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


#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, 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;

  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();
    }

    nTotObjs = 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 != simnfo->getTotIntegrableObjects()){
      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->getTotNmol(); 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[i]);
           
       }


      }
      else{
      //molecule belongs to slave nodes

        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
       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();

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

      }
      
    }
    
  }
  else{
  //actions taken at slave nodes
    for (i=0 ; i < mpiSim->getTotNmol(); 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_Recv(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);

        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->getNumberProcessors(); 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:	1119
Committed:	Mon Apr 19 17:44:48 2004 UTC (20 years, 2 months ago) by tim
File size:	17702 byte(s)
Log Message:	Dump2XYZ is almost working except atoms in rigidbody are double counted
#	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			int vectorSize;
88			int i, j, k;
89			int lineNum = 0;
90			char readBuffer[2000];
91			char* foo;
92			fpos_t *currPos;
93	mmeineke	804	double time;
94	mmeineke	647
95	mmeineke	804
96
97	mmeineke	647	#ifdef IS_MPI
98			if( worldRank == 0 ){
99			#endif // is_mpi
100
101			rewind( inFile );
102
103			currPos = new fpos_t;
104			fgetpos( inFile, currPos );
105	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
106	mmeineke	647	lineNum++;
107	mmeineke	804	if( feof( inFile ) ){
108	mmeineke	647	sprintf( painCave.errMsg,
109			"File \"%s\" ended unexpectedly at line %d\n",
110	tim	1118	inFileName.c_str(),
111	mmeineke	647	lineNum );
112			painCave.isFatal = 1;
113			simError();
114			}
115	tim	1118
116	mmeineke	804	while( !feof( inFile ) ){
117	tim	1119
118			framePos.push_back(currPos);
119	mmeineke	804
120	mmeineke	647	i = atoi(readBuffer);
121
122	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
123	mmeineke	647	lineNum++;
124	mmeineke	804	if( feof( inFile ) ){
125	mmeineke	647	sprintf( painCave.errMsg,
126			"File \"%s\" ended unexpectedly at line %d\n",
127	tim	1118	inFileName.c_str(),
128	mmeineke	647	lineNum );
129			painCave.isFatal = 1;
130			simError();
131			}
132	tim	1118
133	mmeineke	647	for(j=0; j<i; j++){
134
135	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
136	mmeineke	647	lineNum++;
137	mmeineke	804	if( feof( inFile ) ){
138	mmeineke	647	sprintf( painCave.errMsg,
139			"File \"%s\" ended unexpectedly at line %d,"
140			" with atom %d\n",
141	tim	1118	inFileName.c_str(),
142	mmeineke	647	lineNum,
143			j );
144			painCave.isFatal = 1;
145			simError();
146			}
147
148			}
149
150			currPos = new fpos_t;
151			fgetpos( inFile, currPos );
152	mmeineke	804	fgets( readBuffer, sizeof( readBuffer ), inFile );
153	mmeineke	647	lineNum++;
154			}
155
156			delete currPos;
157			rewind( inFile );
158	tim	1118
159	mmeineke	804	isScanned = true;
160
161	mmeineke	647	#ifdef IS_MPI
162			}
163			strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
164			MPIcheckPoint();
165			#endif // is_mpi
166			}
167
168	mmeineke	656	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
169	mmeineke	647
170	mmeineke	656	simnfo = the_simnfo;
171	mmeineke	647
172	mmeineke	656	this->readSet( whichFrame );
173			}
174	gezelter	637
175	mmeineke	656
176
177			void DumpReader :: readSet( int whichFrame ){
178
179	tim	1118	int i, j;
180	gezelter	637
181			#ifdef IS_MPI
182	tim	1118	int done, which_node, which_atom; // loop counter
183			#endif //is_mpi
184	gezelter	637
185	tim	1118	const int BUFFERSIZE = 2000; // size of the read buffer
186			int nTotObjs; // the number of atoms
187			char read_buffer[BUFFERSIZE]; //the line buffer for reading
188
189			char *eof_test; // ptr to see when we reach the end of the file
190	gezelter	637	char *parseErr;
