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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 656 by mmeineke, Tue Jul 29 16:32:37 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
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 <cmath>
5 < #include <vector>
8 > #include <math.h>
9  
10   #include <stdio.h>
11   #include <stdlib.h>
12   #include <string.h>
10 – #include <unistd.h>
11 – #include <sys/types.h>
12 – #include <sys/stat.h>
13  
14 +
15   #include "ReadWrite.hpp"
16   #include "simError.h"
17  
# Line 28 | Line 29 | namespace dumpRead{
29    void anonymousNodeDie( void );
30   #endif // is_mpi
31    
31 –  class FilePos{
32 –    
33 –  public:
34 –    FilePos(){ myPos = NULL; }
35 –    FilePos( fpos_t* thePos ) { myPos = thePos; }
36 –    ~FilePos(){ if( myPos != NULL ) delete myPos; }
37 –
38 –    FilePos &operator=(fpos_t *thePos){ myPos = thePos; return *this; }
39 –
40 –    void setPos( fpos_t *thePos ){ myPos = thePos; }
41 –    fpos_t *getPos( void ){ return myPos; }
42 –  
43 –  private:
44 –    
45 –    fpos_t *myPos
46 –
47 –  };
48 –
49 –  bool operator<(FilePos a, FilePos b){
50 –    return (a.getPos())->__pos < (b.getPos())->__pos; }
51 –
52 –  bool operator==(FilePos a, FilePos b){
53 –    return (a.getPos())->__pos == (b.getPos())->__pos; }
54 –
55 –  vector<FilePos> frameStart;
32   }
33  
34   using namespace dumpRead;
35  
36  
37 < DumpReader :: DumpReader( char *in_name ){
37 > DumpReader :: DumpReader(const char *in_name ){
38  
39    isScanned = false;
40 +  headFP = new FilePos;
41  
42   #ifdef IS_MPI
43    if (worldRank == 0) {
# Line 117 | Line 94 | void DumpReader::scanFile( void ){
94    char readBuffer[2000];
95    char* foo;
96    fpos_t *currPos;
97 +  double time;
98  
99 +  FilePos *currFP;
100 +
101 +
102   #ifdef IS_MPI
103    if( worldRank == 0 ){
104   #endif // is_mpi
# Line 126 | Line 107 | void DumpReader::scanFile( void ){
107      
108      currPos = new fpos_t;
109      fgetpos( inFile, currPos );
110 <    fgets( readBuffer, sizeof( readBuffer ), in_file );
110 >    fgets( readBuffer, sizeof( readBuffer ), inFile );
111      lineNum++;
112 <    if( feof( in_file ) ){
112 >    if( feof( inFile ) ){
113        sprintf( painCave.errMsg,
114                 "File \"%s\" ended unexpectedly at line %d\n",
115                 inName,
# Line 137 | Line 118 | void DumpReader::scanFile( void ){
118        simError();
119      }
120      
121 <    while( !feof( in_file ) ){
122 <      
123 <      frameStart.push_back( FilePos( currPos ) );
121 >    nFrames = 0;
122 >    while( !feof( inFile ) ){
123 >
124 >      headFP->add( currPos );
125 >      nFrames++;
126 >
127        i = atoi(readBuffer);
128        
129 <      fgets( readBuffer, sizeof( readBuffer ), in_file );
129 >      fgets( readBuffer, sizeof( readBuffer ), inFile );
130        lineNum++;    
131 <      if( feof( in_file ) ){
131 >      if( feof( inFile ) ){
132          sprintf( painCave.errMsg,
133                   "File \"%s\" ended unexpectedly at line %d\n",
134                   inName,
# Line 153 | Line 137 | void DumpReader::scanFile( void ){
137          simError();
138        }
139        
140 <      if(outTime){
141 <        foo = strtok( readBuffer, " ,;\t" );
142 <        time = atof( foo );
143 <      }
140 > //       if(outTime){
141 > //      foo = strtok( readBuffer, " ,;\t" );
142 > //      time = atof( foo );
143 > //       }
144        
145        for(j=0; j<i; j++){
146          
147 <        fgets( readBuffer, sizeof( readBuffer ), in_file );
147 >        fgets( readBuffer, sizeof( readBuffer ), inFile );
