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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/InitializeFromFile.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents), Revision 906 by mmeineke, Thu Jan 8 15:44:47 2004 UTC

# Line 1 | Line 1
1 + #define _FILE_OFFSET_BITS 64
2   #include <iostream>
3 < #include <cmath>
3 > #include <math.h>
4  
5   #include <stdio.h>
6   #include <stdlib.h>
# Line 10 | Line 11
11  
12   #include "ReadWrite.hpp"
13   #include "simError.h"
14 + #include "GenericData.hpp"
15  
16   #ifdef IS_MPI
17 + #include <mpi.h>
18   #include "mpiSimulation.hpp"
19 + #define TAKE_THIS_TAG_CHAR 0
20 + #define TAKE_THIS_TAG_INT 1
21  
22 < #define TAKE_THIS_TAG 0
22 > namespace initFile{
23 >  void nodeZeroError( void );
24 >  void anonymousNodeDie( void );
25 > }
26 >
27 > using namespace initFile;
28 >
29   #endif // is_mpi
30  
31 < InitializeFromFile :: InitializeFromFile( char *in_name ){
31 > InitializeFromFile::InitializeFromFile( char *in_name ){
32 >
33   #ifdef IS_MPI
34    if (worldRank == 0) {
35   #endif
# Line 29 | Line 41 | InitializeFromFile :: InitializeFromFile( char *in_nam
41      painCave.isFatal = 1;
42      simError();
43    }
44 <  
44 >
45    strcpy( c_in_name, in_name);
46   #ifdef IS_MPI
47    }
48 < strcpy( checkPointMsg, "Infile opened for reading successfully." );
48 >  else{
49 >          sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50 >  }
51 >  
52 >  strcpy( checkPointMsg, "Infile opened for reading successfully." );
53    MPIcheckPoint();
54   #endif
55 <  return;  
55 >  return;
56   }
57  
58 < InitializeFromFile :: ~InitializeFromFile( ){
58 > InitializeFromFile::~InitializeFromFile( ){
59   #ifdef IS_MPI
60    if (worldRank == 0) {
61   #endif
# Line 60 | Line 76 | InitializeFromFile :: ~InitializeFromFile( ){
76   }
77  
78  
79 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
79 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80  
81 <  int i; // loop counter
81 >  int i, j;
82  
83 + #ifdef IS_MPI
84 +  int done, which_node, which_atom; // loop counter
85 + #endif //is_mpi
86 +
87    const int BUFFERSIZE = 2000; // size of the read buffer
88    int n_atoms; // the number of atoms
89 <  char read_buffer[BUFFERSIZE]; //the line buffer for reading
70 < #ifdef IS_MPI
71 <  char send_buffer[BUFFERSIZE];
72 < #endif
89 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
90  
91 <  char *eof_test; // ptr to see when we reach the end of the file
91 >  char *eof_test; // ptr to see when we reach the end of the file
92    char *parseErr;
76 –  int procIndex;
93  
94 <  entry_plug = the_entry_plug;
94 >  simnfo = the_simnfo;
95  
96  
97   #ifndef IS_MPI
# Line 90 | Line 106 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
106  
107    n_atoms = atoi( read_buffer );
108  
109 <  Atom **atoms = entry_plug->atoms;
94 <  DirectionalAtom* dAtom;
95 <
96 <  if( n_atoms != entry_plug->n_atoms ){
109 >  if( n_atoms != simnfo->n_atoms ){
110      sprintf( painCave.errMsg,
111               "Initialize from File error. %s n_atoms, %d, "
112               "does not match the BASS file's n_atoms, %d.\n",
113 <             c_in_name, n_atoms, entry_plug->n_atoms );
113 >             c_in_name, n_atoms, simnfo->n_atoms );
114      painCave.isFatal = 1;
115      simError();
116    }
117 <  
118 <  //read and toss the comment line
119 <  
117 >
118 >  //read the box mat from the comment line
119 >
120    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
121    if(eof_test == NULL){
122      sprintf( painCave.errMsg,
# Line 112 | Line 125 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
125      simError();
126    }
127  
128 +
129 +
130 +  parseErr = parseCommentLine( read_buffer, simnfo);
131 +  if( parseErr != NULL ){
132 +    strcpy( painCave.errMsg, parseErr );
133 +    painCave.isFatal = 1;
134 +    simError();
135 +  }
136 +
137 +  //parse dump lines
138 +
139    for( i=0; i < n_atoms; i++){
140 <    
140 >
141      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
142      if(eof_test == NULL){
143        sprintf(painCave.errMsg,
# Line 125 | Line 149 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
149        simError();
150      }
151  
152 <    
152 >
153      parseErr = parseDumpLine( read_buffer, i );
154      if( parseErr != NULL ){
155        strcpy( painCave.errMsg, parseErr );
156        painCave.isFatal = 1;
157        simError();
158 <    }    
158 >    }
159    }
160  
161  
162    // MPI Section of code..........
