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root/group/trunk/OOPSE/libmdtools/DumpReader.cpp
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Comparing trunk/OOPSE/libmdtools/DumpReader.cpp (file contents):
Revision 646 by mmeineke, Tue Jul 22 20:05:30 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 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 19 | Line 20
20   #include "mpiSimulation.hpp"
21   #define TAKE_THIS_TAG_CHAR 0
22   #define TAKE_THIS_TAG_INT 1
23 + #endif // is_mpi
24  
23 – namespace dumpRead{
24 –  void nodeZeroError( void );
25 –  void anonymousNodeDie( void );
25  
26 <  
28 <  class FilePos{
29 <  public:
30 <    
26 > DumpReader :: DumpReader(const char *in_name ){
27  
28 <  private:
33 <    
28 >  isScanned = false;
29  
35 –  };
36 –
37 –  vector<FilePos> frameStart;
38 – }
39 –
40 – using namespace dumpRead;
41 –
42 – #endif // is_mpi
43 –
44 – DumpReader :: DumpReader( char *in_name ){
30   #ifdef IS_MPI
31    if (worldRank == 0) {
32   #endif
33  
34 <  c_in_file = fopen(in_name, "r");
35 <  if(c_in_file == NULL){
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 <  strcpy( c_in_name, in_name);
42 >  inFileName = in_name;
43   #ifdef IS_MPI
44    }
45    strcpy( checkPointMsg, "Dump file opened for reading successfully." );
# Line 67 | Line 52 | 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( c_in_file );
58 >  error = fclose( inFile );
59    if( error ){
60      sprintf( painCave.errMsg,
61 <             "Error closing %s\n", c_in_name );
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." );
# Line 83 | Line 75 | DumpReader :: ~DumpReader( ){
75    return;
76   }
77  
78 + int DumpReader::getNframes( void ){
79  
80 +  if( !isScanned )
81 +    scanFile();
82 +  return framePos.size();
83 + }
84  
85 < void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){
85 > void DumpReader::scanFile( void ){
86  
87 <  int i, j, done, which_node, which_atom; // loop counter
87 >  int i, j;
88 >  int lineNum = 0;
89 >  char readBuffer[2000];
90 >  fpos_t *currPos;
91  
92 –  const int BUFFERSIZE = 2000; // size of the read buffer
93 –  int n_atoms; // the number of atoms
94 –  char read_buffer[BUFFERSIZE]; //the line buffer for reading
92   #ifdef IS_MPI
93 <  char send_buffer[BUFFERSIZE];
94 < #endif
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 <  char *eof_test; // ptr to see when we reach the end of the file
112 <  char *parseErr;
113 <  int procIndex;
102 <  double boxMat[9];
103 <  double theBoxMat3[3][3];
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 <  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
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 <             c_in_name );
198 >             inFileName.c_str() );
199      painCave.isFatal = 1;
200      simError();
201    }
116 –  
117 –  n_atoms = atoi( read_buffer );
202  
203 <  Atom **atoms = simnfo->atoms;
120 <  DirectionalAtom* dAtom;
203 >  nTotObjs = atoi( read_buffer );
204  
205 <  if( n_atoms != simnfo->n_atoms ){
205 >  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
206      sprintf( painCave.errMsg,
207               "DumpReader error. %s n_atoms, %d, "
208               "does not match the BASS file's n_atoms, %d.\n",
209 <             c_in_name, n_atoms, simnfo->n_atoms );
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), c_in_file);
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", c_in_name);
219 >             "error in reading commment in %s\n", inFileName.c_str());
220      painCave.isFatal = 1;
221      simError();
222    }
223  
224 <  parseErr = parseCommentLine( read_buffer, time, boxMat );
224 >  parseErr = parseCommentLine( read_buffer, simnfo);
225    if( parseErr != NULL ){
226      strcpy( painCave.errMsg, parseErr );
227      painCave.isFatal = 1;
228      simError();
229    }
230  
231 <  simnfo->setTime( time );
149 <  
150 <  for(i=0;i<3;i++)
151 <    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
152 <  
231 >  //parse dump lines
232  
233 <  simnfo->setBoxM( theBoxMat3 );
155 <  
233 >  for( i=0; i < simnfo->n_mol; i++){
234  
235 <  for( i=0; i < n_atoms; i++){
158 <    
159 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
160 <    if(eof_test == NULL){
161 <      sprintf(painCave.errMsg,
162 <              "error in reading file %s\n"
163 <              "natoms  = %d; index = %d\n"
164 <              "error reading the line from the file.\n",
165 <              c_in_name, n_atoms, i );
166 <      painCave.isFatal = 1;
167 <      simError();
168 <    }
235 >    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
236  
237 <    
238 <    parseErr = parseDumpLine( read_buffer, i );
239 <    if( parseErr != NULL ){
240 <      strcpy( painCave.errMsg, parseErr );
241 <      painCave.isFatal = 1;
242 <      simError();
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  
179 –
259    // MPI Section of code..........
