From 7c1cc8f07592ef4d8b7a90139e4ce548965764bc Mon Sep 17 00:00:00 2001
From: Michael Wedel <michael.wedel@esss.se>
Date: Tue, 6 Oct 2015 21:42:44 +0200
Subject: [PATCH] Refs #13537. Re-adding files after repo-move
---
.../MantidGeometry/Crystal/BasicHKLFilters.h | 162 ++++++++++
.../inc/MantidGeometry/Crystal/HKLFilter.h | 175 +++++++++++
.../inc/MantidGeometry/Crystal/HKLGenerator.h | 182 +++++++++++
.../Crystal/ReflectionGenerator.h | 144 +++++++++
.../Crystal/StructureFactorCalculator.h | 82 +++++
.../StructureFactorCalculatorSummation.h | 64 ++++
.../Geometry/src/Crystal/BasicHKLFilters.cpp | 120 +++++++
Framework/Geometry/src/Crystal/HKLFilter.cpp | 117 +++++++
.../Geometry/src/Crystal/HKLGenerator.cpp | 96 ++++++
.../src/Crystal/ReflectionGenerator.cpp | 146 +++++++++
.../src/Crystal/StructureFactorCalculator.cpp | 83 +++++
.../StructureFactorCalculatorSummation.cpp | 82 +++++
Framework/Geometry/test/BasicHKLFiltersTest.h | 146 +++++++++
Framework/Geometry/test/HKLFilterTest.h | 209 +++++++++++++
Framework/Geometry/test/HKLGeneratorTest.h | 98 ++++++
.../Geometry/test/ReflectionGeneratorTest.h | 126 ++++++++
.../StructureFactorCalculatorSummationTest.h | 75 +++++
.../test/StructureFactorCalculatorTest.h | 107 +++++++
.../geometry/src/Exports/CrystalStructure.cpp | 38 +++
.../src/Exports/ReflectionGenerator.cpp | 77 +++++
.../mantid/geometry/CrystalStructureTest.py | 59 ++++
.../geometry/ReflectionGeneratorTest.py | 69 +++++
.../CrystalStructureAndReflections.rst | 293 ++++++++++++++++++
23 files changed, 2750 insertions(+)
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h
create mode 100644 Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
create mode 100644 Framework/Geometry/src/Crystal/BasicHKLFilters.cpp
create mode 100644 Framework/Geometry/src/Crystal/HKLFilter.cpp
create mode 100644 Framework/Geometry/src/Crystal/HKLGenerator.cpp
create mode 100644 Framework/Geometry/src/Crystal/ReflectionGenerator.cpp
create mode 100644 Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp
create mode 100644 Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp
create mode 100644 Framework/Geometry/test/BasicHKLFiltersTest.h
create mode 100644 Framework/Geometry/test/HKLFilterTest.h
create mode 100644 Framework/Geometry/test/HKLGeneratorTest.h
create mode 100644 Framework/Geometry/test/ReflectionGeneratorTest.h
create mode 100644 Framework/Geometry/test/StructureFactorCalculatorSummationTest.h
create mode 100644 Framework/Geometry/test/StructureFactorCalculatorTest.h
create mode 100644 Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp
create mode 100644 Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp
create mode 100644 Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py
create mode 100644 Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py
create mode 100644 docs/source/concepts/CrystalStructureAndReflections.rst
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h b/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h
new file mode 100644
index 00000000000..8081a3ebe33
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/BasicHKLFilters.h
@@ -0,0 +1,162 @@
+#ifndef MANTID_GEOMETRY_BASICHKLFILTERS_H_
+#define MANTID_GEOMETRY_BASICHKLFILTERS_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include "MantidGeometry/Crystal/ReflectionCondition.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/SpaceGroup.h"
+#include "MantidGeometry/Crystal/UnitCell.h"
+
+#include <strstream>
+
+namespace Mantid {
+namespace Geometry {
+
+/** BasicHKLFilters
+
+ This file contains some implementations of HKLFilter that
+ provide filtering based on things like d-value, space group
+ or centering.
