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Comparing trunk/src/UseTheForce/ForceField.cpp (file contents):
Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 + *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 +
42 + /**
43 + * @file ForceField.cpp
44 + * @author tlin
45 + * @date 11/04/2004
46 + * @time 22:51am
47 + * @version 1.0
48 + */
49 +  
50 + #include <algorithm>
51   #include "UseTheForce/ForceField.hpp"
52 + #include "utils/simError.h"
53 + #include "utils/Tuple.hpp"
54 + #include "UseTheForce/DarkSide/atype_interface.h"
55 + #include "UseTheForce/DarkSide/fForceOptions_interface.h"
56 + #include "UseTheForce/DarkSide/switcheroo_interface.h"
57 + namespace oopse {
58  
59 < AtomType* ForceField::getMatchingAtomType(const string &at) {
59 >  ForceField::ForceField() {
60 >    char* tempPath;
61 >    tempPath = getenv("FORCE_PARAM_PATH");
62  
63 <  map<string, AtomType*>::iterator iter;
64 <  
65 <  iter = atomTypeMap.find(at);
66 <  if (iter != atomTypeMap.end()) {
67 <    return iter->second;
68 <  } else {
11 <    return NULL;
63 >    if (tempPath == NULL) {
64 >      //convert a macro from compiler to a string in c++
65 >      STR_DEFINE(ffPath_, FRC_PATH );
66 >    } else {
67 >      ffPath_ = tempPath;
68 >    }
69    }
13 – }
70  
15 – BondType* ForceField::getMatchingBondType(const string &at1,
16 –                                          const string &at2) {
71  
72 <  map<pair<string,string>, BondType*>::iterator iter;
73 <  vector<BondType*> foundTypes;
72 >  ForceField::~ForceField() {
73 >    deleteAtypes();
74 >    deleteSwitch();
75 >  }
76  
77 <  iter = bondTypeMap.find(pair<at1, at2>);
78 <  if (iter != bondTypeMap.end()) {
79 <    // exact match, so just return it
80 <    return iter->second;
81 <  }
77 >  AtomType* ForceField::getAtomType(const std::string &at) {
78 >    std::vector<std::string> keys;
79 >    keys.push_back(at);
80 >    return atomTypeCont_.find(keys);
81 >  }
82  
83 <  iter = bondTypeMap.find(pair<at2, at1>);
84 <  if (iter != bondTypeMap.end()) {
85 <    // exact match in reverse order, so just return it
86 <    return iter->second;
87 <  }
83 >  BondType* ForceField::getBondType(const std::string &at1,
84 >                                    const std::string &at2) {
85 >    std::vector<std::string> keys;
86 >    keys.push_back(at1);
87 >    keys.push_back(at2);    
88  
89 <  iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
90 <  if (iter != bondTypeMap.end()) {
91 <    foundTypes.push_back(iter->second);
92 <  }
89 >    //try exact match first
90 >    BondType* bondType = bondTypeCont_.find(keys);
91 >    if (bondType) {
92 >      return bondType;
93 >    } else {
94 >      AtomType* atype1;
95 >      AtomType* atype2;
96 >      std::vector<std::string> at1key;
97 >      at1key.push_back(at1);
98 >      atype1 = atomTypeCont_.find(at1key);
99 >  
100 >      std::vector<std::string> at2key;
101 >      at2key.push_back(at2);
102 >      atype2 = atomTypeCont_.find(at2key);
103  
104 <  iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
105 <  if (iter != bondTypeMap.end()) {
106 <    foundTypes.push_back(iter->second);
41 <  }
104 >      // query atom types for their chains of responsibility
105 >      std::vector<AtomType*> at1Chain = atype1->allYourBase();
106 >      std::vector<AtomType*> at2Chain = atype2->allYourBase();
107  
108 <  iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
109 <  if (iter != bondTypeMap.end()) {
45 <    foundTypes.push_back(iter->second);
46 <  }
108 >      std::vector<AtomType*>::iterator i;
109 >      std::vector<AtomType*>::iterator j;
110  
111 <  iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
112 <  if (iter != bondTypeMap.end()) {
113 <    foundTypes.push_back(iter->second);
111 >      int ii = 0;
112 >      int jj = 0;
113 >      int bondTypeScore;
114 >
115 >      std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
116 >
117 >      for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
118 >        jj = 0;
119 >        for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
120 >
121 >          bondTypeScore = ii + jj;
122 >
123 >          std::vector<std::string> myKeys;
124 >          myKeys.push_back((*i)->getName());
125 >          myKeys.push_back((*j)->getName());
126 >
127 >          BondType* bondType = bondTypeCont_.find(myKeys);
128 >          if (bondType) {
