libdiffpy/src/diffpy/srreal/AtomicStructureAdapter.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 AtomicStructureAdapter -- universal structure adapter for

* a non-periodic set of atoms.

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

#include <cassert>

#include <algorithm>

#include <boost/functional/hash.hpp>

#include <diffpy/serialization.ipp>

#include <diffpy/srreal/AtomicStructureAdapter.hpp>

#include <diffpy/srreal/StructureDifference.hpp>

using std::string;

namespace diffpy {

namespace srreal {

//////////////////////////////////////////////////////////////////////////////

// class Atom

//////////////////////////////////////////////////////////////////////////////

bool operator< (const Atom& a0, const Atom& a1)

{

if (a0.atomtype < a1.atomtype) return true;

if (a0.atomtype > a1.atomtype) return false;

R3::Vector::const_iterator p0 = a0.cartesianposition.begin();

R3::Vector::const_iterator p1 = a1.cartesianposition.begin();

for (; p0 != a0.cartesianposition.end(); ++p0, ++p1)

{

if (*p0 < *p1) return true;

if (*p0 > *p1) return false;

}

if (a0.occupancy < a1.occupancy) return true;

if (a0.occupancy > a1.occupancy) return false;

if (a0.anisotropy < a1.anisotropy) return true;

if (a0.anisotropy > a1.anisotropy) return false;

typedef R3::Matrix::array_type::const_iterator CIter;

CIter u0 = a0.cartesianuij.data().begin();

CIter u0last = a0.cartesianuij.data().end();

CIter u1 = a1.cartesianuij.data().begin();

for (; u0 != u0last; ++u0, ++u1)

{

if (*u0 < *u1) return true;

if (*u0 > *u1) return false;

}

return false;

}

bool operator==(const Atom& a0, const Atom& a1)

{

bool rv = (&a0 == &a1) || (

a0.atomtype == a1.atomtype &&

(a0.cartesianposition == a1.cartesianposition) &&

a0.occupancy == a1.occupancy &&

a0.anisotropy == a1.anisotropy &&

a0.cartesianuij == a1.cartesianuij

);

return rv;

}

bool operator!=(const Atom& a0, const Atom& a1)

{

return !(a0 == a1);

}

size_t hash_value(const Atom& a)

{

size_t seed = 0;

boost::hash_combine(seed, a.atomtype);

boost::hash_combine(seed, a.cartesianposition);

boost::hash_combine(seed, a.occupancy);

boost::hash_combine(seed, a.anisotropy);

boost::hash_combine(seed, a.cartesianuij);

return seed;

}

//////////////////////////////////////////////////////////////////////////////

// class AtomicStructureAdapter

//////////////////////////////////////////////////////////////////////////////

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

BaseBondGeneratorPtr AtomicStructureAdapter::createBondGenerator() const

{

BaseBondGeneratorPtr bnds(new BaseBondGenerator(shared_from_this()));

return bnds;

}

int AtomicStructureAdapter::countSites() const

{

return matoms.size();

}

const string& AtomicStructureAdapter::siteAtomType(int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx].atomtype;

}

const R3::Vector& AtomicStructureAdapter::siteCartesianPosition(int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx].cartesianposition;

}

double AtomicStructureAdapter::siteOccupancy(int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx].occupancy;

}

bool AtomicStructureAdapter::siteAnisotropy(int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx].anisotropy;

}

const R3::Matrix& AtomicStructureAdapter::siteCartesianUij(int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx].cartesianuij;

}

// helper for diff

namespace {

typedef std::pair<const Atom*, int> atomindex;

bool cmpatomindex(const atomindex& ai0, const atomindex& ai1)

{

return (*(ai0.first) < *(ai1.first));

}

} // namespace

StructureDifference

AtomicStructureAdapter::diff(StructureAdapterConstPtr other) const

{

using std::min;

typedef boost::shared_ptr<const class AtomicStructureAdapter> Ptr;

StructureDifference sd(this->shared_from_this(), other);

if (sd.stru0 == sd.stru1) return sd;

Ptr pstru0 = boost::static_pointer_cast<Ptr::element_type>(sd.stru0);