260   #else //IS_MPI
261  
# Line 185 | Line 264 | void DumpReader :: getFrame( SimInfo* the_simnfo, int
264  
265    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
266    int haveError;
267 <  
267 >
268    MPI_Status istatus;
269 <  int *AtomToProcMap = mpiSim->getAtomToProcMap();
269 >  int *MolToProcMap = mpiSim->getMolToProcMap();
270 >  int localIndex;
271 >  int nCurObj;
272 >  int nitems;
273  
274 <  
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), c_in_file);
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 %d \n ",c_in_name);
282 >               "Error reading 1st line of %s \n ",inFileName.c_str());
283        haveError = 1;
284        simError();
285      }
286 <    
287 <    n_atoms = atoi( read_buffer );
288 <    
289 <    Atom **atoms = simnfo->atoms;
207 <    DirectionalAtom* dAtom;
208 <
209 <    // Check to see that the number of atoms in the intial configuration file is the
286 >
287 >    nitems = atoi( read_buffer );
288 >
289 >    // Check to see that the number of integrable objects  in the intial configuration file is the
290      // same as declared in simBass.
291 <    
292 <    if( n_atoms != mpiSim->getTotAtoms() ){
291 >
292 >    if( nTotObjs != nitems){
293        sprintf( painCave.errMsg,
294 <               "Initialize from File error. %s n_atoms, %d, "
294 >               "DumpReadererror. %s n_atoms, %d, "
295                 "does not match the BASS file's n_atoms, %d.\n",
296 <               c_in_name, n_atoms, simnfo->n_atoms );
296 >               inFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects());
297        haveError= 1;
298        simError();
299      }
300 <    
301 <    //read the time and boxMat from the comment line
302 <    
303 <    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
300 >
301 >    //read the boxMat from the comment line
302 >
303 >    eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
304      if(eof_test == NULL){
305        sprintf( painCave.errMsg,
306 <               "error in reading commment in %s\n", c_in_name);
306 >               "error in reading commment in %s\n", inFileName.c_str());
307        haveError = 1;
308        simError();
309      }
310 <    
311 <    parseErr = parseCommentLine( read_buffer, time, boxMat );
310 >
311 >    //Every single processor will parse the comment line by itself
312 >    //By using this way, we might lose some efficiency, but if we want to add
313 >    //more parameters into comment line, we only need to modify function
314 >    //parseCommentLine
315 >
316 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
317 >
318 >    parseErr = parseCommentLine( read_buffer, simnfo);
319 >
320      if( parseErr != NULL ){
321        strcpy( painCave.errMsg, parseErr );
322        haveError = 1;
323        simError();
324      }
325  
326 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
327 <    
328 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
329 <    
330 <    if(haveError) nodeZeroError();
331 <    
332 <    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
333 <      
334 <      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
335 <      if(eof_test == NULL){
336 <        sprintf(painCave.errMsg,
249 <                "error in reading file %s\n"
250 <                "natoms  = %d; index = %d\n"
251 <                "error reading the line from the file.\n",
252 <                c_in_name, n_atoms, i );
253 <        haveError= 1;
254 <        simError();
326 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
327 >      which_node = MolToProcMap[i];
328 >      if(which_node == 0){
329 >       //molecules belong to master node
330 >
331 >      localIndex = mpiSim->getGlobalToLocalMol(i);
332 >
333 >      if(localIndex == -1) {
334 >        strcpy(painCave.errMsg, "Molecule not found on node 0!");
335 >        haveError = 1;
336 >        simError();
337        }
256 –    
257 –      if(haveError) nodeZeroError();
338  
339 <      // Get the Node number which wants this atom:
340 <      which_node = AtomToProcMap[i];    
341 <      if (which_node == 0) {
342 <        parseErr = parseDumpLine( read_buffer, i );
343 <        if( parseErr != NULL ){
344 <          strcpy( painCave.errMsg, parseErr );
345 <          haveError = 1;
346 <          simError();
347 <        }    
348 <        if(haveError) nodeZeroError();
349 <      }
339 >       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
340 >       for(j=0; j < integrableObjects.size(); j++){
341 >        
342 >          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
343 >          if(eof_test == NULL){
344 >                sprintf(painCave.errMsg,
345 >                    "error in reading file %s\n"
346 >                    "natoms  = %d; index = %d\n"
347 >                    "error reading the line from the file.\n",
