libdiffpy/src/diffpy/srreal/OverlapCalculator.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 OverlapCalculator -- calculator of atom radii overlaps

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

#include <algorithm>

#include <diffpy/srreal/OverlapCalculator.hpp>

#include <diffpy/srreal/ConstantRadiiTable.hpp>

#include <diffpy/validators.hpp>

#include <diffpy/mathutils.hpp>

#include <diffpy/serialization.ipp>

using namespace std;

using diffpy::validators::ensureNonNull;

namespace diffpy {

namespace srreal {

// Local Constants -----------------------------------------------------------

namespace {

enum {

DISTANCE_OFFSET,

DIRECTION0_OFFSET,

DIRECTION1_OFFSET,

DIRECTION2_OFFSET,

SITE0_OFFSET,

SITE1_OFFSET,

CHUNK_SIZE,

};

template <class T>

vector<T> vectorconvert(const QuantityType& v)

{

vector<T> rv;

rv.reserve(v.size());

QuantityType::const_iterator x = v.begin();

for (; x != v.end(); ++x) rv.push_back(T(*x));

return rv;

}

} // namespace

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

OverlapCalculator::OverlapCalculator()

{

mevaluator->useFullSum(true);

// default configuration

AtomRadiiTablePtr table(new ConstantRadiiTable);

this->setAtomRadiiTable(table);

this->cacheStructureData();

mneighborids_cached = false;

// attributes

this->registerDoubleAttribute("rmaxused", this,

&OverlapCalculator::getRmaxUsed);

};

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

QuantityType OverlapCalculator::overlaps() const

{

int n = this->count();

QuantityType rv;

rv.reserve(n);

for (int idx = 0; idx < n; ++idx)

{

double olp = this->suboverlap(idx);

if (olp <= 0.0) continue;

rv.push_back(olp);

}

return rv;

}

QuantityType OverlapCalculator::distances() const

{

return this->subvector(DISTANCE_OFFSET, OVERLAPPING);

}

vector<R3::Vector> OverlapCalculator::directions() const

{

int n = this->count();

vector<R3::Vector> rv;

rv.reserve(n);

for (int index = 0; index < n; ++index)

{

if (this->suboverlap(index) <= 0.0) continue;

rv.push_back(this->subdirection(index));

}

return rv;

}

vector<int> OverlapCalculator::sites0() const

{

QuantityType rv0 = this->subvector(SITE0_OFFSET, OVERLAPPING);

return vectorconvert<int>(rv0);

}

vector<int> OverlapCalculator::sites1() const

{

QuantityType rv0 = this->subvector(SITE1_OFFSET, OVERLAPPING);

return vectorconvert<int>(rv0);

}

vector<string> OverlapCalculator::types0() const

{

return siteIndicesToTypes(mstructure, this->sites0());

}

vector<string> OverlapCalculator::types1() const

{

return siteIndicesToTypes(mstructure, this->sites1());

}

QuantityType OverlapCalculator::siteSquareOverlaps() const

{

int n = this->count();

int cntsites = this->countSites();

QuantityType rv(cntsites, 0.0);

for (int index = 0; index < n; ++index)

{

double olp = this->suboverlap(index);

if (olp <= 0.0) continue;

double sqoverlap = olp * olp;

int i = int(this->subvalue(SITE0_OFFSET, index));

int j = int(this->subvalue(SITE1_OFFSET, index));

rv[i] += sqoverlap * mstructure->siteOccupancy(j);

}

// overlaps are shared by 2 atoms

QuantityType::iterator xi;

for (xi = rv.begin(); xi != rv.end(); ++xi) *xi /= 2;

return rv;

}

double OverlapCalculator::totalSquareOverlap() const

{

int cntsites = this->countSites();

QuantityType sqoverlap = this->siteSquareOverlaps();

double rv = 0.0;

for (int i = 0; i < cntsites; ++i)

{

rv += sqoverlap[i] *

mstructure->siteMultiplicity(i) * mstructure->siteOccupancy(i);

}

return rv;

}

double OverlapCalculator::meanSquareOverlap() const

{

double totocc = mstructure->totalOccupancy();

double rv = (totocc > 0) ? (this->totalSquareOverlap() / totocc) : 0.0;

return rv;

