| 73 |
|
|
| 74 |
|
MakeStamps *the_stamps; |
| 75 |
|
Globals* the_globals; |
| 76 |
< |
int i; |
| 76 |
> |
int i, j; |
| 77 |
|
|
| 78 |
|
// get the stamps and globals; |
| 79 |
|
the_stamps = stamps; |
| 161 |
|
#endif // is_mpi |
| 162 |
|
|
| 163 |
|
// make an array of molecule stamps that match the components used. |
| 164 |
+ |
// also extract the used stamps out into a separate linked list |
| 165 |
|
|
| 166 |
+ |
simnfo->nComponents = n_components; |
| 167 |
+ |
simnfo->componentsNmol = components_nmol; |
| 168 |
+ |
simnfo->compStamps = comp_stamps; |
| 169 |
+ |
simnfo->headStamp = new LinkedMolStamp(); |
| 170 |
+ |
|
| 171 |
+ |
char* id; |
| 172 |
+ |
LinkedMolStamp* headStamp = simnfo->headStamp; |
| 173 |
+ |
LinkedMolStamp* currentStamp = NULL; |
| 174 |
|
for( i=0; i<n_components; i++ ){ |
| 175 |
|
|
| 176 |
< |
comp_stamps[i] = |
| 177 |
< |
the_stamps->getMolecule( the_components[i]->getType() ); |
| 176 |
> |
id = the_components[i]->getType(); |
| 177 |
> |
comp_stamps[i] = NULL; |
| 178 |
> |
|
| 179 |
> |
// check to make sure the component isn't already in the list |
| 180 |
> |
|
| 181 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 182 |
> |
if( comp_stamps[i] == NULL ){ |
| 183 |
> |
|
| 184 |
> |
// extract the component from the list; |
| 185 |
> |
|
| 186 |
> |
currentStamp = the_stamps->extractMolStamp( id ); |
| 187 |
> |
if( currentStamp == NULL ){ |
| 188 |
> |
sprintf( painCave.errMsg, |
| 189 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
| 190 |
> |
"list of declared molecules\n" |
| 191 |
> |
id ); |
| 192 |
> |
painCave.isFatal = 1; |
| 193 |
> |
simError(); |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
headStamp->add( currentStamp ); |
| 197 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 198 |
> |
} |
| 199 |
|
} |
| 200 |
|
|
| 201 |
+ |
#ifdef IS_MPI |
| 202 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
| 203 |
+ |
MPIcheckPoint(); |
| 204 |
+ |
#endif // is_mpi |
| 205 |
+ |
|
| 206 |
|
|
| 207 |
|
|
| 208 |
+ |
|
| 209 |
|
// caclulate the number of atoms, bonds, bends and torsions |
| 210 |
|
|
| 211 |
|
tot_atoms = 0; |
| 213 |
|
tot_bends = 0; |
| 214 |
|
tot_torsions = 0; |
| 215 |
|
for( i=0; i<n_components; i++ ){ |
| 216 |
< |
|
| 217 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 218 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 219 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 216 |
> |
|
| 217 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
| 218 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
| 219 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
| 220 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
| 221 |
|
} |
| 222 |
|
|
| 234 |
|
|
| 235 |
|
// divide the molecules among processors here. |
| 236 |
|
|
| 237 |
< |
new mpiSimulation( simnfo ); |
| 237 |
> |
mpiSimulation* mpiSim = new mpiSimulation( simnfo ); |
| 238 |
|
|
| 239 |
< |
simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol ); |
| 239 |
> |
mpiSim->divideLabor(); |
| 240 |
> |
|
| 241 |
> |
// set up the local variables |
| 242 |
> |
|
| 243 |
> |
int localMol; |
| 244 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 245 |
> |
|
| 246 |
> |
localMol = 0; |
| 247 |
> |
local_atoms = 0; |
| 248 |
> |
local_bonds = 0; |
| 249 |
> |
local_bends = 0; |
| 250 |
> |
local_torsions = 0; |
| 251 |
> |
for( i=0; i<n_components; i++ ){ |
| 252 |
> |
|
| 253 |
> |
for( j=0; j<components_nmol[i]; j++ ){ |
| 254 |
> |
|
| 255 |
> |
if( mpiSim->getMyMolStart() <= j && |
| 256 |
> |
j <= mpiSim->getMyMolEnd() ){ |
| 257 |
> |
|
| 258 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
| 259 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
| 260 |
> |
local_bends += comp_stamps[i]->getNBends(); |
| 261 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
| 262 |
> |
localMol++; |
| 263 |
> |
} |
| 264 |
> |
} |
| 265 |
> |
} |
| 266 |
|
|
| 267 |
+ |
|
| 268 |
+ |
|
| 269 |
+ |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 270 |
+ |
|
| 271 |
+ |
|
| 272 |
|
#endif // is_mpi |
| 273 |
|
|
| 274 |
|
|
| 593 |
|
the_molecules[molIndex].setNMembers( nMemb ); |
| 594 |
|
the_molecules[molIndex].setStartAtom( molStart ); |
| 595 |
|
the_molecules[molIndex].setEndAtom( molEnd ); |
| 596 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 597 |
|
molIndex++; |
| 598 |
|
|
| 599 |
|
} |
