OOPSE-1.0/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]);

    if (fabs(qSqr) < 1e-6) {
      sprintf(painCave.errMsg,
          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
       return strdup(painCave.errMsg);
    }

    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:	1334
Committed:	Fri Jul 16 18:58:03 2004 UTC (19 years, 11 months ago) by gezelter
File size:	18107 byte(s)
Log Message:	Initial import of OOPSE-1.0 source tree
#	User	Rev	Content
1	gezelter	1334	#define _LARGEFILE_SOURCE64
2			#define _FILE_OFFSET_BITS 64
3
4			#include <sys/types.h>
5			#include <sys/stat.h>
6
7			#include <iostream>
8			#include <math.h>
9
10			#include <stdio.h>
11			#include <stdlib.h>
12			#include <string.h>
13
14
15			#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			#endif // is_mpi
24
25
26			DumpReader :: DumpReader(const char *in_name ){
27
28			isScanned = false;
29
30			#ifdef IS_MPI
31			if (worldRank == 0) {
32			#endif
33
34			inFile = fopen(in_name, "r");
35			if(inFile == NULL){
36			sprintf(painCave.errMsg,
37			"Cannot open file: %s\n", in_name);
38			painCave.isFatal = 1;
39			simError();
40			}
41
42			inFileName = in_name;
43			#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			vector<fpos_t*>::iterator i;
56
57			int error;
58			error = fclose( inFile );
59			if( error ){
60			sprintf( painCave.errMsg,
61			"Error closing %s\n", inFileName.c_str());
62			simError();
63			}
64
65			for(i = framePos.begin(); i != framePos.end(); ++i)
66			delete *i;
67			framePos.clear();
68
69			#ifdef IS_MPI
70			}
71			strcpy( checkPointMsg, "Dump file closed successfully." );
72			MPIcheckPoint();
73			#endif
74
75			return;
76			}
77
78			int DumpReader::getNframes( void ){
79
80			if( !isScanned )
81			scanFile();
82			return framePos.size();
83			}
84
85			void DumpReader::scanFile( void ){
86
87			int i, j;
88			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			fgets( readBuffer, sizeof( readBuffer ), inFile );
101			lineNum++;
102			if( feof( inFile ) ){
103			sprintf( painCave.errMsg,
104			"File \"%s\" ended unexpectedly at line %d\n",
105			inFileName.c_str(),
106			lineNum );
107			painCave.isFatal = 1;
108			simError();
109			}
110
111			while( !feof( inFile ) ){
112
113			framePos.push_back(currPos);
114
115			i = atoi(readBuffer);
116
117			fgets( readBuffer, sizeof( readBuffer ), inFile );
118			lineNum++;
119			if( feof( inFile ) ){
120			sprintf( painCave.errMsg,
121			"File \"%s\" ended unexpectedly at line %d\n",
122			inFileName.c_str(),
123			lineNum );
124			painCave.isFatal = 1;
125			simError();
126			}
127
128			for(j=0; j<i; j++){
129
130			fgets( readBuffer, sizeof( readBuffer ), inFile );
131			lineNum++;
132			if( feof( inFile ) ){
133			sprintf( painCave.errMsg,
134			"File \"%s\" ended unexpectedly at line %d,"
135			" with atom %d\n",
136			inFileName.c_str(),
137			lineNum,
138			j );
139			painCave.isFatal = 1;
140			simError();
141			}
142
143			}
144
145			currPos = new fpos_t;
146			fgetpos( inFile, currPos );
147			fgets( readBuffer, sizeof( readBuffer ), inFile );
148			lineNum++;
149			}
150
151			delete currPos;
152			rewind( inFile );
153
154			isScanned = true;
155
156			#ifdef IS_MPI
157			}
158			strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
159			MPIcheckPoint();
160			#endif // is_mpi
161			}
162
163			void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
164
165			simnfo = the_simnfo;
166
167			this->readSet( whichFrame );
168			}
169
170
171
172			void DumpReader :: readSet( int whichFrame ){
173
174			int i;
175			unsigned int j;
176
177			#ifdef IS_MPI
178			int done, which_node, which_atom; // loop counter
179			#endif //is_mpi
180
181			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			char *parseErr;
187
188			vector<StuntDouble*> integrableObjects;
189
190
191			#ifndef IS_MPI
192
193			fsetpos(inFile, framePos[whichFrame]);
194			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
195			if( eof_test == NULL ){
196			sprintf( painCave.errMsg,
197			"DumpReader error: error reading 1st line of \"%s\"\n",
198			inFileName.c_str() );
199			painCave.isFatal = 1;