+
+ A common use would be to generate a specific list of HKLs,
+ for example all reflections that are allowed according to a certain
+ range of d-values and the reflection conditions of a space group:
+
+ HKLFilter_const_sptr filter =
+ boost::make_shared<HKLFilterDRange>(unitCell, 0.5)
+ & boost::make_shared<HKLFilterSpaceGroup>(spaceGroup);
+
+ HKLGenerator gen(unitCell, 0.5);
+ std::vector<V3D> hkls;
+
+ std::remove_copy_if(gen.begin(), gen.end(), std::back_inserter(hkls),
+ (~filter)->fn());
+
+ An existing list of HKLs could be checked for indices that match the
+ reflection conditions of a space group:
+
+ HKLFilter_const_sptr sgFilter =
+ boost::make_shared<HKLFilterSpaceGroup>(spaceGroup);
+
+ auto matchingHKLCount = std::count_if(hkls.begin(), hkls.end(),
+ sgFilter->fn());
+
+ auto violatingHKLCount = std::count_if(hkls.begin(), hkls.end(),
+ (~sgFilter)->fn());
+
+ Combining HKLGenerator and different HKLFilters provides a very flexible
+ system for creating and processing specific sets of Miller indices that
+ is easy to expand by adding other HKLFilters.
+
+ @author Michael Wedel, ESS
+ @date 23/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+
+/**
+ * A class to filter HKLs by their d-values
+ *
+ * This class takes a UnitCell object and calculates the spacing of
+ * the lattice planes for each HKL. If the lattice spacing is within
+ * the spcified range of values, the reflection is allowed.
+ *
+ * If the first constructor with only dMin is used, dMax is taken to
+ * be the lattice parameter with the largest value. There can not be
+ * a greater interplanar spacing than that value.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterDRange : public HKLFilter {
+public:
+ HKLFilterDRange(const UnitCell &cell, double dMin);
+ HKLFilterDRange(const UnitCell &cell, double dMin, double dMax);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+private:
+ void checkProperDRangeValues();
+
+ UnitCell m_cell;
+ double m_dmin, m_dmax;
+};
+
+/**
+ * A class to filter HKLs according to a space group
+ *
+ * HKLFilterSpaceGroup stores a SpaceGroup object and marks those
+ * reflections as allowed that are allowed according to the
+ * reflection conditions of the space group.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterSpaceGroup : public HKLFilter {
+public:
+ HKLFilterSpaceGroup(const SpaceGroup_const_sptr &spaceGroup);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ SpaceGroup_const_sptr m_spaceGroup;
+};
+
+/**
+ * A class to filter HKLs according to structure factor magnitudes
+ *
+ * This filter takes a StructureFactorCalculator and calculates the
+ * structure factor for each HKL. If F^2 is larger than the specified
+ * minimum, the reflection is considered allowed. The default minimum
+ * is 1e-6.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterStructureFactor : public HKLFilter {
+public:
+ HKLFilterStructureFactor(const StructureFactorCalculator_sptr &calculator,
+ double fSquaredMin = 1.0e-6);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ StructureFactorCalculator_sptr m_calculator;
+ double m_fSquaredMin;
+};
+
+/**
+ * A class to filter HKLs according to a lattice centering
+ *
+ * HKLFilterCentering is a filter that stores a ReflectionCondition object
+ * internally and filters the HKLs according to that.
+ */
+class MANTID_GEOMETRY_DLL HKLFilterCentering : public HKLFilter {
+public:
+ HKLFilterCentering(const ReflectionCondition_sptr ¢ering);
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+
+protected:
+ ReflectionCondition_sptr m_centering;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_BASICHKLFILTERS_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h
new file mode 100644
index 00000000000..ca812aebdef
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLFilter.h
@@ -0,0 +1,175 @@
+#ifndef MANTID_GEOMETRY_HKLFILTER_H_
+#define MANTID_GEOMETRY_HKLFILTER_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/shared_ptr.hpp>
+#include <functional>
+
+namespace Mantid {
+namespace Geometry {
+
+/** HKLFilter
+
+ There are many ways to filter lists of Miller indices HKL. In order
+ to be able to use HKLGenerator with arbitrary filters, HKLFilter provides
+ a general interface for such filters.
+
+ The abstract base class HKLFilter defines a pure virtual method
+ HKLFilter::isAllowed(), which takes a V3D as argument and returns a boolean.
+ Implementing classes can then implement this method, wrapping very different
+ concepts of checking HKLs for certain characteristics.
