| 92 |
|
char *parseErr; |
| 93 |
|
|
| 94 |
|
vector<StuntDouble*> integrableObjects; |
| 95 |
– |
vector<StuntDouble*>::iterator iter; |
| 95 |
|
|
| 96 |
|
simnfo = the_simnfo; |
| 97 |
|
|
| 140 |
|
|
| 141 |
|
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
| 142 |
|
|
| 143 |
< |
for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++) |
| 143 |
> |
for(j = 0; j < integrableObjects.size(); j++){ |
| 144 |
|
|
| 145 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
| 146 |
|
if(eof_test == NULL){ |
| 153 |
|
simError(); |
| 154 |
|
} |
| 155 |
|
|
| 156 |
< |
parseErr = parseDumpLine( read_buffer, *iter); |
| 156 |
> |
parseErr = parseDumpLine( read_buffer, integrableObjects[j]); |
| 157 |
|
if( parseErr != NULL ){ |
| 158 |
|
strcpy( painCave.errMsg, parseErr ); |
| 159 |
|
painCave.isFatal = 1; |
| 160 |
|
simError(); |
| 161 |
|
} |
| 162 |
+ |
} |
| 163 |
|
} |
| 164 |
|
|
| 165 |
– |
|
| 165 |
|
// MPI Section of code.......... |
| 166 |
|
#else //IS_MPI |
| 167 |
|
|
| 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 |
|
|
| 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", |
| 257 |
|
|
| 258 |
|
if(haveError) nodeZeroError(); |
| 259 |
|
|
| 260 |
< |
parseDumpLine(read_buffer, integrableObjects[i]); |
| 260 |
> |
parseDumpLine(read_buffer, integrableObjects[j]); |
| 261 |
|
|
| 262 |
|
} |
| 263 |
|
|
| 266 |
|
else{ |
| 267 |
|
//molecule belongs to slave nodes |
| 268 |
|
|
| 269 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
| 269 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 270 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 271 |
|
|
| 272 |
|
for(j=0; j < integrableObjects.size(); j++){ |
| 296 |
|
} |
| 297 |
|
else{ |
| 298 |
|
//actions taken at slave nodes |
| 299 |
+ |
|
| 300 |
+ |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
| 301 |
+ |
|
| 302 |
+ |
parseErr = parseCommentLine( read_buffer, simnfo); |
| 303 |
+ |
|
| 304 |
+ |
if( parseErr != NULL ){ |
| 305 |
+ |
strcpy( painCave.errMsg, parseErr ); |
| 306 |
+ |
haveError = 1; |
| 307 |
+ |
simError(); |
| 308 |
+ |
} |
| 309 |
+ |
|
| 310 |
|
for (i=0 ; i < mpiSim->getTotNmol(); i++) { |
| 311 |
|
which_node = MolToProcMap[i]; |
| 312 |
|
|
| 325 |
|
|
| 326 |
|
nCurObj = integrableObjects.size(); |
| 327 |
|
|
| 328 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, 0, |
| 329 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 328 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 329 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 330 |
|
|
| 331 |
|
for(j = 0; j < integrableObjects.size(); j++){ |
| 332 |
|
|
| 630 |
|
|
| 631 |
|
//push eta into SimInfo::properties which can be |
| 632 |
|
//retrieved by integrator later |
| 633 |
< |
//entry_plug->setBoxM( theBoxMat3 ); |
| 633 |
> |
|
| 634 |
|
DoubleArrayData* etaValue = new DoubleArrayData(); |
| 635 |
|
etaValue->setID(ETAVALUE_ID); |
| 636 |
|
etaValue->setData(eta, 9); |
