libdiffpy/src/diffpy/srreal/BaseBondGenerator.cpp at develop · cfarrow/libdiffpy · GitHub

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/*****************************************************************************

* diffpy.srreal by DANSE Diffraction group

* Simon J. L. Billinge

* File coded by: Pavol Juhas

* See AUTHORS.txt for a list of people who contributed.

* See LICENSE.txt for license information.

******************************************************************************

* class BaseBondGenerator -- semi-abstract class for generation

* of all atom pairs containing specified anchor atom.

*****************************************************************************/

#include <algorithm>

#include <diffpy/srreal/BaseBondGenerator.hpp>

#include <diffpy/srreal/StructureAdapter.hpp>

#include <diffpy/mathutils.hpp>

using diffpy::mathutils::eps_eq;

namespace diffpy {

namespace srreal {

//using namespace std;

// Constructor ---------------------------------------------------------------

BaseBondGenerator::BaseBondGenerator(StructureAdapterConstPtr stru)

{

msite_anchor = 0;

msite_first = 0;

msite_last = 0;

msite_current = 0;

mstructure = stru;

this->setRmin(0.0);

this->setRmax(DEFAULT_BONDGENERATOR_RMAX);

msite_selected.resize(mstructure->countSites(), true);

if (mstructure->countSites())

{

this->selectAnchorSite(0);

this->selectSiteRange(0, mstructure->countSites());

}

// Public Methods ------------------------------------------------------------

// loop control

void BaseBondGenerator::rewind()

{

msite_current = msite_first;

this->advanceIfSkippedSite();

// avoid calling rewindSymmetry at an invalid site

if (this->finished()) return;

this->rewindSymmetry();

this->advanceWhileInvalid();

}

void BaseBondGenerator::next()

{

this->getNextBond();

this->advanceWhileInvalid();

}

bool BaseBondGenerator::finished() const

{

return msite_current >= msite_last;

}

// configuration

void BaseBondGenerator::selectAnchorSite(int anchor)

{

assert(0 <= anchor && anchor < mstructure->countSites());

msite_anchor = anchor;

mr0 = mstructure->siteCartesianPosition(msite_anchor);

this->setFinishedFlag();

}

void BaseBondGenerator::selectSiteRange(int first, int last)

{

assert(0 <= first && first < mstructure->countSites());

assert(last <= mstructure->countSites());

msite_first = first;

msite_last = last;

std::fill(msite_selected.begin() + first,

msite_selected.begin() + last, true);

this->setFinishedFlag();

}

void BaseBondGenerator::selectSite(int siteindex, bool select)

{

msite_selected[siteindex] = select;

}

void BaseBondGenerator::setRmin(double rmin)

{

if (rmin != mrmin) this->setFinishedFlag();

mrmin = rmin;

}

void BaseBondGenerator::setRmax(double rmax)

{

if (rmax != mrmax) this->setFinishedFlag();

mrmax = rmax;

}

// data query

const double& BaseBondGenerator::getRmin() const

{

return mrmin;

}

const double& BaseBondGenerator::getRmax() const

{

return mrmax;

}

int BaseBondGenerator::site0() const

{

return msite_anchor;

}

int BaseBondGenerator::site1() const

{

return msite_current;

}

int BaseBondGenerator::multiplicity() const

{

return mstructure->siteMultiplicity(this->site0());

}

const R3::Vector& BaseBondGenerator::r0() const

{

return mr0;

}

const R3::Vector& BaseBondGenerator::r1() const

{

return mr1;

}

const double& BaseBondGenerator::distance() const

{

return mdistance;

}

const R3::Vector& BaseBondGenerator::r01() const

{

return mr01;

}

const R3::Matrix& BaseBondGenerator::Ucartesian0() const

{

return mstructure->siteCartesianUij(this->site0());

}

const R3::Matrix& BaseBondGenerator::Ucartesian1() const

{

return mstructure->siteCartesianUij(this->site1());

}

double BaseBondGenerator::msd() const

{

static R3::Vector s;

s = this->r01();

double msd0 = meanSquareDisplacement(this->Ucartesian0(), s,

mstructure->siteAnisotropy(this->site0()));

double msd1 = meanSquareDisplacement(this->Ucartesian1(), s,

mstructure->siteAnisotropy(this->site1()));

double rv = msd0 + msd1;

return rv;

}

// Protected Methods ---------------------------------------------------------

bool BaseBondGenerator::iterateSymmetry()

{

return false;

}

void BaseBondGenerator::rewindSymmetry()

{

mr1 = mstructure->siteCartesianPosition(this->site1());

this->updateDistance();

}

void BaseBondGenerator::getNextBond()

{

if (this->iterateSymmetry()) return;

msite_current += 1;

this->advanceIfSkippedSite();

// avoid calling rewindSymmetry at an invalid site

if (!(this->finished())) this->rewindSymmetry();

}

void BaseBondGenerator::updateDistance()

{

if ((mdistance = fabs(mr01[0] = mr1[0] - mr0[0])) > mrmax) return;

if ((mdistance = fabs(mr01[1] = mr1[1] - mr0[1])) > mrmax) return;

if ((mdistance = fabs(mr01[2] = mr1[2] - mr0[2])) > mrmax) return;

mdistance = R3::norm(mr01);

}

// Private Methods -----------------------------------------------------------

void BaseBondGenerator::advanceIfSkippedSite()

{

while (!this->finished() && !msite_selected[msite_current])

{

++msite_current;

}

void BaseBondGenerator::advanceWhileInvalid()

{

while (!this->finished() &&

(this->bondOutOfRange() || this->atSelfPair()))

{

this->getNextBond();

}

// Private Methods -----------------------------------------------------------

bool BaseBondGenerator::bondOutOfRange() const

{

const double& d = this->distance();

bool rv = (d < this->getRmin()) || (d > this->getRmax());

return rv;

}

bool BaseBondGenerator::atSelfPair() const

{

bool rv = eps_eq(this->distance(), 0.0);

return rv;

}

void BaseBondGenerator::setFinishedFlag()

{

msite_current = msite_last;

}

} // namespace srreal

} // namespace diffpy

// End of file

libdiffpy/src/diffpy/srreal/BaseBondGenerator.cpp at develop · cfarrow/libdiffpy · GitHub

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