+
+ There are two general ways of using HKLFilters. When used "standalone",
+ the isAllowed()-function can be used directly:
+
+ if(filter->isAllowed(hkl)) {
+ // do something
+ }
+
+ For interoperability with STL-algorithms, HKLFilter provides a method that
+ returns a function-object with the filter:
+
+ std::copy_if(generator.begin(), generator.end(),
+ hkls.begin(), filter->fn());
+
+ Often, it's not enough to filter a list by one criterion. To this end,
+ there are two implementations of HKLFilter that provide binary logic
+ operations
+ "and" (HKLFilterAnd) and "or" (HKLFilterOr). They can be constructed from two
+ HKLFilter_const_sptrs, or, more conveniently, by using the operators & and |
+ directly with those types. This makes it possible to combine filters in many
+ ways:
+
+ HKLFilter_const_sptr filter = (filter1 | filter2) & filter3;
+
+ Lastly, the unary logic operation "not" (HKLFilterNot) is implemented. This is
+ important for usability with the pre-C++11 algorithm std::remove_copy_if that
+ works logically reversed compared to std::copy_if:
+
+ std::remove_copy_if(generator.begin(), generator.end(), hkls.begin(),
+ (~filter)->fn());
+
+ For actual implementations of HKLFilter, check out BasicHKLFilters, where some
+ important filters are defined.
+
+ @author Michael Wedel, ESS
+ @date 06/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL HKLFilter {
+public:
+ virtual ~HKLFilter() {}
+
+ std::function<bool(const Kernel::V3D &)> fn() const;
+
+ virtual std::string getDescription() const = 0;
+ virtual bool isAllowed(const Kernel::V3D &hkl) const = 0;
+};
+
+typedef boost::shared_ptr<const HKLFilter> HKLFilter_const_sptr;
+
+/// Base class for unary logic operations for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterUnaryLogicOperation : public HKLFilter {
+public:
+ HKLFilterUnaryLogicOperation(const HKLFilter_const_sptr &filter);
+ ~HKLFilterUnaryLogicOperation() {}
+
+ /// Returns the operand of the function.
+ const HKLFilter_const_sptr &getOperand() const { return m_operand; }
+
+protected:
+ HKLFilter_const_sptr m_operand;
+};
+
+/// Logical "Not"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterNot : public HKLFilterUnaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if filter is a
+ /// null pointer.
+ HKLFilterNot(const HKLFilter_const_sptr &filter)
+ : HKLFilterUnaryLogicOperation(filter) {}
+ ~HKLFilterNot() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+/// Base class for binary logic operations for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterBinaryLogicOperation : public HKLFilter {
+public:
+ HKLFilterBinaryLogicOperation(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs);
+ virtual ~HKLFilterBinaryLogicOperation() {}
+
+ /// Returns the left-hand side operand of the operation.
+ const HKLFilter_const_sptr &getLHS() const { return m_lhs; }
+
+ /// Returns the right-hand side operand of the operation.
+ const HKLFilter_const_sptr &getRHS() const { return m_rhs; }
+
+protected:
+ HKLFilter_const_sptr m_lhs;
+ HKLFilter_const_sptr m_rhs;
+};
+
+/// Logical "And"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterAnd : public HKLFilterBinaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if either of
+ /// the operands is null.
+ HKLFilterAnd(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+ ~HKLFilterAnd() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+/// Logical "Or"-operation for HKLFilter.
+class MANTID_GEOMETRY_DLL HKLFilterOr : public HKLFilterBinaryLogicOperation {
+public:
+ /// Constructor, calls base class constructor, throws exception if either of
+ /// the operands is null.
+ HKLFilterOr(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+ ~HKLFilterOr() {}
+
+ std::string getDescription() const;
+ bool isAllowed(const Kernel::V3D &hkl) const;
+};
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator~(const HKLFilter_const_sptr &filter);
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator&(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs);
+
+MANTID_GEOMETRY_DLL const HKLFilter_const_sptr
+operator|(const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs);
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_HKLFILTER_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h
new file mode 100644
index 00000000000..5c425967731
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/HKLGenerator.h
@@ -0,0 +1,182 @@
+#ifndef MANTID_GEOMETRY_HKLGENERATOR_H_
+#define MANTID_GEOMETRY_HKLGENERATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/UnitCell.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/iterator/iterator_facade.hpp>
+
+namespace Mantid {
+namespace Geometry {
+
+/** HKLGenerator
+
+ HKLGenerator is a pseudo-container that helps in generating actual
+ containers with V3D-objects representing Miller indices (HKL).
