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root/OpenMD/branches/development/src/io/RestReader.cpp
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Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 996 by chrisfen, Wed Jun 28 14:35:14 2006 UTC

# Line 60 | Line 60
60  
61   #ifdef IS_MPI
62   #include <mpi.h>
63 – #include "brains/mpiSimulation.hpp"
63   #define TAKE_THIS_TAG_CHAR 0
64   #define TAKE_THIS_TAG_INT 1
65   #define TAKE_THIS_TAG_DOUBLE 2
# Line 69 | Line 68 | namespace oopse {
68   namespace oopse {
69    
70    RestReader::RestReader( SimInfo* info ) : info_(info){
72 –        
73 –    idealName = "idealCrystal.in";
71      
72 <    isScanned = false;
73 <    
72 >    idealName = "idealCrystal.in";
73 >    
74   #ifdef IS_MPI
75      if (worldRank == 0) {
76   #endif
77 <      
78 <      inIdealFile = fopen(idealName, "r");
79 <      if(inIdealFile == NULL){
77 >
78 >      inIdealFile = new std::ifstream(idealName.c_str());
79 >
80 >      if(inIdealFile->fail()){
81          sprintf(painCave.errMsg,
82 <                "RestReader: Cannot open file: %s\n", idealName);
82 >                "RestReader: Cannot open file: %s\n",
83 >                idealName.c_str());
84          painCave.isFatal = 1;
85          simError();
86        }
87        
89 –      inIdealFileName = idealName;
88   #ifdef IS_MPI
89      }
90      strcpy( checkPointMsg,
91              "File \"idealCrystal.in\" opened successfully for reading." );
92      MPIcheckPoint();
93   #endif
94 +
95      return;  
96    }
97    
# Line 100 | Line 99 | namespace oopse {
99   #ifdef IS_MPI
100      if (worldRank == 0) {
101   #endif
102 <      int error;
103 <      error = fclose( inIdealFile );
104 <      
105 <      if( error ){
107 <        sprintf( painCave.errMsg,
108 <                 "Error closing %s\n", inIdealFileName.c_str());
109 <        simError();
110 <      }
111 <      
112 <      MemoryUtils::deletePointers(framePos);
113 <      
102 >
103 >      delete inIdealFile;
104 >      delete inAngFile;
105 >
106   #ifdef IS_MPI
107      }
108 <    strcpy( checkPointMsg, "Restraint file closed successfully." );
108 >    strcpy( checkPointMsg,
109 >            "File idealCrystal.in (and .zang0 if present) closed successfully." );
110      MPIcheckPoint();
111   #endif
112      
# Line 122 | Line 115 | namespace oopse {
115    
116    
117    void RestReader :: readIdealCrystal(){
118 <    
126 <    int i;
127 <    unsigned int j;
128 <    
118 >        
119   #ifdef IS_MPI
120 <    int done, which_node, which_atom; // loop counter
120 >    int which_node;
121 >    int i, j;
122   #endif //is_mpi
123      
124      const int BUFFERSIZE = 2000; // size of the read buffer
125      int nTotObjs; // the number of atoms
126      char read_buffer[BUFFERSIZE]; //the line buffer for reading
127      
137 –    char *eof_test; // ptr to see when we reach the end of the file
128      char *parseErr;
129      
130      std::vector<StuntDouble*> integrableObjects;
# Line 146 | Line 136 | namespace oopse {
136      
137   #ifndef IS_MPI
138      
139 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
140 <    if( eof_test == NULL ){
139 >    inIdealFile->getline(read_buffer, sizeof(read_buffer));
140 >
141 >    if( inIdealFile->eof() ){
142        sprintf( painCave.errMsg,
143                 "RestraintReader error: error reading 1st line of \"%s\"\n",
144 <               inIdealFileName.c_str() );
144 >               idealName.c_str() );
145        painCave.isFatal = 1;
146        simError();
147      }
# Line 161 | Line 152 | namespace oopse {
152        sprintf( painCave.errMsg,
153                 "RestraintReader error. %s nIntegrable, %d, "
154                 "does not match the meta-data file's nIntegrable, %d.\n",
155 <               inIdealFileName.c_str(), nTotObjs,
155 >               idealName.c_str(),
156 >               nTotObjs,
157                 info_->getNGlobalIntegrableObjects());
158        painCave.isFatal = 1;
159        simError();
160      }
161      
162      // skip over the comment line
163 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
164 <    if(eof_test == NULL){
163 >    inIdealFile->getline(read_buffer, sizeof(read_buffer));
164 >
