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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 1074 by tim, Mon Mar 1 20:01:50 2004 UTC

# Line 1 | Line 1
1   #define _FILE_OFFSET_BITS 64
2  
3 + #include <sys/types.h>
4 + #include <sys/stat.h>
5 +
6   #include <iostream>
7 < #include <cmath>
5 < #include <vector>
7 > #include <math.h>
8  
9   #include <stdio.h>
10   #include <stdlib.h>
11   #include <string.h>
10 – #include <unistd.h>
11 – #include <sys/types.h>
12 – #include <sys/stat.h>
12  
13 +
14   #include "ReadWrite.hpp"
15   #include "simError.h"
16  
# Line 28 | Line 28 | namespace dumpRead{
28    void anonymousNodeDie( void );
29   #endif // is_mpi
30    
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;
31   }
32  
33   using namespace dumpRead;
34  
35  
36 < DumpReader :: DumpReader( char *in_name ){
36 > DumpReader :: DumpReader(const char *in_name ){
37  
38    isScanned = false;
39 +  headFP = new FilePos;
40  
41   #ifdef IS_MPI
42    if (worldRank == 0) {
# Line 117 | Line 93 | void DumpReader::scanFile( void ){
93    char readBuffer[2000];
94    char* foo;
95    fpos_t *currPos;
96 +  double time;
97  
98 +  FilePos *currFP;
99 +
100 +
101   #ifdef IS_MPI
102    if( worldRank == 0 ){
103   #endif // is_mpi
# Line 126 | Line 106 | void DumpReader::scanFile( void ){
106      
107      currPos = new fpos_t;
108      fgetpos( inFile, currPos );
109 <    fgets( readBuffer, sizeof( readBuffer ), in_file );
109 >    fgets( readBuffer, sizeof( readBuffer ), inFile );
110      lineNum++;
111 <    if( feof( in_file ) ){
111 >    if( feof( inFile ) ){
112        sprintf( painCave.errMsg,
113                 "File \"%s\" ended unexpectedly at line %d\n",
114                 inName,
# Line 137 | Line 117 | void DumpReader::scanFile( void ){
117        simError();
118      }
119      
120 <    while( !feof( in_file ) ){
121 <      
122 <      frameStart.push_back( FilePos( currPos ) );
120 >    nFrames = 0;
121 >    while( !feof( inFile ) ){
122 >
123 >      headFP->add( currPos );
124 >      nFrames++;
125 >
126        i = atoi(readBuffer);
127        
128 <      fgets( readBuffer, sizeof( readBuffer ), in_file );
128 >      fgets( readBuffer, sizeof( readBuffer ), inFile );
129        lineNum++;    
130 <      if( feof( in_file ) ){
130 >      if( feof( inFile ) ){
131          sprintf( painCave.errMsg,
132                   "File \"%s\" ended unexpectedly at line %d\n",
133                   inName,
# Line 153 | Line 136 | void DumpReader::scanFile( void ){
136          simError();
137        }
138        
139 <      if(outTime){
140 <        foo = strtok( readBuffer, " ,;\t" );
141 <        time = atof( foo );
142 <      }
139 > //       if(outTime){
140 > //      foo = strtok( readBuffer, " ,;\t" );
141 > //      time = atof( foo );
142 > //       }
143        
144        for(j=0; j<i; j++){
145          
146 <        fgets( readBuffer, sizeof( readBuffer ), in_file );
146 >        fgets( readBuffer, sizeof( readBuffer ), inFile );
147          lineNum++;    
148 <        if( feof( in_file ) ){
148 >        if( feof( inFile ) ){
149            sprintf( painCave.errMsg,
150                     "File \"%s\" ended unexpectedly at line %d,"
151                     " with atom %d\n",
# Line 177 | Line 160 | void DumpReader::scanFile( void ){
160        
161        currPos = new fpos_t;
162        fgetpos( inFile, currPos );
163 <      fgets( readBuffer, sizeof( readBuffer ), in_file );
163 >      fgets( readBuffer, sizeof( readBuffer ), inFile );
164        lineNum++;
165      }
166      
167      delete currPos;
185 –    vectorSize = frameStart.size();
168      rewind( inFile );
169      
170 +    frameStart = new FilePos*[nFrames];
171 +    currFP = headFP;
172 +    for(i=0; i<nFrames; i++){
173 +      
174 +      currFP = currFP->getNext();
175 +      if( currFP == NULL ){
176 +        sprintf( painCave.errMsg,
177 +                 "DumpReader error: scanFile FilePos mismatch at "
178 +                 "nFrames = %d\n",
179 +                 i );
180 +        painCave.isFatal = 1;
181 +        simError();
182 +      }
183 +      
184 +      frameStart[i] = currFP;
185 +    }
186 +
187 +    isScanned = true;
188 +
189   #ifdef IS_MPI
190    }
191    strcpy( checkPointMsg, "Successfully scanned DumpFile\n" );
192    MPIcheckPoint();
193   #endif // is_mpi
193 –
194 –  nFrames = vectorSize;
195 –  isScanned = true;
194   }
195  
196   void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
# Line 220 | Line 218 | void DumpReader :: readSet( int whichFrame ){
218    int procIndex;
219    double boxMat[9];
220    double theBoxMat3[3][3];
221 <  
221 >  double time;
222 >
223    fpos_t *framePos;
224    
225   #ifndef IS_MPI
226    
227 <  framePos = startFrame[whichFrame].getPos();
227 >  framePos = frameStart[whichFrame]->getPos();
228  
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
468 >  double pos[3]; // position place holders
469 >  double vel[3]; // velocity placeholders
470    double q[4]; // the quaternions
471    double jx, jy, jz; // angular velocity placeholders;
472    double qSqr, qLength; // needed to normalize the quaternion vector.