+
+ It's a common task to generate lists of Miller indices. The simplest
+ way of doing that is to simply create a nested loop structure that
+ goes through all combinations of H, K, L within some limits and then
+ put them into a container (vector, list, set, ...):
+
+ for(int h = -hmin; h <= hmax; ++h) {
+ for(int k = -kmin; k <= kmax; ++k) {
+ for(int l = -lmin; l <= lmax; ++l) {
+ hkls.push_back(V3D(h, k, l));
+ }
+ }
+ }
+
+ In most cases the list is not used like that, instead it's filtered
+ using some criteria, for example a certain range of d-spacings or
+ others, so the reflection needs to be checked first:
+
+ ...
+ hkl = V3D(h, k, l)
+ if(isOk(hkl)) {
+ hkls.push_back(hkl);
+ }
+ ...
+
+ Instead of explicitly stating the triple-loop, HKLGenerator provides
+ a shorter way for this process using a const_iterator. The first code
+ example then becomes this:
+
+ HKLGenerator generator(V3D(hmin, kmin, lmin), V3D(hmax, kmax, lmax));
+ for(auto hkl = generator.begin(); hkl != generator.end(); ++hkl) {
+ hkls.push_back(*hkl);
+ }
+
+ Or even shorter, using std::copy:
+
+ HKLGenerator generator(V3D(hmin, kmin, lmin), V3D(hmax, kmax, lmax));
+ std::copy(generator.begin(), generator.end(), std::back_inserter(hkls));
+
+ It's also possible to use filters this way, but in a much easier fashion,
+ using std::copy_remove_if (pre C++11) or std::copy_if (C++11):
+
+ // pre C++11
+ std::copy_remove_if(generator.begin(), generator.end(),
+ std::back_inserter(hkls), isNotOk)
+
+ // C++11
+ std::copy_if(generator.begin(), generator.end(), std::back_inserter(hkls),
+ isOk)
+
+ See the documentation for HKLFilter for more details on how to perform
+ actual filtering.
+
+ Please be aware that the iterator increments infinitely if it passes the
+ specified maximimum HKL. In that case K and L remain constant while H is
+ incremented (until it overflows).
+
+ @author Michael Wedel, ESS
+ @date 23/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL HKLGenerator {
+public:
+ /**
+ * @brief The const_iterator class
+ *
+ * This class uses boost::iterator_facade to provide a const_iterator
+ * interface to HKLGenerator. This makes it very easy to use the standard
+ * library algorithms. It's a forward iterator, so it's not possible to use
+ * operator[] for random access of specific HKLs (this would have to be
+ * done on the generated container if that supports it).
+ *
+ * While the iterators can be instantiated directly, the intention is to
+ * use HKLGenerator::begin() and HKLGenerator::end().
+ */
+ class const_iterator
+ : public boost::iterator_facade<const_iterator, const Kernel::V3D &,
+ boost::forward_traversal_tag> {
+ public:
+ /// Default constructor, requirement from boost::iterator_facade
+ const_iterator() {}
+
+ explicit const_iterator(const Kernel::V3D ¤t);
+
+ explicit const_iterator(const Kernel::V3D &hklMin,
+ const Kernel::V3D &hklMax);
+
+ private:
+ // Required for boost::iterator_facade to work
+ friend class boost::iterator_core_access;
+
+ void increment();
+
+ /// Returns true if other is at the same position
+ inline bool equal(const const_iterator &other) const {
+ return this->m_h == other.m_h && this->m_k == other.m_k &&
+ this->m_l == other.m_l;
+ }
+
+ /// Returns a const reference to the currently pointed at HKL.
+ inline const Kernel::V3D &dereference() const { return m_hkl; }
+
+ int m_h, m_k, m_l;
+ Kernel::V3D m_hkl;
+
+ int m_hMin, m_hMax;
+ int m_kMin, m_kMax;
+ int m_lMin, m_lMax;
+ };
+
+ HKLGenerator(const Kernel::V3D &hklMin, const Kernel::V3D &hklMax);
+ HKLGenerator(const Kernel::V3D &hklMinMax);
+ HKLGenerator(int hMinMax, int kMinMax, int lMinMax);
+ HKLGenerator(const UnitCell &unitCell, double dMin);
+
+ virtual ~HKLGenerator() {}
+
+ /// Returns the number of HKLs to be generated.
+ inline size_t size() const { return m_size; }
+
+ /// Returns an iterator to the beginning of the sequence.
+ inline const const_iterator &begin() const { return m_begin; }
+
+ /// Returns an iterator which "points at" one element past the end.