200			simError();
201			}
202
203			nTotObjs = atoi( read_buffer );
204
205			if( nTotObjs != simnfo->getTotIntegrableObjects() ){
206			sprintf( painCave.errMsg,
207			"DumpReader error. %s n_atoms, %d, "
208			"does not match the BASS file's n_atoms, %d.\n",
209			inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
210			painCave.isFatal = 1;
211			simError();
212			}
213
214			//read the box mat from the comment line
215
216			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
217			if(eof_test == NULL){
218			sprintf( painCave.errMsg,
219			"error in reading commment in %s\n", inFileName.c_str());
220			painCave.isFatal = 1;
221			simError();
222			}
223
224			parseErr = parseCommentLine( read_buffer, simnfo);
225			if( parseErr != NULL ){
226			strcpy( painCave.errMsg, parseErr );
227			painCave.isFatal = 1;
228			simError();
229			}
230
231			//parse dump lines
232
233			for( i=0; i < simnfo->n_mol; i++){
234
235			integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
236
237			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			}
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
268			MPI_Status istatus;
269			int *MolToProcMap = mpiSim->getMolToProcMap();
270			int localIndex;
271			int nCurObj;
272			int nitems;
273
274			nTotObjs = simnfo->getTotIntegrableObjects();
275			haveError = 0;
276			if (worldRank == 0) {
277			fsetpos(inFile, framePos[whichFrame]);
278
279			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
280			if( eof_test == NULL ){
281			sprintf( painCave.errMsg,
282			"Error reading 1st line of %s \n ",inFileName.c_str());
283			haveError = 1;
284			simError();
285			}
286
287			nitems = atoi( read_buffer );
288
289			// Check to see that the number of integrable objects in the intial configuration file is the
290			// same as declared in simBass.
291
292			if( nTotObjs != nitems){
293			sprintf( painCave.errMsg,
294			"DumpReadererror. %s n_atoms, %d, "
295			"does not match the BASS file's n_atoms, %d.\n",
296			inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
297			haveError= 1;
298			simError();
299			}
300
301			//read the boxMat from the comment line
302
303			eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
304			if(eof_test == NULL){
305			sprintf( painCave.errMsg,
306			"error in reading commment in %s\n", inFileName.c_str());
307			haveError = 1;
308			simError();
309			}
310
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			if( parseErr != NULL ){
321			strcpy( painCave.errMsg, parseErr );
322			haveError = 1;
323			simError();
324			}
325
326			for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
327			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			}
338
339			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			parseDumpLine(read_buffer, integrableObjects[j]);
356
357			}
358
359
360			}
361			else{
362			//molecule belongs to slave nodes
363
364			MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
365			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
366
367			for(j=0; j < nCurObj; j++){
368
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
382			MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
383			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
384
385			}
386
387			}
388
389			}
390
391			}
392			else{
393			//actions taken at slave nodes
394			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			for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
405			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
412			if(localIndex == -1) {
413			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
414			haveError = 1;
415			simError();
416			}
417
418			integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
419
420			nCurObj = integrableObjects.size();
421
422			MPI_Send(&nCurObj, 1, MPI_INT, 0,
423			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
424
425			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			#endif
446			}
447
448			char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
449
450			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			double qSqr, qLength; // needed to normalize the quaternion vector.
