ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 837 by tim, Wed Oct 29 00:19:10 2003 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." );
49    MPIcheckPoint();
50   #endif
51 <  return;  
51 >  return;
52   }
53  
54 < InitializeFromFile :: ~InitializeFromFile( ){
54 > InitializeFromFile::~InitializeFromFile( ){
55   #ifdef IS_MPI
56    if (worldRank == 0) {
57   #endif
# Line 60 | Line 72 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
72   }
73  
74  
75 < void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
75 > void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
76  
77 <  int i; // loop counter
77 >  int i, j;
78  
79 + #ifdef IS_MPI
80 +  int done, which_node, which_atom; // loop counter
81 + #endif //is_mpi
82 +
83    const int BUFFERSIZE = 2000; // size of the read buffer
84    int n_atoms; // the number of atoms
85 <  char read_buffer[BUFFERSIZE]; //the line buffer for reading
70 < #ifdef IS_MPI
71 <  char send_buffer[BUFFERSIZE];
72 < #endif
85 >  char read_buffer[BUFFERSIZE]; //the line buffer for reading
86  
87 <  char *eof_test; // ptr to see when we reach the end of the file
87 >  char *eof_test; // ptr to see when we reach the end of the file
88    char *parseErr;
76 –  int procIndex;
89  
90 <  entry_plug = the_entry_plug;
90 >  simnfo = the_simnfo;
91  
92  
93   #ifndef IS_MPI
# Line 90 | Line 102 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
102  
103    n_atoms = atoi( read_buffer );
104  
105 <  Atom **atoms = entry_plug->atoms;
94 <  DirectionalAtom* dAtom;
95 <
96 <  if( n_atoms != entry_plug->n_atoms ){
105 >  if( n_atoms != simnfo->n_atoms ){
106      sprintf( painCave.errMsg,
107               "Initialize from File error. %s n_atoms, %d, "
108               "does not match the BASS file's n_atoms, %d.\n",
109 <             c_in_name, n_atoms, entry_plug->n_atoms );
109 >             c_in_name, n_atoms, simnfo->n_atoms );
110      painCave.isFatal = 1;
111      simError();
112    }
113 <  
114 <  //read and toss the comment line
115 <  
113 >
114 >  //read the box mat from the comment line
115 >
116    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
117    if(eof_test == NULL){
118      sprintf( painCave.errMsg,
# Line 112 | Line 121 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
121      simError();
122    }
123  
124 +
125 +
126 +  parseErr = parseCommentLine( read_buffer, simnfo);
127 +  if( parseErr != NULL ){
128 +    strcpy( painCave.errMsg, parseErr );
129 +    painCave.isFatal = 1;
130 +    simError();
131 +  }
132 +
133 +  //parse dump lines
134 +
135    for( i=0; i < n_atoms; i++){
136 <    
136 >
137      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
138      if(eof_test == NULL){
139        sprintf(painCave.errMsg,
# Line 125 | Line 145 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
145        simError();
146      }
147  
148 <    
148 >
149      parseErr = parseDumpLine( read_buffer, i );
150      if( parseErr != NULL ){
151        strcpy( painCave.errMsg, parseErr );
152        painCave.isFatal = 1;
153        simError();
154 <    }    
154 >    }
155    }
156  
157  
158    // MPI Section of code..........
159   #else //IS_MPI
160  
161 <  int masterIndex;
162 <  int nodeAtomsStart;
143 <  int nodeAtomsEnd;
144 <  int mpiErr;
145 <  int sendError;
161 >  // first thing first, suspend fatalities.
162 >  painCave.isEventLoop = 1;
163  
164 <  MPI_Status istatus[MPI_STATUS_SIZE];
164 >  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
165 >  int haveError;
166  
167 +  MPI_Status istatus;
168 +  int *AtomToProcMap = mpiSim->getAtomToProcMap();
169 +
170 +
171 +  haveError = 0;
172    if (worldRank == 0) {
173 +
174      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
175      if( eof_test == NULL ){
176        sprintf( painCave.errMsg,
177 <               "Error reading 1st line of %d \n ",c_in_name);
178 <      painCave.isFatal = 1;
177 >               "Error reading 1st line of %s \n ",c_in_name);
178 >      haveError = 1;
179        simError();
180      }
181 <    
181 >
182      n_atoms = atoi( read_buffer );
183 <    
160 <    Atom **atoms = entry_plug->atoms;
161 <    DirectionalAtom* dAtom;
162 <
183 >
184      // Check to see that the number of atoms in the intial configuration file is the
185      // same as declared in simBass.
