src/io/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 nIntegrable, %d, "
             "does not match the meta-data file's nIntegrable, %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 derived from the
    // meta-data file.

    if( nTotObjs != nitems){
      sprintf( painCave.errMsg,
               "DumpReader Error. %s nIntegrable, %d, "
               "does not match the meta-data file's nIntegrable, %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 meta-data 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:	2
Committed:	Fri Sep 24 04:16:43 2004 UTC (21 years, 1 month ago) by gezelter
File size:	18157 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	Content
1	#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 nIntegrable, %d, "
208	"does not match the meta-data file's nIntegrable, %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
290	// intial configuration file is the same as derived from the
291	// meta-data file.
292
293	if( nTotObjs != nitems){
294	sprintf( painCave.errMsg,
295	"DumpReader Error. %s nIntegrable, %d, "
296	"does not match the meta-data file's nIntegrable, %d.\n",
297	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
298	haveError= 1;
299	simError();
300	}
301
302	//read the boxMat from the comment line
303
304	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
305	if(eof_test == NULL){
306	sprintf( painCave.errMsg,
307	"error in reading commment in %s\n", inFileName.c_str());
308	haveError = 1;
309	simError();
310	}
311
312	//Every single processor will parse the comment line by itself
313	//By using this way, we might lose some efficiency, but if we want to add
314	//more parameters into comment line, we only need to modify function
315	//parseCommentLine
316
317	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
318
319	parseErr = parseCommentLine( read_buffer, simnfo);
320
321	if( parseErr != NULL ){
322	strcpy( painCave.errMsg, parseErr );
323	haveError = 1;
324	simError();
325	}
326
327	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
328	which_node = MolToProcMap[i];
329	if(which_node == 0){
330	//molecules belong to master node
331
332	localIndex = mpiSim->getGlobalToLocalMol(i);
333
334	if(localIndex == -1) {
335	strcpy(painCave.errMsg, "Molecule not found on node 0!");
336	haveError = 1;
337	simError();
338	}
339
340	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
341	for(j=0; j < integrableObjects.size(); j++){
342
343	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
344	if(eof_test == NULL){
345	sprintf(painCave.errMsg,
346	"error in reading file %s\n"
347	"natoms = %d; index = %d\n"
348	"error reading the line from the file.\n",
349	inFileName.c_str(), nTotObjs, i );
350	haveError= 1;
351	simError();
352	}
353
354	if(haveError) nodeZeroError();
355
356	parseDumpLine(read_buffer, integrableObjects[j]);
357
358	}
359
360
361	}
362	else{
363	//molecule belongs to slave nodes
364
365	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
366	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
367
368	for(j=0; j < nCurObj; j++){
369
370	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
371	if(eof_test == NULL){
372	sprintf(painCave.errMsg,
373	"error in reading file %s\n"
374	"natoms = %d; index = %d\n"
375	"error reading the line from the file.\n",
376	inFileName.c_str(), nTotObjs, i );
377	haveError= 1;
378	simError();
379	}
380
381	if(haveError) nodeZeroError();
382
383	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
384	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
385
386	}
387
388	}
389
390	}
391
392	}
393	else{
394	//actions taken at slave nodes
395	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
396
397	parseErr = parseCommentLine( read_buffer, simnfo);
398
399	if( parseErr != NULL ){
400	strcpy( painCave.errMsg, parseErr );
401	haveError = 1;
402	simError();
403	}
404
405	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
406	which_node = MolToProcMap[i];
407
408	if(which_node == worldRank){
409	//molecule with global index i belongs to this processor
410
411	localIndex = mpiSim->getGlobalToLocalMol(i);
412
413	if(localIndex == -1) {
414	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
415	haveError = 1;
416	simError();
417	}
418
419	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
420
421	nCurObj = integrableObjects.size();
422
423	MPI_Send(&nCurObj, 1, MPI_INT, 0,
424	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
425
426	for(j = 0; j < integrableObjects.size(); j++){
427
428	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
429	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
430
431	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
432
433	if( parseErr != NULL ){
434	strcpy( painCave.errMsg, parseErr );
435	simError();
436	}
437
438	}
439
440	}
441
442	}
443
444	}
445
446	#endif
447	}
448
449	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
450
451	char *foo; // the pointer to the current string token
452
453	double pos[3]; // position place holders
454	double vel[3]; // velocity placeholders
455	double q[4]; // the quaternions
456	double ji[3]; // angular velocity placeholders;
457	double qSqr, qLength; // needed to normalize the quaternion vector.
