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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 637 by gezelter, Thu Jul 17 21:50:01 2003 UTC vs.
Revision 804 by mmeineke, Thu Oct 16 19:16:24 2003 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>
8  
9   #include <stdio.h>
10   #include <stdlib.h>
11   #include <string.h>
7 – #include <unistd.h>
8 – #include <sys/types.h>
9 – #include <sys/stat.h>
12  
13 +
14   #include "ReadWrite.hpp"
15   #include "simError.h"
16  
# Line 16 | Line 19
19   #include "mpiSimulation.hpp"
20   #define TAKE_THIS_TAG_CHAR 0
21   #define TAKE_THIS_TAG_INT 1
22 + #endif // is_mpi
23  
24   namespace dumpRead{
25 +
26 + #ifdef IS_MPI
27    void nodeZeroError( void );
28    void anonymousNodeDie( void );
29 + #endif // is_mpi
30 +  
31   }
32  
33   using namespace dumpRead;
34  
27 – #endif // is_mpi
35  
36   DumpReader :: DumpReader( char *in_name ){
37 +
38 +  isScanned = false;
39 +  headFP = new FilePos;
40 +
41   #ifdef IS_MPI
42    if (worldRank == 0) {
43   #endif
44  
45 <  c_in_file = fopen(in_name, "r");
46 <  if(c_in_file == NULL){
45 >  inFile = fopen(in_name, "r");
46 >  if(inFile == NULL){
47      sprintf(painCave.errMsg,
48              "Cannot open file: %s\n", in_name);
49      painCave.isFatal = 1;
50      simError();
51    }
52    
53 <  strcpy( c_in_name, in_name);
53 >  strcpy( inName, in_name);
54   #ifdef IS_MPI
55    }
56    strcpy( checkPointMsg, "Dump file opened for reading successfully." );
# Line 53 | Line 64 | DumpReader :: ~DumpReader( ){
64    if (worldRank == 0) {
65   #endif
66    int error;
67 <  error = fclose( c_in_file );
67 >  error = fclose( inFile );
68    if( error ){
69      sprintf( painCave.errMsg,
70 <             "Error closing %s\n", c_in_name );
70 >             "Error closing %s\n", inName );
71      simError();
72    }
73   #ifdef IS_MPI
# Line 68 | Line 79 | DumpReader :: ~DumpReader( ){
79    return;
80   }
81  
82 + int DumpReader::getNframes( void ){
83  
84 < void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){
84 >  if( !isScanned ) scanFile();
85 >  return nFrames;
86 > }
87  
88 + void DumpReader::scanFile( void ){
89 +
90 +  int vectorSize;
91 +  int i, j, k;
92 +  int lineNum = 0;
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
104 +    
105 +    rewind( inFile );
106 +    
107 +    currPos = new fpos_t;
108 +    fgetpos( inFile, currPos );
109 +    fgets( readBuffer, sizeof( readBuffer ), inFile );
110 +    lineNum++;
111 +    if( feof( inFile ) ){
112 +      sprintf( painCave.errMsg,
113 +               "File \"%s\" ended unexpectedly at line %d\n",
114 +               inName,
115 +               lineNum );
116 +      painCave.isFatal = 1;
117 +      simError();
118 +    }
119 +    
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 ), inFile );
129 +      lineNum++;    
130 +      if( feof( inFile ) ){
131 +        sprintf( painCave.errMsg,
132 +                 "File \"%s\" ended unexpectedly at line %d\n",
133 +                 inName,
134 +                 lineNum );
135 +        painCave.isFatal = 1;
136 +        simError();
137 +      }
138 +      
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 ), inFile );
147 +        lineNum++;    
148 +        if( feof( inFile ) ){
149 +          sprintf( painCave.errMsg,
150 +                   "File \"%s\" ended unexpectedly at line %d,"
151 +                   " with atom %d\n",
152 +                   inName,
153 +                   lineNum,
154 +                   j );
155 +          painCave.isFatal = 1;
156 +          simError();
157 +        }
158 +        
159 +      }
160 +      
161 +      currPos = new fpos_t;
162 +      fgetpos( inFile, currPos );
163 +      fgets( readBuffer, sizeof( readBuffer ), inFile );
164 +      lineNum++;
165 +    }
166 +    
167 +    delete currPos;
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
194 + }
195 +
196 + void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){
197 +
198 +  simnfo = the_simnfo;
199 +
200 +  this->readSet( whichFrame );
201 + }
202 +
203 +
204 +
205 + void DumpReader :: readSet( int whichFrame ){
206 +
207    int i, j, done, which_node, which_atom; // loop counter
208  
209    const int BUFFERSIZE = 2000; // size of the read buffer
# Line 85 | Line 218 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
218    int procIndex;
219    double boxMat[9];
220    double theBoxMat3[3][3];
221 +  double time;
222  
223 <  simnfo = the_simnfo;
224 <
223 >  fpos_t *framePos;
224 >  
225   #ifndef IS_MPI
226 <  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