165 >    if( inIdealFile->eof() ){
166        sprintf( painCave.errMsg,
167 <               "error in reading commment in %s\n", inIdealFileName.c_str());
167 >               "error in reading commment in %s\n",
168 >               idealName.c_str());
169        painCave.isFatal = 1;
170        simError();
171      }
# Line 188 | Line 182 | namespace oopse {
182        for (integrableObject = mol->beginIntegrableObject(ii);
183             integrableObject != NULL;
184             integrableObject = mol->nextIntegrableObject(ii)) {    
185 <        
186 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
187 <        if(eof_test == NULL){
185 >
186 >        inIdealFile->getline(read_buffer, sizeof(read_buffer));
187 >
188 >        if( inIdealFile->eof() ){
189            sprintf(painCave.errMsg,
190                    "RestReader Error: error in reading file %s\n"
191                    "natoms  = %d; index = %d\n"
192                    "error reading the line from the file.\n",
193 <                  inIdealFileName.c_str(), nTotObjs,
193 >                  idealName.c_str(), nTotObjs,
194                    integrableObject->getGlobalIndex() );
195            painCave.isFatal = 1;
196            simError();
# Line 217 | Line 212 | namespace oopse {
212      painCave.isEventLoop = 1;
213      
214      int masterNode = 0;
220 –    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
215      
216      MPI_Status istatus;
223 –    int localIndex;
217      int nCurObj;
218      int nitems;
219 <    
220 <    nTotObjs = info_->getTotIntegrableObjects();
219 >    int haveError;
220 >
221 >    nTotObjs = info_->getNGlobalIntegrableObjects();
222      haveError = 0;
223 <    
223 >
224      if (worldRank == masterNode) {
225 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
226 <      if( eof_test == NULL ){
225 >      inIdealFile->getline(read_buffer, sizeof(read_buffer));
226 >
227 >      if( inIdealFile->eof() ){
228          sprintf( painCave.errMsg,
229 <                 "Error reading 1st line of %s \n ",inIdealFileName.c_str());
229 >                 "Error reading 1st line of %s \n ",idealName.c_str());
230          painCave.isFatal = 1;
231          simError();
232        }
# Line 245 | Line 240 | namespace oopse {
240          sprintf( painCave.errMsg,
241                   "RestraintReader Error. %s nIntegrable, %d, "
242                   "does not match the meta-data file's nIntegrable, %d.\n",
243 <                 inIdealFileName.c_str(), nTotObjs,
243 >                 idealName.c_str(), nTotObjs,
244                   info_->getNGlobalIntegrableObjects());
245          painCave.isFatal = 1;
246          simError();
247        }
248        
249        // skip over the comment line
250 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
251 <      if(eof_test == NULL){
250 >      inIdealFile->getline(read_buffer, sizeof(read_buffer));
251 >
252 >      if( inIdealFile->eof() ){
253          sprintf( painCave.errMsg,
254 <                 "error in reading commment in %s\n", inIdealFileName.c_str());
254 >                 "error in reading commment in %s\n", idealName.c_str());
255          painCave.isFatal = 1;
256          simError();
257        }
258 <      
258 >
259 >      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
260 >
261        for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
262 <        int which_node = info_->getMolToProc(i);
262 >        which_node = info_->getMolToProc(i);
263          
264          if(which_node == masterNode){
265            //molecules belong to master node
266            
267 <          localIndex = info_->getMoleculeByGlobalIndex(i);
267 >          mol = info_->getMoleculeByGlobalIndex(i);
268            
269 <          if(localIndex == NULL) {
270 <            strcpy(painCave.errMsg,
271 <                   "RestReader Error: Molecule not found on node %d!",
272 <                   worldRank);
269 >          if(mol == NULL) {
270 >            sprintf(painCave.errMsg,
271 >                    "RestReader Error: Molecule not found on node %d!\n",
272 >                    worldRank);
273              painCave.isFatal = 1;
274              simError();
275            }
# Line 280 | Line 278 | namespace oopse {
278                 integrableObject != NULL;
