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root/OpenMD/trunk/src/brains/ForceField.cpp
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branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 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    
50   #include <algorithm>
51 < #include "UseTheForce/ForceField.hpp"
51 > #include "brains/ForceField.hpp"
52   #include "utils/simError.h"
53 < #include "utils/Tuple.hpp"
53 >
54 > #include "io/OptionSectionParser.hpp"
55 > #include "io/BaseAtomTypesSectionParser.hpp"
56 > #include "io/DirectionalAtomTypesSectionParser.hpp"
57 > #include "io/AtomTypesSectionParser.hpp"
58 > #include "io/BendTypesSectionParser.hpp"
59 > #include "io/BondTypesSectionParser.hpp"
60 > #include "io/ChargeAtomTypesSectionParser.hpp"
61 > #include "io/EAMAtomTypesSectionParser.hpp"
62 > #include "io/FluctuatingChargeAtomTypesSectionParser.hpp"
63 > #include "io/GayBerneAtomTypesSectionParser.hpp"
64 > #include "io/InversionTypesSectionParser.hpp"
65 > #include "io/LennardJonesAtomTypesSectionParser.hpp"
66 > #include "io/MultipoleAtomTypesSectionParser.hpp"
67 > #include "io/NonBondedInteractionsSectionParser.hpp"
68 > #include "io/PolarizableAtomTypesSectionParser.hpp"
69 > #include "io/SCAtomTypesSectionParser.hpp"
70 > #include "io/ShapeAtomTypesSectionParser.hpp"
71 > #include "io/StickyAtomTypesSectionParser.hpp"
72 > #include "io/StickyPowerAtomTypesSectionParser.hpp"
73 > #include "io/TorsionTypesSectionParser.hpp"
74 >
75 > #include "types/LennardJonesAdapter.hpp"
76 > #include "types/EAMAdapter.hpp"
77 > #include "types/SuttonChenAdapter.hpp"
78 > #include "types/GayBerneAdapter.hpp"
79 > #include "types/StickyAdapter.hpp"
80 >
81   namespace OpenMD {
82  
83 <  ForceField::ForceField() {
83 >  ForceField::ForceField(std::string ffName) {
84  
85      char* tempPath;
86      tempPath = getenv("FORCE_PARAM_PATH");
# Line 65 | Line 91 | namespace OpenMD {
91      } else {
92        ffPath_ = tempPath;
93      }
94 +
95 +    setForceFieldFileName(ffName + ".frc");
96 +
97 +    /**
98 +     * The order of adding section parsers is important.
99 +     *
100 +     * OptionSectionParser must come first to set options for other
101 +     * parsers
102 +     *
103 +     * DirectionalAtomTypesSectionParser should be added before
104 +     * AtomTypesSectionParser, and these two section parsers will
105 +     * actually create "real" AtomTypes (AtomTypesSectionParser will
106 +     * create AtomType and DirectionalAtomTypesSectionParser will
107 +     * create DirectionalAtomType, which is a subclass of AtomType and
108 +     * should come first).
109 +     *
110 +     * Other AtomTypes Section Parsers will not create the "real"
111 +     * AtomType, they only add and set some attributes of the AtomType
112 +     * (via the Adapters). Thus ordering of these is not important.
113 +     * AtomTypesSectionParser should be added before other atom type
114 +     *
115 +     * The order of BondTypesSectionParser, BendTypesSectionParser and
116 +     * TorsionTypesSectionParser, etc. are not important.
