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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 823 by chuckv, Thu Dec 29 16:03:11 2005 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 46 | Line 46
46   * @time 13:51am
47   * @version 1.0
48   */
49 <
49 > #include <exception>
50   #include <iostream>
51   #include <sstream>
52   #include <string>
# Line 102 | Line 102 | Globals* SimCreator::parseFile(const std::string mdFil
102                  streamSize = ppStream.str().size() +1;
103                  commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
104  
105 <                commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
105 >                commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
106              
107                  
108              } else {
# Line 147 | Line 147 | Globals* SimCreator::parseFile(const std::string mdFil
147               simParams = treeParser.walkTree(parser.getAST());
148  
149          }
150 +
151        
152        catch(antlr::MismatchedCharException& e) {
153 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
153 >          sprintf(painCave.errMsg,
154 >                  "parser exception: %s %s:%d:%d\n",
155 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
156 >          painCave.isFatal = 1;
157 >          simError();          
158        }
159        catch(antlr::MismatchedTokenException &e) {
160 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
160 >          sprintf(painCave.errMsg,
161 >                  "parser exception: %s %s:%d:%d\n",
162 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
163 >          painCave.isFatal = 1;
164 >          simError();  
165        }
166        catch(antlr::NoViableAltForCharException &e) {
167 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
167 >          sprintf(painCave.errMsg,
168 >                  "parser exception: %s %s:%d:%d\n",
169 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
170 >          painCave.isFatal = 1;
171 >          simError();  
172        }
173        catch(antlr::NoViableAltException &e) {
174 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
174 >          sprintf(painCave.errMsg,
175 >                  "parser exception: %s %s:%d:%d\n",
176 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
177 >          painCave.isFatal = 1;
178 >          simError();  
179        }
180 +      
181          catch(antlr::TokenStreamRecognitionException& e) {
182 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
182 >          sprintf(painCave.errMsg,
183 >                  "parser exception: %s %s:%d:%d\n",
184 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
185 >          painCave.isFatal = 1;
186 >          simError();  
187          }
188 +        
189          catch(antlr::TokenStreamIOException& e) {
190 <          cerr<< "parser exception: " << e.getMessage() << endl;
190 >          sprintf(painCave.errMsg,
191 >                  "parser exception: %s\n",
192 >                  e.getMessage().c_str());
193 >          painCave.isFatal = 1;
194 >          simError();
195          }
196 +        
197          catch(antlr::TokenStreamException& e) {
198 <          cerr<< "parser exception: " << e.getMessage() << endl;
198 >          sprintf(painCave.errMsg,
199 >                  "parser exception: %s\n",
200 >                  e.getMessage().c_str());
201 >          painCave.isFatal = 1;
202 >          simError();
203          }        
204         catch (antlr::RecognitionException& e) {
205 <          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
205 >          sprintf(painCave.errMsg,
206 >                  "parser exception: %s %s:%d:%d\n",
207 >                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
208 >          painCave.isFatal = 1;
209 >          simError();          
210         }
211         catch (antlr::CharStreamException& e) {
212 <            cerr << "parser exception: " << e.getMessage() << endl;
212 >          sprintf(painCave.errMsg,
213 >                  "parser exception: %s\n",
214 >                  e.getMessage().c_str());
215 >          painCave.isFatal = 1;
216 >          simError();        
217         }
218 <        catch (exception& e) {
219 <            cerr << "parser exception: " << e.what() << endl;
220 <        }
218 >       catch (OOPSEException& e) {
219 >          sprintf(painCave.errMsg,
220 >                  "%s\n",
221 >                  e.getMessage().c_str());
222 >          painCave.isFatal = 1;
223 >          simError();
224 >       }
225 >       catch (std::exception& e) {
226 >          sprintf(painCave.errMsg,
227 >                  "parser exception: %s\n",
228 >                  e.what());
229 >          painCave.isFatal = 1;
230 >          simError();
231 >       }
232  
233          return simParams;
234    }
# Line 228 | Line 279 | Globals* SimCreator::parseFile(const std::string mdFil
279      //create SimInfo
280      SimInfo * info = new SimInfo(ff, simParams);
281      
282 <    //gather parameters (SimCreator only retrieves part of the parameters)
282 >    //gather parameters (SimCreator only retrieves part of the
283 >    //parameters)
284      gatherParameters(info, mdFileName);
285      
286      //divide the molecules and determine the global index of molecules
# Line 240 | Line 292 | Globals* SimCreator::parseFile(const std::string mdFil
292      createMolecules(info);
293      
294      
295 <    //allocate memory for DataStorage(circular reference, need to break it)
295 >    //allocate memory for DataStorage(circular reference, need to
296 >    //break it)
297      info->setSnapshotManager(new SimSnapshotManager(info));
298      
299 <    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
300 <    //global index will never change again). Local indices of atoms and rigidbodies are already set by
301 <    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager.
299 >    //set the global index of atoms, rigidbodies and cutoffgroups
300 >    //(only need to be set once, the global index will never change
301 >    //again). Local indices of atoms and rigidbodies are already set
302 >    //by MoleculeCreator class which actually delegates the
303 >    //responsibility to LocalIndexManager.
304      setGlobalIndex(info);
305      
306 <    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
307 <    //atoms don't have the global index yet  (their global index are all initialized to -1).
308 <    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
309 <    //we can determine the beginning global indices of atoms before they get created.
306 >    //Although addExcludePairs is called inside SimInfo's addMolecule
307 >    //method, at that point atoms don't have the global index yet
308 >    //(their global index are all initialized to -1).  Therefore we
309 >    //have to call addExcludePairs explicitly here. A way to work
310 >    //around is that we can determine the beginning global indices of
311 >    //atoms before they get created.
312      SimInfo::MoleculeIterator mi;
313      Molecule* mol;
314      for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
# Line 295 | Line 352 | Globals* SimCreator::parseFile(const std::string mdFil
352    
353   #ifdef IS_MPI
354    void SimCreator::divideMolecules(SimInfo *info) {
355 <    double numerator;
356 <    double denominator;
357 <    double precast;
358 <    double x;
359 <    double y;
360 <    double a;
355 >    RealType numerator;
356 >    RealType denominator;
357 >    RealType precast;
358 >    RealType x;
359 >    RealType y;
360 >    RealType a;
361      int old_atoms;
362      int add_atoms;
363      int new_atoms;
# Line 412 | Line 469 | Globals* SimCreator::parseFile(const std::string mdFil
469            //           Pacc(x) = exp(- a * x)
470            // where a = penalty / (average atoms per molecule)
471            
472 <          x = (double)(new_atoms - nTarget);
472 >          x = (RealType)(new_atoms - nTarget);
473            y = myRandom->rand();
474            
475            if (y < exp(- a * x)) {

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