}

double OverlapCalculator::flipDiffTotal(int i, int j) const

{

int cntsites = this->countSites();

if (i < 0 || i >= cntsites || j < 0 || j >= cntsites)

{

const char* emsg = "Index out of range.";

throw invalid_argument(emsg);

}

bool sameradii = (i == j) ||

(mstructure_cache.siteradii[i] == mstructure_cache.siteradii[j]);

if (sameradii) return 0.0;

// here we have to remove the overlap contributions for i and j

double rv = 0.0;

const list<int>& ineighbors = this->getNeighborIds(i);

const list<int>& jneighbors = this->getNeighborIds(j);

boost::unordered_set<int> allids;

allids.insert(ineighbors.begin(), ineighbors.end());

allids.insert(jneighbors.begin(), jneighbors.end());

boost::unordered_set<int>::const_iterator idx;

for (idx = allids.begin(); idx != allids.end(); ++idx)

{

int i1 = int(this->subvalue(SITE0_OFFSET, *idx));

int j1 = int(this->subvalue(SITE1_OFFSET, *idx));

double sqscale =

((i1 == j1) ? 1 : 2) *

mstructure->siteOccupancy(i1) * mstructure->siteOccupancy(j1) *

mstructure->siteMultiplicity(i1) / 2;

double olp0 = this->suboverlap(*idx);

double olp1 = this->suboverlap(*idx, i, j);

rv -= sqscale * olp0 * olp0;

rv += sqscale * olp1 * olp1;

}

return rv;

}

double OverlapCalculator::flipDiffMean(int i, int j) const

{

double totocc = mstructure->totalOccupancy();

double rv = (totocc > 0) ? (this->flipDiffTotal(i, j) / totocc) : 0.0;

return rv;

}

vector<R3::Vector> OverlapCalculator::gradients() const

{

using diffpy::mathutils::eps_gt;

int n = this->count();

int cntsites = this->countSites();

vector<R3::Vector> rv(cntsites, R3::Vector(0.0, 0.0, 0.0));

R3::Vector gij;

for (int index = 0; index < n; ++index)

{

double olp = this->suboverlap(index);

if (olp <= 0.0) continue;

const double& dst = this->subvalue(DISTANCE_OFFSET, index);

assert(eps_gt(dst, 0.0));

int j = int(this->subvalue(SITE1_OFFSET, index));

gij = -2.0 * olp / dst * this->subdirection(index);

rv[j] += gij;

}

return rv;

}

boost::unordered_set<int> OverlapCalculator::getNeighborSites(int i) const

{

boost::unordered_set<int> rv;

const list<int>& ineighbors = this->getNeighborIds(i);

list<int>::const_iterator idx;

for (idx = ineighbors.begin(); idx != ineighbors.end(); ++idx)

{

double olp = this->suboverlap(*idx);

if (olp <= 0.0) continue;

assert(i == int(this->subvalue(SITE0_OFFSET, *idx)));

int j1 = int(this->subvalue(SITE1_OFFSET, *idx));

rv.insert(j1);

}

return rv;

}

QuantityType OverlapCalculator::coordinations() const

{

int cntsites = this->countSites();

QuantityType rv(cntsites, 0.0);

int n = this->count();

for (int index = 0; index < n; ++index)

{

double olp = this->suboverlap(index);

if (olp <= 0.0) continue;

int j0 = int(this->subvalue(SITE0_OFFSET, index));

int j1 = int(this->subvalue(SITE1_OFFSET, index));

rv[j0] += mstructure->siteOccupancy(j1);

}

return rv;

}

boost::unordered_map<string,double>

OverlapCalculator::coordinationByTypes(int i) const

{

boost::unordered_map<string,double> rv;

const list<int>& ineighbors = this->getNeighborIds(i);

list<int>::const_iterator idx;

for (idx = ineighbors.begin(); idx != ineighbors.end(); ++idx)

{

double olp = this->suboverlap(*idx);

if (olp <= 0.0) continue;

int j0 = int(this->subvalue(SITE0_OFFSET, *idx));

int j1 = int(this->subvalue(SITE1_OFFSET, *idx));

if (j0 == i)

