> Where are kr, kth, vn_half, etc. defined? They don't seem to be explicitly
> stated in the gaff.dat file. For example, kr is defined as
These things are usually in the appropriate journal articles. So for example:
> bondcalc.kr = KCAL_TO_KJ * parameter->_dpar[0];
Since Open Babel uses kJ/mol by default, this is a conversion for the
stretching constant.
> Can someone explain what _dpar[0]? I surmise that it references a number in
> gaff.dat in some fashion though I'm not sure how. All I need to know is which
> number _dpar[0] corresponds to in the .dat file, and how this correspondence
> is achieved.
The _dpar are floating-point constants, and the _ipar are integer constants (in
all of the Open Babel force field classes).
You can see how they're parsed in bool OBForceFieldGaff::ParseParamFile()
So for example, I see:
> parameter._a = vs[0]; //KNDSYM
> parameter._dpar.push_back(atof(vs[1].c_str())); // AMASS
> parameter._dpar.push_back(atof(vs[2].c_str())); // ATPOL [A^3]
Hope that helps,
-Geoff
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