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;
  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->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[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->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_Send(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);

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

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

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

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

        }
          
      }
      
    }

  }

#endif
}

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

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

  double pos[3]; // position place holders
  double vel[3]; // velocity placeholders
  double q[4]; // the quaternions
  double ji[3]; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.


  // set the string tokenizer

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

  // check the atom name to the current atom

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

  // get the positions

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

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

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


  // get the velocities

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

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

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


  // add the positions and velocities to the atom

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

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

  // get the quaternions

  if( sd->isDirectional() ){

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

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

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

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      inFileName.c_str() );
      return strdup( painCave.errMsg );
    }
    q[3] = atof( foo );

    // get the angular velocities

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

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

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


    // check that the quaternion vector is normalized

    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);

    qLength = sqrt( qSqr );
    q[0] = q[0] / qLength;
    q[1] = q[1] / qLength;
    q[2] = q[2] / qLength;
    q[3] = q[3] / qLength;

    // add quaternion and angular velocities

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


  return NULL;
}


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

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

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

  // set the string tokenizer

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

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

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

  //get H-Matrix

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

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

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

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

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

  return NULL;
}

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

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


  MPI_Finalize();
  exit (0);

}

void DumpReader::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}
#endif
Revision:	1198
Committed:	Thu May 27 00:48:12 2004 UTC (21 years, 5 months ago) by tim
File size:	17958 byte(s)
Log Message:	in the progress of fixing MPI version of cutoff group
#	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 vectorSize;
88	int i, j, k;
89	int lineNum = 0;
90	char readBuffer[2000];
91	char* foo;
92	fpos_t *currPos;
93	double time;
94
95
96
97	#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	fgets( readBuffer, sizeof( readBuffer ), inFile );
106	lineNum++;
107	if( feof( inFile ) ){
108	sprintf( painCave.errMsg,
109	"File \"%s\" ended unexpectedly at line %d\n",
110	inFileName.c_str(),
111	lineNum );
112	painCave.isFatal = 1;
113	simError();
114	}
115
116	while( !feof( inFile ) ){
117
118	framePos.push_back(currPos);
119
120	i = atoi(readBuffer);
121
122	fgets( readBuffer, sizeof( readBuffer ), inFile );
123	lineNum++;
124	if( feof( inFile ) ){
125	sprintf( painCave.errMsg,
126	"File \"%s\" ended unexpectedly at line %d\n",
127	inFileName.c_str(),
128	lineNum );
129	painCave.isFatal = 1;
130	simError();
131	}
132
133	for(j=0; j<i; j++){
134
135	fgets( readBuffer, sizeof( readBuffer ), inFile );
136	lineNum++;
137	if( feof( inFile ) ){
138	sprintf( painCave.errMsg,
139	"File \"%s\" ended unexpectedly at line %d,"
140	" with atom %d\n",