186 <    
186 >
187      if( n_atoms != mpiSim->getTotAtoms() ){
188        sprintf( painCave.errMsg,
189                 "Initialize from File error. %s n_atoms, %d, "
190                 "does not match the BASS file's n_atoms, %d.\n",
191 <               c_in_name, n_atoms, entry_plug->n_atoms );
192 <      painCave.isFatal = 1;
191 >               c_in_name, n_atoms, simnfo->n_atoms );
192 >      haveError= 1;
193        simError();
194      }
195 <    
196 <    //read and toss the comment line
197 <    
195 >
196 >    //read the boxMat from the comment line
197 >
198      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
199      if(eof_test == NULL){
200        sprintf( painCave.errMsg,
201                 "error in reading commment in %s\n", c_in_name);
202 <      painCave.isFatal = 1;
202 >      haveError = 1;
203        simError();
204      }
205 <  
206 <    // Read Proc 0 share of the xyz file...
207 <    masterIndex = 0;
208 <    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
209 <    
205 >
206 >    //Every single processor will parse the comment line by itself
207 >    //By using this way, we might lose some efficiency, but if we want to add
208 >    //more parameters into comment line, we only need to modify function
209 >    //parseCommentLine
210 >
211 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
212 >
213 >    parseErr = parseCommentLine( read_buffer, simnfo);
214 >
215 >    if( parseErr != NULL ){
216 >      strcpy( painCave.errMsg, parseErr );
217 >      haveError = 1;
218 >      simError();
219 >    }
220 >
221 >    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
222 >
223        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
224        if(eof_test == NULL){
225          sprintf(painCave.errMsg,
# Line 193 | Line 227 | void InitializeFromFile :: read_xyz( SimInfo* the_entr
227                  "natoms  = %d; index = %d\n"
228                  "error reading the line from the file.\n",
229                  c_in_name, n_atoms, i );
230 <        painCave.isFatal = 1;
230 >        haveError= 1;
231          simError();
232        }
233 <    
234 <      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 <  }
233 >
234 >      if(haveError) nodeZeroError();
235  
236 <  sprintf(checkPointMsg,
237 <          "Node 0 has successfully read positions from input file.");
238 <  MPIcheckPoint();
236 >      // Get the Node number which wants this atom:
237 >      which_node = AtomToProcMap[i];
238 >      if (which_node == 0) {
239 >        parseErr = parseDumpLine( read_buffer, i );
240 >        if( parseErr != NULL ){
241 >          strcpy( painCave.errMsg, parseErr );
242 >          haveError = 1;
243 >          simError();
244 >        }
245 >        if(haveError) nodeZeroError();
246 >      }
247  
248 <  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215 <         procIndex++){
216 <    if (worldRank == 0) {
248 >      else {
249  
250 <      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
251 <               istatus);
250 >        myStatus = 1;
251 >        MPI_Send(&myStatus, 1, MPI_INT, which_node,
252 >                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
253 >        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
254 >                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
255 >        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
256 >                 MPI_COMM_WORLD);
257 >        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
258 >                 MPI_COMM_WORLD, &istatus);
259  
260 <      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();
260 >        if(!myStatus) nodeZeroError();
261        }
262 <      sendError = 0;
263 <      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
264 <      
265 <      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
266 <        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
267 <        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();
262 >    }
263 >    myStatus = -1;
264 >    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
265 >      MPI_Send( &myStatus, 1, MPI_INT, j,
266 >                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
267 >    }
268  
269 <        masterIndex++;
270 <      }
269 >  } else {
270 >
271 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
272 >
273 >    parseErr = parseCommentLine( read_buffer, simnfo);
274 >
275 >    if( parseErr != NULL ){
276 >      strcpy( painCave.errMsg, parseErr );
277 >      haveError = 1;
278 >      simError();
279      }
280  
281  
282 <    else if(worldRank == procIndex){
283 <      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();
282 >    done = 0;
283 >    while (!done) {
284  
285 <      for ( i = 0; i < entry_plug->n_atoms; i++){
285 >      MPI_Recv(&myStatus, 1, MPI_INT, 0,
286 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
287  
288 <        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);
288 >      if(!myStatus) anonymousNodeDie();
289  
290 +      if(myStatus < 0) break;
291  
292 <          strcpy( painCave.errMsg, parseErr );
293 <          painCave.isFatal = 1;
294 <          simError();
295 <        }
296 <        sendError = 0;
297 <        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
292 >      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
293 >               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
294 >      MPI_Recv(&which_atom, 1, MPI_INT, 0,
295 >               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
296 >
297 >      myStatus = 1;
298 >      parseErr = parseDumpLine( read_buffer, which_atom );
299 >      if( parseErr != NULL ){
300 >        strcpy( painCave.errMsg, parseErr );
301 >        myStatus = 0;;
302 >        simError();
303        }
304 +
305 +      MPI_Send( &myStatus, 1, MPI_INT, 0,
306 +                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
307 +
308      }
295 –    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296 –    MPIcheckPoint();
309    }
310  
311 + // last  thing last, enable  fatalities.
