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root/OpenMD/trunk/src/brains/ForceField.cpp
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Comparing:
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1782 by gezelter, Wed Aug 22 02:28:28 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   /**
# Line 48 | Line 49
49   */
50    
51   #include <algorithm>
52 < #include "UseTheForce/ForceField.hpp"
52 > #include "brains/ForceField.hpp"
53   #include "utils/simError.h"
54 < #include "utils/Tuple.hpp"
54 >
55 > #include "io/OptionSectionParser.hpp"
56 > #include "io/BaseAtomTypesSectionParser.hpp"
57 > #include "io/DirectionalAtomTypesSectionParser.hpp"
58 > #include "io/AtomTypesSectionParser.hpp"
59 > #include "io/BendTypesSectionParser.hpp"
60 > #include "io/BondTypesSectionParser.hpp"
61 > #include "io/ChargeAtomTypesSectionParser.hpp"
62 > #include "io/EAMAtomTypesSectionParser.hpp"
63 > #include "io/FluctuatingChargeAtomTypesSectionParser.hpp"
64 > #include "io/GayBerneAtomTypesSectionParser.hpp"
65 > #include "io/InversionTypesSectionParser.hpp"
66 > #include "io/LennardJonesAtomTypesSectionParser.hpp"
67 > #include "io/MultipoleAtomTypesSectionParser.hpp"
68 > #include "io/NonBondedInteractionsSectionParser.hpp"
69 > #include "io/PolarizableAtomTypesSectionParser.hpp"
70 > #include "io/SCAtomTypesSectionParser.hpp"
71 > #include "io/ShapeAtomTypesSectionParser.hpp"
72 > #include "io/StickyAtomTypesSectionParser.hpp"
73 > #include "io/StickyPowerAtomTypesSectionParser.hpp"
74 > #include "io/TorsionTypesSectionParser.hpp"
75 >
76 > #include "types/LennardJonesAdapter.hpp"
77 > #include "types/EAMAdapter.hpp"
78 > #include "types/SuttonChenAdapter.hpp"
79 > #include "types/GayBerneAdapter.hpp"
80 > #include "types/StickyAdapter.hpp"
81 >
82   namespace OpenMD {
83  
84 <  ForceField::ForceField() {
84 >  ForceField::ForceField(std::string ffName) {
85  
86      char* tempPath;
87      tempPath = getenv("FORCE_PARAM_PATH");
# Line 64 | Line 92 | namespace OpenMD {
92      } else {
93        ffPath_ = tempPath;
94      }
95 +
96 +    setForceFieldFileName(ffName + ".frc");
97 +
98 +    /**
99 +     * The order of adding section parsers is important.
100 +     *
101 +     * OptionSectionParser must come first to set options for other
102 +     * parsers
103 +     *
104 +     * DirectionalAtomTypesSectionParser should be added before
105 +     * AtomTypesSectionParser, and these two section parsers will
106 +     * actually create "real" AtomTypes (AtomTypesSectionParser will
107 +     * create AtomType and DirectionalAtomTypesSectionParser will
108 +     * create DirectionalAtomType, which is a subclass of AtomType and
109 +     * should come first).
110 +     *
111 +     * Other AtomTypes Section Parsers will not create the "real"
112 +     * AtomType, they only add and set some attributes of the AtomType
113 +     * (via the Adapters). Thus ordering of these is not important.
114 +     * AtomTypesSectionParser should be added before other atom type
115 +     *
116 +     * The order of BondTypesSectionParser, BendTypesSectionParser and
117 +     * TorsionTypesSectionParser, etc. are not important.
118 +     */
119 +
120 +    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
121 +    spMan_.push_back(new BaseAtomTypesSectionParser());
122 +    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
123 +    spMan_.push_back(new AtomTypesSectionParser());
124 +
125 +    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
126 +    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
127 +    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
128 +    spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_));
129 +    spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_));
130 +    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
131 +    spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
132 +    spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
133 +    spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
134 +    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
135 +    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
136 +
137 +    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
138 +    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
139 +    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
140 +    spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
141 +
142 +    spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));    
143 +  }
144 +
145 +  void ForceField::parse(const std::string& filename) {
146 +    ifstrstream* ffStream;
147 +
148 +    ffStream = openForceFieldFile(filename);
149 +
150 +    spMan_.parse(*ffStream, *this);
151 +
152 +    ForceField::AtomTypeContainer::MapTypeIterator i;
153 +    AtomType* at;
154 +
155 +    for (at = atomTypeCont_.beginType(i); at != NULL;
156 +         at = atomTypeCont_.nextType(i)) {
157 +
158 +      // useBase sets the responsibilities, and these have to be done
159 +      // after the atomTypes and Base types have all been scanned:
160 +
161 +      std::vector<AtomType*> ayb = at->allYourBase();      
162 +      if (ayb.size() > 1) {
163 +        for (int j = ayb.size()-1; j > 0; j--) {
164 +          
165 +          ayb[j-1]->useBase(ayb[j]);
166 +
167 +        }
168 +      }
169 +    }
170 +
171 +    delete ffStream;
172    }
173  
174    /**
# Line 634 | Line 739 | namespace OpenMD {
739    }
740    
741    RealType ForceField::getRcutFromAtomType(AtomType* at) {
742 <    /**@todo */
638 <    GenericData* data;
639 <    RealType rcut = 0.0;
742 >    RealType rcut(0.0);
743      
744 <    if (at->isLennardJones()) {
745 <      data = at->getPropertyByName("LennardJones");
746 <      if (data != NULL) {
644 <        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
645 <        
646 <        if (ljData != NULL) {
647 <          LJParam ljParam = ljData->getData();
648 <          
649 <          //by default use 2.5*sigma as cutoff radius
650 <          rcut = 2.5 * ljParam.sigma;
651 <          
652 <        } else {
653 <          sprintf( painCave.errMsg,
654 <                   "Can not cast GenericData to LJParam\n");
655 <          painCave.severity = OPENMD_ERROR;
656 <          painCave.isFatal = 1;
657 <          simError();          
658 <        }            
659 <      } else {
660 <        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
661 <        painCave.severity = OPENMD_ERROR;
662 <        painCave.isFatal = 1;
663 <        simError();          
664 <      }
744 >    LennardJonesAdapter lja = LennardJonesAdapter(at);
745 >    if (lja.isLennardJones()) {
746 >      rcut = 2.5 * lja.getSigma();
747      }
748 +    EAMAdapter ea = EAMAdapter(at);
749 +    if (ea.isEAM()) {
750 +      rcut = max(rcut, ea.getRcut());
751 +    }
752 +    SuttonChenAdapter sca = SuttonChenAdapter(at);
753 +    if (sca.isSuttonChen()) {
754 +      rcut = max(rcut, 2.0 * sca.getAlpha());
755 +    }
756 +    GayBerneAdapter gba = GayBerneAdapter(at);
757 +    if (gba.isGayBerne()) {
758 +      rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
759 +    }
760 +    StickyAdapter sa = StickyAdapter(at);
761 +    if (sa.isSticky()) {
762 +      rcut = max(rcut, max(sa.getRu(), sa.getRup()));
763 +    }
764 +
765      return rcut;    
766    }
767    

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