348 >                    inFileName.c_str(), nTotObjs, i );
349 >                haveError= 1;
350 >                simError();
351 >          }
352 >          
353 >          if(haveError) nodeZeroError();
354 >
355 >          parseDumpLine(read_buffer, integrableObjects[j]);
356 >          
357 >       }
358 >
359 >
360 >      }
361 >      else{
362 >      //molecule belongs to slave nodes
363 >
364 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
365 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
366        
367 <      else {
368 <      
369 <        myStatus = 1;
370 <        MPI_Send(&myStatus, 1, MPI_INT, which_node,
371 <                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
372 <        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
373 <                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
374 <        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
375 <                 MPI_COMM_WORLD);
376 <        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
377 <                 MPI_COMM_WORLD, &istatus);
378 <        
379 <        if(!myStatus) nodeZeroError();
367 >       for(j=0; j < nCurObj; j++){
368 >        
369 >          eof_test = fgets(read_buffer, sizeof(read_buffer), inFile);
370 >          if(eof_test == NULL){
371 >                sprintf(painCave.errMsg,
372 >                    "error in reading file %s\n"
373 >                    "natoms  = %d; index = %d\n"
374 >                    "error reading the line from the file.\n",
375 >                    inFileName.c_str(), nTotObjs, i );
376 >                haveError= 1;
377 >                simError();
378 >          }
379 >          
380 >          if(haveError) nodeZeroError();
381 >
382 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
383 >                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
384 >          
385 >       }
386 >
387        }
388 +      
389      }
286 –    myStatus = -1;
287 –    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
288 –      MPI_Send( &myStatus, 1, MPI_INT, j,
289 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
290 –    }
390      
391 <  } else {
392 <    
393 <    MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
394 <    MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
391 >  }
392 >  else{
393 >  //actions taken at slave nodes
394 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
395  
396 <    done = 0;
298 <    while (!done) {
396 >    parseErr = parseCommentLine( read_buffer, simnfo);
397  
398 <      MPI_Recv(&myStatus, 1, MPI_INT, 0,
399 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
398 >    if( parseErr != NULL ){
399 >      strcpy( painCave.errMsg, parseErr );
400 >      haveError = 1;
401 >      simError();
402 >    }
403 >  
404 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
405 >      which_node = MolToProcMap[i];
406        
407 <      if(!myStatus) anonymousNodeDie();
407 >      if(which_node == worldRank){
408 >      //molecule with global index i belongs to this processor
409        
410 <      if(myStatus < 0) break;
410 >        localIndex = mpiSim->getGlobalToLocalMol(i);
411  
412 <      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
413 <               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
414 <      MPI_Recv(&which_atom, 1, MPI_INT, 0,
415 <               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
416 <      
417 <      myStatus = 1;
418 <      parseErr = parseDumpLine( read_buffer, which_atom );
419 <      if( parseErr != NULL ){
420 <        strcpy( painCave.errMsg, parseErr );
421 <        myStatus = 0;;
422 <        simError();
412 >        if(localIndex == -1) {
413 >          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
414 >          haveError = 1;
415 >          simError();
416 >        }
417 >
418 >        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        
419 >
420 >        nCurObj = integrableObjects.size();
421 >        
422 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
423 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
424 >
425 >        for(j = 0; j < integrableObjects.size(); j++){
426 >
427 >          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
428 >                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
429 >
430 >          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
431 >
432 >          if( parseErr != NULL ){
433 >                strcpy( painCave.errMsg, parseErr );
434 >                simError();
435 >          }
436 >
437 >        }
438 >          
439        }
440        
320 –      MPI_Send( &myStatus, 1, MPI_INT, 0,
321 –                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
322 –      
441      }
442 +
443    }
325 –    
326 – // last  thing last, enable  fatalities.