312 +  painCave.isEventLoop = 0;
313 +
314 +
315 +
316   #endif
317   }
318  
319 + char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
320  
321 < char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
321 >  char *foo; // the pointer to the current string token
322  
323 <  char *foo; // the pointer to the current string token
324 <  
307 <  double rx, ry, rz; // position place holders
308 <  double vx, vy, vz; // velocity placeholders
323 >  double pos[3]; // position place holders
324 >  double vel[3]; // velocity placeholders
325    double q[4]; // the quaternions
326    double jx, jy, jz; // angular velocity placeholders;
327    double qSqr, qLength; // needed to normalize the quaternion vector.
328 <  
329 <  Atom **atoms = entry_plug->atoms;
328 >
329 >  Atom **atoms = simnfo->atoms;
330    DirectionalAtom* dAtom;
315 –  
316 –  int n_atoms;
331  
332 +  int n_atoms, atomIndex;
333 +
334   #ifdef IS_MPI
335 +  int j;
336 +
337    n_atoms = mpiSim->getTotAtoms();
338 +  atomIndex=-1;
339 +  for (j=0; j < mpiSim->getMyNlocal(); j++) {
340 +    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
341 +  }
342 +  if (atomIndex == -1) {
343 +    sprintf( painCave.errMsg,
344 +             "Initialize from file error. Atom at index %d "
345 +             "in file %s does not exist on processor %d .\n",
346 +             globalIndex, c_in_name, mpiSim->getMyNode() );
347 +    return strdup( painCave.errMsg );
348 +  }
349   #else
350 <  n_atoms = entry_plug->n_atoms;
350 >  n_atoms = simnfo->n_atoms;
351 >  atomIndex = globalIndex;
352   #endif // is_mpi
353  
324 –
354    // set the string tokenizer
355 <  
355 >
356    foo = strtok(readLine, " ,;\t");
357 <  
357 >
358    // check the atom name to the current atom
359 <  
359 >
360    if( strcmp( foo, atoms[atomIndex]->getType() ) ){
361      sprintf( painCave.errMsg,
362               "Initialize from file error. Atom %s at index %d "
# Line 336 | Line 365 | char* InitializeFromFile::parseDumpLine(char* readLine
365               foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
366      return strdup( painCave.errMsg );
367    }
368 <    
368 >
369    // get the positions
370  
371    foo = strtok(NULL, " ,;\t");
# Line 347 | Line 376 | char* InitializeFromFile::parseDumpLine(char* readLine
376               c_in_name, n_atoms, atomIndex );
377      return strdup( painCave.errMsg );
378    }
379 <  rx = atof( foo );
380 <  
379 >  pos[0] = atof( foo );
380 >
381    foo = strtok(NULL, " ,;\t");
382    if(foo == NULL){
383      sprintf( painCave.errMsg,
# Line 357 | Line 386 | char* InitializeFromFile::parseDumpLine(char* readLine
386               c_in_name, n_atoms, atomIndex );
387      return strdup( painCave.errMsg );
388    }
389 <  ry = atof( foo );
390 <    
389 >  pos[1] = atof( foo );
390 >
391    foo = strtok(NULL, " ,;\t");
392    if(foo == NULL){
393      sprintf( painCave.errMsg,
# Line 367 | Line 396 | char* InitializeFromFile::parseDumpLine(char* readLine
396               c_in_name, n_atoms, atomIndex );
397      return strdup( painCave.errMsg );
398    }
399 <  rz = atof( foo );    
399 >  pos[2] = atof( foo );
400  
401  
402    // get the velocities
# Line 380 | Line 409 | char* InitializeFromFile::parseDumpLine(char* readLine
409               c_in_name, n_atoms, atomIndex );
410      return strdup( painCave.errMsg );
411    }
412 <  vx = atof( foo );
413 <    
412 >  vel[0] = atof( foo );
413 >
414    foo = strtok(NULL, " ,;\t");
415    if(foo == NULL){
416      sprintf( painCave.errMsg,
# Line 390 | Line 419 | char* InitializeFromFile::parseDumpLine(char* readLine
419               c_in_name, n_atoms, atomIndex );
420      return strdup( painCave.errMsg );
421    }
422 <  vy = atof( foo );
423 <    
422 >  vel[1] = atof( foo );
423 >
424    foo = strtok(NULL, " ,;\t");
425    if(foo == NULL){