226 >  
227 >  framePos = frameStart[whichFrame]->getPos();
228 >
229 >  
230 >
231 >
232 >  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
233    if( eof_test == NULL ){
234      sprintf( painCave.errMsg,
235               "DumpReader error: error reading 1st line of \"%s\"\n",
236 <             c_in_name );
236 >             inName );
237      painCave.isFatal = 1;
238      simError();
239    }
# Line 107 | Line 247 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
247      sprintf( painCave.errMsg,
248               "DumpReader error. %s n_atoms, %d, "
249               "does not match the BASS file's n_atoms, %d.\n",
250 <             c_in_name, n_atoms, simnfo->n_atoms );
250 >             inName, n_atoms, simnfo->n_atoms );
251      painCave.isFatal = 1;
252      simError();
253    }
254    
255    //read the box mat from the comment line
256    
257 <  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
257 >  eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
258    if(eof_test == NULL){
259      sprintf( painCave.errMsg,
260 <             "error in reading commment in %s\n", c_in_name);
260 >             "error in reading commment in %s\n", inName);
261      painCave.isFatal = 1;
262      simError();
263    }
# Line 140 | Line 280 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
280  
281    for( i=0; i < n_atoms; i++){
282      
283 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
283 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
284      if(eof_test == NULL){
285        sprintf(painCave.errMsg,
286                "error in reading file %s\n"
287                "natoms  = %d; index = %d\n"
288                "error reading the line from the file.\n",
289 <              c_in_name, n_atoms, i );
289 >              inName, n_atoms, i );
290        painCave.isFatal = 1;
291        simError();
292      }
# Line 177 | Line 317 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
317    haveError = 0;
318    if (worldRank == 0) {
319  
320 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
320 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
321      if( eof_test == NULL ){
322        sprintf( painCave.errMsg,
323 <               "Error reading 1st line of %d \n ",c_in_name);
323 >               "Error reading 1st line of %d \n ",inName);
324        haveError = 1;
325        simError();
326      }
# Line 197 | Line 337 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
337        sprintf( painCave.errMsg,
338                 "Initialize from File error. %s n_atoms, %d, "
339                 "does not match the BASS file's n_atoms, %d.\n",
340 <               c_in_name, n_atoms, simnfo->n_atoms );
340 >               inName, n_atoms, simnfo->n_atoms );
341        haveError= 1;
342        simError();
343      }
344      
345      //read the time and boxMat from the comment line
346      
347 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
347 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
348      if(eof_test == NULL){
349        sprintf( painCave.errMsg,
350 <               "error in reading commment in %s\n", c_in_name);
350 >               "error in reading commment in %s\n", inName);
351        haveError = 1;
352        simError();
353      }
# Line 219 | Line 359 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
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 227 | Line 367 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
367      
368      for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
369        
370 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
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 <                c_in_name, n_atoms, i );
376 >                inName, n_atoms, i );
377          haveError= 1;
378          simError();
379        }
# Line 275 | Line 415 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
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 325 | 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 346 | Line 486 | char* DumpReader::parseDumpLine(char* readLine, int gl
486      sprintf( painCave.errMsg,
487               "Initialize from file error. Atom at index %d "
488               "in file %s does not exist on processor %d .\n",
489 <             globalIndex, c_in_name, mpiSim->getMyNode() );
489 >             globalIndex, inName, mpiSim->getMyNode() );
490      return strdup( painCave.errMsg );
491    }  
492   #else
# Line 365 | Line 505 | char* DumpReader::parseDumpLine(char* readLine, int gl
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, c_in_name, atoms[atomIndex]->getType() );
