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root/group/trunk/OOPSE/libmdtools/InitializeFromFile.cpp
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Comparing trunk/OOPSE/libmdtools/InitializeFromFile.cpp (file contents):
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 2004 UTC

# Line 16 | Line 16
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
19 > #define TAKE_THIS_TAG_CHAR 3134
20 > #define TAKE_THIS_TAG_INT 3135
21  
22   namespace initFile{
23    void nodeZeroError( void );
# Line 175 | Line 175 | void InitializeFromFile :: readInit( SimInfo* the_simn
175    int *MolToProcMap = mpiSim->getMolToProcMap();
176    int localIndex;
177    int nCurObj;
178 +  int nItems;
179  
180 +  nTotObjs = simnfo->getTotIntegrableObjects();
181    haveError = 0;
182    if (worldRank == 0) {
183  
# Line 187 | Line 189 | void InitializeFromFile :: readInit( SimInfo* the_simn
189        simError();
190      }
191  
192 <    nTotObjs = atoi( read_buffer );
192 >    nItems = atoi( read_buffer );
193  
194      // Check to see that the number of integrable objects  in the intial configuration file is the
195      // same as declared in simBass.
196  
197 <    if( nTotObjs != simnfo->getTotIntegrableObjects()){
197 >    if( nTotObjs != nItems){
198        sprintf( painCave.errMsg,
199                 "Initialize from File error. %s n_atoms, %d, "
200                 "does not match the BASS file's n_atoms, %d.\n",
# Line 218 | Line 220 | void InitializeFromFile :: readInit( SimInfo* the_simn
220  
221      MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222  
223 +
224      parseErr = parseCommentLine( read_buffer, simnfo);
225  
226      if( parseErr != NULL ){
# Line 226 | Line 229 | void InitializeFromFile :: readInit( SimInfo* the_simn
229        simError();
230      }
231  
232 <    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
232 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
233        which_node = MolToProcMap[i];
234        if(which_node == 0){
235         //molecules belong to master node
# Line 255 | Line 258 | void InitializeFromFile :: readInit( SimInfo* the_simn
258            
259            if(haveError) nodeZeroError();
260  
261 <          parseDumpLine(read_buffer, integrableObjects[i]);
261 >          parseDumpLine(read_buffer, integrableObjects[j]);
262            
263         }
264  
# Line 264 | Line 267 | void InitializeFromFile :: readInit( SimInfo* the_simn
267        else{
268        //molecule belongs to slave nodes
269  
270 <        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
270 >        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272 <      
273 <       for(j=0; j < integrableObjects.size(); j++){
272 >
273 >       for(j=0; j < nCurObj; j++){
274          
275            eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276            if(eof_test == NULL){
# Line 284 | Line 287 | void InitializeFromFile :: readInit( SimInfo* the_simn
287  
288              MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289                        TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290 <          
290 >
291         }
292  
293        }
# Line 294 | Line 297 | void InitializeFromFile :: readInit( SimInfo* the_simn
297    }
298    else{
299    //actions taken at slave nodes
300 <    for (i=0 ; i < mpiSim->getTotNmol(); i++) {
300 >
301 >    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302 >
303 >    parseErr = parseCommentLine( read_buffer, simnfo);
304 >
305 >    if( parseErr != NULL ){
306 >      strcpy( painCave.errMsg, parseErr );
307 >      haveError = 1;
308 >      simError();
309 >    }
310 >  
311 >    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
312        which_node = MolToProcMap[i];
313        
314        if(which_node == worldRank){
# Line 312 | Line 326 | void InitializeFromFile :: readInit( SimInfo* the_simn
326  
327          nCurObj = integrableObjects.size();
328          
329 <        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
330 <                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
329 >        MPI_Send(&nCurObj, 1, MPI_INT, 0,
330 >                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331  
332          for(j = 0; j < integrableObjects.size(); j++){
333  
# Line 504 | Line 518 | char* InitializeFromFile::parseDumpLine(char* readLine
518  
519      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520  
521 +    if (fabs(qSqr) < 1e-6) {
522 +      sprintf(painCave.errMsg,
523 +          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
524 +       return strdup(painCave.errMsg);
525 +    }
526 +    
527      qLength = sqrt( qSqr );
528      q[0] = q[0] / qLength;
529      q[1] = q[1] / qLength;
# Line 617 | Line 637 | char* InitializeFromFile::parseCommentLine(char* readL
637      
638      //push eta into SimInfo::properties which can be
639      //retrieved by integrator later
640 <    //entry_plug->setBoxM( theBoxMat3 );
640 >    
641      DoubleArrayData* etaValue = new DoubleArrayData();
642      etaValue->setID(ETAVALUE_ID);
643      etaValue->setData(eta, 9);
# Line 635 | Line 655 | void initFile::nodeZeroError( void ){
655    int j, myStatus;
656  
657    myStatus = 0;
658 <  for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
658 >  for (j = 0; j < mpiSim->getNProcessors(); j++) {
659      MPI_Send( &myStatus, 1, MPI_INT, j,
660                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661    }

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