426      sprintf( painCave.errMsg,
# Line 400 | Line 429 | char* InitializeFromFile::parseDumpLine(char* readLine
429               c_in_name, n_atoms, atomIndex );
430      return strdup( painCave.errMsg );
431    }
432 <  vz = atof( foo );
433 <    
434 <    
432 >  vel[2] = atof( foo );
433 >
434 >
435    // get the quaternions
436 <    
436 >
437    if( atoms[atomIndex]->isDirectional() ){
438 <      
438 >
439      foo = strtok(NULL, " ,;\t");
440      if(foo == NULL){
441        sprintf(painCave.errMsg,
# Line 416 | Line 445 | char* InitializeFromFile::parseDumpLine(char* readLine
445        return strdup( painCave.errMsg );
446      }
447      q[0] = atof( foo );
448 <      
448 >
449      foo = strtok(NULL, " ,;\t");
450      if(foo == NULL){
451        sprintf( painCave.errMsg,
# Line 426 | Line 455 | char* InitializeFromFile::parseDumpLine(char* readLine
455        return strdup( painCave.errMsg );
456      }
457      q[1] = atof( foo );
458 <      
458 >
459      foo = strtok(NULL, " ,;\t");
460      if(foo == NULL){
461        sprintf( painCave.errMsg,
# Line 436 | Line 465 | char* InitializeFromFile::parseDumpLine(char* readLine
465        return strdup( painCave.errMsg );
466      }
467      q[2] = atof( foo );
468 <      
468 >
469      foo = strtok(NULL, " ,;\t");
470      if(foo == NULL){
471        sprintf( painCave.errMsg,
# Line 446 | Line 475 | char* InitializeFromFile::parseDumpLine(char* readLine
475        return strdup( painCave.errMsg );
476      }
477      q[3] = atof( foo );
478 <      
478 >
479      // get the angular velocities
480 <      
480 >
481      foo = strtok(NULL, " ,;\t");
482      if(foo == NULL){
483        sprintf( painCave.errMsg,
# Line 458 | Line 487 | char* InitializeFromFile::parseDumpLine(char* readLine
487        return strdup( painCave.errMsg );
488      }
489      jx = atof( foo );
490 <      
490 >
491      foo = strtok(NULL, " ,;\t");
492      if(foo == NULL){
493        sprintf( painCave.errMsg,
# Line 468 | Line 497 | char* InitializeFromFile::parseDumpLine(char* readLine
497        return strdup( painCave.errMsg );
498      }
499      jy = atof(foo );
500 <      
500 >
501      foo = strtok(NULL, " ,;\t");
502      if(foo == NULL){
503        sprintf( painCave.errMsg,
# Line 478 | Line 507 | char* InitializeFromFile::parseDumpLine(char* readLine
507        return strdup( painCave.errMsg );
508      }
509      jz = atof( foo );
510 <      
510 >
511      dAtom = ( DirectionalAtom* )atoms[atomIndex];
512  
513      // check that the quaternion vector is normalized
514  
515      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
516 <      
516 >
517      qLength = sqrt( qSqr );
518      q[0] = q[0] / qLength;
519      q[1] = q[1] / qLength;
520      q[2] = q[2] / qLength;
521      q[3] = q[3] / qLength;
522 <      
522 >
523      dAtom->setQ( q );
524 <      
524 >
525      // add the angular velocities
526  
527      dAtom->setJx( jx );
528      dAtom->setJy( jy );
529      dAtom->setJz( jz );
530    }
531 <    
531 >
532    // add the positions and velocities to the atom
504 –    
505 –  atoms[atomIndex]->setX( rx );
506 –  atoms[atomIndex]->setY( ry );
507 –  atoms[atomIndex]->setZ( rz );
508 –    
509 –  atoms[atomIndex]->set_vx( vx );
510 –  atoms[atomIndex]->set_vy( vy );
511 –  atoms[atomIndex]->set_vz( vz );
533  
534 +  atoms[atomIndex]->setPos( pos );
535 +  atoms[atomIndex]->setVel( vel );
536 +
537    return NULL;
538   }
539 +
540 +
541 + char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
542 +
543 +  double currTime;
544 +  double boxMat[9];
545 +  double theBoxMat3[3][3];
546 +  double chi;
547 +  double integralOfChidt;
548 +  double eta[9];
549 +
550 +  char *foo; // the pointer to the current string token
551 +
552 +  // set the string tokenizer
553 +
554 +  foo = strtok(readLine, " ,;\t");
555 +  // set the timeToken.
