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; |