508 >             foo, atomIndex, inName, atoms[atomIndex]->getType() );
509      return strdup( painCave.errMsg );
510    }
511      
# Line 376 | Line 516 | char* DumpReader::parseDumpLine(char* readLine, int gl
516      sprintf( painCave.errMsg,
517               "error in reading postition x from %s\n"
518               "natoms  = %d, index = %d\n",
519 <             c_in_name, n_atoms, atomIndex );
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){
526      sprintf( painCave.errMsg,
527               "error in reading postition y from %s\n"
528               "natoms  = %d, index = %d\n",
529 <             c_in_name, n_atoms, atomIndex );
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){
536      sprintf( painCave.errMsg,
537               "error in reading postition z from %s\n"
538               "natoms  = %d, index = %d\n",
539 <             c_in_name, n_atoms, atomIndex );
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 409 | Line 549 | char* DumpReader::parseDumpLine(char* readLine, int gl
549      sprintf( painCave.errMsg,
550               "error in reading velocity x from %s\n"
551               "natoms  = %d, index = %d\n",
552 <             c_in_name, n_atoms, atomIndex );
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){
559      sprintf( painCave.errMsg,
560               "error in reading velocity y from %s\n"
561               "natoms  = %d, index = %d\n",
562 <             c_in_name, n_atoms, atomIndex );
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){
569      sprintf( painCave.errMsg,
570               "error in reading velocity z from %s\n"
571               "natoms  = %d, index = %d\n",
572 <             c_in_name, n_atoms, atomIndex );
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 444 | Line 584 | char* DumpReader::parseDumpLine(char* readLine, int gl
584        sprintf(painCave.errMsg,
585                "error in reading quaternion 0 from %s\n"
586                "natoms  = %d, index = %d\n",
587 <              c_in_name, n_atoms, atomIndex );
587 >              inName, n_atoms, atomIndex );
588        return strdup( painCave.errMsg );
589      }
590      q[0] = atof( foo );
# Line 454 | Line 594 | char* DumpReader::parseDumpLine(char* readLine, int gl
594        sprintf( painCave.errMsg,
595                 "error in reading quaternion 1 from %s\n"
596                 "natoms  = %d, index = %d\n",
597 <               c_in_name, n_atoms, atomIndex );
597 >               inName, n_atoms, atomIndex );
598        return strdup( painCave.errMsg );
599      }
600      q[1] = atof( foo );
# Line 464 | Line 604 | char* DumpReader::parseDumpLine(char* readLine, int gl
604        sprintf( painCave.errMsg,
605                 "error in reading quaternion 2 from %s\n"
606                 "natoms  = %d, index = %d\n",
607 <               c_in_name, n_atoms, atomIndex );
607 >               inName, n_atoms, atomIndex );
608        return strdup( painCave.errMsg );
609      }
610      q[2] = atof( foo );
# Line 474 | Line 614 | char* DumpReader::parseDumpLine(char* readLine, int gl
614        sprintf( painCave.errMsg,
615                 "error in reading quaternion 3 from %s\n"
616                 "natoms  = %d, index = %d\n",
617 <               c_in_name, n_atoms, atomIndex );
617 >               inName, n_atoms, atomIndex );
618        return strdup( painCave.errMsg );
619      }
620      q[3] = atof( foo );
# Line 486 | Line 626 | char* DumpReader::parseDumpLine(char* readLine, int gl
626        sprintf( painCave.errMsg,
627                 "error in reading angular momentum jx from %s\n"
628                 "natoms  = %d, index = %d\n",
629 <               c_in_name, n_atoms, atomIndex );
629 >               inName, n_atoms, atomIndex );
630        return strdup( painCave.errMsg );
631      }
632      jx = atof( foo );
# Line 496 | Line 636 | char* DumpReader::parseDumpLine(char* readLine, int gl
636        sprintf( painCave.errMsg,
637                 "error in reading angular momentum jy from %s\n"
638                 "natoms  = %d, index = %d\n",
639 <               c_in_name, n_atoms, atomIndex );
639 >               inName, n_atoms, atomIndex );
640        return strdup( painCave.errMsg );
641      }
642      jy = atof(foo );
# Line 506 | Line 646 | char* DumpReader::parseDumpLine(char* readLine, int gl
646        sprintf( painCave.errMsg,
647                 "error in reading angular momentum jz from %s\n"
648                 "natoms  = %d, index = %d\n",
