# | Line 161 | Line 161 | void SimSetup::createSim( void ){ | |
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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; |
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