279                 integrableObject = mol->nextIntegrableObject(ii)){
280              
281 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
281 >            inIdealFile->getline(read_buffer, sizeof(read_buffer));
282              
283 <            if(eof_test == NULL){
283 >            if( inIdealFile->eof() ){
284                sprintf(painCave.errMsg,
285                        "RestReader Error: error in reading file %s\n"
286                        "natoms  = %d; index = %d\n"
287                        "error reading the line from the file.\n",
288 <                      inIdealFileName.c_str(), nTotObjs, i );
288 >                      idealName.c_str(), nTotObjs, i );
289                painCave.isFatal = 1;
290                simError();
291              }
292 <            
293 <            parseIdealLine(read_buffer, integrableObjects[j]);
292 >        
293 >            parseIdealLine(read_buffer, integrableObject);
294 >        
295            }
296 +
297          } else {
298            //molecule belongs to slave nodes
299            
300            MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
301                     TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
302            
303 <          for(j=0; j < nCurObj; j++){
304 <            
305 <            eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile);
306 <            if(eof_test == NULL){
303 >          for(j = 0; j < nCurObj; j++){
304 >            inIdealFile->getline(read_buffer, sizeof(read_buffer));
305 >
306 >            if( inIdealFile->eof() ){
307                sprintf(painCave.errMsg,
308                        "RestReader Error: error in reading file %s\n"
309                        "natoms  = %d; index = %d\n"
310                        "error reading the line from the file.\n",
311 <                      inIdealFileName.c_str(), nTotObjs, i );
311 >                      idealName.c_str(), nTotObjs, i );
312                painCave.isFatal = 1;
313                simError();
314              }
315              
316 <            if(haveError) nodeZeroError();
317 <            
318 <            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
316 >            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
317                       TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
318            }
319          }
320        }
321      } else {
322 <      //actions taken at slave nodes
322 >      //actions taken at slave nodes
323 >      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
324 >
325        for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
326 <        int which_node = info_->getMolToProc(i);
327 <        
326 >        int which_node = info_->getMolToProc(i);
327 >
328          if(which_node == worldRank){
329            //molecule with global index i belongs to this processor
330            
331 <          localIndex = info_->getMoleculeByGlobalIndex(i);
331 >          mol = info_->getMoleculeByGlobalIndex(i);
332            
333 <          if(localIndex == NULL) {
333 >          if(mol == NULL) {
334              sprintf(painCave.errMsg,
335                      "RestReader Error: molecule not found on node %d\n",
336                      worldRank);
# Line 338 | Line 338 | namespace oopse {
338              simError();
339            }
340            
341 <          nCurObj = localIndex->getNIntegrableObjects();
341 >          nCurObj = mol->getNIntegrableObjects();
342            
343            MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
344                     TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
# Line 365 | Line 365 | namespace oopse {
365    
366    char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
367      
368 <    char *foo; // the pointer to the current string token
369 <    
370 <    double pos[3];        // position place holders
371 <    double q[4];          // the quaternions
372 <    double RfromQ[3][3];  // the rotation matrix
373 <    double normalize;     // to normalize the reference unit vector
374 <    double uX, uY, uZ;    // reference unit vector place holders
375 <    double uselessToken;
368 >    RealType pos[3];        // position place holders
369 >    RealType q[4];          // the quaternions
370 >    RealType RfromQ[3][3];  // the rotation matrix
371 >    RealType normalize;     // to normalize the reference unit vector
372 >    RealType uX, uY, uZ;    // reference unit vector place holders
373 >    RealType uselessToken;
374      StringTokenizer tokenizer(readLine);
375      int nTokens;
376      
377      nTokens = tokenizer.countTokens();
378 <    
378 >
379      if (nTokens < 14) {
380        sprintf(painCave.errMsg,
381                "RestReader Error: Not enough Tokens.\n");
# Line 386 | Line 384 | namespace oopse {
384      }
385      
386      std::string name = tokenizer.nextToken();
387 <    
387 >
388      if (name != sd->getType()) {
389        
390        sprintf(painCave.errMsg,
391                "RestReader Error: Atom type [%s] in %s does not "
392                "match Atom Type [%s] in .md file.\n",
393 <              name.c_str(), inIdealFileName.c_str(),
393 >              name.c_str(), idealName.c_str(),
394                sd->getType().c_str());
395        painCave.isFatal = 1;
396        simError();        
# Line 401 | Line 399 | namespace oopse {
399      pos[0] = tokenizer.nextTokenAsDouble();
400      pos[1] = tokenizer.nextTokenAsDouble();
401      pos[2] = tokenizer.nextTokenAsDouble();
402 <    
402 >
403      // store the positions in the stuntdouble as generic data doubles
404      DoubleGenericData* refPosX = new DoubleGenericData();
405      refPosX->setID("refPosX");
406      refPosX->setData(pos[0]);
407      sd->addProperty(refPosX);
408 <    
408 >
409      DoubleGenericData* refPosY = new DoubleGenericData();
410      refPosY->setID("refPosY");
411      refPosY->setData(pos[1]);
# Line 417 | Line 415 | namespace oopse {
415      refPosZ->setID("refPosZ");
416      refPosZ->setData(pos[2]);
417      sd->addProperty(refPosZ);
418 <    
418 >
419      // we don't need the velocities
420      uselessToken = tokenizer.nextTokenAsDouble();
421      uselessToken = tokenizer.nextTokenAsDouble();
# Line 471 | Line 469 | namespace oopse {
469    void RestReader::readZangle(){
470      
471      int i;
474 –    unsigned int j;
472      int isPresent;
473      
474      Molecule* mol;
# Line 480 | Line 477 | namespace oopse {
477      Molecule::IntegrableObjectIterator ii;
478      
479   #ifdef IS_MPI
480 <    int done, which_node, which_atom; // loop counter
484 <    int nProc;
480 >    int which_node;
481      MPI_Status istatus;
482   #endif //is_mpi
483      
484      const int BUFFERSIZE = 2000; // size of the read buffer
485 <    int nTotObjs; // the number of atoms
485 >    unsigned int nTotObjs; // the number of atoms
486      char read_buffer[BUFFERSIZE]; //the line buffer for reading
487      
492 –    char *eof_test; // ptr to see when we reach the end of the file
493 –    char *parseErr;
494 –    
488      std::vector<StuntDouble*> vecParticles;
489 <    std::vector<double> tempZangs;
489 >    std::vector<RealType> tempZangs;
490        
491 <    inAngFileName = info_->getRestFileName();
491 >    angFile = info_->getRestFileName();
492      
493 <    inAngFileName += "0";
493 >    angFile += "0";
494      
495      // open the omega value file for reading
496   #ifdef IS_MPI
497      if (worldRank == 0) {
498   #endif
499        isPresent = 1;
500 <      inAngFile = fopen(inAngFileName.c_str(), "r");
501 <      if(!inAngFile){
500 >      
501 >      inAngFile = new std::ifstream(angFile.c_str());
502 >      
503 >      if(inAngFile->fail()){
504          sprintf(painCave.errMsg,
505                  "Restraints Warning: %s file is not present\n"
506                  "\tAll omega values will be initialized to zero. If the\n"
507                  "\tsimulation is starting from the idealCrystal.in reference\n"
508                  "\tconfiguration, this is the desired action. If this is not\n"
509                  "\tthe case, the energy calculations will be incorrect.\n",
510 <                inAngFileName.c_str());
510 >                angFile.c_str());
511          painCave.severity = OOPSE_WARNING;
512          painCave.isFatal = 0;
513          simError();  
# Line 530 | Line 525 | namespace oopse {
525        }
526        
527   #ifdef IS_MPI
528 +      if (!isPresent) {
529 +        // master node zeroes out its zAngles if .zang0 isn't present
530 +        zeroZangle();
531 +        return;
532 +      }
533 +
534      }
535      
536      // listen to node 0 to see if we should exit this function
# Line 547 | Line 548 | namespace oopse {
548      
549   #ifndef IS_MPI
550      
551 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
552 <    if( eof_test == NULL ){
551 >    // read the first line and die if there is a failure
552 >    inAngFile->getline(read_buffer, sizeof(read_buffer));
553 >
554 >    if( inAngFile->eof() ){
555        sprintf( painCave.errMsg,
556                 "RestraintReader error: error reading 1st line of \"%s\"\n",
557 <               inAngFileName.c_str() );
557 >               angFile.c_str() );
558        painCave.isFatal = 1;
559        simError();
560      }
561 +
562 +    // read the file and load the values into a vector
563 +    inAngFile->getline(read_buffer, sizeof(read_buffer));
564      
565 <    eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
560 <    while ( eof_test != NULL ) {
565 >    while ( !inAngFile->eof() ) {
566        // check for and ignore blank lines
567        if ( read_buffer != NULL )
568          tempZangs.push_back( atof(read_buffer) );
569 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
569 >
570 >      inAngFile->getline(read_buffer, sizeof(read_buffer));
571      }
572      
573      nTotObjs = info_->getNGlobalIntegrableObjects();
# Line 569 | Line 575 | namespace oopse {
575      if( nTotObjs != tempZangs.size() ){
576        sprintf( painCave.errMsg,
577                 "RestraintReader zAngle reading error. %s nIntegrable, %d, "
578 <               "does not match the meta-data file's nIntegrable, %d.\n",
579 <               inAngFileName.c_str(), tempZangs.size(), nTotObjs );
578 >               "does not match the meta-data file's nIntegrable, %i.\n",
579 >               angFile.c_str(),
580 >               tempZangs.size(),
581 >               nTotObjs );
582        painCave.isFatal = 1;
583        simError();
584      }
# Line 594 | Line 602 | namespace oopse {
602      
603      // first thing first, suspend fatalities.
604      painCave.isEventLoop = 1;
605 <    
606 <    int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
607 <    int haveError, index;
608 <    
609 <    int *MolToProcMap = mpiSim->getMolToProcMap();
610 <    int localIndex;
605 >
606 >    int masterNode = 0;
607 >
608 >    int haveError;
609 >    int intObjIndex;    
610 >    int intObjIndexTransfer;    
611 >
612 >    int j;
613      int nCurObj;
614 <    double angleTranfer;
614 >    RealType angleTransfer;
615      
616 <    nTotObjs = info_->getTotIntegrableObjects();
616 >    nTotObjs = info_->getNGlobalIntegrableObjects();
617      haveError = 0;
618 <    if (worldRank == 0) {
618 >
619 >    if (worldRank == masterNode) {
620        
621 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
622 <      if( eof_test == NULL ){
621 >      inAngFile->getline(read_buffer, sizeof(read_buffer));
622 >
623 >      if( inAngFile->eof() ){
624          sprintf( painCave.errMsg,
625 <                 "Error reading 1st line of %s \n ",inAngFileName.c_str());
625 >                 "Error reading 1st line of %s \n ",angFile.c_str());
626          haveError = 1;
627          simError();
628        }
629        
630 <      // let node 0 load the temporary angle vector
631 <      eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
632 <      while ( eof_test != NULL ) {
630 >      // let the master node read the file and load the temporary angle vector
631 >      inAngFile->getline(read_buffer, sizeof(read_buffer));
632 >
633 >      while ( !inAngFile->eof() ) {
634          // check for and ignore blank lines
635          if ( read_buffer != NULL )
636            tempZangs.push_back( atof(read_buffer) );
637 <        eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile);
637 >
638 >        inAngFile->getline(read_buffer, sizeof(read_buffer));
639        }
640 <      
640 >
641        // Check to see that the number of integrable objects in the
642        // intial configuration file is the same as derived from the
643        // meta-data file.
# Line 631 | Line 645 | namespace oopse {
645          sprintf( painCave.errMsg,
646                   "RestraintReader zAngle reading Error. %s nIntegrable, %d, "
647                   "does not match the meta-data file's nIntegrable, %d.\n",
648 <                 inAngFileName.c_str(), tempZangs.size(), nTotObjs);
648 >                 angFile.c_str(),
649 >                 tempZangs.size(),
650 >                 nTotObjs);
651          haveError= 1;
652          simError();
653        }
654        
655 <    }
656 <    // At this point, node 0 has a tempZangs vector completed, and
641 <    // everyone else has nada
642 <    index = 0;
643 <    
644 <    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
645 <      // Get the Node number which has this atom
646 <      which_node = MolToProcMap[i];
655 >      // At this point, node 0 has a tempZangs vector completed, and
656 >      // everyone else has nada
657        
658 <      if (worldRank == 0) {
659 <        if (which_node == 0) {
660 <          localIndex = mpiSim->getGlobalToLocalMol(i);
661 <          
662 <          if(localIndex == -1) {
663 <            strcpy(painCave.errMsg, "Molecule not found on node 0!");
664 <            haveError = 1;
658 >      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
659 >        // Get the Node number which has this atom
660 >        which_node = info_->getMolToProc(i);
661 >        
662 >        if (which_node == masterNode) {
663 >          mol = info_->getMoleculeByGlobalIndex(i);
664 >
665 >          if(mol == NULL) {
666 >            strcpy(painCave.errMsg, "Molecule not found on node 0!");
667 >            haveError = 1;
668 >            simError();
669 >          }
670 >
671 >          for (integrableObject = mol->beginIntegrableObject(ii);
672 >               integrableObject != NULL;
673 >               integrableObject = mol->nextIntegrableObject(ii)){
674 >            intObjIndex = integrableObject->getGlobalIndex();
675 >            integrableObject->setZangle(tempZangs[intObjIndex]);
676 >          }    
677 >          
678 >        } else {
679 >          // I am MASTER OF THE UNIVERSE, but I don't own this molecule
680 >          // listen for the number of integrableObjects in the molecule
681 >          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
682 >                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
683 >          
684 >          for(j=0; j < nCurObj; j++){          
685 >            // listen for which integrableObject we need to send the value for
686 >            MPI_Recv(&intObjIndexTransfer, 1, MPI_INT, which_node,
687 >                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
688 >            angleTransfer = tempZangs[intObjIndexTransfer];
689 >            // send the value to the node so it can initialize the object
690 >            MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
691 >                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);              
692 >          }
693 >        }
694 >      }
695 >    } else {
696 >      // I am SLAVE TO THE MASTER
697 >      for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
698 >        which_node = info_->getMolToProc(i);
699 >
700 >        if (which_node == worldRank) {
701 >          
702 >          // BUT I OWN THIS MOLECULE!!!
703 >          
704 >          mol = info_->getMoleculeByGlobalIndex(i);
705 >
706 >          if(mol == NULL) {
707 >            sprintf(painCave.errMsg,
708 >                    "RestReader Error: molecule not found on node %d\n",
709 >                    worldRank);
710 >            painCave.isFatal = 1;
711              simError();
712            }
713 <          
714 <          vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
715 <          for(j = 0; j < vecParticles.size(); j++){      
716 <            vecParticles[j]->setZangle(tempZangs[index]);
717 <            index++;
718 <          }    
719 <          
720 <        } else {
721 <          // I am MASTER OF THE UNIVERSE, but I don't own this molecule
722 <          
723 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
724 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
725 <          
726 <          for(j=0; j < nCurObj; j++){            
727 <            angleTransfer = tempZangs[index];
728 <            MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
729 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);              
730 <            index++;
731 <          }
732 <          
677 <        }
678 <        
679 <      } else {
680 <        // I am SLAVE TO THE MASTER
681 <        
682 <        if (which_node == worldRank) {
683 <          
684 <          // BUT I OWN THIS MOLECULE!!!