191	mmeineke	804
192	tim	1118	vector<StuntDouble*> integrableObjects;
193
194
195	mmeineke	656	#ifndef IS_MPI
196	gezelter	637
197	tim	1118	fsetpos(inFile, framePos[whichFrame]);
198	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
199	gezelter	637	if( eof_test == NULL ){
200			sprintf( painCave.errMsg,
201	tim	1119	"DumpReader error: error reading 1st line of \"%s\"\n",
202	tim	1118	inFileName.c_str() );
203	gezelter	637	painCave.isFatal = 1;
204			simError();
205			}
206
207	tim	1118	nTotObjs = atoi( read_buffer );
208	gezelter	637
209	tim	1118	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
210	gezelter	637	sprintf( painCave.errMsg,
211	tim	1119	"DumpReader error. %s n_atoms, %d, "
212	gezelter	637	"does not match the BASS file's n_atoms, %d.\n",
213	tim	1118	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
214	gezelter	637	painCave.isFatal = 1;
215			simError();
216			}
217	tim	1118
218			//read the box mat from the comment line
219
220	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
221	gezelter	637	if(eof_test == NULL){
222			sprintf( painCave.errMsg,
223	tim	1118	"error in reading commment in %s\n", inFileName.c_str());
224	gezelter	637	painCave.isFatal = 1;
225			simError();
226			}
227
228	tim	1118	parseErr = parseCommentLine( read_buffer, simnfo);
229	gezelter	637	if( parseErr != NULL ){
230			strcpy( painCave.errMsg, parseErr );
231			painCave.isFatal = 1;
232			simError();
233			}
234
235	tim	1118	//parse dump lines
236	gezelter	637
237	tim	1118	for( i=0; i < simnfo->n_mol; i++){
238	gezelter	637
239	tim	1118	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
240	gezelter	637
241	tim	1118	for(j = 0; j < integrableObjects.size(); j++){
242
243			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
244			if(eof_test == NULL){
245			sprintf(painCave.errMsg,
246			"error in reading file %s\n"
247			"natoms = %d; index = %d\n"
248			"error reading the line from the file.\n",
249			inFileName.c_str(), nTotObjs, i );
250			painCave.isFatal = 1;
251			simError();
252			}
253
254			parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
255			if( parseErr != NULL ){
256			strcpy( painCave.errMsg, parseErr );
257			painCave.isFatal = 1;
258			simError();
259			}
260	gezelter	637	}
261			}
262
263			// MPI Section of code..........
264			#else //IS_MPI
265
266			// first thing first, suspend fatalities.
267			painCave.isEventLoop = 1;
268
269			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
270			int haveError;
271	tim	1118
272	gezelter	637	MPI_Status istatus;
273	tim	1118	int *MolToProcMap = mpiSim->getMolToProcMap();
274			int localIndex;
275			int nCurObj;
276	gezelter	637
277			haveError = 0;
278			if (worldRank == 0) {
279	tim	1118	fsetpos(inFile, framePos[whichFrame]);
280
281	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
282	gezelter	637	if( eof_test == NULL ){
283			sprintf( painCave.errMsg,
284	tim	1118	"Error reading 1st line of %s \n ",inFileName.c_str());
285	gezelter	637	haveError = 1;
286			simError();
287			}
288	tim	1118
289			nTotObjs = atoi( read_buffer );
290
291			// Check to see that the number of integrable objects in the intial configuration file is the
292	gezelter	637	// same as declared in simBass.
293	tim	1118
294			if( nTotObjs != simnfo->getTotIntegrableObjects()){
295	gezelter	637	sprintf( painCave.errMsg,
296	tim	1119	"DumpReadererror. %s n_atoms, %d, "
297	gezelter	637	"does not match the BASS file's n_atoms, %d.\n",
298	tim	1118	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
299	gezelter	637	haveError= 1;
300			simError();
301			}
302	tim	1118
303			//read the boxMat from the comment line
304
305	mmeineke	647	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
306	gezelter	637	if(eof_test == NULL){
307			sprintf( painCave.errMsg,
308	tim	1118	"error in reading commment in %s\n", inFileName.c_str());
309	gezelter	637	haveError = 1;
310			simError();
311			}
312	tim	1118
313			//Every single processor will parse the comment line by itself
314			//By using this way, we might lose some efficiency, but if we want to add
315			//more parameters into comment line, we only need to modify function