163   #else //IS_MPI
164  
165 <  int masterIndex;
166 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
165 >  // first thing first, suspend fatalities.
166 >  painCave.isEventLoop = 1;
167  
168 <  MPI_Status istatus[MPI_STATUS_SIZE];
168 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
169 >  int haveError;
170  
171 +  MPI_Status istatus;
172 +  int *AtomToProcMap = mpiSim->getAtomToProcMap();
173 +
174 +
175 +  haveError = 0;
176    if (worldRank == 0) {
177 +
178      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
179      if( eof_test == NULL ){
180        sprintf( painCave.errMsg,
181 <               "Error reading 1st line of %d \n ",c_in_name);
182 <      painCave.isFatal = 1;
181 >               "Error reading 1st line of %s \n ",c_in_name);
182 >      haveError = 1;
183        simError();
184      }
185 <    
185 >
186      n_atoms = atoi( read_buffer );
187 <    
160 <    Atom **atoms = entry_plug->atoms;
161 <    DirectionalAtom* dAtom;
162 <
187 >
188      // Check to see that the number of atoms in the intial configuration file is the
189      // same as declared in simBass.
190 <    
190 >
191      if( n_atoms != mpiSim->getTotAtoms() ){
192        sprintf( painCave.errMsg,
193                 "Initialize from File error. %s n_atoms, %d, "
194                 "does not match the BASS file's n_atoms, %d.\n",
195 <               c_in_name, n_atoms, entry_plug->n_atoms );
196 <      painCave.isFatal = 1;
195 >               c_in_name, n_atoms, simnfo->n_atoms );
196 >      haveError= 1;
197        simError();
198      }
199 <    
200 <    //read and toss the comment line
201 <    
199 >
200 >    //read the boxMat from the comment line
201 >
202      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
203      if(eof_test == NULL){
204        sprintf( painCave.errMsg,
205                 "error in reading commment in %s\n", c_in_name);
206 <      painCave.isFatal = 1;
206 >      haveError = 1;
207        simError();
208      }
209 <  
210 <    // Read Proc 0 share of the xyz file...
211 <    masterIndex = 0;
212 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
213 <    
209 >
210 >    //Every single processor will parse the comment line by itself
211 >    //By using this way, we might lose some efficiency, but if we want to add
212 >    //more parameters into comment line, we only need to modify function
213 >    //parseCommentLine
214 >
215 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
216 >
217 >    parseErr = parseCommentLine( read_buffer, simnfo);
218 >
219 >    if( parseErr != NULL ){
220 >      strcpy( painCave.errMsg, parseErr );
221 >      haveError = 1;
222 >      simError();
223 >    }
224 >
225 >    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
226 >
227        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
228        if(eof_test == NULL){
229          sprintf(painCave.errMsg,
# Line 193 | Line 231 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
231                  "natoms  = %d; index = %d\n"
232                  "error reading the line from the file.\n",
233                  c_in_name, n_atoms, i );
234 <        painCave.isFatal = 1;
234 >        haveError= 1;
235          simError();
236        }
237 <    
238 <      parseErr = parseDumpLine( read_buffer, i );
201 <      if( parseErr != NULL ){
202 <        strcpy( painCave.errMsg, parseErr );
203 <        painCave.isFatal = 1;
204 <        simError();
205 <      }    
206 <      masterIndex++;
207 <    }
208 <  }
237 >
238 >      if(haveError) nodeZeroError();
239  
240 <  sprintf(checkPointMsg,
241 <          "Node 0 has successfully read positions from input file.");
242 <  MPIcheckPoint();
240 >      // Get the Node number which wants this atom:
241 >      which_node = AtomToProcMap[i];
242 >      if (which_node == 0) {
243 >        parseErr = parseDumpLine( read_buffer, i );
244 >        if( parseErr != NULL ){
245 >          strcpy( painCave.errMsg, parseErr );
246 >          haveError = 1;
247 >          simError();
248 >        }
249 >        if(haveError) nodeZeroError();
250 >      }
251  
252 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215 <         procIndex++){
216 <    if (worldRank == 0) {
252 >      else {
253  
254 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
255 <               istatus);
254 >        myStatus = 1;
255 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
256 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
257 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
258 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
259 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
260 >                 MPI_COMM_WORLD);
261 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
262 >                 MPI_COMM_WORLD, &istatus);
263  
264 <      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
222 <               istatus);
223 <      // Make sure where node 0 is reading from, matches where the receiving node
224 <      // expects it to be.