129 >            foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
130 >          }
131 >          jj++;
132 >        }
133 >        ii++;
134 >      }
135 >
136 >
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    }
153    
154 <  if (foundTypes.empty()) {
155 <    return NULL;
156 <  } else {
157 <    
154 >  BendType* ForceField::getBendType(const std::string &at1,
155 >                                    const std::string &at2,
156 >                                    const std::string &at3) {
157 >    std::vector<std::string> keys;
158 >    keys.push_back(at1);
159 >    keys.push_back(at2);    
160 >    keys.push_back(at3);    
161  
162 <
162 >    //try exact match first
163 >    BendType* bendType = bendTypeCont_.find(keys);
164 >    if (bendType) {
165 >      return bendType;
166 >    } else {
167  
168 +      AtomType* atype1;
169 +      AtomType* atype2;
170 +      AtomType* atype3;
171 +      std::vector<std::string> at1key;
172 +      at1key.push_back(at1);
173 +      atype1 = atomTypeCont_.find(at1key);
174 +  
175 +      std::vector<std::string> at2key;
176 +      at2key.push_back(at2);
177 +      atype2 = atomTypeCont_.find(at2key);
178  
179 +      std::vector<std::string> at3key;
180 +      at3key.push_back(at3);
181 +      atype3 = atomTypeCont_.find(at3key);
182  
183 <  
183 >      // query atom types for their chains of responsibility
184 >      std::vector<AtomType*> at1Chain = atype1->allYourBase();
185 >      std::vector<AtomType*> at2Chain = atype2->allYourBase();
186 >      std::vector<AtomType*> at3Chain = atype3->allYourBase();
187  
188 +      std::vector<AtomType*>::iterator i;
189 +      std::vector<AtomType*>::iterator j;
190 +      std::vector<AtomType*>::iterator k;
191  
192 < BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
193 <                                          const string &at3);
194 < TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
195 <                                                const string &at3, const string &at4);
192 >      int ii = 0;
193 >      int jj = 0;
194 >      int kk = 0;
195 >      int IKscore;
196  
197 < double ForceField::getRcutForAtomType(AtomType* at);
197 >      std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
198  
199 +      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
200 +        ii = 0;
201 +        for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
202 +          kk = 0;
203 +          for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
204 +          
205 +            IKscore = ii + kk;
206  
207 < vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
208 <  
209 <   vector<vector<string> > results;
207 >            std::vector<std::string> myKeys;
208 >            myKeys.push_back((*i)->getName());
209 >            myKeys.push_back((*j)->getName());
210 >            myKeys.push_back((*k)->getName());
211  
212 <  
212 >            BendType* bendType = bendTypeCont_.find(myKeys);
213 >            if (bendType) {
214 >              foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
215 >            }
216 >            kk++;
217 >          }
218 >          ii++;
219 >        }
220 >        jj++;
221 >      }
222 >      
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  
238 +  TorsionType* ForceField::getTorsionType(const std::string &at1,
239 +                                          const std::string &at2,
240 +                                          const std::string &at3,
241 +                                          const std::string &at4) {
242 +    std::vector<std::string> keys;
243 +    keys.push_back(at1);
244 +    keys.push_back(at2);    
245 +    keys.push_back(at3);    
246 +    keys.push_back(at4);    
247  
80 –   vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
81 –    
82 –     int nStrings;
83 –     vector<string> oneResult;
84 –     vector<vector<string> > allResults;
248  
249 <     nStrings = myAts.size();
249 >    //try exact match first
250 >    TorsionType* torsionType = torsionTypeCont_.find(keys);
251 >    if (torsionType) {
252 >      return torsionType;
253 >    } else {
254  
255 <     if (nStrings == 1) {
256 <       oneResult.push_back(wildcardCharacter);
257 <       allResults.push_back(oneResult);
258 <       return allResults;
259 <     } else {
260 <      
261 <       for (i=0; i < nStrings; i++) {
262 <         oneResult = myAts;