117 +     */
118 +
119 +    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
120 +    spMan_.push_back(new BaseAtomTypesSectionParser());
121 +    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
122 +    spMan_.push_back(new AtomTypesSectionParser());
123 +
124 +    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
125 +    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
126 +    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
127 +    spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_));
128 +    spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_));
129 +    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
130 +    spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
131 +    spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
132 +    spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
133 +    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
134 +    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
135 +
136 +    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
137 +    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
138 +    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
139 +    spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
140 +
141 +    spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));    
142    }
143  
144 +  void ForceField::parse(const std::string& filename) {
145 +    ifstrstream* ffStream;
146 +
147 +    ffStream = openForceFieldFile(filename);
148 +
149 +    spMan_.parse(*ffStream, *this);
150 +
151 +    ForceField::AtomTypeContainer::MapTypeIterator i;
152 +    AtomType* at;
153 +
154 +    for (at = atomTypeCont_.beginType(i); at != NULL;
155 +         at = atomTypeCont_.nextType(i)) {
156 +
157 +      // useBase sets the responsibilities, and these have to be done
158 +      // after the atomTypes and Base types have all been scanned:
159 +
160 +      std::vector<AtomType*> ayb = at->allYourBase();      
161 +      if (ayb.size() > 1) {
162 +        for (int j = ayb.size()-1; j > 0; j--) {
163 +          
164 +          ayb[j-1]->useBase(ayb[j]);
165 +
166 +        }
167 +      }
168 +    }
169 +
170 +    delete ffStream;
171 +  }
172 +
173    /**
174     * getAtomType by string
175     *
# Line 124 | 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 144 | 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      
151 –        int bestScore = foundBonds[0].first;
254          std::vector<std::string> theKeys = foundBonds[0].second;
255          
256          BondType* bestType = bondTypeCont_.find(theKeys);
# Line 206 | 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 230 | Line 332 | namespace OpenMD {
332          jj++;
333        }
334        
335 <      if (foundBends.size() > 0) {
335 >      if (!foundBends.empty()) {
336          std::sort(foundBends.begin(), foundBends.end());
235 –        int jscore = foundBends[0].first;
236 –        int ikscore = foundBends[0].second;
337          std::vector<std::string> theKeys = foundBends[0].third;      
338          
339          BendType* bestType = bendTypeCont_.find(theKeys);  
# Line 302 | 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 332 | Line 432 | namespace OpenMD {
432          jj++;
433        }
434        
435 <      if (foundTorsions.size() > 0) {
435 >      if (!foundTorsions.empty()) {
436          std::sort(foundTorsions.begin(), foundTorsions.end());
337 –        int jkscore = foundTorsions[0].first;
338 –        int ilscore = foundTorsions[0].second;
437          std::vector<std::string> theKeys = foundTorsions[0].third;
438          
439          TorsionType* bestType = torsionTypeCont_.find(theKeys);
# Line 403 | 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 433 | Line 531 | namespace OpenMD {
531          jj++;
532        }
533          
534 <      if (foundInversions.size() > 0) {
534 >      if (!foundInversions.empty()) {
535          std::sort(foundInversions.begin(), foundInversions.end());
438 –        int iscore = foundInversions[0].first;
439 –        int jklscore = foundInversions[0].second;
536          std::vector<std::string> theKeys = foundInversions[0].third;
537          
538          InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
# Line 482 | 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 502 | 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());
508 <        
509 <        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 635 | Line 729 | namespace OpenMD {
729    }
730    
731    RealType ForceField::getRcutFromAtomType(AtomType* at) {
732 <    /**@todo */
639 <    GenericData* data;
640 <    RealType rcut = 0.0;
732 >    RealType rcut(0.0);
733      
734 <    if (at->isLennardJones()) {
735 <      data = at->getPropertyByName("LennardJones");
736 <      if (data != NULL) {
645 <        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
646 <        
647 <        if (ljData != NULL) {
648 <          LJParam ljParam = ljData->getData();
649 <          
650 <          //by default use 2.5*sigma as cutoff radius
651 <          rcut = 2.5 * ljParam.sigma;
652 <          
653 <        } else {
654 <          sprintf( painCave.errMsg,
655 <                   "Can not cast GenericData to LJParam\n");
656 <          painCave.severity = OPENMD_ERROR;
657 <          painCave.isFatal = 1;
658 <          simError();          
659 <        }            
660 <      } else {
661 <        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662 <        painCave.severity = OPENMD_ERROR;
663 <        painCave.isFatal = 1;
664 <        simError();          
665 <      }
734 >    LennardJonesAdapter lja = LennardJonesAdapter(at);
735 >    if (lja.isLennardJones()) {
736 >      rcut = 2.5 * lja.getSigma();
737      }
738 +    EAMAdapter ea = EAMAdapter(at);
739 +    if (ea.isEAM()) {
740 +      rcut = max(rcut, ea.getRcut());
741 +    }
742 +    SuttonChenAdapter sca = SuttonChenAdapter(at);
743 +    if (sca.isSuttonChen()) {
744 +      rcut = max(rcut, 2.0 * sca.getAlpha());
745 +    }
746 +    GayBerneAdapter gba = GayBerneAdapter(at);
747 +    if (gba.isGayBerne()) {
748 +      rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
749 +    }
750 +    StickyAdapter sa = StickyAdapter(at);
751 +    if (sa.isSticky()) {
752 +      rcut = max(rcut, max(sa.getRu(), sa.getRup()));
753 +    }
754 +
755      return rcut;    
756    }
757    
# Line 673 | 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());
764 >    ffStream->open(forceFieldFilename.c_str(), ifstream::in | ifstream::binary);
765 >
766      if(!ffStream->is_open()){
767  
768        forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
769 <      ffStream->open( forceFieldFilename.c_str() );
769 >      ffStream->open( forceFieldFilename.c_str(),  
770 >                      ifstream::in | ifstream::binary );
771  
772        //if current directory does not contain the force field file,
773        //try to open it in the path        

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