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Comparing branches/development/src/nonbonded/SC.cpp (file contents):
Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 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   #include <stdio.h>
# Line 53 | Line 54 | namespace OpenMD {
54    SC::SC() : name_("SC"), initialized_(false), forceField_(NULL),
55               scRcut_(0.0), np_(3000) {}
56    
56 –  SCParam SC::getSCParam(AtomType* atomType) {
57 –    
58 –    // Do sanity checking on the AtomType we were passed before
59 –    // building any data structures:
60 –    if (!atomType->isSC()) {
61 –      sprintf( painCave.errMsg,
62 –               "SC::getSCParam was passed an atomType (%s) that does not\n"
63 –               "\tappear to be a Sutton-Chen (SC) atom.\n",
64 –               atomType->getName().c_str());
65 –      painCave.severity = OPENMD_ERROR;
66 –      painCave.isFatal = 1;
67 –      simError();
68 –    }
69 –    
70 –    GenericData* data = atomType->getPropertyByName("SC");
71 –    if (data == NULL) {
72 –      sprintf( painCave.errMsg, "SC::getSCParam could not find SC\n"
73 –               "\tparameters for atomType %s.\n",
74 –               atomType->getName().c_str());
75 –      painCave.severity = OPENMD_ERROR;
76 –      painCave.isFatal = 1;
77 –      simError();
78 –    }
79 –    
80 –    SCParamGenericData* scData = dynamic_cast<SCParamGenericData*>(data);
81 –    if (scData == NULL) {
82 –      sprintf( painCave.errMsg,
83 –               "SC::getSCParam could not convert GenericData to SCParamGenericData\n"
84 –               "\tfor atom type %s\n", atomType->getName().c_str());
85 –      painCave.severity = OPENMD_ERROR;
86 –      painCave.isFatal = 1;
87 –      simError();          
88 –    }
89 –    
90 –    return scData->getData();
91 –  }
92 –
93 –  RealType SC::getC(AtomType* atomType) {    
94 –    SCParam scParam = getSCParam(atomType);
95 –    return scParam.c;
96 –  }
97 –
98 –  RealType SC::getM(AtomType* atomType) {    
99 –    SCParam scParam = getSCParam(atomType);
100 –    return scParam.m;
101 –  }
102 –
57    RealType SC::getM(AtomType* atomType1, AtomType* atomType2) {    
58 <    RealType m1 = getM(atomType1);
59 <    RealType m2 = getM(atomType2);
58 >    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
59 >    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
60 >    RealType m1 = sca1.getM();
61 >    RealType m2 = sca2.getM();
62      return 0.5 * (m1 + m2);
63    }
64  
109 –  RealType SC::getN(AtomType* atomType) {    
110 –    SCParam scParam = getSCParam(atomType);
111 –    return scParam.n;
112 –  }
113 –
65    RealType SC::getN(AtomType* atomType1, AtomType* atomType2) {    
66 <    RealType n1 = getN(atomType1);
67 <    RealType n2 = getN(atomType2);
66 >    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
67 >    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
68 >    RealType n1 = sca1.getN();
69 >    RealType n2 = sca2.getN();
70      return 0.5 * (n1 + n2);
71    }
72  
120 –  RealType SC::getAlpha(AtomType* atomType) {    
121 –    SCParam scParam = getSCParam(atomType);
122 –    return scParam.alpha;
123 –  }
124 –
73    RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) {    
74 <    RealType alpha1 = getAlpha(atomType1);
75 <    RealType alpha2 = getAlpha(atomType2);
74 >    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
75 >    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
76 >    RealType alpha1 = sca1.getAlpha();
77 >    RealType alpha2 = sca2.getAlpha();
78  
79      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
80      std::string DistanceMix = fopts.getDistanceMixingRule();
# Line 134 | Line 84 | namespace OpenMD {
84        return sqrt(alpha1 * alpha2);
85      else
86        return 0.5 * (alpha1 + alpha2);
137 –  }
138 –
139 –  RealType SC::getEpsilon(AtomType* atomType) {    
140 –    SCParam scParam = getSCParam(atomType);
141 –    return scParam.epsilon;
87    }
88  
89 <  RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) {    
90 <    RealType epsilon1 = getEpsilon(atomType1);
91 <    RealType epsilon2 = getEpsilon(atomType2);
89 >  RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) {  
90 >    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
91 >    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
92 >    RealType epsilon1 = sca1.getEpsilon();
93 >    RealType epsilon2 = sca2.getEpsilon();
94      return sqrt(epsilon1 * epsilon2);
95    }
96  
# Line 155 | Line 102 | namespace OpenMD {
102  
103      for (at = atomTypes->beginType(i); at != NULL;
104           at = atomTypes->nextType(i)) {
105 <      if (at->isSC())
105 >      SuttonChenAdapter sca = SuttonChenAdapter(at);
106 >      if (sca.isSuttonChen())
107          addType(at);
108      }    
109      initialized_ = true;
# Line 165 | Line 113 | namespace OpenMD {
113  
114    void SC::addType(AtomType* atomType){
115  
116 +    SuttonChenAdapter sca = SuttonChenAdapter(atomType);
117      SCAtomData scAtomData;
118      
119 <    scAtomData.c = getC(atomType);
120 <    scAtomData.m = getM(atomType);
121 <    scAtomData.n = getN(atomType);
122 <    scAtomData.alpha = getAlpha(atomType);
123 <    scAtomData.epsilon = getEpsilon(atomType);
119 >    scAtomData.c = sca.getC();
120 >    scAtomData.m = sca.getM();
121 >    scAtomData.n = sca.getN();
122 >    scAtomData.alpha = sca.getAlpha();
123 >    scAtomData.epsilon = sca.getEpsilon();
124      scAtomData.rCut = 2.0 * scAtomData.alpha;
125  
126      // add it to the map:
178 –    AtomTypeProperties atp = atomType->getATP();    
127  
128      pair<map<int,AtomType*>::iterator,bool> ret;    
129 <    ret = SClist.insert( pair<int, AtomType*>(atp.ident, atomType) );
129 >    ret = SClist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
130      if (ret.second == false) {
131        sprintf( painCave.errMsg,
132                 "SC already had a previous entry with ident %d\n",
133 <               atp.ident);
133 >               atomType->getIdent() );
134        painCave.severity = OPENMD_INFO;
135        painCave.isFatal = 0;
136        simError();        

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