141	inFileName.c_str(),
142	lineNum,
143	j );
144	painCave.isFatal = 1;
145	simError();
146	}
147
148	}
149
150	currPos = new fpos_t;
151	fgetpos( inFile, currPos );
152	fgets( readBuffer, sizeof( readBuffer ), inFile );
153	lineNum++;
154	}
155
156	delete currPos;
157	rewind( inFile );
158
159	isScanned = true;
160
161	#ifdef IS_MPI
162	}
163	strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
164	MPIcheckPoint();
165	#endif // is_mpi
166	}
167
168	void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
169
170	simnfo = the_simnfo;
171
172	this->readSet( whichFrame );
173	}
174
175
176
177	void DumpReader :: readSet( int whichFrame ){
178
179	int i, j;
180
181	#ifdef IS_MPI
182	int done, which_node, which_atom; // loop counter
183	#endif //is_mpi
184
185	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	char *parseErr;
191
192	vector<StuntDouble*> integrableObjects;
193
194
195	#ifndef IS_MPI
196
197	fsetpos(inFile, framePos[whichFrame]);
198	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
199	if( eof_test == NULL ){
200	sprintf( painCave.errMsg,
201	"DumpReader error: error reading 1st line of \"%s\"\n",
202	inFileName.c_str() );
203	painCave.isFatal = 1;
204	simError();
205	}
206
207	nTotObjs = atoi( read_buffer );
208
209	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
210	sprintf( painCave.errMsg,
211	"DumpReader error. %s n_atoms, %d, "
212	"does not match the BASS file's n_atoms, %d.\n",
213	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
214	painCave.isFatal = 1;
215	simError();
216	}
217
218	//read the box mat from the comment line
219
220	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
221	if(eof_test == NULL){
222	sprintf( painCave.errMsg,
223	"error in reading commment in %s\n", inFileName.c_str());
224	painCave.isFatal = 1;
225	simError();
226	}
227
228	parseErr = parseCommentLine( read_buffer, simnfo);
229	if( parseErr != NULL ){
230	strcpy( painCave.errMsg, parseErr );
231	painCave.isFatal = 1;
232	simError();
233	}
234
235	//parse dump lines
236
237	for( i=0; i < simnfo->n_mol; i++){
238
239	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
240
241	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	}
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
272	MPI_Status istatus;
273	int *MolToProcMap = mpiSim->getMolToProcMap();
274	int localIndex;
275	int nCurObj;
276	int nitems;
277
278	nTotObjs = simnfo->getTotIntegrableObjects();
279	haveError = 0;
280	if (worldRank == 0) {
281	fsetpos(inFile, framePos[whichFrame]);
282
283	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
284	if( eof_test == NULL ){
285	sprintf( painCave.errMsg,
286	"Error reading 1st line of %s \n ",inFileName.c_str());
287	haveError = 1;
288	simError();
289	}
290
291	nitems = atoi( read_buffer );
292
293	// Check to see that the number of integrable objects in the intial configuration file is the
294	// same as declared in simBass.
295
296	if( nTotObjs != nitems){
297	sprintf( painCave.errMsg,
298	"DumpReadererror. %s n_atoms, %d, "
299	"does not match the BASS file's n_atoms, %d.\n",
300	inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
301	haveError= 1;
302	simError();
303	}
304
305	//read the boxMat from the comment line
306
307	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
308	if(eof_test == NULL){
309	sprintf( painCave.errMsg,
310	"error in reading commment in %s\n", inFileName.c_str());
311	haveError = 1;
312	simError();
313	}
314
315	//Every single processor will parse the comment line by itself
316	//By using this way, we might lose some efficiency, but if we want to add
317	//more parameters into comment line, we only need to modify function
318	//parseCommentLine
319
320	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
321
322	parseErr = parseCommentLine( read_buffer, simnfo);
323
324	if( parseErr != NULL ){
325	strcpy( painCave.errMsg, parseErr );
326	haveError = 1;
327	simError();
328	}
329
330	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
331	which_node = MolToProcMap[i];
332	if(which_node == 0){
333	//molecules belong to master node
334
335	localIndex = mpiSim->getGlobalToLocalMol(i);
336
337	if(localIndex == -1) {
338	strcpy(painCave.errMsg, "Molecule not found on node 0!");
339	haveError = 1;
340	simError();
341	}
342
343	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
344	for(j=0; j < integrableObjects.size(); j++){
345
346	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
347	if(eof_test == NULL){
348	sprintf(painCave.errMsg,
349	"error in reading file %s\n"
350	"natoms = %d; index = %d\n"
351	"error reading the line from the file.\n",
352	inFileName.c_str(), nTotObjs, i );
353	haveError= 1;
354	simError();
355	}
356
357	if(haveError) nodeZeroError();
358
