OrientationSphere::OrientationSphere(const ActionOptions&ao):
Action(ao),
MultiColvarFunction(ao)
{
// Resize everything that stores a vector now that we know the
// number of components
unsigned ncomponents=getBaseMultiColvar(0)->getNumberOfQuantities() - 5;
catom_orient.resize( ncomponents );
catom_der.resize( ncomponents );
this_orient.resize( ncomponents );
// Weight of this does not have derivatives
weightHasDerivatives=false;
// Read in the switching function
std::string sw, errors; parse("SWITCH",sw);
if(sw.length()>0){
switchingFunction.set(sw,errors);
} else {
double r_0=-1.0, d_0; int nn, mm;
parse("NN",nn); parse("MM",mm);
parse("R_0",r_0); parse("D_0",d_0);
if( r_0<0.0 ) error("you must set a value for R_0");
switchingFunction.set(nn,mm,r_0,d_0);
}
log.printf(" degree of overlap in orientation between central molecule and those within %s\n",( switchingFunction.description() ).c_str() );
// Set the link cell cutoff
setLinkCellCutoff( 2.*switchingFunction.inverse( getTolerance() ) );
// Finish the setup of the object
buildSymmetryFunctionLists();
// And check everything has been read in correctly
checkRead();
}
OrientationSphere::OrientationSphere(const ActionOptions&ao):
Action(ao),
MultiColvarFunction(ao)
{
if( getNumberOfBaseMultiColvars()>1 ) warning("not sure if orientation sphere works with more than one base multicolvar - check numerical derivatives");
// Read in the switching function
std::string sw, errors; parse("SWITCH",sw);
if(sw.length()>0){
switchingFunction.set(sw,errors);
} else {
double r_0=-1.0, d_0; int nn, mm;
parse("NN",nn); parse("MM",mm);
parse("R_0",r_0); parse("D_0",d_0);
if( r_0<0.0 ) error("you must set a value for R_0");
switchingFunction.set(nn,mm,r_0,d_0);
}
log.printf(" degree of overlap in orientation between central molecule and those within %s\n",( switchingFunction.description() ).c_str() );
// Set the link cell cutoff
rcut2 = switchingFunction.get_dmax()*switchingFunction.get_dmax();
setLinkCellCutoff( switchingFunction.get_dmax() );
// Finish the setup of the object
buildSymmetryFunctionLists();
}