556 +
557 +  if(foo == NULL){
558 +    sprintf( painCave.errMsg,
559 +             "error in reading Time from %s\n",
560 +             c_in_name );
561 +    return strdup( painCave.errMsg );
562 +  }
563 +
564 +  currTime = atof( foo );
565 +  entry_plug->setTime( currTime );
566 +
567 +  //get H-Matrix
568 +
569 +  for(int i = 0 ; i < 9; i++){
570 +    foo = strtok(NULL, " ,;\t");
571 +    if(foo == NULL){
572 +      sprintf( painCave.errMsg,
573 +               "error in reading H[%d] from %s\n", i, c_in_name );
574 +      return strdup( painCave.errMsg );
575 +    }
576 +    boxMat[i] = atof( foo );
577 +  }
578 +
579 +  for(int i=0;i<3;i++)
580 +    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
581 +
582 +  //set H-Matrix
583 +  entry_plug->setBoxM( theBoxMat3 );
584 +
585 +  //get chi and integralOfChidt, they should appear by pair
586 +  foo = strtok(NULL, " ,;\t\n");
587 +  if(foo != NULL){
588 +    chi = atof(foo);
589 +
590 +    foo = strtok(NULL, " ,;\t\n");
591 +    if(foo == NULL){
592 +      sprintf( painCave.errMsg,
593 +               "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
594 +      return strdup( painCave.errMsg );
595 +    }
596 +    integralOfChidt = atof( foo );
597 +
598 +    //push chi and integralOfChidt into SimInfo::properties which can be
599 +    //retrieved by integrator later
600 +    DoubleData* chiValue = new DoubleData();
601 +    chiValue->setID(CHIVALUE_ID);
602 +    chiValue->setData(chi);
603 +    entry_plug->addProperty(chiValue);
604 +
605 +    DoubleData* integralOfChidtValue = new DoubleData();
606 +    integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
607 +    integralOfChidtValue->setData(integralOfChidt);
608 +    entry_plug->addProperty(integralOfChidtValue);
609 +
610 +  }
611 +  else
612 +    return NULL;
613 +
614 +  //get eta
615 +  for(int i = 0 ; i < 9; i++){
616 +    foo = strtok(NULL, " ,;\t");
617 +    if(foo == NULL){
618 +      sprintf( painCave.errMsg,
619 +               "error in reading eta[%d] from %s\n", i, c_in_name );
620 +      return strdup( painCave.errMsg );
621 +    }
622 +    eta[i] = atof( foo );
623 +  }
624 +
625 +  //push eta into SimInfo::properties which can be
626 +  //retrieved by integrator later
627 +  //entry_plug->setBoxM( theBoxMat3 );
628 +  DoubleArrayData* etaValue = new DoubleArrayData();
629 +  etaValue->setID(ETAVALUE_ID);
630 +  etaValue->setData(eta, 9);
631 +  entry_plug->addProperty(etaValue);
632 +
633 +
634 +  return NULL;
635 + }
636 +
637 + #ifdef IS_MPI
638 +
639 + // a couple of functions to let us escape the read loop
640 +
641 + void initFile::nodeZeroError( void ){
642 +  int j, myStatus;
643 +
644 +  myStatus = 0;
645 +  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
646 +    MPI_Send( &myStatus, 1, MPI_INT, j,
647 +              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
648 +  }
649 +
650 +
651 +  MPI_Finalize();
652 +  exit (0);
653 +
654 + }
655 +
656 + void initFile::anonymousNodeDie( void ){
657 +
658 +  MPI_Finalize();
659 +  exit (0);
660 + }
661 +
662 + #endif //is_mpi

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines