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54 lines
1.7 KiB
C++
54 lines
1.7 KiB
C++
// $Id: nucJC.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___NUC_JC
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#define ___NUC_JC
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#include <cmath>
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#include "replacementModel.h"
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namespace nucDef {
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const MDOUBLE Alp = 4.0;
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const MDOUBLE odAl = 1.0/Alp; // one divided by alphabet
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const MDOUBLE om_odAl = 1.0-odAl; // one minus odAl;
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const MDOUBLE alDiv_omalp = Alp/(Alp-1.0);
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const MDOUBLE m_alDiv_omalp = -alDiv_omalp;
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}
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class nucJC : public replacementModel {
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public:
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const int alphabetSize() const {return 4;}
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virtual replacementModel* clone() const { return new nucJC(*this); }
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explicit nucJC(){};
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const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
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// return ((i==j) ? 0.25+0.75*exp(-4.0/3.0*d): 0.25-0.25*exp(-4.0/3.0*d));
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return ((i==j) ? nucDef::odAl+nucDef::om_odAl*exp(nucDef::m_alDiv_omalp*d): nucDef::odAl-nucDef::odAl*exp(nucDef::m_alDiv_omalp*d));
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}
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const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
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// return ((i==j) ? -exp(-4.0/3.0*d): exp(-4.0/3.0*d)/3.0);
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return ((i==j) ? -exp(nucDef::m_alDiv_omalp*d): exp(nucDef::m_alDiv_omalp*d)/(nucDef::Alp-1));
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}
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const MDOUBLE freq(const int i) const {return 0.25;};
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const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
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// return ((i==j) ? 4.0/3.0*exp(-4.0/3.0*d): -4.0/3.0*exp(-4.0/3.0*d));
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return ((i==j) ? nucDef::alDiv_omalp*exp(nucDef::m_alDiv_omalp*d): nucDef::m_alDiv_omalp*exp(nucDef::m_alDiv_omalp*d));
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}
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const MDOUBLE Q(const int i, const int j) const {
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return ((i == j) ? ( - 1.0) : (1.0 / 3.0));
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}
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};
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#endif
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// note: according to the new C++ rules, the clone function should be like this:
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// virtual nucJC* clone() const { return new nucJC(*this); }
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// however, not all compiler support it yet. look at More Effective C++ page 126.
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