458
459
460	// set the string tokenizer
461
462	foo = strtok(readLine, " ,;\t");
463
464	// check the atom name to the current atom
465
466	if( strcmp( foo, sd->getType() ) ){
467	sprintf( painCave.errMsg,
468	"DumpReader error. Does not"
469	" match the meta-data atom %s.\n",
470	sd->getType() );
471	return strdup( painCave.errMsg );
472	}
473
474	// get the positions
475
476	foo = strtok(NULL, " ,;\t");
477	if(foo == NULL){
478	sprintf( painCave.errMsg,
479	"error in reading postition x from %s\n",
480	inFileName.c_str());
481	return strdup( painCave.errMsg );
482	}
483	pos[0] = atof( foo );
484
485	foo = strtok(NULL, " ,;\t");
486	if(foo == NULL){
487	sprintf( painCave.errMsg,
488	"error in reading postition y from %s\n",
489	inFileName.c_str());
490	return strdup( painCave.errMsg );
491	}
492	pos[1] = atof( foo );
493
494	foo = strtok(NULL, " ,;\t");
495	if(foo == NULL){
496	sprintf( painCave.errMsg,
497	"error in reading postition z from %s\n",
498	inFileName.c_str());
499	return strdup( painCave.errMsg );
500	}
501	pos[2] = atof( foo );
502
503
504	// get the velocities
505
506	foo = strtok(NULL, " ,;\t");
507	if(foo == NULL){
508	sprintf( painCave.errMsg,
509	"error in reading velocity x from %s\n",
510	inFileName.c_str() );
511	return strdup( painCave.errMsg );
512	}
513	vel[0] = atof( foo );
514
515	foo = strtok(NULL, " ,;\t");
516	if(foo == NULL){
517	sprintf( painCave.errMsg,
518	"error in reading velocity x from %s\n",
519	inFileName.c_str() );
520	return strdup( painCave.errMsg );
521	}
522	vel[1] = atof( foo );
523
524	foo = strtok(NULL, " ,;\t");
525	if(foo == NULL){
526	sprintf( painCave.errMsg,
527	"error in reading velocity x from %s\n",
528	inFileName.c_str() );
529	return strdup( painCave.errMsg );
530	}
531	vel[2] = atof( foo );
532
533
534	// add the positions and velocities to the atom
535
536	sd->setPos( pos );
537	sd->setVel( vel );
538
539	if (!sd->isDirectional())
540	return NULL;
541
542	// get the quaternions
543
544	if( sd->isDirectional() ){
545
546	foo = strtok(NULL, " ,;\t");
547	if(foo == NULL){
548	sprintf( painCave.errMsg,
549	"error in reading velocity x from %s\n",
550	inFileName.c_str() );
551	return strdup( painCave.errMsg );
552	}
553	q[0] = atof( foo );
554
555	foo = strtok(NULL, " ,;\t");
556	if(foo == NULL){
557	sprintf( painCave.errMsg,
558	"error in reading velocity x from %s\n",
559	inFileName.c_str() );
560	return strdup( painCave.errMsg );
561	}
562	q[1] = atof( foo );
563
564	foo = strtok(NULL, " ,;\t");
565	if(foo == NULL){
566	sprintf( painCave.errMsg,
567	"error in reading velocity x from %s\n",
568	inFileName.c_str() );
569	return strdup( painCave.errMsg );
570	}
571	q[2] = atof( foo );
572
573	foo = strtok(NULL, " ,;\t");
574	if(foo == NULL){
575	sprintf( painCave.errMsg,
576	"error in reading velocity x from %s\n",
577	inFileName.c_str() );
578	return strdup( painCave.errMsg );
579	}
580	q[3] = atof( foo );
581
582	// get the angular velocities
583
584	foo = strtok(NULL, " ,;\t");
585	if(foo == NULL){
586	sprintf( painCave.errMsg,
587	"error in reading velocity x from %s\n",
588	inFileName.c_str() );
589	return strdup( painCave.errMsg );
590	}
591	ji[0] = atof( foo );
592
593	foo = strtok(NULL, " ,;\t");
594	if(foo == NULL){
595	sprintf( painCave.errMsg,
596	"error in reading velocity x from %s\n",
597	inFileName.c_str() );
598	return strdup( painCave.errMsg );
599	}
600	ji[1] = atof(foo );
601
602	foo = strtok(NULL, " ,;\t");
603	if(foo == NULL){
604	sprintf( painCave.errMsg,
605	"error in reading velocity x from %s\n",
606	inFileName.c_str() );
607	return strdup( painCave.errMsg );
608	}
609	ji[2] = atof( foo );
610
611
612	// check that the quaternion vector is normalized
613
614	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
615
616	if (fabs(qSqr) < 1e-6) {
617	sprintf(painCave.errMsg,
618	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
619	return strdup(painCave.errMsg);
620	}
621
622	qLength = sqrt( qSqr );
623	q[0] = q[0] / qLength;
624	q[1] = q[1] / qLength;
625	q[2] = q[2] / qLength;
626	q[3] = q[3] / qLength;
627
628	// add quaternion and angular velocities
629
630	sd->setQ( q );
631	sd->setJ( ji );
632	}
633
634
635
636	return NULL;
637	}
638
639
640	char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
641
642	double currTime;
643	double boxMat[9];
644	double theBoxMat3[3][3];
645	double chi;
646	double integralOfChidt;
647	double eta[9];
648
649	char *foo; // the pointer to the current string token
650
651	// set the string tokenizer
652
653	foo = strtok(readLine, " ,;\t");
654	// set the timeToken.