359	parseDumpLine(read_buffer, integrableObjects[j]);
360
361	}
362
363
364	}
365	else{
366	//molecule belongs to slave nodes
367
368	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
369	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
370
371	for(j=0; j < nCurObj; j++){
372
373	eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
374	if(eof_test == NULL){
375	sprintf(painCave.errMsg,
376	"error in reading file %s\n"
377	"natoms = %d; index = %d\n"
378	"error reading the line from the file.\n",
379	inFileName.c_str(), nTotObjs, i );
380	haveError= 1;
381	simError();
382	}
383
384	if(haveError) nodeZeroError();
385
386	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
387	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
388
389	}
390
391	}
392
393	}
394
395	}
396	else{
397	//actions taken at slave nodes
398	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
399
400	parseErr = parseCommentLine( read_buffer, simnfo);
401
402	if( parseErr != NULL ){
403	strcpy( painCave.errMsg, parseErr );
404	haveError = 1;
405	simError();
406	}
407
408	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
409	which_node = MolToProcMap[i];
410
411	if(which_node == worldRank){
412	//molecule with global index i belongs to this processor
413
414	localIndex = mpiSim->getGlobalToLocalMol(i);
415
416	if(localIndex == -1) {
417	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
418	haveError = 1;
419	simError();
420	}
421
422	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
423
424	nCurObj = integrableObjects.size();
425
426	MPI_Send(&nCurObj, 1, MPI_INT, 0,
427	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
428
429	for(j = 0; j < integrableObjects.size(); j++){
430
431	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
432	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
433
434	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
435
436	if( parseErr != NULL ){
437	strcpy( painCave.errMsg, parseErr );
438	simError();
439	}
440
441	}
442
443	}
444
445	}
446
447	}
448
449	#endif
450	}
451
452	char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
453
454	char *foo; // the pointer to the current string token
455
456	double pos[3]; // position place holders
457	double vel[3]; // velocity placeholders
458	double q[4]; // the quaternions
459	double ji[3]; // angular velocity placeholders;
460	double qSqr, qLength; // needed to normalize the quaternion vector.
461
462
463	// set the string tokenizer
464
465	foo = strtok(readLine, " ,;\t");
466
467	// check the atom name to the current atom
468
469	if( strcmp( foo, sd->getType() ) ){
470	sprintf( painCave.errMsg,
471	"DumpReader error. Does not"
472	" match the BASS atom %s.\n",
473	sd->getType() );
474	return strdup( painCave.errMsg );
475	}
476
477	// get the positions
478
479	foo = strtok(NULL, " ,;\t");
480	if(foo == NULL){
481	sprintf( painCave.errMsg,
482	"error in reading postition x from %s\n",
483	inFileName.c_str());
484	return strdup( painCave.errMsg );
485	}
486	pos[0] = atof( foo );
487
488	foo = strtok(NULL, " ,;\t");
489	if(foo == NULL){
490	sprintf( painCave.errMsg,
491	"error in reading postition y from %s\n",
492	inFileName.c_str());
493	return strdup( painCave.errMsg );
494	}
495	pos[1] = atof( foo );
496
497	foo = strtok(NULL, " ,;\t");
498	if(foo == NULL){
499	sprintf( painCave.errMsg,
500	"error in reading postition z from %s\n",
501	inFileName.c_str());
502	return strdup( painCave.errMsg );
503	}
504	pos[2] = atof( foo );
505
506
507	// get the velocities
508
509	foo = strtok(NULL, " ,;\t");
510	if(foo == NULL){
511	sprintf( painCave.errMsg,
512	"error in reading velocity x from %s\n",
513	inFileName.c_str() );
514	return strdup( painCave.errMsg );
515	}
516	vel[0] = atof( foo );
517
518	foo = strtok(NULL, " ,;\t");
519	if(foo == NULL){
520	sprintf( painCave.errMsg,
521	"error in reading velocity x from %s\n",
522	inFileName.c_str() );
523	return strdup( painCave.errMsg );
524	}
525	vel[1] = atof( foo );
526
527	foo = strtok(NULL, " ,;\t");
528	if(foo == NULL){
529	sprintf( painCave.errMsg,
530	"error in reading velocity x from %s\n",
531	inFileName.c_str() );
532	return strdup( painCave.errMsg );
533	}
534	vel[2] = atof( foo );
535
536
537	// add the positions and velocities to the atom
538
539	sd->setPos( pos );
540	sd->setVel( vel );
541
542	if (!sd->isDirectional())
543	return NULL;
544
545	// get the quaternions
546
547	if( sd->isDirectional() ){
548
549	foo = strtok(NULL, " ,;\t");
550	if(foo == NULL){
551	sprintf( painCave.errMsg,
552	"error in reading velocity x from %s\n",
553	inFileName.c_str() );
554	return strdup( painCave.errMsg );
555	}
556	q[0] = atof( foo );
557
558	foo = strtok(NULL, " ,;\t");
559	if(foo == NULL){
560	sprintf( painCave.errMsg,
561	"error in reading velocity x from %s\n",