225 <
226 <      if (masterIndex != nodeAtomsStart){
227 <        sendError = 1;
228 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
229 <        sprintf(painCave.errMsg,
230 <                "Initialize from file error: atoms start index (%d) for "
231 <                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
232 <        painCave.isFatal = 1;
233 <        simError();
264 >        if(!myStatus) nodeZeroError();
265        }
266 <      sendError = 0;
267 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
268 <      
269 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
270 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
271 <        if(eof_test == NULL){
241 <          
242 <          sprintf(read_buffer,"ERROR");
243 <          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
244 <          
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 <                  c_in_name, n_atoms, i );
250 <          painCave.isFatal = 1;
251 <          simError();
252 <        }
253 <        
254 <        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
255 <        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
256 <                          istatus);
257 <        if (sendError) MPIcheckPoint();
266 >    }
267 >    myStatus = -1;
268 >    for (j = 1; j < mpiSim->getNumberProcessors(); j++) {
269 >      MPI_Send( &myStatus, 1, MPI_INT, j,
270 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
271 >    }
272  
273 <        masterIndex++;
274 <      }
273 >  } else {
274 >
275 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
276 >
277 >    parseErr = parseCommentLine( read_buffer, simnfo);
278 >
279 >    if( parseErr != NULL ){
280 >      strcpy( painCave.errMsg, parseErr );
281 >      haveError = 1;
282 >      simError();
283      }
284  
285  
286 <    else if(worldRank == procIndex){
287 <      nodeAtomsStart = mpiSim->getMyAtomStart();
266 <      nodeAtomsEnd = mpiSim->getMyAtomEnd();
267 <      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
268 <      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
269 <      
270 <      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
271 <               istatus);
272 <      if (sendError) MPIcheckPoint();
286 >    done = 0;
287 >    while (!done) {
288  
289 <      for ( i = 0; i < entry_plug->n_atoms; i++){
289 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
290 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
291  
292 <        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
277 <                          istatus);
278 <        
279 <        if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
280 <        
281 <        parseErr = parseDumpLine( read_buffer, i );
282 <        if( parseErr != NULL ){
283 <          sendError = 1;
284 <          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
292 >      if(!myStatus) anonymousNodeDie();
293  
294 +      if(myStatus < 0) break;
295  
296 <          strcpy( painCave.errMsg, parseErr );
297 <          painCave.isFatal = 1;
298 <          simError();
299 <        }
300 <        sendError = 0;
301 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
296 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
297 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
298 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
299 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
300 >
301 >      myStatus = 1;
302 >      parseErr = parseDumpLine( read_buffer, which_atom );
303 >      if( parseErr != NULL ){
304 >        strcpy( painCave.errMsg, parseErr );
305 >        myStatus = 0;;
306 >        simError();
307        }
308 +
309 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
310 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
311 +
312      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
313    }
314  
315 + // last  thing last, enable  fatalities.
