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root/OpenMD/branches/development/src/brains/ForceField.cpp
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Comparing:
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
branches/development/src/brains/ForceField.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
44   * @file ForceField.cpp
45   * @author tlin
46   * @date 11/04/2004
46 – * @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"
54 < #include "UseTheForce/DarkSide/atype_interface.h"
55 < #include "UseTheForce/DarkSide/fForceOptions_interface.h"
56 < #include "UseTheForce/DarkSide/switcheroo_interface.h"
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 67 | 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 <  ForceField::~ForceField() {
148 <    deleteAtypes();
149 <    deleteSwitch();
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 +   *
176 +   * finds the requested atom type in this force field using the string
177 +   * name of the atom type.
178 +   */
179    AtomType* ForceField::getAtomType(const std::string &at) {
180      std::vector<std::string> keys;
181      keys.push_back(at);
182      return atomTypeCont_.find(keys);
183 +  }
184 +
185 +  /**
186 +   * getAtomType by ident
187 +   *
188 +   * finds the requested atom type in this force field using the
189 +   * integer ident instead of the string name of the atom type.
190 +   */
191 +  AtomType* ForceField::getAtomType(int ident) {  
192 +    std::string at = atypeIdentToName.find(ident)->second;
193 +    return getAtomType(at);
194    }
195  
196    BondType* ForceField::getBondType(const std::string &at1,
# Line 440 | Line 552 | namespace OpenMD {
552    }
553    
554    NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
555 +    
556      std::vector<std::string> keys;
557      keys.push_back(at1);
558      keys.push_back(at2);    
# Line 449 | Line 562 | namespace OpenMD {
562      if (nbiType) {
563        return nbiType;
564      } else {
565 <      //if no exact match found, try wild card match
566 <      return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
567 <    }    
565 >      AtomType* atype1;
566 >      AtomType* atype2;
567 >      std::vector<std::string> at1key;
568 >      at1key.push_back(at1);
569 >      atype1 = atomTypeCont_.find(at1key);
570 >      
571 >      std::vector<std::string> at2key;
572 >      at2key.push_back(at2);
573 >      atype2 = atomTypeCont_.find(at2key);
574 >      
575 >      // query atom types for their chains of responsibility
576 >      std::vector<AtomType*> at1Chain = atype1->allYourBase();
577 >      std::vector<AtomType*> at2Chain = atype2->allYourBase();
578 >      
579 >      std::vector<AtomType*>::iterator i;
580 >      std::vector<AtomType*>::iterator j;
581 >      
582 >      int ii = 0;
583 >      int jj = 0;
584 >      int nbiTypeScore;
585 >      
586 >      std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
587 >      
588 >      for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
589 >        jj = 0;
590 >        for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
591 >          
592 >          nbiTypeScore = ii + jj;
593 >          
594 >          std::vector<std::string> myKeys;
595 >          myKeys.push_back((*i)->getName());
596 >          myKeys.push_back((*j)->getName());
597 >          
598 >          NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
599 >          if (nbiType) {
600 >            foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
601 >          }
602 >          jj++;
603 >        }
604 >        ii++;
605 >      }
606 >      
607 >      
608 >      if (foundNBI.size() > 0) {
609 >        // sort the foundNBI by the score:
610 >        std::sort(foundNBI.begin(), foundNBI.end());
611 >        
612 >        int bestScore = foundNBI[0].first;
613 >        std::vector<std::string> theKeys = foundNBI[0].second;
614 >        
615 >        NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);        
616 >        return bestType;
617 >      } else {
618 >        //if no exact match found, try wild card match
619 >        return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
620 >      }
621 >    }
622    }
623    
624    BondType* ForceField::getExactBondType(const std::string &at1,
# Line 507 | Line 674 | namespace OpenMD {
674    bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
675      std::vector<std::string> keys;
676      keys.push_back(at);
677 +    atypeIdentToName[atomType->getIdent()] = at;
678      return atomTypeCont_.add(keys, atomType);
679    }
680  
681    bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
682      std::vector<std::string> keys;
683      keys.push_back(at);
684 +    atypeIdentToName[atomType->getIdent()] = at;
685      return atomTypeCont_.replace(keys, atomType);
686    }
687  
# Line 569 | Line 738 | namespace OpenMD {
738    }
739    
740    RealType ForceField::getRcutFromAtomType(AtomType* at) {
741 <    /**@todo */
573 <    GenericData* data;
574 <    RealType rcut = 0.0;
741 >    RealType rcut(0.0);
742      
743 <    if (at->isLennardJones()) {
744 <      data = at->getPropertyByName("LennardJones");
745 <      if (data != NULL) {
579 <        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
580 <        
581 <        if (ljData != NULL) {
582 <          LJParam ljParam = ljData->getData();
583 <          
584 <          //by default use 2.5*sigma as cutoff radius
585 <          rcut = 2.5 * ljParam.sigma;
586 <          
587 <        } else {
588 <          sprintf( painCave.errMsg,
589 <                   "Can not cast GenericData to LJParam\n");
590 <          painCave.severity = OPENMD_ERROR;
591 <          painCave.isFatal = 1;
592 <          simError();          
593 <        }            
594 <      } else {
595 <        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
596 <        painCave.severity = OPENMD_ERROR;
597 <        painCave.isFatal = 1;
598 <        simError();          
599 <      }
743 >    LennardJonesAdapter lja = LennardJonesAdapter(at);
744 >    if (lja.isLennardJones()) {
745 >      rcut = 2.5 * lja.getSigma();
746      }
747 +    EAMAdapter ea = EAMAdapter(at);
748 +    if (ea.isEAM()) {
749 +      rcut = max(rcut, ea.getRcut());
750 +    }
751 +    SuttonChenAdapter sca = SuttonChenAdapter(at);
752 +    if (sca.isSuttonChen()) {
753 +      rcut = max(rcut, 2.0 * sca.getAlpha());
754 +    }
755 +    GayBerneAdapter gba = GayBerneAdapter(at);
756 +    if (gba.isGayBerne()) {
757 +      rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
758 +    }
759 +    StickyAdapter sa = StickyAdapter(at);
760 +    if (sa.isSticky()) {
761 +      rcut = max(rcut, max(sa.getRu(), sa.getRup()));
762 +    }
763 +
764      return rcut;    
765    }
766    
# Line 631 | Line 794 | namespace OpenMD {
794      return ffStream;
795    }
796  
634 –  void ForceField::setFortranForceOptions(){
635 –    ForceOptions theseFortranOptions;
636 –    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
637 –    setfForceOptions(&theseFortranOptions);
638 –  }
797   } //end namespace OpenMD

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