{

const string& tp = mstructure->siteAtomType(j1);

rv[tp] += mstructure->siteOccupancy(j1);

}

else

{

assert(j1 == i);

const string& tp = mstructure->siteAtomType(j0);

rv[tp] += mstructure->siteOccupancy(j0) *

mstructure->siteMultiplicity(j0) /

mstructure->siteMultiplicity(j1);

}

return rv;

}

vector< boost::unordered_set<int> > OverlapCalculator::neighborhoods() const

{

int cntsites = this->countSites();

typedef boost::unordered_set<int> SiteSet;

typedef std::vector< boost::shared_ptr<SiteSet> > SiteSetPointers;

SiteSetPointers rvptr(cntsites);

int n = this->count();

for (int index = 0; index < n; ++index)

{

double olp = this->suboverlap(index);

if (olp <= 0.0) continue;

int j0 = int(this->subvalue(SITE0_OFFSET, index));

int j1 = int(this->subvalue(SITE1_OFFSET, index));

if (!rvptr[j0].get())

{

rvptr[j0].reset(new SiteSet);

rvptr[j0]->insert(j0);

}

if (!rvptr[j1].get())

{

rvptr[j0]->insert(j1);

rvptr[j1] = rvptr[j0];

}

assert(rvptr[j0].get() && rvptr[j1].get());

if (rvptr[j0].get() == rvptr[j1].get()) continue;

// here we need to unify the j0 and j1 sets

SiteSetPointers::value_type ss1 = rvptr[j1];

SiteSet::const_iterator idx1 = ss1->begin();

for (; idx1 != ss1->end(); ++idx1)

{

rvptr[j0]->insert(*idx1);

rvptr[*idx1] = rvptr[j0];

}

// replace any unassigned items with a self-neighborhoods

for (int i = 0; i < cntsites; ++i)

{

if (rvptr[i].get()) continue;

rvptr[i].reset(new SiteSet(&i, &i + 1));

}

boost::unordered_set<const SiteSet*> duplicate;

vector< boost::unordered_set<int> > rv;

SiteSetPointers::const_iterator ssp;

for (ssp = rvptr.begin(); ssp != rvptr.end(); ++ssp)

{

if (duplicate.count(ssp->get())) continue;

duplicate.insert(ssp->get());

rv.push_back(**ssp);

}

return rv;

}

void OverlapCalculator::setAtomRadiiTable(AtomRadiiTablePtr table)

{

ensureNonNull("AtomRadiiTable", table);

matomradiitable = table;

}

void OverlapCalculator::setAtomRadiiTableByType(const std::string& tp)

{

matomradiitable = AtomRadiiTable::createByType(tp);

}

AtomRadiiTablePtr& OverlapCalculator::getAtomRadiiTable()

{

return matomradiitable;

}

const AtomRadiiTablePtr& OverlapCalculator::getAtomRadiiTable() const

{

return matomradiitable;

}

double OverlapCalculator::getRmaxUsed() const

{

assert(this->countSites() == int(mstructure_cache.siteradii.size()));

double rv = min(this->getRmax(), mstructure_cache.maxseparation);

return rv;

}

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

void OverlapCalculator::resetValue()

{

mvalue.clear();

mneighborids.clear();

mneighborids_cached = false;

this->cacheStructureData();

this->PairQuantity::resetValue();

}

void OverlapCalculator::configureBondGenerator(BaseBondGenerator& bnds) const

{

bnds.setRmax(this->getRmaxUsed());

}

void OverlapCalculator::addPairContribution(

const BaseBondGenerator& bnds, int summationscale)

{

assert(summationscale == 1);

assert(bnds.distance() <= mstructure_cache.maxseparation);

const R3::Vector& r01 = bnds.r01();

int baseidx = mvalue.size();

mvalue.insert(mvalue.end(), CHUNK_SIZE, 0.0);

mvalue[baseidx + DISTANCE_OFFSET] = bnds.distance();

mvalue[baseidx + DIRECTION0_OFFSET] = r01[0];

mvalue[baseidx + DIRECTION1_OFFSET] = r01[1];

mvalue[baseidx + DIRECTION2_OFFSET] = r01[2];

mvalue[baseidx + SITE0_OFFSET] = bnds.site0();

mvalue[baseidx + SITE1_OFFSET] = bnds.site1();