263 <         replace(oneResult.begin(), oneResult.end(),
255 >      AtomType* atype1;
256 >      AtomType* atype2;
257 >      AtomType* atype3;
258 >      AtomType* atype4;
259 >      std::vector<std::string> at1key;
260 >      at1key.push_back(at1);
261 >      atype1 = atomTypeCont_.find(at1key);
262 >  
263 >      std::vector<std::string> at2key;
264 >      at2key.push_back(at2);
265 >      atype2 = atomTypeCont_.find(at2key);
266 >
267 >      std::vector<std::string> at3key;
268 >      at3key.push_back(at3);
269 >      atype3 = atomTypeCont_.find(at3key);
270 >
271 >      std::vector<std::string> at4key;
272 >      at4key.push_back(at4);
273 >      atype4 = atomTypeCont_.find(at4key);
274 >
275 >      // query atom types for their chains of responsibility
276 >      std::vector<AtomType*> at1Chain = atype1->allYourBase();
277 >      std::vector<AtomType*> at2Chain = atype2->allYourBase();
278 >      std::vector<AtomType*> at3Chain = atype3->allYourBase();
279 >      std::vector<AtomType*> at4Chain = atype4->allYourBase();
280 >
281 >      std::vector<AtomType*>::iterator i;
282 >      std::vector<AtomType*>::iterator j;
283 >      std::vector<AtomType*>::iterator k;
284 >      std::vector<AtomType*>::iterator l;
285 >
286 >      int ii = 0;
287 >      int jj = 0;
288 >      int kk = 0;
289 >      int ll = 0;
290 >      int ILscore;
291 >      int JKscore;
292 >
293 >      std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
294 >
295 >      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
296 >        kk = 0;
297 >        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
298 >          ii = 0;      
299 >          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
300 >            ll = 0;
301 >            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
302 >          
303 >              ILscore = ii + ll;
304 >              JKscore = jj + kk;
305 >
306 >              std::vector<std::string> myKeys;
307 >              myKeys.push_back((*i)->getName());
308 >              myKeys.push_back((*j)->getName());
309 >              myKeys.push_back((*k)->getName());
310 >              myKeys.push_back((*l)->getName());
311 >
312 >              TorsionType* torsionType = torsionTypeCont_.find(myKeys);
313 >              if (torsionType) {
314 >                foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
315 >              }
316 >              ll++;
317 >            }
318 >            ii++;
319 >          }
320 >          kk++;
321 >        }
322 >        jj++;
323 >      }
324 >      
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_);
336 >      }
337 >    }
338 >  }
339 >
340 >  InversionType* ForceField::getInversionType(const std::string &at1,
341 >                                              const std::string &at2,
342 >                                              const std::string &at3,
343 >                                              const std::string &at4) {
344 >    std::vector<std::string> keys;
345 >    keys.push_back(at1);
346 >    keys.push_back(at2);    
347 >    keys.push_back(at3);    
348 >    keys.push_back(at4);    
349 >
350 >    //try exact match first
351 >    InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
352 >    if (inversionType) {
353 >      return inversionType;
354 >    } else {
355 >      
356 >      AtomType* atype1;
357 >      AtomType* atype2;
358 >      AtomType* atype3;
359 >      AtomType* atype4;
360 >      std::vector<std::string> at1key;
361 >      at1key.push_back(at1);
362 >      atype1 = atomTypeCont_.find(at1key);
363 >      
364 >      std::vector<std::string> at2key;
365 >      at2key.push_back(at2);
366 >      atype2 = atomTypeCont_.find(at2key);
367 >      
368 >      std::vector<std::string> at3key;
369 >      at3key.push_back(at3);
370 >      atype3 = atomTypeCont_.find(at3key);
371 >      
372 >      std::vector<std::string> at4key;
373 >      at4key.push_back(at4);
374 >      atype4 = atomTypeCont_.find(at4key);
375 >
376 >      // query atom types for their chains of responsibility
377 >      std::vector<AtomType*> at1Chain = atype1->allYourBase();
378 >      std::vector<AtomType*> at2Chain = atype2->allYourBase();
379 >      std::vector<AtomType*> at3Chain = atype3->allYourBase();
380 >      std::vector<AtomType*> at4Chain = atype4->allYourBase();
381 >
382 >      std::vector<AtomType*>::iterator i;