316 +  painCave.isEventLoop = 0;
317 +
318 +
319 +
320   #endif
321   }
322  
323 + char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
324  
325 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
325 >  char *foo; // the pointer to the current string token
326  
327 <  char *foo; // the pointer to the current string token
328 <  
307 <  double rx, ry, rz; // position place holders
308 <  double vx, vy, vz; // velocity placeholders
327 >  double pos[3]; // position place holders
328 >  double vel[3]; // velocity placeholders
329    double q[4]; // the quaternions
330    double jx, jy, jz; // angular velocity placeholders;
331    double qSqr, qLength; // needed to normalize the quaternion vector.
332 <  
333 <  Atom **atoms = entry_plug->atoms;
332 >
333 >  Atom **atoms = simnfo->atoms;
334    DirectionalAtom* dAtom;
315 –  
316 –  int n_atoms;
335  
336 +  int n_atoms, atomIndex;
337 +
338   #ifdef IS_MPI
339 +  int j;
340 +
341    n_atoms = mpiSim->getTotAtoms();
342 +  atomIndex=-1;
343 +  for (j=0; j < mpiSim->getMyNlocal(); j++) {
344 +    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
345 +  }
346 +  if (atomIndex == -1) {
347 +    sprintf( painCave.errMsg,
348 +             "Initialize from file error. Atom at index %d "
349 +             "in file %s does not exist on processor %d .\n",
350 +             globalIndex, c_in_name, mpiSim->getMyNode() );
351 +    return strdup( painCave.errMsg );
352 +  }
353   #else
354 <  n_atoms = entry_plug->n_atoms;
354 >  n_atoms = simnfo->n_atoms;
355 >  atomIndex = globalIndex;
356   #endif // is_mpi
357  
324 –
358    // set the string tokenizer
359 <  
359 >
360    foo = strtok(readLine, " ,;\t");
361 <  
361 >
362    // check the atom name to the current atom
363 <  
363 >
364    if( strcmp( foo, atoms[atomIndex]->getType() ) ){
365      sprintf( painCave.errMsg,
366               "Initialize from file error. Atom %s at index %d "
# Line 336 | Line 369 | char* InitializeFromFile::parseDumpLine(char* readLine
369               foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
370      return strdup( painCave.errMsg );
371    }
372 <    
372 >
373    // get the positions
374  
375    foo = strtok(NULL, " ,;\t");
# Line 347 | Line 380 | char* InitializeFromFile::parseDumpLine(char* readLine
380               c_in_name, n_atoms, atomIndex );
381      return strdup( painCave.errMsg );
382    }
383 <  rx = atof( foo );
384 <  
383 >  pos[0] = atof( foo );
384 >
385    foo = strtok(NULL, " ,;\t");
386    if(foo == NULL){
387      sprintf( painCave.errMsg,
# Line 357 | Line 390 | char* InitializeFromFile::parseDumpLine(char* readLine
390               c_in_name, n_atoms, atomIndex );
391      return strdup( painCave.errMsg );
392    }
393 <  ry = atof( foo );
394 <    
393 >  pos[1] = atof( foo );
394 >
395    foo = strtok(NULL, " ,;\t");
396    if(foo == NULL){
397      sprintf( painCave.errMsg,
# Line 367 | Line 400 | char* InitializeFromFile::parseDumpLine(char* readLine
400               c_in_name, n_atoms, atomIndex );
401      return strdup( painCave.errMsg );
402    }
403 <  rz = atof( foo );    
403 >  pos[2] = atof( foo );
404  
405  
406    // get the velocities
# Line 380 | Line 413 | char* InitializeFromFile::parseDumpLine(char* readLine
413               c_in_name, n_atoms, atomIndex );
414      return strdup( painCave.errMsg );
415    }
416 <  vx = atof( foo );
417 <    
416 >  vel[0] = atof( foo );
417 >
418    foo = strtok(NULL, " ,;\t");
419    if(foo == NULL){
420      sprintf( painCave.errMsg,
# Line 390 | Line 423 | char* InitializeFromFile::parseDumpLine(char* readLine
423               c_in_name, n_atoms, atomIndex );
424      return strdup( painCave.errMsg );
425    }
426 <  vy = atof( foo );
427 <    
426 >  vel[1] = atof( foo );
427 >