+ inline const const_iterator &end() const { return m_end; }
+
+private:
+ size_t getSize(const Kernel::V3D &min, const Kernel::V3D &max) const;
+
+ const_iterator getBeginIterator() const;
+ const_iterator getEndIterator() const;
+ Kernel::V3D getEndHKL() const;
+
+ Kernel::V3D m_hklMin;
+ Kernel::V3D m_hklMax;
+
+ size_t m_size;
+
+ const_iterator m_begin;
+ const_iterator m_end;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_HKLGENERATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h
new file mode 100644
index 00000000000..439fcfa162d
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/ReflectionGenerator.h
@@ -0,0 +1,144 @@
+#ifndef MANTID_GEOMETRY_REFLECTIONGENERATOR_H_
+#define MANTID_GEOMETRY_REFLECTIONGENERATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/HKLFilter.h"
+
+namespace Mantid {
+namespace Geometry {
+
+enum struct ReflectionConditionFilter {
+ None,
+ Centering,
+ SpaceGroup,
+ StructureFactor
+};
+
+/** ReflectionGenerator
+
+ ReflectionGenerator is a class that provides the means to perform some
+ common tasks involving generation of reflections. While the combination
+ of HKLGenerator and HKLFilter is very flexible, very often a limited set
+ of operations has to be performed repeatedly, involving the crystal
+ structure.
+
+ ReflectionGenerator is constructed from a CrystalStructure object, which
+ is then stored internally. Additionally, a default filter for reflection
+ conditions can be set, which is applied for HKL-generation in addition
+ to a DRangeFilter. For more flexibility, a method is provided that accepts
+ an HKLFilter as additional argument, this filter is then added to the
+ DRangeFilter.
+
+ This way it's very simple to obtain for example a list of unique reflections
+ for a given crystal structure:
+
+ CrystalStructure structure("5.43 5.43 5.43",
+ "F d -3 m", "Si 0 0 0 1.0 0.05");
+ ReflectionGenerator generator(structure);
+
+ // Get all unique HKLs between 0.5 and 5.0 Angstrom
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.5, 5.0);
+
+ Additionally there are methods to obtain structure factors and d-values
+ for a given list of HKLs.
+
+ The generated reflection lists can be filtered by several criteria to remove
+ reflections that are not allowed. In the default case, the reflection
+ conditions of the space group are used. Alternatively, the reflections can be
+ filtered according to the centering of the lattice or, with some more
+ computational effort, by their structure factors.
+
+ The default filter method can be supplied to the constructor in the form of
+ the enum ReflectionConditionFilter. Furthermore, it's possible to provide
+ self-defined filters in overloaded versions of the HKL generation methods.
+ These can also be generated by using a small helper method that creates
+ the filters and populates them with values associated to the stored crystal
+ structure:
+
+
+ ReflectionGenerator generator(
+ CrystalStructure("5.43 5.43 5.43",
+ "F d -3 m", "Si 0 0 0 1.0 0.05"));
+ auto filter = generator.getReflectionConditionFilter(
+ ReflectionConditionFilter::StructureFactor);
+
+ The filter can then be used in connection with HKLGenerator or the HKL-
+ generation methods of ReflectionGenerator.
+
+ An example where structure factors are required can be found in a very
+ common crystal structure, the structure of Silicon. Silicon crystallizes
+ in the space group Fd-3m (No. 227) and the asymmetric unit consists of
+ one Si-atom at the position (1/8, 1/8, 1/8) (for origin choice 2, with the
+ inversion at the origin). Looking up this space group in the International
+ Tables for Crystallography A reveals that placing a scatterer at this
+ position introduces a new reflection condition for general reflections hkl:
+
+ h = 2n + 1 (reflections with odd h are allowed)
+ or h + k + l = 4n
+
+ This means that for example the reflection family {2 2 2} is not allowed,
+ even though the F-centering would allow it. Using the structure factor
+ calculation filter solves this problem.