562	inFileName.c_str() );
563	return strdup( painCave.errMsg );
564	}
565	q[1] = atof( foo );
566
567	foo = strtok(NULL, " ,;\t");
568	if(foo == NULL){
569	sprintf( painCave.errMsg,
570	"error in reading velocity x from %s\n",
571	inFileName.c_str() );
572	return strdup( painCave.errMsg );
573	}
574	q[2] = atof( foo );
575
576	foo = strtok(NULL, " ,;\t");
577	if(foo == NULL){
578	sprintf( painCave.errMsg,
579	"error in reading velocity x from %s\n",
580	inFileName.c_str() );
581	return strdup( painCave.errMsg );
582	}
583	q[3] = atof( foo );
584
585	// get the angular velocities
586
587	foo = strtok(NULL, " ,;\t");
588	if(foo == NULL){
589	sprintf( painCave.errMsg,
590	"error in reading velocity x from %s\n",
591	inFileName.c_str() );
592	return strdup( painCave.errMsg );
593	}
594	ji[0] = atof( foo );
595
596	foo = strtok(NULL, " ,;\t");
597	if(foo == NULL){
598	sprintf( painCave.errMsg,
599	"error in reading velocity x from %s\n",
600	inFileName.c_str() );
601	return strdup( painCave.errMsg );
602	}
603	ji[1] = atof(foo );
604
605	foo = strtok(NULL, " ,;\t");
606	if(foo == NULL){
607	sprintf( painCave.errMsg,
608	"error in reading velocity x from %s\n",
609	inFileName.c_str() );
610	return strdup( painCave.errMsg );
611	}
612	ji[2] = atof( foo );
613
614
615	// check that the quaternion vector is normalized
616
617	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
618
619	qLength = sqrt( qSqr );
620	q[0] = q[0] / qLength;
621	q[1] = q[1] / qLength;
622	q[2] = q[2] / qLength;
623	q[3] = q[3] / qLength;
624
625	// add quaternion and angular velocities
626
627	sd->setQ( q );
628	sd->setJ( ji );
629	}
630
631
632
633	return NULL;
634	}
635
636
637	char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
638
639	double currTime;
640	double boxMat[9];
641	double theBoxMat3[3][3];
642	double chi;
643	double integralOfChidt;
644	double eta[9];
645
646	char *foo; // the pointer to the current string token
647
648	// set the string tokenizer
649
650	foo = strtok(readLine, " ,;\t");
651	// set the timeToken.
652
653	if(foo == NULL){
654	sprintf( painCave.errMsg,
655	"error in reading Time from %s\n",
656	inFileName.c_str() );
657	return strdup( painCave.errMsg );
658	}
659
660	currTime = atof( foo );
661	entry_plug->setTime( currTime );
662
663	//get H-Matrix
664
665	for(int i = 0 ; i < 9; i++){
666	foo = strtok(NULL, " ,;\t");
667	if(foo == NULL){
668	sprintf( painCave.errMsg,
669	"error in reading H[%d] from %s\n", i, inFileName.c_str() );
670	return strdup( painCave.errMsg );
671	}
672	boxMat[i] = atof( foo );
673	}
674
675	for(int i=0;i<3;i++)
676	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
677
678	//set H-Matrix
679	entry_plug->setBoxM( theBoxMat3 );
680
681	//get chi and integralOfChidt, they should appear by pair
682
683	if( entry_plug->useInitXSstate ){
684	foo = strtok(NULL, " ,;\t\n");
685	if(foo != NULL){
686	chi = atof(foo);
687
688	foo = strtok(NULL, " ,;\t\n");
689	if(foo == NULL){
690	sprintf( painCave.errMsg,
691	"chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
692	return strdup( painCave.errMsg );
693	}
694	integralOfChidt = atof( foo );
695
696	//push chi and integralOfChidt into SimInfo::properties which can be
697	//retrieved by integrator later
698	DoubleData* chiValue = new DoubleData();
699	chiValue->setID(CHIVALUE_ID);
700	chiValue->setData(chi);
701	entry_plug->addProperty(chiValue);
702
703	DoubleData* integralOfChidtValue = new DoubleData();
704	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
705	integralOfChidtValue->setData(integralOfChidt);
706	entry_plug->addProperty(integralOfChidtValue);
707
708	}
709	else
710	return NULL;
711
712	//get eta
713	foo = strtok(NULL, " ,;\t\n");
714	if(foo != NULL ){
715
716	for(int i = 0 ; i < 9; i++){
717
718	if(foo == NULL){
719	sprintf( painCave.errMsg,
720	"error in reading eta[%d] from %s\n", i, inFileName.c_str() );
721	return strdup( painCave.errMsg );
722	}
723	eta[i] = atof( foo );
724	foo = strtok(NULL, " ,;\t\n");
725	}
726	}
727	else
728	return NULL;
729
730	//push eta into SimInfo::properties which can be
731	//retrieved by integrator later
732	//entry_plug->setBoxM( theBoxMat3 );
733	DoubleArrayData* etaValue = new DoubleArrayData();
734	etaValue->setID(ETAVALUE_ID);
735	etaValue->setData(eta, 9);
736	entry_plug->addProperty(etaValue);
737	}
738
739	return NULL;
740	}
741
742	#ifdef IS_MPI
743	void DumpReader::nodeZeroError( void ){
744	int j, myStatus;
745
746	myStatus = 0;
747	for (j = 0; j < mpiSim->getNprocessors(); j++) {
748	MPI_Send( &myStatus, 1, MPI_INT, j,
749	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
750	}
751
752
753	MPI_Finalize();
754	exit (0);
755
756	}
757
758	void DumpReader::anonymousNodeDie( void ){
759
760	MPI_Finalize();
761	exit (0);
762	}
763	#endif