148          lineNum++;    
149 <        if( feof( in_file ) ){
149 >        if( feof( inFile ) ){
150            sprintf( painCave.errMsg,
151                     "File \"%s\" ended unexpectedly at line %d,"
152                     " with atom %d\n",
# Line 177 | Line 161 | void DumpReader::scanFile( void ){
161        
162        currPos = new fpos_t;
163        fgetpos( inFile, currPos );
164 <      fgets( readBuffer, sizeof( readBuffer ), in_file );
164 >      fgets( readBuffer, sizeof( readBuffer ), inFile );
165        lineNum++;
166      }
167      
168      delete currPos;
185 –    vectorSize = frameStart.size();
169      rewind( inFile );
170      
171 +    frameStart = new FilePos*[nFrames];
172 +    currFP = headFP;
173 +    for(i=0; i<nFrames; i++){
174 +      
175 +      currFP = currFP->getNext();
176 +      if( currFP == NULL ){
177 +        sprintf( painCave.errMsg,
178 +                 "DumpReader error: scanFile FilePos mismatch at "
179 +                 "nFrames = %d\n",
180 +                 i );
181 +        painCave.isFatal = 1;
182 +        simError();
183 +      }
184 +      
185 +      frameStart[i] = currFP;
186 +    }
187 +
188 +    isScanned = true;
189 +
190   #ifdef IS_MPI
191    }
192    strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
193    MPIcheckPoint();
194   #endif // is_mpi
193 –
194 –  nFrames = vectorSize;
195 –  isScanned = true;
195   }
196  
197   void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
# Line 220 | Line 219 | void DumpReader :: readSet( int whichFrame ){
219    int procIndex;
220    double boxMat[9];
221    double theBoxMat3[3][3];
222 <  
222 >  double time;
223 >
224    fpos_t *framePos;
225 +  framePos = frameStart[whichFrame]->getPos();
226    
227   #ifndef IS_MPI
228    
229 <  framePos = startFrame[whichFrame].getPos();
229 <
229 >  fsetpos(inFile, framePos);
230    
231  
232 –
232    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
233    if( eof_test == NULL ){
234      sprintf( painCave.errMsg,
# Line 317 | Line 316 | void DumpReader :: readSet( int whichFrame ){
316    
317    haveError = 0;
318    if (worldRank == 0) {
319 <
319 >    fsetpos(inFile, framePos);
320      eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
321      if( eof_test == NULL ){
322        sprintf( painCave.errMsg,
# Line 360 | Line 359 | void DumpReader :: readSet( int whichFrame ){
359        simError();
360      }
361  
362 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
362 >    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
363      
364      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
365      
# Line 416 | Line 415 | void DumpReader :: readSet( int whichFrame ){
415      
416    } else {
417      
418 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
418 >    MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
419      MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
420  
421      done = 0;
# Line 466 | Line 465 | char* DumpReader::parseDumpLine(char* readLine, int gl
465  
466    char *foo; // the pointer to the current string token
467    
468 <  double rx, ry, rz; // position place holders
469 <  double vx, vy, vz; // velocity placeholders
470 <  double q[4]; // the quaternions
471 <  double jx, jy, jz; // angular velocity placeholders;
468 >  double pos[3];        // position place holders
469 >  double vel[3];        // velocity placeholders
470 >  double q[4];          // the quaternions
471 >  double ji[3];         // angular velocity placeholders;
472    double qSqr, qLength; // needed to normalize the quaternion vector.