+
+ @author Michael Wedel, ESS
+ @date 30/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL ReflectionGenerator {
+public:
+ ReflectionGenerator(const CrystalStructure &crystalStructure,
+ ReflectionConditionFilter defaultFilter =
+ ReflectionConditionFilter::SpaceGroup);
+ ~ReflectionGenerator() {}
+
+ const CrystalStructure &getCrystalStructure() const;
+
+ HKLFilter_const_sptr getDRangeFilter(double dMin, double dMax) const;
+ HKLFilter_const_sptr
+ getReflectionConditionFilter(ReflectionConditionFilter filter);
+
+ std::vector<Kernel::V3D> getHKLs(double dMin, double dMax) const;
+ std::vector<Kernel::V3D>
+ getHKLs(double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const;
+
+ std::vector<Kernel::V3D> getUniqueHKLs(double dMin, double dMax) const;
+ std::vector<Kernel::V3D>
+ getUniqueHKLs(double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const;
+
+ std::vector<double> getDValues(const std::vector<Kernel::V3D> &hkls) const;
+ std::vector<double> getFsSquared(const std::vector<Kernel::V3D> &hkls) const;
+
+private:
+ CrystalStructure m_crystalStructure;
+ StructureFactorCalculator_sptr m_sfCalculator;
+ HKLFilter_const_sptr m_defaultHKLFilter;
+};
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_REFLECTIONGENERATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h
new file mode 100644
index 00000000000..04b51ff0b49
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculator.h
@@ -0,0 +1,82 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/** StructureFactorCalculator
+
+ This is a base class for concrete structure factor calculators. It is used
+ to logically separate this calculation from CrystalStructure so that different
+ methods of calculation can be used. For actual implementations please consult
+ the available sub-classes.
+
+ @author Michael Wedel, ESS
+ @date 05/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL StructureFactorCalculator {
+public:
+ StructureFactorCalculator();
+ virtual ~StructureFactorCalculator() {}
+
+ void setCrystalStructure(const CrystalStructure &crystalStructure);
+
+ /// In implementations this method should return the structure factor for the
+ /// specified HKL.
+ virtual StructureFactor getF(const Kernel::V3D &hkl) const = 0;
+ virtual double getFSquared(const Kernel::V3D &hkl) const;
+
+ virtual std::vector<StructureFactor>
+ getFs(const std::vector<Kernel::V3D> &hkls) const;
+ virtual std::vector<double>
+ getFsSquared(const std::vector<Kernel::V3D> &hkls) const;
+
+protected:
+ virtual void
+ crystalStructureSetHook(const CrystalStructure &crystalStructure);
+};
+
+typedef boost::shared_ptr<StructureFactorCalculator>
+ StructureFactorCalculator_sptr;
+
+namespace StructureFactorCalculatorFactory {
+/// Small templated factory function that creates the desired calculator
+/// and initializes it by setting the crystal structure.
+template <typename T>
+StructureFactorCalculator_sptr
+create(const CrystalStructure &crystalStructure) {
+ boost::shared_ptr<T> calculator = boost::make_shared<T>();
+ calculator->setCrystalStructure(crystalStructure);
+
+ return calculator;
+}
+}
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATOR_H_ */
diff --git a/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
new file mode 100644
index 00000000000..5cfed836be0
--- /dev/null
+++ b/Framework/Geometry/inc/MantidGeometry/Crystal/StructureFactorCalculatorSummation.h
@@ -0,0 +1,64 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_
+
+#include "MantidGeometry/DllConfig.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/** StructureFactorCalculatorSummation
+
+ This implementation of StructureFactorCalculator uses the summation method
+ provided by BraggScatterer and its sub-classes. It obtains all scatterers in
+ the unit cell by combining the space group and the scatterers located in the
+ asymmetric unit (both taken from CrystalStructure) and stores them.
+
+ @author Michael Wedel, ESS
+ @date 05/09/2015
+
+ Copyright © 2015 ISIS Rutherford Appleton Laboratory, NScD Oak Ridge
+ National Laboratory & European Spallation Source
+
+ This file is part of Mantid.
+
+ Mantid is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+
+ Mantid is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+ File change history is stored at: <https://github.com/mantidproject/mantid>
+ Code Documentation is available at: <http://doxygen.mantidproject.org>
+*/
+class MANTID_GEOMETRY_DLL StructureFactorCalculatorSummation
+ : public StructureFactorCalculator {
+public:
+ StructureFactorCalculatorSummation();
+ virtual ~StructureFactorCalculatorSummation() {}
+
+ StructureFactor getF(const Kernel::V3D &hkl) const;
+
+protected:
+ void crystalStructureSetHook(const CrystalStructure &crystalStructure);
+
+ void updateUnitCellScatterers(const CrystalStructure &crystalStructure);
+ std::string getV3DasString(const Kernel::V3D &point) const;
+
+ CompositeBraggScatterer_sptr m_unitCellScatterers;
+};
+
+typedef boost::shared_ptr<StructureFactorCalculatorSummation>
+ StructureFactorSummation_sptr;
+
+} // namespace Geometry
+} // namespace Mantid
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATION_H_ */
diff --git a/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp b/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp
new file mode 100644
index 00000000000..9dfec3038a8
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/BasicHKLFilters.cpp
@@ -0,0 +1,120 @@
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+
+namespace Mantid {
+namespace Geometry {
+
+/// Constructor, dMax is set to the largest lattice parameter.