Ptr pstru1 = boost::dynamic_pointer_cast<Ptr::element_type>(sd.stru1);

if (!pstru1) return this->StructureAdapter::diff(other);

assert(pstru0);

assert(pstru1);

const AtomicStructureAdapter& astru0 = *pstru0;

const AtomicStructureAdapter& astru1 = *pstru1;

sd.pop0.reserve(astru0.countSites());

sd.add1.reserve(astru1.countSites());

// try fast side-by-side comparison for equal length structures

if (astru0.countSites() == astru1.countSites())

{

sd.diffmethod = StructureDifference::Method::SIDEBYSIDE;

const_iterator ai0 = astru0.matoms.begin();

const_iterator ai1 = astru1.matoms.begin();

for (int i = 0; ai0 != astru0.matoms.end(); ++i, ++ai0, ++ai1)

{

if (*ai0 != *ai1)

{

sd.pop0.push_back(i);

sd.add1.push_back(i);

}

if (!sd.allowsfastupdate()) break;

}

if (sd.allowsfastupdate()) return sd;

}

// here the structures are either of different length or differ too much

// when compared side by side. Let's start from a blank slate.

sd.pop0.clear();

sd.add1.clear();

// let's build sorted vectors of atoms in stru0 and stru1

sd.diffmethod = StructureDifference::Method::SORTED;

std::vector<atomindex> satoms0, satoms1;

satoms0.reserve(astru0.countSites());

const_iterator ai = astru0.matoms.begin();

for (int i = 0; ai != astru0.matoms.end(); ++ai, ++i)

{

satoms0.push_back(atomindex(&(*ai), i));

}

// use negative index for stru1 atoms so we can tell them apart

// in the output of set_symmetric_difference

satoms1.reserve(astru1.countSites());

ai = astru1.matoms.begin();

for (int i = -1; ai != astru1.matoms.end(); ++ai, --i)

{

satoms1.push_back(atomindex(&(*ai), i));

}

sort(satoms0.begin(), satoms0.end(), cmpatomindex);

sort(satoms1.begin(), satoms1.end(), cmpatomindex);

std::vector<atomindex> symdiffatoms(satoms0.size() + satoms1.size());

std::vector<atomindex>::iterator ii;

ii = std::set_symmetric_difference(satoms0.begin(), satoms0.end(),

satoms1.begin(), satoms1.end(),

symdiffatoms.begin(), cmpatomindex);

symdiffatoms.erase(ii, symdiffatoms.end());

for (ii = symdiffatoms.begin(); ii != symdiffatoms.end(); ++ii)

{

if (ii->second >= 0) sd.pop0.push_back(ii->second);

else sd.add1.push_back(-1 * ii->second - 1);

}

assert(sd.pop0.size() <= min(satoms0.size(), symdiffatoms.size()));

assert(sd.add1.size() <= min(satoms1.size(), symdiffatoms.size()));

sort(sd.pop0.begin(), sd.pop0.end());

sort(sd.add1.begin(), sd.add1.end());

return sd;

}

void AtomicStructureAdapter::insert(int idx, const Atom& atom)

{

assert(0 <= idx && idx <= this->countSites());

matoms.insert(matoms.begin() + idx, atom);

}

void AtomicStructureAdapter::append(const Atom& atom)

{

matoms.push_back(atom);

}

void AtomicStructureAdapter::remove(int idx)

{

assert(0 <= idx && idx < this->countSites());

matoms.erase(matoms.begin() + idx);

}

Atom& AtomicStructureAdapter::operator[](int idx)

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx];

}

const Atom& AtomicStructureAdapter::operator[](int idx) const

{

assert(0 <= idx && idx < this->countSites());

return matoms[idx];

}

} // namespace srreal

} // namespace diffpy

// Serialization -------------------------------------------------------------

DIFFPY_INSTANTIATE_SERIALIZATION(diffpy::srreal::AtomicStructureAdapter)

BOOST_CLASS_EXPORT_IMPLEMENT(diffpy::srreal::AtomicStructureAdapter)

// End of file

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

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