316			//parseCommentLine
317
318			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
319
320			parseErr = parseCommentLine( read_buffer, simnfo);
321
322	gezelter	637	if( parseErr != NULL ){
323			strcpy( painCave.errMsg, parseErr );
324			haveError = 1;
325			simError();
326			}
327
328	tim	1118	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
329			which_node = MolToProcMap[i];
330			if(which_node == 0){
331			//molecules belong to master node
332
333			localIndex = mpiSim->getGlobalToLocalMol(i);
334
335			if(localIndex == -1) {
336			strcpy(painCave.errMsg, "Molecule not found on node 0!");
337			haveError = 1;
338			simError();
339	gezelter	637	}
340
341	tim	1118	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
342			for(j=0; j < integrableObjects.size(); j++){
343
344			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
345			if(eof_test == NULL){
346			sprintf(painCave.errMsg,
347			"error in reading file %s\n"
348			"natoms = %d; index = %d\n"
349			"error reading the line from the file.\n",
350			inFileName.c_str(), nTotObjs, i );
351			haveError= 1;
352			simError();
353			}
354
355			if(haveError) nodeZeroError();
356
357			parseDumpLine(read_buffer, integrableObjects[i]);
358
359			}
360
361
362	gezelter	637	}
363	tim	1118	else{
364			//molecule belongs to slave nodes
365	gezelter	637
366	tim	1118	MPI_Recv(&nCurObj, 1, MPI_INT, 0,
367	gezelter	637	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
368
369	tim	1118	for(j=0; j < integrableObjects.size(); j++){
370
371			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
372			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			inFileName.c_str(), nTotObjs, i );
378			haveError= 1;
379			simError();
380			}
381
382			if(haveError) nodeZeroError();
383	gezelter	637
384	tim	1118	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
385			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
386
387			}
388
389	gezelter	637	}
390
391			}
392	tim	1118
393	gezelter	637	}
394	tim	1118	else{
395			//actions taken at slave nodes
396			for (i=0 ; i < mpiSim->getTotNmol(); i++) {
397			which_node = MolToProcMap[i];
398
399			if(which_node == worldRank){
400			//molecule with global index i belongs to this processor
401
402			localIndex = mpiSim->getGlobalToLocalMol(i);
403	gezelter	637
404	tim	1118	if(localIndex == -1) {
405			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
406			haveError = 1;
407			simError();
408			}
409	gezelter	637
410	tim	1118	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
411	gezelter	637
412	tim	1118	nCurObj = integrableObjects.size();
413
414			MPI_Recv(&nCurObj, 1, MPI_INT, 0,
415			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
416	gezelter	637
417	tim	1118	for(j = 0; j < integrableObjects.size(); j++){
418
419			MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
420			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
421
422			parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
423
424			if( parseErr != NULL ){
425			strcpy( painCave.errMsg, parseErr );
426			simError();
427			}
428
429			}
430
431			}
432
433			}
434
435			}
436
437	gezelter	637	#endif
438			}
439
440	tim	1118	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
441	gezelter	637
442	tim	1118	char *foo; // the pointer to the current string token
443
444			double pos[3]; // position place holders
445			double vel[3]; // velocity placeholders
446			double q[4]; // the quaternions
447			double ji[3]; // angular velocity placeholders;
448	gezelter	637	double qSqr, qLength; // needed to normalize the quaternion vector.
449
450
451			// set the string tokenizer
452	tim	1118
453	gezelter	637	foo = strtok(readLine, " ,;\t");
454	tim	1118
455	gezelter	637	// check the atom name to the current atom
456	tim	1118
457			if( strcmp( foo, sd->getType() ) ){
458			sprintf( painCave.errMsg,
459	tim	1119	"DumpReader error. Does not"
460	tim	1118	" match the BASS atom %s.\n",
461			sd->getType() );
462			return strdup( painCave.errMsg );
463			}
464
465	gezelter	637	// get the positions
466
467			foo = strtok(NULL, " ,;\t");
468			if(foo == NULL){
469			sprintf( painCave.errMsg,
