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Comparing trunk/src/brains/ForceField.cpp (file contents):
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC vs.
Revision 1905 by gezelter, Wed Jul 17 20:39:58 2013 UTC

# Line 35 | Line 35
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 44 | Line 44
44   * @file ForceField.cpp
45   * @author tlin
46   * @date 11/04/2004
47 – * @time 22:51am
47   * @version 1.0
48   */
49    
# Line 81 | Line 80 | namespace OpenMD {
80  
81   namespace OpenMD {
82  
83 <  ForceField::ForceField(std::string ffName) {
83 >  ForceField::ForceField(std::string ffName): wildCardAtomTypeName_("X") {
84  
85      char* tempPath;
86      tempPath = getenv("FORCE_PARAM_PATH");
# Line 228 | Line 227 | namespace OpenMD {
227  
228        std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
229  
230 <      for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
230 >      for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
231          jj = 0;
232 <        for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
232 >        for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
233  
234            bondTypeScore = ii + jj;
235  
# Line 248 | Line 247 | namespace OpenMD {
247        }
248  
249  
250 <      if (foundBonds.size() > 0) {
250 >      if (!foundBonds.empty()) {
251          // sort the foundBonds by the score:
252          std::sort(foundBonds.begin(), foundBonds.end());
253      
255 –        int bestScore = foundBonds[0].first;
254          std::vector<std::string> theKeys = foundBonds[0].second;
255          
256          BondType* bestType = bondTypeCont_.find(theKeys);
# Line 310 | Line 308 | namespace OpenMD {
308  
309        std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
310  
311 <      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
311 >      for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
312          ii = 0;
313 <        for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
313 >        for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
314            kk = 0;
315 <          for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
315 >          for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
316            
317              IKscore = ii + kk;
318  
# Line 334 | Line 332 | namespace OpenMD {
332          jj++;
333        }
334        
335 <      if (foundBends.size() > 0) {
335 >      if (!foundBends.empty()) {
336          std::sort(foundBends.begin(), foundBends.end());
339 –        int jscore = foundBends[0].first;
340 –        int ikscore = foundBends[0].second;
337          std::vector<std::string> theKeys = foundBends[0].third;      
338          
339          BendType* bestType = bendTypeCont_.find(theKeys);  
# Line 406 | Line 402 | namespace OpenMD {
402  
403        std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
404  
405 <      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
405 >      for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
406          kk = 0;
407 <        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
407 >        for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
408            ii = 0;      
409 <          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
409 >          for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
410              ll = 0;
411 <            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
411 >            for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
412            
413                ILscore = ii + ll;
414                JKscore = jj + kk;
# Line 436 | Line 432 | namespace OpenMD {
432          jj++;
433        }
434        
435 <      if (foundTorsions.size() > 0) {
435 >      if (!foundTorsions.empty()) {
436          std::sort(foundTorsions.begin(), foundTorsions.end());
441 –        int jkscore = foundTorsions[0].first;
442 –        int ilscore = foundTorsions[0].second;
437          std::vector<std::string> theKeys = foundTorsions[0].third;
438          
439          TorsionType* bestType = torsionTypeCont_.find(theKeys);
# Line 507 | Line 501 | namespace OpenMD {
501        
502        std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
503        
504 <      for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
504 >      for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
505          kk = 0;
506 <        for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
506 >        for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
507            ii = 0;      
508 <          for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
508 >          for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
509              ll = 0;
510 <            for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
510 >            for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
511                
512                Iscore = ii;
513                JKLscore = jj + kk + ll;
# Line 537 | Line 531 | namespace OpenMD {
531          jj++;
532        }
533          
534 <      if (foundInversions.size() > 0) {
534 >      if (!foundInversions.empty()) {
535          std::sort(foundInversions.begin(), foundInversions.end());
542 –        int iscore = foundInversions[0].first;
543 –        int jklscore = foundInversions[0].second;
536          std::vector<std::string> theKeys = foundInversions[0].third;
537          
538          InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
# Line 586 | Line 578 | namespace OpenMD {
578        
579        std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
580        
581 <      for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
581 >      for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
582          jj = 0;
583 <        for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
583 >        for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
584            
585            nbiTypeScore = ii + jj;
586            
# Line 606 | Line 598 | namespace OpenMD {
598        }
599        
600        
601 <      if (foundNBI.size() > 0) {
601 >      if (!foundNBI.empty()) {
602          // sort the foundNBI by the score:
603 <        std::sort(foundNBI.begin(), foundNBI.end());
612 <        
613 <        int bestScore = foundNBI[0].first;
603 >        std::sort(foundNBI.begin(), foundNBI.end());      
604          std::vector<std::string> theKeys = foundNBI[0].second;
605          
606          NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);        
# Line 771 | Line 761 | namespace OpenMD {
761      ifstrstream* ffStream = new ifstrstream();
762      
763      //try to open the force filed file in current directory first    
764 <    ffStream->open(forceFieldFilename.c_str(), ifstream::in | ifstream::binary);
775 <
764 >    ffStream->open(forceFieldFilename.c_str());
765      if(!ffStream->is_open()){
766  
767        forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
768 <      ffStream->open( forceFieldFilename.c_str(),  
780 <                      ifstream::in | ifstream::binary );
768 >      ffStream->open( forceFieldFilename.c_str() );
769  
770        //if current directory does not contain the force field file,
771        //try to open it in the path        

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