}

void OverlapCalculator::executeParallelMerge(const std::string& pdata)

{

istringstream storage(pdata, ios::binary);

diffpy::serialization::iarchive ia(storage, ios::binary);

QuantityType pvalue;

ia >> pvalue;

mvalue.insert(mvalue.end(), pvalue.begin(), pvalue.end());

}

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

int OverlapCalculator::count() const

{

int rv = int(mvalue.size()) / CHUNK_SIZE;

return rv;

}

QuantityType OverlapCalculator::subvector(int offset,

OverlapCalculator::OverlapFlag flag) const

{

assert(0 <= offset && offset < CHUNK_SIZE);

assert(flag == ALLVALUES || flag == OVERLAPPING);

int n = this->count();

QuantityType rv;

rv.reserve(n);

for (int index = 0; index < n; ++index)

{

if (OVERLAPPING == flag && this->suboverlap(index) <= 0.0) continue;

rv.push_back(this->subvalue(offset, index));

}

return rv;

}

const double& OverlapCalculator::subvalue(int offset, int index) const

{

assert(0 <= offset && offset < CHUNK_SIZE);

assert(0 <= index && index < this->count());

return mvalue[offset + CHUNK_SIZE * index];

}

const R3::Vector& OverlapCalculator::subdirection(int index) const

{

static R3::Vector rv;

rv[0] = this->subvalue(DIRECTION0_OFFSET, index);

rv[1] = this->subvalue(DIRECTION1_OFFSET, index);

rv[2] = this->subvalue(DIRECTION2_OFFSET, index);

return rv;

}

double OverlapCalculator::suboverlap(int index, int flipi, int flipj) const

{

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

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

int i = int(this->subvalue(SITE0_OFFSET, index));

int j = int(this->subvalue(SITE1_OFFSET, index));

const double& radiusi = (flipi == flipj) ? mstructure_cache.siteradii[i] :

(i == flipi) ? mstructure_cache.siteradii[flipj] :

(i == flipj) ? mstructure_cache.siteradii[flipi] :

mstructure_cache.siteradii[i];

const double& radiusj = (flipi == flipj) ? mstructure_cache.siteradii[j] :

(j == flipi) ? mstructure_cache.siteradii[flipj] :

(j == flipj) ? mstructure_cache.siteradii[flipi] :

mstructure_cache.siteradii[j];

const double& dij = this->subvalue(DISTANCE_OFFSET, index);

double sepij = radiusi + radiusj;

double rv = (dij < sepij) ? (sepij - dij) : 0.0;

return rv;

}

void OverlapCalculator::cacheStructureData()

{

int cntsites = this->countSites();

mstructure_cache.siteradii.resize(cntsites);

const AtomRadiiTablePtr& table = this->getAtomRadiiTable();

for (int i = 0; i < cntsites; ++i)

{

const string& smbl = mstructure->siteAtomType(i);

mstructure_cache.siteradii[i] = table->lookup(smbl);

}

double maxradius = mstructure_cache.siteradii.empty() ?

0.0 : *max_element(mstructure_cache.siteradii.begin(),

mstructure_cache.siteradii.end());

mstructure_cache.maxseparation = 2 * maxradius;

}

const std::list<int>&

OverlapCalculator::getNeighborIds(int k) const

{

typedef std::list<int> NbList;

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

if (!mneighborids_cached)

{

assert(mneighborids.empty());

int n = this->count();

for (int idx = 0; idx < n; ++idx)

{

int i = int(this->subvalue(SITE0_OFFSET, idx));

mneighborids[i].push_back(idx);

}

mneighborids_cached = true;

}

static NbList noneighbors;

NeighborIdsStorage::const_iterator nbit = mneighborids.find(k);

const NbList& rv =

(nbit == mneighborids.end()) ? noneighbors : nbit->second;

return rv;

}

} // namespace srreal

} // namespace diffpy

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

DIFFPY_INSTANTIATE_SERIALIZATION(diffpy::srreal::OverlapCalculator)

BOOST_CLASS_EXPORT_IMPLEMENT(diffpy::srreal::OverlapCalculator)

// End of file

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

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