327 –  painCave.isEventLoop = 0;
444  
329 –  simnfo->setTime( time );
330 –
331 –  for(i=0;i<3;i++)
332 –    for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
333 –
334 –  simnfo->setBoxM( theBoxMat3 );
335 –
336 –  
445   #endif
446   }
447  
448 < char* DumpReader::parseDumpLine(char* readLine, int globalIndex){
448 > char* DumpReader::parseDumpLine(char* readLine, StuntDouble* sd){
449  
450 <  char *foo; // the pointer to the current string token
451 <  
452 <  double rx, ry, rz; // position place holders
453 <  double vx, vy, vz; // velocity placeholders
450 >  char *foo; // the pointer to the current string token
451 >
452 >  double pos[3]; // position place holders
453 >  double vel[3]; // velocity placeholders
454    double q[4]; // the quaternions
455 <  double jx, jy, jz; // angular velocity placeholders;
455 >  double ji[3]; // angular velocity placeholders;
456    double qSqr, qLength; // needed to normalize the quaternion vector.
349 –  
350 –  Atom **atoms = simnfo->atoms;
351 –  DirectionalAtom* dAtom;
352 –  
353 –  int j, n_atoms, atomIndex;
457  
355 – #ifdef IS_MPI
356 –  n_atoms = mpiSim->getTotAtoms();
357 –  atomIndex=-1;        
358 –  for (j=0; j < mpiSim->getMyNlocal(); j++) {
359 –    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
360 –  }
361 –  if (atomIndex == -1) {
362 –    sprintf( painCave.errMsg,
363 –             "Initialize from file error. Atom at index %d "
364 –             "in file %s does not exist on processor %d .\n",
365 –             globalIndex, c_in_name, mpiSim->getMyNode() );
366 –    return strdup( painCave.errMsg );
367 –  }  
368 – #else
369 –  n_atoms = simnfo->n_atoms;
370 –  atomIndex = globalIndex;
371 – #endif // is_mpi
458  
459    // set the string tokenizer
460 <  
460 >
461    foo = strtok(readLine, " ,;\t");
462 <  
462 >
463    // check the atom name to the current atom
464 <  
465 <  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
464 >
465 >  if( strcmp( foo, sd->getType() ) ){
466      sprintf( painCave.errMsg,
467 <             "Initialize from file error. Atom %s at index %d "
382 <             "in file %s does not"
467 >             "DumpReader error.  Does not"
468               " match the BASS atom %s.\n",
469 <             foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
469 >             sd->getType() );
470      return strdup( painCave.errMsg );
471    }
472 <    
472 >
473    // get the positions
474  
475    foo = strtok(NULL, " ,;\t");
476    if(foo == NULL){
477      sprintf( painCave.errMsg,
478 <             "error in reading postition x from %s\n"
479 <             "natoms  = %d, index = %d\n",
395 <             c_in_name, n_atoms, atomIndex );
478 >             "error in reading postition x from %s\n",
479 >             inFileName.c_str());
480      return strdup( painCave.errMsg );
481    }
482 <  rx = atof( foo );
483 <  
482 >  pos[0] = atof( foo );
483 >
484    foo = strtok(NULL, " ,;\t");
485    if(foo == NULL){
486      sprintf( painCave.errMsg,
487 <             "error in reading postition y from %s\n"
488 <             "natoms  = %d, index = %d\n",
405 <             c_in_name, n_atoms, atomIndex );
487 >             "error in reading postition y from %s\n",
488 >             inFileName.c_str());
489      return strdup( painCave.errMsg );
490    }
491 <  ry = atof( foo );
492 <    
491 >  pos[1] = atof( foo );
492 >
493    foo = strtok(NULL, " ,;\t");
494    if(foo == NULL){
495      sprintf( painCave.errMsg,
496 <             "error in reading postition z from %s\n"
497 <             "natoms  = %d, index = %d\n",
415 <             c_in_name, n_atoms, atomIndex );
496 >             "error in reading postition z from %s\n",
497 >             inFileName.c_str());