470	tim	1118	"error in reading postition x from %s\n",
471			inFileName.c_str());
472	gezelter	637	return strdup( painCave.errMsg );
473			}
474	mmeineke	804	pos[0] = atof( foo );
475	tim	1118
476	gezelter	637	foo = strtok(NULL, " ,;\t");
477			if(foo == NULL){
478			sprintf( painCave.errMsg,
479	tim	1118	"error in reading postition y from %s\n",
480			inFileName.c_str());
481	gezelter	637	return strdup( painCave.errMsg );
482			}
483	mmeineke	804	pos[1] = atof( foo );
484	tim	1118
485	gezelter	637	foo = strtok(NULL, " ,;\t");
486			if(foo == NULL){
487			sprintf( painCave.errMsg,
488	tim	1118	"error in reading postition z from %s\n",
489			inFileName.c_str());
490	gezelter	637	return strdup( painCave.errMsg );
491			}
492	tim	1118	pos[2] = atof( foo );
493	gezelter	637
494
495			// get the velocities
496
497			foo = strtok(NULL, " ,;\t");
498			if(foo == NULL){
499			sprintf( painCave.errMsg,
500	tim	1118	"error in reading velocity x from %s\n",
501			inFileName.c_str() );
502	gezelter	637	return strdup( painCave.errMsg );
503			}
504	mmeineke	804	vel[0] = atof( foo );
505	tim	1118
506	gezelter	637	foo = strtok(NULL, " ,;\t");
507			if(foo == NULL){
508			sprintf( painCave.errMsg,
509	tim	1118	"error in reading velocity x from %s\n",
510			inFileName.c_str() );
511	gezelter	637	return strdup( painCave.errMsg );
512			}
513	mmeineke	804	vel[1] = atof( foo );
514	tim	1118
515	gezelter	637	foo = strtok(NULL, " ,;\t");
516			if(foo == NULL){
517			sprintf( painCave.errMsg,
518	tim	1118	"error in reading velocity x from %s\n",
519			inFileName.c_str() );
520	gezelter	637	return strdup( painCave.errMsg );
521			}
522	mmeineke	804	vel[2] = atof( foo );
523	tim	1118
524
525			// add the positions and velocities to the atom
526
527			sd->setPos( pos );
528			sd->setVel( vel );
529
530			if (!sd->isDirectional())
531			return NULL;
532
533	gezelter	637	// get the quaternions
534	tim	1118
535			if( sd->isDirectional() ){
536
537	gezelter	637	foo = strtok(NULL, " ,;\t");
538			if(foo == NULL){
539	tim	1118	sprintf( painCave.errMsg,
540			"error in reading velocity x from %s\n",
541			inFileName.c_str() );
542	gezelter	637	return strdup( painCave.errMsg );
543			}
544			q[0] = atof( foo );
545	tim	1118
546	gezelter	637	foo = strtok(NULL, " ,;\t");
547			if(foo == NULL){
548			sprintf( painCave.errMsg,
549	tim	1118	"error in reading velocity x from %s\n",
550			inFileName.c_str() );
551	gezelter	637	return strdup( painCave.errMsg );
552			}
553			q[1] = atof( foo );
554	tim	1118
555	gezelter	637	foo = strtok(NULL, " ,;\t");
556			if(foo == NULL){
557			sprintf( painCave.errMsg,
558	tim	1118	"error in reading velocity x from %s\n",
559			inFileName.c_str() );
560	gezelter	637	return strdup( painCave.errMsg );
561			}
562			q[2] = atof( foo );
563	tim	1118
564	gezelter	637	foo = strtok(NULL, " ,;\t");
565			if(foo == NULL){
566			sprintf( painCave.errMsg,
567	tim	1118	"error in reading velocity x from %s\n",
568			inFileName.c_str() );
569	gezelter	637	return strdup( painCave.errMsg );
570			}
571			q[3] = atof( foo );
572	tim	1118
573	gezelter	637	// get the angular velocities
574	tim	1118
575	gezelter	637	foo = strtok(NULL, " ,;\t");
576			if(foo == NULL){
577			sprintf( painCave.errMsg,
578	tim	1118	"error in reading velocity x from %s\n",
579			inFileName.c_str() );
580	gezelter	637	return strdup( painCave.errMsg );
581			}
582	gezelter	1097	ji[0] = atof( foo );
583	tim	1118
584	gezelter	637	foo = strtok(NULL, " ,;\t");
585			if(foo == NULL){
586			sprintf( painCave.errMsg,
587	tim	1118	"error in reading velocity x from %s\n",
588			inFileName.c_str() );
589	gezelter	637	return strdup( painCave.errMsg );
590			}
591	gezelter	1097	ji[1] = atof(foo );
592	tim	1118
593	gezelter	637	foo = strtok(NULL, " ,;\t");
594			if(foo == NULL){
595			sprintf( painCave.errMsg,
596	tim	1118	"error in reading velocity x from %s\n",
597			inFileName.c_str() );
598	gezelter	637	return strdup( painCave.errMsg );
599			}
600	gezelter	1097	ji[2] = atof( foo );
601	gezelter	637
602	tim	1118
603	gezelter	637	// check that the quaternion vector is normalized
604
605			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
606	tim	1118