655
656	if(foo == NULL){
657	sprintf( painCave.errMsg,
658	"error in reading Time from %s\n",
659	inFileName.c_str() );
660	return strdup( painCave.errMsg );
661	}
662
663	currTime = atof( foo );
664	entry_plug->setTime( currTime );
665
666	//get H-Matrix
667
668	for(int i = 0 ; i < 9; i++){
669	foo = strtok(NULL, " ,;\t");
670	if(foo == NULL){
671	sprintf( painCave.errMsg,
672	"error in reading H[%d] from %s\n", i, inFileName.c_str() );
673	return strdup( painCave.errMsg );
674	}
675	boxMat[i] = atof( foo );
676	}
677
678	for(int i=0;i<3;i++)
679	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
680
681	//set H-Matrix
682	entry_plug->setBoxM( theBoxMat3 );
683
684	//get chi and integralOfChidt, they should appear by pair
685
686	if( entry_plug->useInitXSstate ){
687	foo = strtok(NULL, " ,;\t\n");
688	if(foo != NULL){
689	chi = atof(foo);
690
691	foo = strtok(NULL, " ,;\t\n");
692	if(foo == NULL){
693	sprintf( painCave.errMsg,
694	"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
695	return strdup( painCave.errMsg );
696	}
697	integralOfChidt = atof( foo );
698
699	//push chi and integralOfChidt into SimInfo::properties which can be
700	//retrieved by integrator later
701	DoubleData* chiValue = new DoubleData();
702	chiValue->setID(CHIVALUE_ID);
703	chiValue->setData(chi);
704	entry_plug->addProperty(chiValue);
705
706	DoubleData* integralOfChidtValue = new DoubleData();
707	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
708	integralOfChidtValue->setData(integralOfChidt);
709	entry_plug->addProperty(integralOfChidtValue);
710
711	}
712	else
713	return NULL;
714
715	//get eta
716	foo = strtok(NULL, " ,;\t\n");
717	if(foo != NULL ){
718
719	for(int i = 0 ; i < 9; i++){
720
721	if(foo == NULL){
722	sprintf( painCave.errMsg,
723	"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
724	return strdup( painCave.errMsg );
725	}
726	eta[i] = atof( foo );
727	foo = strtok(NULL, " ,;\t\n");
728	}
729	}
730	else
731	return NULL;
732
733	//push eta into SimInfo::properties which can be
734	//retrieved by integrator later
735	//entry_plug->setBoxM( theBoxMat3 );
736	DoubleArrayData* etaValue = new DoubleArrayData();
737	etaValue->setID(ETAVALUE_ID);
738	etaValue->setData(eta, 9);
739	entry_plug->addProperty(etaValue);
740	}
741
742	return NULL;
743	}
744
745	#ifdef IS_MPI
746	void DumpReader::nodeZeroError( void ){
747	int j, myStatus;
748
749	myStatus = 0;
750	for (j = 0; j < mpiSim->getNProcessors(); j++) {
751	MPI_Send( &myStatus, 1, MPI_INT, j,
752	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
753	}
754
755
756	MPI_Finalize();
757	exit (0);
758
759	}
760
761	void DumpReader::anonymousNodeDie( void ){
762
763	MPI_Finalize();
764	exit (0);
765	}
766	#endif