383 >      std::vector<AtomType*>::iterator j;
384 >      std::vector<AtomType*>::iterator k;
385 >      std::vector<AtomType*>::iterator l;
386 >
387 >      int ii = 0;
388 >      int jj = 0;
389 >      int kk = 0;
390 >      int ll = 0;
391 >      int Iscore;
392 >      int JKLscore;
393 >      
394 >      std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
395 >      
396 >      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
397 >        kk = 0;
398 >        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
399 >          ii = 0;      
400 >          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
401 >            ll = 0;
402 >            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
403 >              
404 >              Iscore = ii;
405 >              JKLscore = jj + kk + ll;
406 >              
407 >              std::vector<std::string> myKeys;
408 >              myKeys.push_back((*i)->getName());
409 >              myKeys.push_back((*j)->getName());
410 >              myKeys.push_back((*k)->getName());
411 >              myKeys.push_back((*l)->getName());
412 >              
413 >              InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
414 >              if (inversionType) {
415 >                foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
416 >              }
417 >              ll++;
418 >            }
419 >            ii++;
420 >          }
421 >          kk++;
422 >        }
423 >        jj++;
424 >      }
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_);
437 >      }
438 >    }
439 >  }
440 >  
441 >  NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
442 >    std::vector<std::string> keys;
443 >    keys.push_back(at1);
444 >    keys.push_back(at2);    
445 >    
446 >    //try exact match first
447 >    NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
448 >    if (nbiType) {
449 >      return nbiType;
450 >    } else {
451 >      //if no exact match found, try wild card match
452 >      return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
453 >    }    
454 >  }
455 >  
456 >  BondType* ForceField::getExactBondType(const std::string &at1,
457 >                                         const std::string &at2){
458 >    std::vector<std::string> keys;
459 >    keys.push_back(at1);
460 >    keys.push_back(at2);    
461 >    return bondTypeCont_.find(keys);
462 >  }
463 >  
464 >  BendType* ForceField::getExactBendType(const std::string &at1,
465 >                                         const std::string &at2,
466 >                                         const std::string &at3){
467 >    std::vector<std::string> keys;
468 >    keys.push_back(at1);
469 >    keys.push_back(at2);    
470 >    keys.push_back(at3);    
471 >    return bendTypeCont_.find(keys);
472 >  }
473 >  
474 >  TorsionType* ForceField::getExactTorsionType(const std::string &at1,
475 >                                               const std::string &at2,
476 >                                               const std::string &at3,
477 >                                               const std::string &at4){
478 >    std::vector<std::string> keys;
479 >    keys.push_back(at1);
480 >    keys.push_back(at2);    
481 >    keys.push_back(at3);    
482 >    keys.push_back(at4);  
483 >    return torsionTypeCont_.find(keys);
484 >  }
485 >  
486 >  InversionType* ForceField::getExactInversionType(const std::string &at1,
487 >                                                   const std::string &at2,
488 >                                                   const std::string &at3,
489 >                                                   const std::string &at4){
490 >    std::vector<std::string> keys;
491 >    keys.push_back(at1);
492 >    keys.push_back(at2);    
493 >    keys.push_back(at3);    
494 >    keys.push_back(at4);  
495 >    return inversionTypeCont_.find(keys);
496 >  }
497 >  
498 >  NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
499 >    std::vector<std::string> keys;
500 >    keys.push_back(at1);
501 >    keys.push_back(at2);    
502 >    return nonBondedInteractionTypeCont_.find(keys);
503 >  }
504 >  
505 >
506 >  bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
507 >    std::vector<std::string> keys;
508 >    keys.push_back(at);
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;
521 >    keys.push_back(at1);
522 >    keys.push_back(at2);    