498      return strdup( painCave.errMsg );
499    }
500 <  rz = atof( foo );    
500 >  pos[2] = atof( foo );
501  
502  
503    // get the velocities
# Line 423 | Line 505 | char* DumpReader::parseDumpLine(char* readLine, int gl
505    foo = strtok(NULL, " ,;\t");
506    if(foo == NULL){
507      sprintf( painCave.errMsg,
508 <             "error in reading velocity x from %s\n"
509 <             "natoms  = %d, index = %d\n",
428 <             c_in_name, n_atoms, atomIndex );
508 >             "error in reading velocity x from %s\n",
509 >             inFileName.c_str() );
510      return strdup( painCave.errMsg );
511    }
512 <  vx = atof( foo );
513 <    
512 >  vel[0] = atof( foo );
513 >
514    foo = strtok(NULL, " ,;\t");
515    if(foo == NULL){
516      sprintf( painCave.errMsg,
517 <             "error in reading velocity y from %s\n"
518 <             "natoms  = %d, index = %d\n",
438 <             c_in_name, n_atoms, atomIndex );
517 >             "error in reading velocity x from %s\n",
518 >             inFileName.c_str() );
519      return strdup( painCave.errMsg );
520    }
521 <  vy = atof( foo );
522 <    
521 >  vel[1] = atof( foo );
522 >
523    foo = strtok(NULL, " ,;\t");
524    if(foo == NULL){
525      sprintf( painCave.errMsg,
526 <             "error in reading velocity z from %s\n"
527 <             "natoms  = %d, index = %d\n",
448 <             c_in_name, n_atoms, atomIndex );
526 >             "error in reading velocity x from %s\n",
527 >             inFileName.c_str() );
528      return strdup( painCave.errMsg );
529    }
530 <  vz = atof( foo );
531 <    
532 <    
530 >  vel[2] = atof( foo );
531 >
532 >
533 >  // add the positions and velocities to the atom
534 >
535 >  sd->setPos( pos );
536 >  sd->setVel( vel );
537 >
538 >  if (!sd->isDirectional())
539 >    return NULL;
540 >
541    // get the quaternions
542 <    
543 <  if( atoms[atomIndex]->isDirectional() ){
544 <      
542 >
543 >  if( sd->isDirectional() ){
544 >
545      foo = strtok(NULL, " ,;\t");
546      if(foo == NULL){
547 <      sprintf(painCave.errMsg,
548 <              "error in reading quaternion 0 from %s\n"
549 <              "natoms  = %d, index = %d\n",
463 <              c_in_name, n_atoms, atomIndex );
547 >      sprintf( painCave.errMsg,
548 >                     "error in reading velocity x from %s\n",
549 >                      inFileName.c_str() );
550        return strdup( painCave.errMsg );
551      }
552      q[0] = atof( foo );
553 <      
553 >
554      foo = strtok(NULL, " ,;\t");
555      if(foo == NULL){
556        sprintf( painCave.errMsg,
557 <               "error in reading quaternion 1 from %s\n"
558 <               "natoms  = %d, index = %d\n",
473 <               c_in_name, n_atoms, atomIndex );
557 >                     "error in reading velocity x from %s\n",
558 >                      inFileName.c_str() );
559        return strdup( painCave.errMsg );
560      }
561      q[1] = atof( foo );
562 <      
562 >
563      foo = strtok(NULL, " ,;\t");
564      if(foo == NULL){
565        sprintf( painCave.errMsg,
566 <               "error in reading quaternion 2 from %s\n"
567 <               "natoms  = %d, index = %d\n",
483 <               c_in_name, n_atoms, atomIndex );
566 >                     "error in reading velocity x from %s\n",
567 >                      inFileName.c_str() );
568        return strdup( painCave.errMsg );
569      }
570      q[2] = atof( foo );
571 <      
571 >
572      foo = strtok(NULL, " ,;\t");
573      if(foo == NULL){
574        sprintf( painCave.errMsg,
575 <               "error in reading quaternion 3 from %s\n"
576 <               "natoms  = %d, index = %d\n",
