plug->useInitXSstate ){
680			foo = strtok(NULL, " ,;\t\n");
681			if(foo != NULL){
682			chi = atof(foo);
683
684			foo = strtok(NULL, " ,;\t\n");
685			if(foo == NULL){
686			sprintf( painCave.errMsg,
687			"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
688			return strdup( painCave.errMsg );
689			}
690			integralOfChidt = atof( foo );
691
692			//push chi and integralOfChidt into SimInfo::properties which can be
693			//retrieved by integrator later
694			DoubleData* chiValue = new DoubleData();
695			chiValue->setID(CHIVALUE_ID);
696			chiValue->setData(chi);
697			entry_plug->addProperty(chiValue);
698
699			DoubleData* integralOfChidtValue = new DoubleData();
700			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
701			integralOfChidtValue->setData(integralOfChidt);
702			entry_plug->addProperty(integralOfChidtValue);
703
704			}
705			else
706			return NULL;
707	mmeineke	847
708	tim	1118	//get eta
709	mmeineke	847	foo = strtok(NULL, " ,;\t\n");
710	tim	1118	if(foo != NULL ){
711
712			for(int i = 0 ; i < 9; i++){
713
714			if(foo == NULL){
715			sprintf( painCave.errMsg,
716			"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
717			return strdup( painCave.errMsg );
718			}
719			eta[i] = atof( foo );
720			foo = strtok(NULL, " ,;\t\n");
721			}
722	mmeineke	847	}
723	tim	1118	else
724			return NULL;
725	mmeineke	847
726	tim	1118	//push eta into SimInfo::properties which can be
727	mmeineke	847	//retrieved by integrator later
728	tim	1118	//entry_plug->setBoxM( theBoxMat3 );
729			DoubleArrayData* etaValue = new DoubleArrayData();
730			etaValue->setID(ETAVALUE_ID);
731			etaValue->setData(eta, 9);
732			entry_plug->addProperty(etaValue);
733	mmeineke	847	}
734	tim	1118
735	mmeineke	847	return NULL;
736	gezelter	637	}
737
738			#ifdef IS_MPI
739	tim	1118	void DumpReader::nodeZeroError( void ){
740			int j, myStatus;
741	gezelter	637
742			myStatus = 0;
743	gezelter	1203	for (j = 0; j < mpiSim->getNProcessors(); j++) {
744	tim	1118	MPI_Send( &myStatus, 1, MPI_INT, j,
745	gezelter	637	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
746	tim	1118	}
747	gezelter	637
748	tim	1118
749	gezelter	637	MPI_Finalize();
750			exit (0);
751	tim	1118
752	gezelter	637	}
753
754	tim	1118	void DumpReader::anonymousNodeDie( void ){
755	gezelter	637
756			MPI_Finalize();
757			exit (0);
758			}
759	tim	1198	#endif