+HKLFilterDRange::HKLFilterDRange(const UnitCell &cell, double dMin)
+ : m_cell(cell), m_dmin(dMin) {
+ m_dmax = std::max(m_cell.a(), std::max(m_cell.b(), m_cell.c()));
+
+ checkProperDRangeValues();
+}
+
+/// Constructor with explicit dMax.
+HKLFilterDRange::HKLFilterDRange(const UnitCell &cell, double dMin, double dMax)
+ : m_cell(cell), m_dmin(dMin), m_dmax(dMax) {
+ checkProperDRangeValues();
+}
+
+/// Returns a description containing the parameters of the filter.
+std::string HKLFilterDRange::getDescription() const {
+ std::ostringstream strm;
+ strm << "(" << m_dmin << " <= d <= " << m_dmax << ")";
+
+ return strm.str();
+}
+
+/// Returns true if the d-value of the HKL is within the specified range.
+bool HKLFilterDRange::isAllowed(const Kernel::V3D &hkl) const {
+ double d = m_cell.d(hkl);
+
+ return d >= m_dmin && d <= m_dmax;
+}
+
+/// Throws exception if m_dMin or m_dMax is <= 0 or if m_dMax < m_dMin.
+void HKLFilterDRange::checkProperDRangeValues() {
+ if (m_dmin <= 0.0) {
+ throw std::range_error("dMin cannot be <= 0.");
+ }
+
+ if (m_dmax <= 0.0) {
+ throw std::range_error("dMax cannot be <= 0.");
+ }
+
+ if (m_dmax <= m_dmin) {
+ throw std::range_error("dMax cannot be smaller than dMin.");
+ }
+}
+
+/// Constructor, throws exception if the supplied pointer is invalid.
+HKLFilterSpaceGroup::HKLFilterSpaceGroup(
+ const SpaceGroup_const_sptr &spaceGroup)
+ : m_spaceGroup(spaceGroup) {
+ if (!m_spaceGroup) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterSpaceGroup from null space group.");
+ }
+}
+
+/// Returns a description of the filter that contains the space group symbol.
+std::string HKLFilterSpaceGroup::getDescription() const {
+ std::ostringstream strm;
+ strm << "(Space group: " << m_spaceGroup->hmSymbol() << ")";
+
+ return strm.str();
+}
+
+/// Returns true if the reflection is allowed by the space group reflection
+/// conditions.
+bool HKLFilterSpaceGroup::isAllowed(const Kernel::V3D &hkl) const {
+ return m_spaceGroup->isAllowedReflection(hkl);
+}
+
+/// Constructor, throws exception if the calculator pointer is invalid.
+HKLFilterStructureFactor::HKLFilterStructureFactor(
+ const StructureFactorCalculator_sptr &calculator, double fSquaredMin)
+ : m_calculator(calculator), m_fSquaredMin(fSquaredMin) {
+ if (!m_calculator) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterStructureFactor from null calculator.");
+ }
+}
+
+/// Returns a description for the filter that contains the minimum F^2.
+std::string HKLFilterStructureFactor::getDescription() const {
+ std::ostringstream strm;
+ strm << "(F^2 > " << m_fSquaredMin << ")";
+
+ return strm.str();
+}
+
+/// Returns true if F^2(hkl) is larger than the stored minimum.
+bool HKLFilterStructureFactor::isAllowed(const Kernel::V3D &hkl) const {
+ return m_calculator->getFSquared(hkl) > m_fSquaredMin;
+}
+
+/// Constructor, throws exception if pointer is null.
+HKLFilterCentering::HKLFilterCentering(
+ const ReflectionCondition_sptr ¢ering)
+ : m_centering(centering) {
+ if (!m_centering) {
+ throw std::runtime_error(
+ "Cannot construct HKLFilterCentering from null centering.");
+ }
+}
+
+/// Returns a description with the centering symbol.
+std::string HKLFilterCentering::getDescription() const {
+ return "(Centering: " + m_centering->getSymbol() + ")";
+}
+
+/// Returns true if the HKL is allowed according to the lattice centering.