428    foo = strtok(NULL, " ,;\t");
429    if(foo == NULL){
430      sprintf( painCave.errMsg,
# Line 400 | Line 433 | char* InitializeFromFile::parseDumpLine(char* readLine
433               c_in_name, n_atoms, atomIndex );
434      return strdup( painCave.errMsg );
435    }
436 <  vz = atof( foo );
437 <    
438 <    
436 >  vel[2] = atof( foo );
437 >
438 >
439    // get the quaternions
440 <    
440 >
441    if( atoms[atomIndex]->isDirectional() ){
442 <      
442 >
443      foo = strtok(NULL, " ,;\t");
444      if(foo == NULL){
445        sprintf(painCave.errMsg,
# Line 416 | Line 449 | char* InitializeFromFile::parseDumpLine(char* readLine
449        return strdup( painCave.errMsg );
450      }
451      q[0] = atof( foo );
452 <      
452 >
453      foo = strtok(NULL, " ,;\t");
454      if(foo == NULL){
455        sprintf( painCave.errMsg,
# Line 426 | Line 459 | char* InitializeFromFile::parseDumpLine(char* readLine
459        return strdup( painCave.errMsg );
460      }
461      q[1] = atof( foo );
462 <      
462 >
463      foo = strtok(NULL, " ,;\t");
464      if(foo == NULL){
465        sprintf( painCave.errMsg,
# Line 436 | Line 469 | char* InitializeFromFile::parseDumpLine(char* readLine
469        return strdup( painCave.errMsg );
470      }
471      q[2] = atof( foo );
472 <      
472 >
473      foo = strtok(NULL, " ,;\t");
474      if(foo == NULL){
475        sprintf( painCave.errMsg,
# Line 446 | Line 479 | char* InitializeFromFile::parseDumpLine(char* readLine
479        return strdup( painCave.errMsg );
480      }
481      q[3] = atof( foo );
482 <      
482 >
483      // get the angular velocities
484 <      
484 >
485      foo = strtok(NULL, " ,;\t");
486      if(foo == NULL){
487        sprintf( painCave.errMsg,
# Line 458 | Line 491 | char* InitializeFromFile::parseDumpLine(char* readLine
491        return strdup( painCave.errMsg );
492      }
493      jx = atof( foo );
494 <      
494 >
495      foo = strtok(NULL, " ,;\t");
496      if(foo == NULL){
497        sprintf( painCave.errMsg,
# Line 468 | Line 501 | char* InitializeFromFile::parseDumpLine(char* readLine
501        return strdup( painCave.errMsg );
502      }
503      jy = atof(foo );
504 <      
504 >
505      foo = strtok(NULL, " ,;\t");
506      if(foo == NULL){
507        sprintf( painCave.errMsg,
# Line 478 | Line 511 | char* InitializeFromFile::parseDumpLine(char* readLine
511        return strdup( painCave.errMsg );
512      }
513      jz = atof( foo );
514 <      
514 >
515      dAtom = ( DirectionalAtom* )atoms[atomIndex];
516  
517      // check that the quaternion vector is normalized
518  
519      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520 <      
520 >
521      qLength = sqrt( qSqr );
522      q[0] = q[0] / qLength;
523      q[1] = q[1] / qLength;
524      q[2] = q[2] / qLength;
525      q[3] = q[3] / qLength;
526 <      
526 >
527      dAtom->setQ( q );
528 <      
528 >
529      // add the angular velocities
530  
531      dAtom->setJx( jx );
532      dAtom->setJy( jy );
533      dAtom->setJz( jz );
534    }
535 <    
535 >
536    // add the positions and velocities to the atom
537 <    
538 <  atoms[atomIndex]->setX( rx );
539 <  atoms[atomIndex]->setY( ry );
540 <  atoms[atomIndex]->setZ( rz );
537 >
538 >  atoms[atomIndex]->setPos( pos );
539 >  atoms[atomIndex]->setVel( vel );
540 >
541 >  return NULL;
542 > }
543 >
544 >
545 > char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
546 >
547 >  double currTime;
548 >  double boxMat[9];
549 >  double theBoxMat3[3][3];
550 >  double chi;
551 >  double integralOfChidt;
552 >  double eta[9];
553 >
554 >  char *foo; // the pointer to the current string token
555 >
556 >  // set the string tokenizer
557 >
558 >  foo = strtok(readLine, " ,;\t");
559 >  // set the timeToken.