493 <               c_in_name, n_atoms, atomIndex );
575 >                     "error in reading velocity x from %s\n",
576 >                      inFileName.c_str() );
577        return strdup( painCave.errMsg );
578      }
579      q[3] = atof( foo );
580 <      
580 >
581      // get the angular velocities
582 <      
582 >
583      foo = strtok(NULL, " ,;\t");
584      if(foo == NULL){
585        sprintf( painCave.errMsg,
586 <               "error in reading angular momentum jx from %s\n"
587 <               "natoms  = %d, index = %d\n",
505 <               c_in_name, n_atoms, atomIndex );
586 >                     "error in reading velocity x from %s\n",
587 >                      inFileName.c_str() );
588        return strdup( painCave.errMsg );
589      }
590 <    jx = atof( foo );
591 <      
590 >    ji[0] = atof( foo );
591 >
592      foo = strtok(NULL, " ,;\t");
593      if(foo == NULL){
594        sprintf( painCave.errMsg,
595 <               "error in reading angular momentum jy from %s\n"
596 <               "natoms  = %d, index = %d\n",
515 <               c_in_name, n_atoms, atomIndex );
595 >                     "error in reading velocity x from %s\n",
596 >                      inFileName.c_str() );
597        return strdup( painCave.errMsg );
598      }
599 <    jy = atof(foo );
600 <      
599 >    ji[1] = atof(foo );
600 >
601      foo = strtok(NULL, " ,;\t");
602      if(foo == NULL){
603        sprintf( painCave.errMsg,
604 <               "error in reading angular momentum jz from %s\n"
605 <               "natoms  = %d, index = %d\n",
525 <               c_in_name, n_atoms, atomIndex );
604 >                     "error in reading velocity x from %s\n",
605 >                      inFileName.c_str() );
606        return strdup( painCave.errMsg );
607      }
608 <    jz = atof( foo );
529 <      
530 <    dAtom = ( DirectionalAtom* )atoms[atomIndex];
608 >    ji[2] = atof( foo );
609  
610 +
611      // check that the quaternion vector is normalized
612  
613      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
614 <      
614 >
615 >    if (fabs(qSqr) < 1e-6) {
616 >      sprintf(painCave.errMsg,
617 >          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
618 >       return strdup(painCave.errMsg);
619 >    }
620 >
621      qLength = sqrt( qSqr );
622      q[0] = q[0] / qLength;
623      q[1] = q[1] / qLength;
624      q[2] = q[2] / qLength;
625      q[3] = q[3] / qLength;
541 –      
542 –    dAtom->setQ( q );
543 –      
544 –    // add the angular velocities
626  
627 <    dAtom->setJx( jx );
628 <    dAtom->setJy( jy );
629 <    dAtom->setJz( jz );
627 >    // add quaternion and angular velocities
628 >
629 >    sd->setQ( q );
630 >    sd->setJ( ji );
631    }
632 <    
551 <  // add the positions and velocities to the atom
552 <    
553 <  atoms[atomIndex]->setX( rx );
554 <  atoms[atomIndex]->setY( ry );
555 <  atoms[atomIndex]->setZ( rz );
556 <    
557 <  atoms[atomIndex]->set_vx( vx );
558 <  atoms[atomIndex]->set_vy( vy );
559 <  atoms[atomIndex]->set_vz( vz );
632 >
633  
634 +
635    return NULL;
636   }
637  
638  
639 < char* DumpReader::parseCommentLine(char* readLine, double time,
566 <                                   double boxMat[9]){
639 > char* DumpReader::parseCommentLine(char* readLine, SimInfo* entry_plug){
640  
641 <  char *foo; // the pointer to the current string token
642 <  int j;
641 >  double currTime;
642 >  double boxMat[9];
643 >  double theBoxMat3[3][3];
644 >  double chi;
645 >  double integralOfChidt;
646 >  double eta[9];
647  
648 +  char *foo; // the pointer to the current string token
649 +
650    // set the string tokenizer
651 <  
651 >
652    foo = strtok(readLine, " ,;\t");
653 +  // set the timeToken.
