void CReflCalc::Init(ReflSettings* InitStruct)
{
lambda = InitStruct->Wavelength;
k0 = 2.0*M_PI/lambda;
objectivefunction = InitStruct->Objectivefunction;
m_bforcenorm = InitStruct->Forcenorm;
m_dnormfactor = 1.0;
m_dQSpread = InitStruct->QErr/100;
m_bXRonly = InitStruct->XRonly;
m_bImpNorm = InitStruct->Impnorm;
//Setup OpenMP - currently a maximum of 8 processors is allowed. After a certain number
//of data points, there will not be much of a benefit to allowing additional processors
//to work on the calculation. If more than 2-300 data points are being analyzed, it would
//make sense to increase this number
if(MAX_OMP_THREADS > omp_get_num_procs())
m_iuseableprocessors = omp_get_num_procs();
else
m_iuseableprocessors = MAX_OMP_THREADS;
//For Debugging Purposes
#ifdef SINGLEPROCDEBUG
m_iuseableprocessors = 1;
#endif
omp_set_num_threads(m_iuseableprocessors);
SetupRef(InitStruct);
}
/** Called every time the trajectory changes. Set up FrameMask for the new
* parmtop and allocate space for selected atoms from the Frame.
*/
Action::RetType Action_Rmsd::Setup(Topology* currentParm, Topology** parmAddress) {
// Target setup
if (SetupRmsMask(*currentParm, "rmsd")) return Action::ERR;
// Reference setup
if (SetupRef(*currentParm, TgtMask().Nselected(), "rmsd"))
return Action::ERR;
// Per residue rmsd setup
if (perres_) {
// If RefParm is still NULL probably 'first', set now.
if (RefParm_ == 0)
RefParm_ = currentParm;
if (perResSetup(currentParm, RefParm_)) return Action::ERR;
}
return Action::OK;
}