560 >
561 >  if(foo == NULL){
562 >    sprintf( painCave.errMsg,
563 >             "error in reading Time from %s\n",
564 >             c_in_name );
565 >    return strdup( painCave.errMsg );
566 >  }
567 >
568 >  currTime = atof( foo );
569 >  entry_plug->setTime( currTime );
570 >
571 >  //get H-Matrix
572 >
573 >  for(int i = 0 ; i < 9; i++){
574 >    foo = strtok(NULL, " ,;\t");
575 >    if(foo == NULL){
576 >      sprintf( painCave.errMsg,
577 >               "error in reading H[%d] from %s\n", i, c_in_name );
578 >      return strdup( painCave.errMsg );
579 >    }
580 >    boxMat[i] = atof( foo );
581 >  }
582 >
583 >  for(int i=0;i<3;i++)
584 >    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
585 >
586 >  //set H-Matrix
587 >  entry_plug->setBoxM( theBoxMat3 );
588 >
589 >  //get chi and integralOfChidt, they should appear by pair
590 >
591 >  if( entry_plug->useInitXSstate ){
592 >    foo = strtok(NULL, " ,;\t\n");
593 >    if(foo != NULL){
594 >      chi = atof(foo);
595 >      
596 >      foo = strtok(NULL, " ,;\t\n");
597 >      if(foo == NULL){
598 >        sprintf( painCave.errMsg,
599 >                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
600 >        return strdup( painCave.errMsg );
601 >      }
602 >      integralOfChidt = atof( foo );
603 >      
604 >      //push chi and integralOfChidt into SimInfo::properties which can be
605 >      //retrieved by integrator later
606 >      DoubleData* chiValue = new DoubleData();
607 >      chiValue->setID(CHIVALUE_ID);
608 >      chiValue->setData(chi);
609 >      entry_plug->addProperty(chiValue);
610 >      
611 >      DoubleData* integralOfChidtValue = new DoubleData();
612 >      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
613 >      integralOfChidtValue->setData(integralOfChidt);
614 >      entry_plug->addProperty(integralOfChidtValue);
615 >      
616 >    }
617 >    else
618 >      return NULL;
619      
620 <  atoms[atomIndex]->set_vx( vx );
621 <  atoms[atomIndex]->set_vy( vy );
622 <  atoms[atomIndex]->set_vz( vz );
620 >    //get eta
621 >    for(int i = 0 ; i < 9; i++){
622 >      foo = strtok(NULL, " ,;\t");
623 >      if(foo == NULL){
624 >        sprintf( painCave.errMsg,
625 >                 "error in reading eta[%d] from %s\n", i, c_in_name );
626 >        return strdup( painCave.errMsg );
627 >      }
628 >      eta[i] = atof( foo );
629 >    }
630 >    
631 >    //push eta into SimInfo::properties which can be
632 >    //retrieved by integrator later
633 >    //entry_plug->setBoxM( theBoxMat3 );
634 >    DoubleArrayData* etaValue = new DoubleArrayData();
635 >    etaValue->setID(ETAVALUE_ID);
636 >    etaValue->setData(eta, 9);
637 >    entry_plug->addProperty(etaValue);
638 >  }
639  
640    return NULL;
641   }
642 +
643 + #ifdef IS_MPI
644 +
645 + // a couple of functions to let us escape the read loop
646 +
647 + void initFile::nodeZeroError( void ){
648 +  int j, myStatus;
649 +
650 +  myStatus = 0;
651 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
652 +    MPI_Send( &myStatus, 1, MPI_INT, j,
653 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
654 +  }
655 +
656 +
657 +  MPI_Finalize();
658 +  exit (0);
659 +
660 + }
661 +
662 + void initFile::anonymousNodeDie( void ){
663 +
664 +  MPI_Finalize();
665 +  exit (0);
666 + }
667 +
668 + #endif //is_mpi

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