473    
474    Atom **atoms = simnfo->atoms;
# Line 498 | Line 497 | char* DumpReader::parseDumpLine(char* readLine, int gl
497    // set the string tokenizer
498    
499    foo = strtok(readLine, " ,;\t");
500 <  
500 >  atoms[atomIndex]->setType(foo);
501    // check the atom name to the current atom
502    
503 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
504 <    sprintf( painCave.errMsg,
505 <             "Initialize from file error. Atom %s at index %d "
506 <             "in file %s does not"
507 <             " match the BASS atom %s.\n",
508 <             foo, atomIndex, inName, atoms[atomIndex]->getType() );
509 <    return strdup( painCave.errMsg );
510 <  }
503 >  //if( strcmp( foo, atoms[atomIndex]->getType() ) ){
504 >  //  sprintf( painCave.errMsg,
505 >  //    "Initialize from file error. Atom %s at index %d "
506 >  //     "in file %s does not"
507 >  //     " match the BASS atom %s.\n",
508 >  //     foo, atomIndex, inName, atoms[atomIndex]->getType() );
509 >  //  return strdup( painCave.errMsg );
510 >  //}
511      
512    // get the positions
513  
# Line 520 | Line 519 | char* DumpReader::parseDumpLine(char* readLine, int gl
519               inName, n_atoms, atomIndex );
520      return strdup( painCave.errMsg );
521    }
522 <  rx = atof( foo );
522 >  pos[0] = atof( foo );
523    
524    foo = strtok(NULL, " ,;\t");
525    if(foo == NULL){
# Line 530 | Line 529 | char* DumpReader::parseDumpLine(char* readLine, int gl
529               inName, n_atoms, atomIndex );
530      return strdup( painCave.errMsg );
531    }
532 <  ry = atof( foo );
532 >  pos[1] = atof( foo );
533      
534    foo = strtok(NULL, " ,;\t");
535    if(foo == NULL){
# Line 540 | Line 539 | char* DumpReader::parseDumpLine(char* readLine, int gl
539               inName, n_atoms, atomIndex );
540      return strdup( painCave.errMsg );
541    }
542 <  rz = atof( foo );    
542 >  pos[2] = atof( foo );    
543  
544  
545    // get the velocities
# Line 553 | Line 552 | char* DumpReader::parseDumpLine(char* readLine, int gl
552               inName, n_atoms, atomIndex );
553      return strdup( painCave.errMsg );
554    }
555 <  vx = atof( foo );
555 >  vel[0] = atof( foo );
556      
557    foo = strtok(NULL, " ,;\t");
558    if(foo == NULL){
# Line 563 | Line 562 | char* DumpReader::parseDumpLine(char* readLine, int gl
562               inName, n_atoms, atomIndex );
563      return strdup( painCave.errMsg );
564    }
565 <  vy = atof( foo );
565 >  vel[1] = atof( foo );
566      
567    foo = strtok(NULL, " ,;\t");
568    if(foo == NULL){
# Line 573 | Line 572 | char* DumpReader::parseDumpLine(char* readLine, int gl
572               inName, n_atoms, atomIndex );
573      return strdup( painCave.errMsg );
574    }
575 <  vz = atof( foo );
575 >  vel[2] = atof( foo );
576      
577      
578    // get the quaternions
# Line 630 | Line 629 | char* DumpReader::parseDumpLine(char* readLine, int gl
629                 inName, n_atoms, atomIndex );
630        return strdup( painCave.errMsg );
631      }
632 <    jx = atof( foo );
632 >    ji[0] = atof( foo );
633        
634      foo = strtok(NULL, " ,;\t");
635      if(foo == NULL){
# Line 640 | Line 639 | char* DumpReader::parseDumpLine(char* readLine, int gl
639                 inName, n_atoms, atomIndex );
640        return strdup( painCave.errMsg );
641      }
642 <    jy = atof(foo );
642 >    ji[1] = atof(foo );
643        
644      foo = strtok(NULL, " ,;\t");
645      if(foo == NULL){
# Line 650 | Line 649 | char* DumpReader::parseDumpLine(char* readLine, int gl
649                 inName, n_atoms, atomIndex );
650        return strdup( painCave.errMsg );
651      }
