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// ************************************************************************************************
//
// BornAgain: simulate and fit reflection and scattering
//
//! @file Sample/Particle/Mesocrystal.cpp
//! @brief Implements class Mesocrystal.
//!
//! @homepage http://www.bornagainproject.org
//! @license GNU General Public License v3 or higher (see COPYING)
//! @copyright Forschungszentrum Jülich GmbH 2018
//! @authors Scientific Computing Group at MLZ (see CITATION, AUTHORS)
//
// ************************************************************************************************
#include "Sample/Particle/Mesocrystal.h"
#include "Base/Type/Span.h"
#include "Base/Util/Assert.h"
#include "Sample/Lattice/ISelectionRule.h"
#include "Sample/Lattice/Lattice3D.h"
#include "Sample/Particle/Crystal.h"
#include "Sample/Particle/IFormfactor.h"
#include "Sample/Particle/Particle.h"
#include "Sample/Scattering/Rotations.h"
#include <algorithm>
Mesocrystal::Mesocrystal(Crystal* crystal, IFormfactor* formfactor)
: m_crystal(crystal)
, m_meso_formfactor(formfactor)
{
}
Mesocrystal::Mesocrystal(const Crystal& crystal, const IFormfactor& formfactor)
: Mesocrystal(crystal.clone(), formfactor.clone())
{
}
Mesocrystal::~Mesocrystal() = default;
Mesocrystal* Mesocrystal::clone() const
{
auto* result = new Mesocrystal(m_crystal->clone(), m_meso_formfactor->clone());
result->setAbundance(m_abundance);
if (rotation())
result->rotate(*rotation());
result->translate(particlePosition());
return result;
}
std::vector<const INode*> Mesocrystal::nodeChildren() const
{
return std::vector<const INode*>()
<< IParticle::nodeChildren() << m_crystal << m_meso_formfactor;
}
const Crystal& Mesocrystal::particleStructure() const
{
ASSERT(m_crystal);
return *m_crystal;
}
Span Mesocrystal::zSpan() const
{
return m_meso_formfactor->spanZ(rotation()) + particlePosition().z();
}
std::vector<R3> Mesocrystal::calcBasisPositions() const
{
std::vector<I3> basisIndexes = calcBasisIndexes().basisIndexes;
std::vector<R3> result(basisIndexes.size());
size_t counter = 0;
for (const I3& index : basisIndexes)
result[counter++] = index.x() * m_crystal->lattice()->basisVectorA()
+ index.y() * m_crystal->lattice()->basisVectorB()
+ index.z() * m_crystal->lattice()->basisVectorC();
return result;
}
ShapeIndexes Mesocrystal::calcBasisIndexes() const
{
const Lattice3D& lattice = *m_crystal->lattice();
R3 shift = m_crystal->basis()->particlePosition();
auto contains = [&](const I3& index) -> bool {
R3 position = index.x() * lattice.basisVectorA() + index.y() * lattice.basisVectorB()
+ index.z() * lattice.basisVectorC();
return m_meso_formfactor->contains(position + shift);
};
// positive and negative boundaries are changeable
struct Limits {
int i_min = 0, i_max = 1;
int j_min = 0, j_max = 1;
int k_min = 0, k_max = 1;
} limits;
// On the first pass we find min and max indices along each axis WITHOUT selection rule
auto check_and_add_particle = [&](int i, int j, int k) {
if (contains(I3(i, j, k))) {
// if boundary particle belongs to the outer shape, extend the boundaries
if (i == limits.i_min)
limits.i_min--;
if (i == limits.i_max)
limits.i_max++;
if (j == limits.j_min)
limits.j_min--;
if (j == limits.j_max)
limits.j_max++;
if (k == limits.k_min)
limits.k_min--;
if (k == limits.k_max)
limits.k_max++;
}
};
auto iterate_i = [&](int j, int k) {
for (int i = 1; i <= limits.i_max; i++)
check_and_add_particle(i, j, k);
for (int i = 0; i >= limits.i_min; i--)
check_and_add_particle(i, j, k);
};
auto iterate_j = [&](int k) {
for (int j = 1; j <= limits.j_max; j++)
iterate_i(j, k);
for (int j = 0; j >= limits.j_min; j--)
iterate_i(j, k);
};
auto iterate_k = [&] {
for (int k = 1; k <= limits.k_max; k++)
iterate_j(k);
for (int k = 0; k >= limits.k_min; k--)
iterate_j(k);
};
iterate_k();
// min and max indexes belonging to the outer shape
I3 min_index(limits.i_min + 1, limits.j_min + 1, limits.k_min + 1);
I3 max_index(limits.i_max - 1, limits.j_max - 1, limits.k_max - 1);
I3 range = max_index - min_index;
// On the second pass we find indices WITH selection rule
auto contains_shifted = [&](int i, int j, int k) -> bool {
const I3 shifted_index = I3(i, j, k) + min_index;
if (lattice.selectionRule() && !lattice.selectionRule()->coordinateSelected(shifted_index))
return false;
return contains(shifted_index);
};
// reuse to find updated index range WITH selection rule
limits = {range.x(), 0, range.y(), 0, range.z(), 0};
// For each [i,j] point we collect continuous ranges of k indexes and store them as of pairs
// (k_begin, k_end). These ranges will be used to efficiently sum the geometric progression.
std::vector<std::vector<std::vector<std::pair<int, int>>>> k_pairs(
range.x() + 1, std::vector<std::vector<std::pair<int, int>>>(range.y() + 1));
std::vector<I3> basisIndexes;
for (int i = 0; i <= range.x(); i++) {
for (int j = 0; j <= range.y(); j++) {
for (int k = 0; k <= range.z(); k++) {
if (!contains_shifted(i, j, k))
continue;
basisIndexes.push_back(I3(i, j, k) + min_index);
limits.i_min = std::min(limits.i_min, i);
limits.j_min = std::min(limits.j_min, j);
limits.k_min = std::min(limits.k_min, k);
limits.i_max = std::max(limits.i_max, i);
limits.j_max = std::max(limits.j_max, j);
limits.k_max = std::max(limits.k_max, k);
// open pair
if (k == 0 || !contains_shifted(i, j, k - 1))
k_pairs[i][j].push_back(std::make_pair(k, k));
// close pair
if (k == range.z() || !contains_shifted(i, j, k + 1))
k_pairs[i][j].back().second = k;
}
}
}
// min and max indexes belonging to the outer shape with selection rule
const I3 upd_min_index = I3(limits.i_min, limits.j_min, limits.k_min) + min_index;
const I3 upd_max_index = I3(limits.i_max, limits.j_max, limits.k_max) + min_index;
return {upd_min_index, upd_max_index, basisIndexes, k_pairs};
}
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