# 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 674 | Line 673 | char* DumpReader::parseDumpLine(char* readLine, int gl
673    }
674      
675    // 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 );
676  
677 +  atoms[atomIndex]->setPos( pos );
678 +  atoms[atomIndex]->setVel( vel );
679 +
680    return NULL;
681   }
682  
683  
684 < char* DumpReader::parseCommentLine(char* readLine, double time,
684 > char* DumpReader::parseCommentLine(char* readLine, double &time,
685                                     double boxMat[9]){
686  
687    char *foo; // the pointer to the current string token
688    int j;
689 +  double chi, integralOfChidt;
690 +  double eta[9];
691  
692    // set the string tokenizer
693    
# Line 792 | Line 788 | char* DumpReader::parseCommentLine(char* readLine, dou
788    boxMat[8] = atof( foo );    
789  
790    return NULL;
791 +
792 +  //get chi and integralOfChidt, they should appear by pair
793 +  foo = strtok(NULL, " ,;\t\n");
794 +  if(foo != NULL){
795 +    chi = atof(foo);
796 +    
797 +    foo = strtok(NULL, " ,;\t\n");
798 +    if(foo == NULL){
799 +      sprintf( painCave.errMsg,
800 +               "chi and integralOfChidt should appear by pair in %s\n", inName );
801 +      return strdup( painCave.errMsg );
802 +    }
803 +    integralOfChidt = atof( foo );
804 +    
805 +    //push chi and integralOfChidt into SimInfo::properties which can be
806 +    //retrieved by integrator later
807 +    DoubleData* chiValue = new DoubleData();
808 +    chiValue->setID(CHIVALUE_ID);
809 +    chiValue->setData(chi);
810 +    simnfo->addProperty(chiValue);
811 +    
812 +    DoubleData* integralOfChidtValue = new DoubleData();
813 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
814 +    integralOfChidtValue->setData(integralOfChidt);
815 +    simnfo->addProperty(integralOfChidtValue);
816 +    
817 +  }
818 +  else
819 +    return NULL;
820 +  
821 +  //get eta
822 +  for(int i = 0 ; i < 9; i++){
823 +    foo = strtok(NULL, " ,;\t");
824 +    if(foo == NULL){
825 +      sprintf( painCave.errMsg,
826 +               "error in reading eta[%d] from %s\n", i, inName );
827 +      return strdup( painCave.errMsg );
828 +    }
829 +    eta[i] = atof( foo );
830 +  }
831 +  
832 +  //push eta into SimInfo::properties which can be
833 +  //retrieved by integrator later
834 +  //simnfo->setBoxM( theBoxMat3 );
835 +  DoubleArrayData* etaValue = new DoubleArrayData();
836 +  etaValue->setID(ETAVALUE_ID);
837 +  etaValue->setData(eta, 9);
838 +  simnfo->addProperty(etaValue);
839 +  
840 +  
841 +  return NULL;
842 +  
843 +  
844 +
845   }
846  
847  
# Line 799 | Line 849 | void initFile::nodeZeroError( void ){
849  
850   // a couple of functions to let us escape the read loop
851  
852 < void initFile::nodeZeroError( void ){
852 > void dumpRead::nodeZeroError( void ){
853    int j, myStatus;
854    
855    myStatus = 0;
# Line 814 | Line 864 | void initFile::anonymousNodeDie( void ){
864    
865   }
866  
867 < void initFile::anonymousNodeDie( void ){
867 > void dumpRead::anonymousNodeDie( void ){
868  
869    MPI_Finalize();
870    exit (0);

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