654 +
655    if(foo == NULL){
656      sprintf( painCave.errMsg,
657 <             "error in reading time from %s\n",
658 <             c_in_name );
657 >             "error in reading Time from %s\n",
658 >             inFileName.c_str() );
659      return strdup( painCave.errMsg );
660    }
580 –  time = atof( foo );
661  
662 <  // get the Hx vector
662 >  currTime = atof( foo );
663 >  entry_plug->setTime( currTime );
664  
665 <  foo = strtok(NULL, " ,;\t");
666 <  if(foo == NULL){
667 <    sprintf( painCave.errMsg,
668 <             "error in reading Hx[0] from %s\n",
669 <             c_in_name );
670 <    return strdup( painCave.errMsg );
665 >  //get H-Matrix
666 >
667 >  for(int i = 0 ; i < 9; i++){
668 >    foo = strtok(NULL, " ,;\t");
669 >    if(foo == NULL){
670 >      sprintf( painCave.errMsg,
671 >               "error in reading H[%d] from %s\n", i, inFileName.c_str() );
672 >      return strdup( painCave.errMsg );
673 >    }
674 >    boxMat[i] = atof( foo );
675    }
591 –  boxMat[0] = atof( foo );
592 –  
593 –  foo = strtok(NULL, " ,;\t");
594 –  if(foo == NULL){
595 –    sprintf( painCave.errMsg,
596 –             "error in reading Hx[1] from %s\n",
597 –             c_in_name );
598 –    return strdup( painCave.errMsg );
599 –  }
600 –  boxMat[1] = atof( foo );
601 –    
602 –  foo = strtok(NULL, " ,;\t");
603 –  if(foo == NULL){
604 –    sprintf( painCave.errMsg,
605 –             "error in reading Hx[2] from %s\n",
606 –             c_in_name );
607 –    return strdup( painCave.errMsg );
608 –  }
609 –  boxMat[2] = atof( foo );    
676  
677 <  // get the Hy vector
677 >  for(int i=0;i<3;i++)
678 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
679  
680 <  foo = strtok(NULL, " ,;\t");
681 <  if(foo == NULL){
615 <    sprintf( painCave.errMsg,
616 <             "error in reading Hy[0] from %s\n",
617 <             c_in_name );
618 <    return strdup( painCave.errMsg );
619 <  }
620 <  boxMat[3] = atof( foo );
621 <  
622 <  foo = strtok(NULL, " ,;\t");
623 <  if(foo == NULL){
624 <    sprintf( painCave.errMsg,
625 <             "error in reading Hy[1] from %s\n",
626 <             c_in_name );
627 <    return strdup( painCave.errMsg );
628 <  }
629 <  boxMat[4] = atof( foo );
630 <    
631 <  foo = strtok(NULL, " ,;\t");
632 <  if(foo == NULL){
633 <    sprintf( painCave.errMsg,
634 <             "error in reading Hy[2] from %s\n",
635 <             c_in_name );
636 <    return strdup( painCave.errMsg );
637 <  }
638 <  boxMat[5] = atof( foo );    
680 >  //set H-Matrix
681 >  entry_plug->setBoxM( theBoxMat3 );
682  
683 <  // get the Hz vector
683 >  //get chi and integralOfChidt, they should appear by pair
684  
685 <  foo = strtok(NULL, " ,;\t");
686 <  if(foo == NULL){
687 <    sprintf( painCave.errMsg,
688 <             "error in reading Hz[0] from %s\n",
689 <             c_in_name );
690 <    return strdup( painCave.errMsg );
685 >  if( entry_plug->useInitXSstate ){
686 >    foo = strtok(NULL, " ,;\t\n");
687 >    if(foo != NULL){
688 >      chi = atof(foo);
689 >      
690 >      foo = strtok(NULL, " ,;\t\n");
691 >      if(foo == NULL){
692 >        sprintf( painCave.errMsg,