457
458
459			// set the string tokenizer
460
461			foo = strtok(readLine, " ,;\t");
462
463			// check the atom name to the current atom
464
465			if( strcmp( foo, sd->getType() ) ){
466			sprintf( painCave.errMsg,
467			"DumpReader error. Does not"
468			" match the BASS atom %s.\n",
469			sd->getType() );
470			return strdup( painCave.errMsg );
471			}
472
473			// get the positions
474
475			foo = strtok(NULL, " ,;\t");
476			if(foo == NULL){
477			sprintf( painCave.errMsg,
478			"error in reading postition x from %s\n",
479			inFileName.c_str());
480			return strdup( painCave.errMsg );
481			}
482			pos[0] = atof( foo );
483
484			foo = strtok(NULL, " ,;\t");
485			if(foo == NULL){
486			sprintf( painCave.errMsg,
487			"error in reading postition y from %s\n",
488			inFileName.c_str());
489			return strdup( painCave.errMsg );
490			}
491			pos[1] = atof( foo );
492
493			foo = strtok(NULL, " ,;\t");
494			if(foo == NULL){
495			sprintf( painCave.errMsg,
496			"error in reading postition z from %s\n",
497			inFileName.c_str());
498			return strdup( painCave.errMsg );
499			}
500			pos[2] = atof( foo );
501
502
503			// get the velocities
504
505			foo = strtok(NULL, " ,;\t");
506			if(foo == NULL){
507			sprintf( painCave.errMsg,
508			"error in reading velocity x from %s\n",
509			inFileName.c_str() );
510			return strdup( painCave.errMsg );
511			}
512			vel[0] = atof( foo );
513
514			foo = strtok(NULL, " ,;\t");
515			if(foo == NULL){
516			sprintf( painCave.errMsg,
517			"error in reading velocity x from %s\n",
518			inFileName.c_str() );
519			return strdup( painCave.errMsg );
520			}
521			vel[1] = atof( foo );
522
523			foo = strtok(NULL, " ,;\t");
524			if(foo == NULL){
525			sprintf( painCave.errMsg,
526			"error in reading velocity x from %s\n",
527			inFileName.c_str() );
528			return strdup( painCave.errMsg );
529			}
530			vel[2] = atof( foo );
531
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			// get the quaternions
542
543			if( sd->isDirectional() ){
544
545			foo = strtok(NULL, " ,;\t");
546			if(foo == NULL){
547			sprintf( painCave.errMsg,
548			"error in reading velocity x from %s\n",
549			inFileName.c_str() );
550			return strdup( painCave.errMsg );
551			}
552			q[0] = atof( foo );
553
554			foo = strtok(NULL, " ,;\t");
555			if(foo == NULL){
556			sprintf( painCave.errMsg,
557			"error in reading velocity x from %s\n",
558			inFileName.c_str() );
559			return strdup( painCave.errMsg );
560			}
561			q[1] = atof( foo );
562
563			foo = strtok(NULL, " ,;\t");
564			if(foo == NULL){
565			sprintf( painCave.errMsg,
566			"error in reading velocity x from %s\n",
567			inFileName.c_str() );
568			return strdup( painCave.errMsg );
569			}
570			q[2] = atof( foo );
571
572			foo = strtok(NULL, " ,;\t");
573			if(foo == NULL){
574			sprintf( painCave.errMsg,
575			"error in reading velocity x from %s\n",
576			inFileName.c_str() );
577			return strdup( painCave.errMsg );
578			}
579			q[3] = atof( foo );
580
581			// get the angular velocities
582
583			foo = strtok(NULL, " ,;\t");
584			if(foo == NULL){
585			sprintf( painCave.errMsg,
586			"error in reading velocity x from %s\n",
587			inFileName.c_str() );
588			return strdup( painCave.errMsg );
589			}
590			ji[0] = atof( foo );
591
592			foo = strtok(NULL, " ,;\t");
593			if(foo == NULL){
594			sprintf( painCave.errMsg,
595			"error in reading velocity x from %s\n",
596			inFileName.c_str() );
597			return strdup( painCave.errMsg );
598			}
599			ji[1] = atof(foo );
600
601			foo = strtok(NULL, " ,;\t");
602			if(foo == NULL){
603			sprintf( painCave.errMsg,
604			"error in reading velocity x from %s\n",
605			inFileName.c_str() );
606			return strdup( painCave.errMsg );
607			}
608			ji[2] = atof( foo );
609
610
611			// 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
615			if (fabs(qSqr) < 1e-6) {
616			sprintf(painCave.errMsg,
617			"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
618			return strdup(painCave.errMsg);
619			}
620
621			qLength = sqrt( qSqr );
622			q[0] = q[0] / qLength;
623			q[1] = q[1] / qLength;
624			q[2] = q[2] / qLength;
625			q[3] = q[3] / qLength;
626
627			// add quaternion and angular velocities
628
629			sd->setQ( q );
630			sd->setJ( ji );
631			}
632
633
634
635			return NULL;
636			}
637
638
639			char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
640
641			double currTime;
642			double boxMat[9];
643			double theBoxMat3[3][3];
644			double chi;
645			double integralOfChidt;
646			double eta[9];
647
648			char *foo; // the pointer to the current string token
649
650			// set the string tokenizer
651
652			foo = strtok(readLine, " ,;\t");
653			// set the timeToken.