649 <               c_in_name, n_atoms, atomIndex );
649 >               inName, n_atoms, atomIndex );
650        return strdup( painCave.errMsg );
651      }
652      jz = atof( foo );
# Line 533 | Line 673 | char* DumpReader::parseDumpLine(char* readLine, int gl
673    }
674      
675    // add the positions and velocities to the atom
536 –    
537 –  atoms[atomIndex]->setX( rx );
538 –  atoms[atomIndex]->setY( ry );
539 –  atoms[atomIndex]->setZ( rz );
540 –    
541 –  atoms[atomIndex]->set_vx( vx );
542 –  atoms[atomIndex]->set_vy( vy );
543 –  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
# Line 558 | Line 693 | char* DumpReader::parseCommentLine(char* readLine, dou
693    if(foo == NULL){
694      sprintf( painCave.errMsg,
695               "error in reading time from %s\n",
696 <             c_in_name );
696 >             inName );
697      return strdup( painCave.errMsg );
698    }
699    time = atof( foo );
# Line 569 | Line 704 | char* DumpReader::parseCommentLine(char* readLine, dou
704    if(foo == NULL){
705      sprintf( painCave.errMsg,
706               "error in reading Hx[0] from %s\n",
707 <             c_in_name );
707 >             inName );
708      return strdup( painCave.errMsg );
709    }
710    boxMat[0] = atof( foo );
# Line 578 | Line 713 | char* DumpReader::parseCommentLine(char* readLine, dou
713    if(foo == NULL){
714      sprintf( painCave.errMsg,
715               "error in reading Hx[1] from %s\n",
716 <             c_in_name );
716 >             inName );
717      return strdup( painCave.errMsg );
718    }
719    boxMat[1] = atof( foo );
# Line 587 | Line 722 | char* DumpReader::parseCommentLine(char* readLine, dou
722    if(foo == NULL){
723      sprintf( painCave.errMsg,
724               "error in reading Hx[2] from %s\n",
725 <             c_in_name );
725 >             inName );
726      return strdup( painCave.errMsg );
727    }
728    boxMat[2] = atof( foo );    
# Line 598 | Line 733 | char* DumpReader::parseCommentLine(char* readLine, dou
733    if(foo == NULL){
734      sprintf( painCave.errMsg,
735               "error in reading Hy[0] from %s\n",
736 <             c_in_name );
736 >             inName );
737      return strdup( painCave.errMsg );
738    }
739    boxMat[3] = atof( foo );
# Line 607 | Line 742 | char* DumpReader::parseCommentLine(char* readLine, dou
742    if(foo == NULL){
743      sprintf( painCave.errMsg,
744               "error in reading Hy[1] from %s\n",
745 <             c_in_name );
745 >             inName );
746      return strdup( painCave.errMsg );
747    }
748    boxMat[4] = atof( foo );
# Line 616 | Line 751 | char* DumpReader::parseCommentLine(char* readLine, dou
751    if(foo == NULL){
752      sprintf( painCave.errMsg,
753               "error in reading Hy[2] from %s\n",
754 <             c_in_name );
754 >             inName );
755      return strdup( painCave.errMsg );
756    }
757    boxMat[5] = atof( foo );    
# Line 627 | Line 762 | char* DumpReader::parseCommentLine(char* readLine, dou
762    if(foo == NULL){
763      sprintf( painCave.errMsg,
764               "error in reading Hz[0] from %s\n",
765 <             c_in_name );
765 >             inName );
766      return strdup( painCave.errMsg );
767    }
768    boxMat[6] = atof( foo );
# Line 636 | Line 771 | char* DumpReader::parseCommentLine(char* readLine, dou
771    if(foo == NULL){
772      sprintf( painCave.errMsg,
773               "error in reading Hz[1] from %s\n",
774 <             c_in_name );
774 >             inName );
775      return strdup( painCave.errMsg );
776    }
777    boxMat[7] = atof( foo );
# Line 645 | Line 780 | char* DumpReader::parseCommentLine(char* readLine, dou
780    if(foo == NULL){
781      sprintf( painCave.errMsg,
782               "error in reading Hz[2] from %s\n",
783 <             c_in_name );
783 >             inName );
784      return strdup( painCave.errMsg );
785    }
786    boxMat[8] = atof( foo );    
# Line 658 | Line 793 | char* DumpReader::parseCommentLine(char* readLine, dou
793  
794   // a couple of functions to let us escape the read loop
795  
796 < void initFile::nodeZeroError( void ){
796 > void dumpRead::nodeZeroError( void ){
797    int j, myStatus;
798    
799    myStatus = 0;
# Line 673 | Line 808 | void initFile::nodeZeroError( void ){
808    
809   }
810  
811 < void initFile::anonymousNodeDie( void ){
811 > void dumpRead::anonymousNodeDie( void ){
812  
813    MPI_Finalize();
814    exit (0);

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