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root/OpenMD/trunk/src/brains/ForceField.cpp
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Comparing trunk/src/UseTheForce/ForceField.cpp (file contents):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 54 | Line 54
54   #include "UseTheForce/DarkSide/atype_interface.h"
55   #include "UseTheForce/DarkSide/fForceOptions_interface.h"
56   #include "UseTheForce/DarkSide/switcheroo_interface.h"
57 < namespace oopse {
57 > namespace OpenMD {
58  
59    ForceField::ForceField() {
60      char* tempPath;
# Line 133 | Line 133 | namespace oopse {
133          ii++;
134        }
135  
136 –      // sort the foundBonds by the score:
136  
137 <      std::sort(foundBonds.begin(), foundBonds.end());
138 <      
139 <      int bestScore = foundBonds[0].first;
140 <      std::vector<std::string> theKeys = foundBonds[0].second;
141 <
142 <      std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";      
143 <      BondType* bestType = bondTypeCont_.find(theKeys);
144 <      if (bestType)
145 <        return bestType;
146 <      else {
147 <        //if no exact match found, try wild card match
148 <        return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
137 >      if (foundBonds.size() > 0) {
138 >        // sort the foundBonds by the score:
139 >        std::sort(foundBonds.begin(), foundBonds.end());
140 >    
141 >        int bestScore = foundBonds[0].first;
142 >        std::vector<std::string> theKeys = foundBonds[0].second;
143 >        
144 >        BondType* bestType = bondTypeCont_.find(theKeys);
145 >        
146 >        return bestType;
147 >      } else {
148 >        //if no exact match found, try wild card match
149 >        return bondTypeCont_.find(keys, wildCardAtomTypeName_);      
150        }
151      }
152    }
# Line 220 | Line 220 | namespace oopse {
220          jj++;
221        }
222        
223 <      std::sort(foundBends.begin(), foundBends.end());
224 <
225 <      int jscore = foundBends[0].first;
226 <      int ikscore = foundBends[0].second;
227 <      std::vector<std::string> theKeys = foundBends[0].third;
228 <
229 <      std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";      
230 <
231 <      BendType* bestType = bendTypeCont_.find(theKeys);  
232 <      if (bestType)
233 <        return bestType;
234 <      else {
235 <      
223 >      if (foundBends.size() > 0) {
224 >        std::sort(foundBends.begin(), foundBends.end());
225 >        int jscore = foundBends[0].first;
226 >        int ikscore = foundBends[0].second;
227 >        std::vector<std::string> theKeys = foundBends[0].third;      
228 >        
229 >        BendType* bestType = bendTypeCont_.find(theKeys);  
230 >        return bestType;
231 >      } else {        
232          //if no exact match found, try wild card match
233          return bendTypeCont_.find(keys, wildCardAtomTypeName_);      
234        }
235      }
236    }
237  
242 –
238    TorsionType* ForceField::getTorsionType(const std::string &at1,
239                                            const std::string &at2,
240                                            const std::string &at3,
# Line 327 | Line 322 | namespace oopse {
322          jj++;
323        }
324        
325 <      std::sort(foundTorsions.begin(), foundTorsions.end());
326 <
327 <      int jkscore = foundTorsions[0].first;
328 <      int ilscore = foundTorsions[0].second;
329 <      std::vector<std::string> theKeys = foundTorsions[0].third;
330 <
331 <      std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
332 <
338 <      
339 <      TorsionType* bestType = torsionTypeCont_.find(theKeys);
340 <      if (bestType) {
341 <        return bestType;
325 >      if (foundTorsions.size() > 0) {
326 >        std::sort(foundTorsions.begin(), foundTorsions.end());
327 >        int jkscore = foundTorsions[0].first;
328 >        int ilscore = foundTorsions[0].second;
329 >        std::vector<std::string> theKeys = foundTorsions[0].third;
330 >        
331 >        TorsionType* bestType = torsionTypeCont_.find(theKeys);
332 >        return bestType;
333        } else {
334          //if no exact match found, try wild card match
335          return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
# Line 357 | Line 348 | namespace oopse {
348      keys.push_back(at4);    
349  
350      //try exact match first
351 <    InversionType* inversionType = inversionTypeCont_.find(keys);
351 >    InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
352      if (inversionType) {
353        return inversionType;
354      } else {
# Line 419 | Line 410 | namespace oopse {
410                myKeys.push_back((*k)->getName());
411                myKeys.push_back((*l)->getName());
412                
413 <              InversionType* inversionType = inversionTypeCont_.find(myKeys);
413 >              InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
414                if (inversionType) {
415                  foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
416                }
# Line 431 | Line 422 | namespace oopse {
422          }
423          jj++;
424        }
425 <      
426 <      std::sort(foundInversions.begin(), foundInversions.end());
427 <      
428 <      int iscore = foundInversions[0].first;
429 <      int jklscore = foundInversions[0].second;
430 <      std::vector<std::string> theKeys = foundInversions[0].third;
431 <      
432 <      std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
433 <      
443 <      
444 <      InversionType* bestType = inversionTypeCont_.find(theKeys);
445 <      if (bestType) {
446 <        return bestType;
425 >        
426 >      if (foundInversions.size() > 0) {
427 >        std::sort(foundInversions.begin(), foundInversions.end());
428 >        int iscore = foundInversions[0].first;
429 >        int jklscore = foundInversions[0].second;
430 >        std::vector<std::string> theKeys = foundInversions[0].third;
431 >        
432 >        InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
433 >        return bestType;
434        } else {
435          //if no exact match found, try wild card match
436          return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
# Line 522 | Line 509 | namespace oopse {
509      return atomTypeCont_.add(keys, atomType);
510    }
511  
512 +  bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
513 +    std::vector<std::string> keys;
514 +    keys.push_back(at);
515 +    return atomTypeCont_.replace(keys, atomType);
516 +  }
517 +
518    bool ForceField::addBondType(const std::string &at1, const std::string &at2,
519                                 BondType* bondType) {
520      std::vector<std::string> keys;
# Line 593 | Line 586 | namespace oopse {
586          } else {
587            sprintf( painCave.errMsg,
588                     "Can not cast GenericData to LJParam\n");
589 <          painCave.severity = OOPSE_ERROR;
589 >          painCave.severity = OPENMD_ERROR;
590            painCave.isFatal = 1;
591            simError();          
592          }            
593        } else {
594          sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
595 <        painCave.severity = OOPSE_ERROR;
595 >        painCave.severity = OPENMD_ERROR;
596          painCave.isFatal = 1;
597          simError();          
598        }
# Line 629 | Line 622 | namespace oopse {
622                   "\tHave you tried setting the FORCE_PARAM_PATH environment "
623                   "variable?\n",
624                   forceFieldFilename.c_str() );
625 <        painCave.severity = OOPSE_ERROR;
625 >        painCave.severity = OPENMD_ERROR;
626          painCave.isFatal = 1;
627          simError();
628        }
# Line 642 | Line 635 | namespace oopse {
635      forceFieldOptions_.makeFortranOptions(theseFortranOptions);
636      setfForceOptions(&theseFortranOptions);
637    }
638 < } //end namespace oopse
638 > } //end namespace OpenMD

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