654
655			if(foo == NULL){
656			sprintf( painCave.errMsg,
657			"error in reading Time from %s\n",
658			inFileName.c_str() );
659			return strdup( painCave.errMsg );
660			}
661
662			currTime = atof( foo );
663			entry_plug->setTime( currTime );
664
665			//get H-Matrix
666
667			for(int i = 0 ; i < 9; i++){
668			foo = strtok(NULL, " ,;\t");
669			if(foo == NULL){
670			sprintf( painCave.errMsg,
671			"error in reading H[%d] from %s\n", i, inFileName.c_str() );
672			return strdup( painCave.errMsg );
673			}
674			boxMat[i] = atof( foo );
675			}
676
677			for(int i=0;i<3;i++)
678			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
679
680			//set H-Matrix
681			entry_plug->setBoxM( theBoxMat3 );
682
683			//get chi and integralOfChidt, they should appear by pair
684
685			if( entry_plug->useInitXSstate ){
686			foo = strtok(NULL, " ,;\t\n");
687			if(foo != NULL){
688			chi = atof(foo);
689
690			foo = strtok(NULL, " ,;\t\n");
691			if(foo == NULL){
692			sprintf( painCave.errMsg,
693			"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
694			return strdup( painCave.errMsg );
695			}
696			integralOfChidt = atof( foo );
697
698			//push chi and integralOfChidt into SimInfo::properties which can be
699			//retrieved by integrator later
700			DoubleData* chiValue = new DoubleData();
701			chiValue->setID(CHIVALUE_ID);
702			chiValue->setData(chi);
703			entry_plug->addProperty(chiValue);
704
705			DoubleData* integralOfChidtValue = new DoubleData();
706			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
707			integralOfChidtValue->setData(integralOfChidt);
708			entry_plug->addProperty(integralOfChidtValue);
709
710			}
711			else
712			return NULL;
713
714			//get eta
715			foo = strtok(NULL, " ,;\t\n");
716			if(foo != NULL ){
717
718			for(int i = 0 ; i < 9; i++){
719
720			if(foo == NULL){
721			sprintf( painCave.errMsg,
722			"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
723			return strdup( painCave.errMsg );
724			}
725			eta[i] = atof( foo );
726			foo = strtok(NULL, " ,;\t\n");
727			}
728			}
729			else
730			return NULL;
731
732			//push eta into SimInfo::properties which can be
733			//retrieved by integrator later
734			//entry_plug->setBoxM( theBoxMat3 );
735			DoubleArrayData* etaValue = new DoubleArrayData();
736			etaValue->setID(ETAVALUE_ID);
737			etaValue->setData(eta, 9);
738			entry_plug->addProperty(etaValue);
739			}
740
741			return NULL;
742			}
743
744			#ifdef IS_MPI
745			void DumpReader::nodeZeroError( void ){
746			int j, myStatus;
747
748			myStatus = 0;
749			for (j = 0; j < mpiSim->getNProcessors(); j++) {
750			MPI_Send( &myStatus, 1, MPI_INT, j,
751			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
752			}
753
754
755			MPI_Finalize();
756			exit (0);
757
758			}
759
760			void DumpReader::anonymousNodeDie( void ){
761
762			MPI_Finalize();
763			exit (0);
764			}
765			#endif