652 <    jz = atof( foo );
652 >    ji[2] = atof( foo );
653        
654      dAtom = ( DirectionalAtom* )atoms[atomIndex];
655  
# Line 668 | Line 667 | char* DumpReader::parseDumpLine(char* readLine, int gl
667        
668      // add the angular velocities
669  
670 <    dAtom->setJx( jx );
672 <    dAtom->setJy( jy );
673 <    dAtom->setJz( jz );
670 >    dAtom->setJ( ji );
671    }
672      
673    // add the positions and velocities to the atom
677 –    
678 –  atoms[atomIndex]->setX( rx );
679 –  atoms[atomIndex]->setY( ry );
680 –  atoms[atomIndex]->setZ( rz );
681 –    
682 –  atoms[atomIndex]->set_vx( vx );
683 –  atoms[atomIndex]->set_vy( vy );
684 –  atoms[atomIndex]->set_vz( vz );
674  
675 +  atoms[atomIndex]->setPos( pos );
676 +  atoms[atomIndex]->setVel( vel );
677 +
678    return NULL;
679   }
680  
681  
682 < char* DumpReader::parseCommentLine(char* readLine, double time,
682 > char* DumpReader::parseCommentLine(char* readLine, double &time,
683                                     double boxMat[9]){
684  
685    char *foo; // the pointer to the current string token
686    int j;
687 +  double chi, integralOfChidt;
688 +  double eta[9];
689  
690    // set the string tokenizer
691    
# Line 792 | Line 786 | char* DumpReader::parseCommentLine(char* readLine, dou
786    boxMat[8] = atof( foo );    
787  
788    return NULL;
789 +
790 +  //get chi and integralOfChidt, they should appear by pair
791 +  foo = strtok(NULL, " ,;\t\n");
792 +  if(foo != NULL){
793 +    chi = atof(foo);
794 +    
795 +    foo = strtok(NULL, " ,;\t\n");
796 +    if(foo == NULL){
797 +      sprintf( painCave.errMsg,
798 +               "chi and integralOfChidt should appear by pair in %s\n", inName );
799 +      return strdup( painCave.errMsg );
800 +    }
801 +    integralOfChidt = atof( foo );
802 +    
803 +    //push chi and integralOfChidt into SimInfo::properties which can be
804 +    //retrieved by integrator later
805 +    DoubleData* chiValue = new DoubleData();
806 +    chiValue->setID(CHIVALUE_ID);
807 +    chiValue->setData(chi);
808 +    simnfo->addProperty(chiValue);
809 +    
810 +    DoubleData* integralOfChidtValue = new DoubleData();
811 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
812 +    integralOfChidtValue->setData(integralOfChidt);
813 +    simnfo->addProperty(integralOfChidtValue);
814 +    
815 +  }
816 +  else
817 +    return NULL;
818 +  
819 +  //get eta
820 +  for(int i = 0 ; i < 9; i++){
821 +    foo = strtok(NULL, " ,;\t");
822 +    if(foo == NULL){
823 +      sprintf( painCave.errMsg,
824 +               "error in reading eta[%d] from %s\n", i, inName );
825 +      return strdup( painCave.errMsg );
826 +    }
827 +    eta[i] = atof( foo );
828 +  }
829 +  
830 +  //push eta into SimInfo::properties which can be
831 +  //retrieved by integrator later
832 +  //simnfo->setBoxM( theBoxMat3 );
833 +  DoubleArrayData* etaValue = new DoubleArrayData();
834 +  etaValue->setID(ETAVALUE_ID);
835 +  etaValue->setData(eta, 9);
836 +  simnfo->addProperty(etaValue);
837 +  
838 +  
839 +  return NULL;
840 +  
841 +  
842 +
843   }
844  
845  
# Line 799 | Line 847 | char* DumpReader::parseCommentLine(char* readLine, dou
847  
848   // a couple of functions to let us escape the read loop
849  
850 < void initFile::nodeZeroError( void ){
850 > void dumpRead::nodeZeroError( void ){
851    int j, myStatus;
852    
853    myStatus = 0;
# Line 814 | Line 862 | void initFile::nodeZeroError( void ){
862    
863   }
864  
865 < void initFile::anonymousNodeDie( void ){
865 > void dumpRead::anonymousNodeDie( void ){
866  
867    MPI_Finalize();
868    exit (0);

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