523 >    return bondTypeCont_.add(keys, bondType);    
524 >  }
525 >  
526 >  bool ForceField::addBendType(const std::string &at1, const std::string &at2,
527 >                               const std::string &at3, BendType* bendType) {
528 >    std::vector<std::string> keys;
529 >    keys.push_back(at1);
530 >    keys.push_back(at2);    
531 >    keys.push_back(at3);    
532 >    return bendTypeCont_.add(keys, bendType);
533 >  }
534 >  
535 >  bool ForceField::addTorsionType(const std::string &at1,
536 >                                  const std::string &at2,
537 >                                  const std::string &at3,
538 >                                  const std::string &at4,
539 >                                  TorsionType* torsionType) {
540 >    std::vector<std::string> keys;
541 >    keys.push_back(at1);
542 >    keys.push_back(at2);    
543 >    keys.push_back(at3);    
544 >    keys.push_back(at4);    
545 >    return torsionTypeCont_.add(keys, torsionType);
546 >  }
547 >
548 >  bool ForceField::addInversionType(const std::string &at1,
549 >                                    const std::string &at2,
550 >                                    const std::string &at3,
551 >                                    const std::string &at4,
552 >                                    InversionType* inversionType) {
553 >    std::vector<std::string> keys;
554 >    keys.push_back(at1);
555 >    keys.push_back(at2);    
556 >    keys.push_back(at3);    
557 >    keys.push_back(at4);    
558 >    return inversionTypeCont_.add(keys, inversionType);
559 >  }
560 >  
561 >  bool ForceField::addNonBondedInteractionType(const std::string &at1,
562 >                                               const std::string &at2,
563 >                                               NonBondedInteractionType* nbiType) {
564 >    std::vector<std::string> keys;
565 >    keys.push_back(at1);
566 >    keys.push_back(at2);    
567 >    return nonBondedInteractionTypeCont_.add(keys, nbiType);
568 >  }
569 >  
570 >  RealType ForceField::getRcutFromAtomType(AtomType* at) {
571 >    /**@todo */
572 >    GenericData* data;
573 >    RealType rcut = 0.0;
574 >    
575 >    if (at->isLennardJones()) {
576 >      data = at->getPropertyByName("LennardJones");
577 >      if (data != NULL) {
578 >        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
579 >        
580 >        if (ljData != NULL) {
581 >          LJParam ljParam = ljData->getData();
582 >          
583 >          //by default use 2.5*sigma as cutoff radius
584 >          rcut = 2.5 * ljParam.sigma;
585 >          
586 >        } else {
587 >          sprintf( painCave.errMsg,
588 >                   "Can not cast GenericData to LJParam\n");
589 >          painCave.severity = OOPSE_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;
596 >        painCave.isFatal = 1;
597 >        simError();          
598 >      }
599 >    }
600 >    return rcut;    
601 >  }
602 >  
603 >
604 >  ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
605 >    std::string forceFieldFilename(filename);
606 >    ifstrstream* ffStream = new ifstrstream();
607 >    
608 >    //try to open the force filed file in current directory first    
609 >    ffStream->open(forceFieldFilename.c_str());
610 >    if(!ffStream->is_open()){
611 >
612 >      forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
613 >      ffStream->open( forceFieldFilename.c_str() );
614 >
615 >      //if current directory does not contain the force field file,
616 >      //try to open it in the path        
617 >      if(!ffStream->is_open()){
618 >
619 >        sprintf( painCave.errMsg,
620 >                 "Error opening the force field parameter file:\n"
621 >                 "\t%s\n"
622 >                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
623 >                 "variable?\n",
624 >                 forceFieldFilename.c_str() );
625 >        painCave.severity = OOPSE_ERROR;
626 >        painCave.isFatal = 1;
627 >        simError();
628 >      }
629 >    }  
630 >    return ffStream;
631 >  }
632 >
633 >  void ForceField::setFortranForceOptions(){
634 >    ForceOptions theseFortranOptions;
635 >    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
636 >    setfForceOptions(&theseFortranOptions);
637 >  }
638 > } //end namespace oopse

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