693 >                 "chi and integralOfChidt should appear by pair in %s\n", inFileName.c_str() );
694 >        return strdup( painCave.errMsg );
695 >      }
696 >      integralOfChidt = atof( foo );
697 >      
698 >      //push chi and integralOfChidt into SimInfo::properties which can be
699 >      //retrieved by integrator later
700 >      DoubleData* chiValue = new DoubleData();
701 >      chiValue->setID(CHIVALUE_ID);
702 >      chiValue->setData(chi);
703 >      entry_plug->addProperty(chiValue);
704 >      
705 >      DoubleData* integralOfChidtValue = new DoubleData();
706 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
707 >      integralOfChidtValue->setData(integralOfChidt);
708 >      entry_plug->addProperty(integralOfChidtValue);
709 >      
710 >    }
711 >    else
712 >      return NULL;
713 >    
714 >    //get eta
715 >    foo = strtok(NULL, " ,;\t\n");
716 >    if(foo != NULL ){
717 >  
718 >      for(int i = 0 ; i < 9; i++){
719 >        
720 >        if(foo == NULL){
721 >          sprintf( painCave.errMsg,
722 >                   "error in reading eta[%d] from %s\n", i, inFileName.c_str() );
723 >          return strdup( painCave.errMsg );
724 >        }
725 >        eta[i] = atof( foo );
726 >        foo = strtok(NULL, " ,;\t\n");
727 >      }
728 >    }
729 >    else
730 >      return NULL;
731 >    
732 >    //push eta into SimInfo::properties which can be
733 >    //retrieved by integrator later
734 >    //entry_plug->setBoxM( theBoxMat3 );
735 >    DoubleArrayData* etaValue = new DoubleArrayData();
736 >    etaValue->setID(ETAVALUE_ID);
737 >    etaValue->setData(eta, 9);
738 >    entry_plug->addProperty(etaValue);
739    }
649 –  boxMat[6] = atof( foo );
650 –  
651 –  foo = strtok(NULL, " ,;\t");
652 –  if(foo == NULL){
653 –    sprintf( painCave.errMsg,
654 –             "error in reading Hz[1] from %s\n",
655 –             c_in_name );
656 –    return strdup( painCave.errMsg );
657 –  }
658 –  boxMat[7] = atof( foo );
659 –    
660 –  foo = strtok(NULL, " ,;\t");
661 –  if(foo == NULL){
662 –    sprintf( painCave.errMsg,
663 –             "error in reading Hz[2] from %s\n",
664 –             c_in_name );
665 –    return strdup( painCave.errMsg );
666 –  }
667 –  boxMat[8] = atof( foo );    
740  
741    return NULL;
742   }
743  
672 –
744   #ifdef IS_MPI
745 <
675 < // a couple of functions to let us escape the read loop
676 <
677 < void initFile::nodeZeroError( void ){
745 > void DumpReader::nodeZeroError( void ){
746    int j, myStatus;
747 <  
747 >
748    myStatus = 0;
749 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
750 <    MPI_Send( &myStatus, 1, MPI_INT, j,
749 >  for (j = 0; j < mpiSim->getNProcessors(); j++) {
750 >    MPI_Send( &myStatus, 1, MPI_INT, j,
751                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
752 <  }  
685 <  
752 >  }
753  
754 +
755    MPI_Finalize();
756    exit (0);
757 <  
757 >
758   }
759  
760 < void initFile::anonymousNodeDie( void ){
760 > void DumpReader::anonymousNodeDie( void ){
761  
762    MPI_Finalize();
763    exit (0);
764   }
765 <
698 < #endif //is_mpi
765 > #endif

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