607	gezelter	637	qLength = sqrt( qSqr );
608			q[0] = q[0] / qLength;
609			q[1] = q[1] / qLength;
610			q[2] = q[2] / qLength;
611			q[3] = q[3] / qLength;
612
613	tim	1118	// add quaternion and angular velocities
614
615			sd->setQ( q );
616			sd->setJ( ji );
617	gezelter	637	}
618
619	mmeineke	804
620	tim	1118
621	gezelter	637	return NULL;
622			}
623
624
625	tim	1118	char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
626	gezelter	637
627	tim	1118	double currTime;
628			double boxMat[9];
629			double theBoxMat3[3][3];
630			double chi;
631			double integralOfChidt;
632	mmeineke	847	double eta[9];
633	gezelter	637
634	tim	1118	char *foo; // the pointer to the current string token
635
636	gezelter	637	// set the string tokenizer
637	tim	1118
638	gezelter	637	foo = strtok(readLine, " ,;\t");
639	tim	1118	// set the timeToken.
640
641	gezelter	637	if(foo == NULL){
642			sprintf( painCave.errMsg,
643	tim	1118	"error in reading Time from %s\n",
644			inFileName.c_str() );
645	gezelter	637	return strdup( painCave.errMsg );
646			}
647
648	tim	1118	currTime = atof( foo );
649			entry_plug->setTime( currTime );
650	gezelter	637
651	tim	1118	//get H-Matrix
652	gezelter	637
653	tim	1118	for(int i = 0 ; i < 9; i++){
654			foo = strtok(NULL, " ,;\t");
655			if(foo == NULL){
656			sprintf( painCave.errMsg,
657			"error in reading H[%d] from %s\n", i, inFileName.c_str() );
658			return strdup( painCave.errMsg );
659			}
660			boxMat[i] = atof( foo );
661	gezelter	637	}
662
663	tim	1118	for(int i=0;i<3;i++)
664			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
665	gezelter	637
666	tim	1118	//set H-Matrix
667			entry_plug->setBoxM( theBoxMat3 );
668	gezelter	637
669	tim	1118	//get chi and integralOfChidt, they should appear by pair
670	mmeineke	847
671	tim	1118	if( entry_plug->useInitXSstate ){
672			foo = strtok(NULL, " ,;\t\n");
673			if(foo != NULL){
674			chi = atof(foo);
675
676			foo = strtok(NULL, " ,;\t\n");
677			if(foo == NULL){
678			sprintf( painCave.errMsg,
679			"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
680			return strdup( painCave.errMsg );
681			}
682			integralOfChidt = atof( foo );
683
684			//push chi and integralOfChidt into SimInfo::properties which can be
685			//retrieved by integrator later
686			DoubleData* chiValue = new DoubleData();
687			chiValue->setID(CHIVALUE_ID);
688			chiValue->setData(chi);
689			entry_plug->addProperty(chiValue);
690
691			DoubleData* integralOfChidtValue = new DoubleData();
692			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
693			integralOfChidtValue->setData(integralOfChidt);
694			entry_plug->addProperty(integralOfChidtValue);
695
696			}
697			else
698			return NULL;
699	mmeineke	847
700	tim	1118	//get eta
701	mmeineke	847	foo = strtok(NULL, " ,;\t\n");
702	tim	1118	if(foo != NULL ){
703
704			for(int i = 0 ; i < 9; i++){
705
706			if(foo == NULL){
707			sprintf( painCave.errMsg,
708			"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
709			return strdup( painCave.errMsg );
710			}
711			eta[i] = atof( foo );
712			foo = strtok(NULL, " ,;\t\n");
713			}
714	mmeineke	847	}
715	tim	1118	else
716			return NULL;
717	mmeineke	847
718	tim	1118	//push eta into SimInfo::properties which can be
719	mmeineke	847	//retrieved by integrator later
720	tim	1118	//entry_plug->setBoxM( theBoxMat3 );
721			DoubleArrayData* etaValue = new DoubleArrayData();
722			etaValue->setID(ETAVALUE_ID);
723			etaValue->setData(eta, 9);
724			entry_plug->addProperty(etaValue);
725	mmeineke	847	}
726	tim	1118
727	mmeineke	847	return NULL;
728	gezelter	637	}
729
730			#ifdef IS_MPI
731	tim	1118	void DumpReader::nodeZeroError( void ){
732			int j, myStatus;
733	gezelter	637
734			myStatus = 0;
735	tim	1118	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
736			MPI_Send( &myStatus, 1, MPI_INT, j,
737	gezelter	637	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
738	tim	1118	}
739	gezelter	637
740	tim	1118
741	gezelter	637	MPI_Finalize();
742			exit (0);
743	tim	1118
744	gezelter	637	}
745
746	tim	1118	void DumpReader::anonymousNodeDie( void ){
747	gezelter	637
748			MPI_Finalize();
749			exit (0);
750			}
751	tim	1118	#endif