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root/OpenMD/branches/development/src/nonbonded/Sticky.cpp
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Comparing branches/development/src/nonbonded/Sticky.cpp (file contents):
Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

# Line 46 | Line 46
46   #include <cmath>
47   #include "nonbonded/Sticky.hpp"
48   #include "nonbonded/LJ.hpp"
49 + #include "types/StickyAdapter.hpp"
50   #include "utils/simError.h"
51  
52   using namespace std;
53   namespace OpenMD {
54    
55    Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
55 –  
56 –  StickyParam Sticky::getStickyParam(AtomType* atomType) {
57 –    
58 –    // Do sanity checking on the AtomType we were passed before
59 –    // building any data structures:
60 –    if (!atomType->isSticky() && !atomType->isStickyPower()) {
61 –      sprintf( painCave.errMsg,
62 –               "Sticky::getStickyParam was passed an atomType (%s) that does\n"
63 –               "\tnot appear to be a Sticky atom.\n",
64 –               atomType->getName().c_str());
65 –      painCave.severity = OPENMD_ERROR;
66 –      painCave.isFatal = 1;
67 –      simError();
68 –    }
69 –    
70 –    DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
71 –    GenericData* data = daType->getPropertyByName("Sticky");
72 –    if (data == NULL) {
73 –      sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n"
74 –               "\tSticky parameters for atomType %s.\n",
75 –               daType->getName().c_str());
76 –      painCave.severity = OPENMD_ERROR;
77 –      painCave.isFatal = 1;
78 –      simError();
79 –    }
80 –    
81 –    StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data);
82 –    if (stickyData == NULL) {
83 –      sprintf( painCave.errMsg,
84 –               "Sticky::getStickyParam could not convert GenericData to\n"
85 –               "\tStickyParamGenericData for atom type %s\n",
86 –               daType->getName().c_str());
87 –      painCave.severity = OPENMD_ERROR;
88 –      painCave.isFatal = 1;
89 –      simError();          
90 –    }
56      
92 –    return stickyData->getData();
93 –  }
94 –  
57    void Sticky::initialize() {    
58      
59      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 104 | Line 66 | namespace OpenMD {
66      for (at = atomTypes->beginType(i); at != NULL;
67           at = atomTypes->nextType(i)) {
68        
69 <      if (at->isSticky() || at->isStickyPower())
70 <        addType(at);
69 >      StickyAdapter sa = StickyAdapter(at);
70 >      if (sa.isSticky()) addType(at);
71      }
72      
73      initialized_ = true;
# Line 113 | Line 75 | namespace OpenMD {
75        
76    void Sticky::addType(AtomType* atomType){
77      // add it to the map:
116 –    AtomTypeProperties atp = atomType->getATP();    
78      
79      pair<map<int,AtomType*>::iterator,bool> ret;    
80 <    ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
80 >    ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(),
81 >                                                 atomType) );
82      if (ret.second == false) {
83        sprintf( painCave.errMsg,
84                 "Sticky already had a previous entry with ident %d\n",
85 <               atp.ident);
85 >               atomType->getIdent() );
86        painCave.severity = OPENMD_INFO;
87        painCave.isFatal = 0;
88        simError();        
# Line 128 | Line 90 | namespace OpenMD {
90      
91      RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi;
92      
93 <    StickyParam sticky1 = getStickyParam(atomType);
93 >    StickyAdapter sticky1 = StickyAdapter(atomType);
94  
95      // Now, iterate over all known types and add to the mixing map:
96      
# Line 136 | Line 98 | namespace OpenMD {
98      for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
99        
100        AtomType* atype2 = (*it).second;
101 <    
102 <      StickyParam sticky2 = getStickyParam(atype2);
101 >      
102 >      StickyAdapter sticky2 = StickyAdapter(atype2);
103  
104        StickyInteractionData mixer;        
105            
# Line 146 | Line 108 | namespace OpenMD {
108        // Lorentz- Berthelot mixing rules (which happen to do the right thing
109        // when atomType and atype2 happen to be the same.
110        
111 <      mixer.rl   = 0.5 * ( sticky1.rl + sticky2.rl );
112 <      mixer.ru   = 0.5 * ( sticky1.ru + sticky2.ru );
113 <      mixer.rlp  = 0.5 * ( sticky1.rlp + sticky2.rlp );
114 <      mixer.rup  = 0.5 * ( sticky1.rup + sticky2.rup );
111 >      mixer.rl   = 0.5 * ( sticky1.getRl() + sticky2.getRl() );
112 >      mixer.ru   = 0.5 * ( sticky1.getRu() + sticky2.getRu() );
113 >      mixer.rlp  = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() );
114 >      mixer.rup  = 0.5 * ( sticky1.getRup() + sticky2.getRup() );
115        mixer.rbig = max(mixer.ru, mixer.rup);
116 <      mixer.w0  = sqrt( sticky1.w0   * sticky2.w0  );
117 <      mixer.v0  = sqrt( sticky1.v0   * sticky2.v0  );
118 <      mixer.v0p = sqrt( sticky1.v0p  * sticky2.v0p );
119 <      mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower();
116 >      mixer.w0  = sqrt( sticky1.getW0()   * sticky2.getW0()  );
117 >      mixer.v0  = sqrt( sticky1.getW0()   * sticky2.getV0()  );
118 >      mixer.v0p = sqrt( sticky1.getV0p()  * sticky2.getV0p() );
119 >      mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower();
120  
121        CubicSpline* s = new CubicSpline();
122        s->addPoint(mixer.rl, 1.0);

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