685 <          
686 <          localIndex = mpiSim->getGlobalToLocalMol(i);
687 <          vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
688 <          nCurObj = vecParticles.size();
689 <          
690 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
691 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
692 <          
693 <          for(j = 0; j < vecParticles.size(); j++){
694 <            
695 <            MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
696 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
697 <            vecParticles[j]->setZangle(angleTransfer);
698 <          }    
699 <        }
713 >
714 >          nCurObj = mol->getNIntegrableObjects();
715 >          // send the number of integrableObjects in the molecule
716 >          MPI_Send(&nCurObj, 1, MPI_INT, 0,
717 >                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
718 >          
719 >          for (integrableObject = mol->beginIntegrableObject(ii);
720 >               integrableObject != NULL;
721 >               integrableObject = mol->nextIntegrableObject(ii)){
722 >            intObjIndexTransfer = integrableObject->getGlobalIndex();
723 >            // send the global index of the integrableObject
724 >            MPI_Send(&intObjIndexTransfer, 1, MPI_INT, 0,
725 >                     TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
726 >            // listen for the value we want to set locally
727 >            MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
728 >                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
729 >
730 >            integrableObject->setZangle(angleTransfer);
731 >          }    
732 >        }
733        }
734 <    }
734 >    }
735   #endif
736    }
737    
738    void RestReader :: zeroZangle(){
739      
707 –    int i;
708 –    unsigned int j;
709 –    int nTotObjs; // the number of atoms
710 –    
740      Molecule* mol;
741      StuntDouble* integrableObject;
742      SimInfo::MoleculeIterator mi;
743      Molecule::IntegrableObjectIterator ii;
744 <    
716 <    std::vector<StuntDouble*> vecParticles;
717 <    
744 >    
745   #ifndef IS_MPI
746      // set all zAngles to 0.0
747      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 733 | Line 760 | namespace oopse {
760      painCave.isEventLoop = 1;
761      
762      int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
763 <    int haveError, index;
763 >    int haveError;
764      int which_node;
765      
739 –    MPI_Status istatus;
740 –    int *MolToProcMap = mpiSim->getMolToProcMap();
741 –    int localIndex;
742 –    int nCurObj;
743 –    double angleTranfer;
744 –    
745 –    nTotObjs = info_->getTotIntegrableObjects();
766      haveError = 0;
767 <    
768 <    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
767 >
768 >    for (int i=0 ; i < info_->getNGlobalMolecules(); i++) {
769 >
770        // Get the Node number which has this atom
771 <      which_node = MolToProcMap[i];
772 <      
773 <      // let's let node 0 pass out constant values to all the processors
774 <      if (worldRank == 0) {
775 <        if (which_node == 0) {
776 <          localIndex = mpiSim->getGlobalToLocalMol(i);
777 <          
778 <          if(localIndex == -1) {
779 <            strcpy(painCave.errMsg, "Molecule not found on node 0!");
780 <            haveError = 1;
781 <            simError();
782 <          }
783 <          
784 <          vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
785 <          for(j = 0; j < vecParticles.size(); j++){      
786 <            vecParticles[j]->setZangle( 0.0 );
787 <          }    
788 <          
789 <        } else {
790 <          // I am MASTER OF THE UNIVERSE, but I don't own this molecule
791 <          
771 <          MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
772 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
773 <          
774 <          for(j=0; j < nCurObj; j++){            
775 <            angleTransfer = 0.0;
776 <            MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node,
777 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);              
778 <            index++;
779 <          }
780 <        }
781 <      } else {
782 <        // I am SLAVE TO THE MASTER
783 <        
784 <        if (which_node == worldRank) {
785 <          
786 <          // BUT I OWN THIS MOLECULE!!!
787 <          
788 <          localIndex = mpiSim->getGlobalToLocalMol(i);
789 <          vecParticles = (info_->molecules[localIndex]).getIntegrableObjects();
790 <          nCurObj = vecParticles.size();
791 <          
792 <          MPI_Send(&nCurObj, 1, MPI_INT, 0,
793 <                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
794 <          
795 <          for(j = 0; j < vecParticles.size(); j++){
796 <            
797 <            MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0,
798 <                     TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
799 <            vecParticles[j]->setZangle(angleTransfer);
800 <          }    
801 <        }
771 >      which_node = info_->getMolToProc(i);
772 >        
773 >      // each processor zeroes its own integrable objects
774 >      if (which_node == worldRank) {
775 >        mol = info_->getMoleculeByGlobalIndex(i);
776 >        
777 >        if(mol == NULL) {
778 >          sprintf( painCave.errMsg,
779 >                  "Molecule not found on node %i!",
780 >                  which_node );
781 >          haveError = 1;
782 >          simError();
783 >        }
784 >        
785 >        for (integrableObject = mol->beginIntegrableObject(ii);
786 >             integrableObject != NULL;
787 >             integrableObject = mol->nextIntegrableObject(ii)){
788 >          
789 >          integrableObject->setZangle( 0.0 );
790 >          
791 >        }
792        }
793      }
794 +
795   #endif
796    }
797    

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