+bool HKLFilterCentering::isAllowed(const Kernel::V3D &hkl) const {
+ return m_centering->isAllowed(static_cast<int>(hkl.X()),
+ static_cast<int>(hkl.Y()),
+ static_cast<int>(hkl.Z()));
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/HKLFilter.cpp b/Framework/Geometry/src/Crystal/HKLFilter.cpp
new file mode 100644
index 00000000000..ed218cb7fdb
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/HKLFilter.cpp
@@ -0,0 +1,117 @@
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include <boost/make_shared.hpp>
+#include <stdexcept>
+
+namespace Mantid {
+namespace Geometry {
+
+/**
+ * Returns a function object that wraps HKLFilter::isAllowed
+ *
+ * This method uses std::bind to create a function object that
+ * represents the HKLFilter::isAllowed() method. This way it's
+ * possible to pass the function to STL-algorithms easily (see
+ * class documentation).
+ *
+ * @return Function object with filter function for V3D.s
+ */
+std::function<bool(const Kernel::V3D &)> HKLFilter::fn() const {
+ return std::bind(&HKLFilter::isAllowed, this, std::placeholders::_1);
+}
+
+/// Stores the supplied filter, throws exception if filter is null.
+HKLFilterUnaryLogicOperation::HKLFilterUnaryLogicOperation(
+ const HKLFilter_const_sptr &filter)
+ : m_operand(filter) {
+ if (!m_operand) {
+ throw std::runtime_error(
+ "Cannot create HKLFilterUnaryLogicOperation from null operand.");
+ }
+}
+
+/// Returns a description of the HKLFilterNot.
+std::string HKLFilterNot::getDescription() const {
+ return "!" + m_operand->getDescription();
+}
+
+/// Returns true if the wrapped filter returns false and false otherwise.
+bool HKLFilterNot::isAllowed(const Kernel::V3D &hkl) const {
+ return !(m_operand->isAllowed(hkl));
+}
+
+/// Stores the left-hand and right-hand side operators, throws exception if
+/// either is null.
+HKLFilterBinaryLogicOperation::HKLFilterBinaryLogicOperation(
+ const HKLFilter_const_sptr &lhs, const HKLFilter_const_sptr &rhs)
+ : m_lhs(lhs), m_rhs(rhs) {
+ if (!m_lhs || !m_rhs) {
+ throw std::runtime_error("Cannot construct HKLFilterBinaryLogicOperation "
+ "with one or more null-operands.");
+ }
+}
+
+/// Returns a description of the HKLFilterAnd.
+std::string HKLFilterAnd::getDescription() const {
+ return "(" + m_lhs->getDescription() + " & " + m_rhs->getDescription() + ")";
+}
+
+/// Returns true if both wrapped filters return true.
+bool HKLFilterAnd::isAllowed(const Kernel::V3D &hkl) const {
+ return m_lhs->isAllowed(hkl) && m_rhs->isAllowed(hkl);
+}
+
+/// Returns a description of the HKLFilterOr.
+std::string HKLFilterOr::getDescription() const {
+ return "(" + m_lhs->getDescription() + " | " + m_rhs->getDescription() + ")";
+}
+
+/// Returns true if either of the wrapped filters returns true.
+bool HKLFilterOr::isAllowed(const Kernel::V3D &hkl) const {
+ return m_lhs->isAllowed(hkl) || m_rhs->isAllowed(hkl);
+}
+
+/**
+ * Constructs an HKLFilterNot from the operand
+ *
+ * This function makes it easy to construct HKLFilterNot by using the
+ * operator ~, which inverts the wrapped filter.
+ *
+ * @param filter :: HKLFilter to invert.
+ * @return HKLFilterNot with the wrapped filter.
+ */
+const HKLFilter_const_sptr operator~(const HKLFilter_const_sptr &filter) {
+ return boost::make_shared<const HKLFilterNot>(filter);
+}
+
+/**
+ * Constructs an HKLFilterAnd from the operands
+ *
+ * This function makes it easy to construct HKLFilterAnd by using the
+ * operator & directly on HKLFilter_const_sptr.
+ *
+ * @param lhs :: Left-hand side HKLFilter operand.
+ * @param rhs :: Right-hand side HKLFilter operand.
+ * @return HKLFilterAnd with two wrapped filters.
+ */
+const HKLFilter_const_sptr operator&(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs) {
+ return boost::make_shared<const HKLFilterAnd>(lhs, rhs);
+}
+
+/**
+ * Constructs an HKLFilterOr from the operands
+ *
+ * This function makes it easy to construct HKLFilterOr by using the
+ * operator | directly on HKLFilter_const_sptr.
+ *
+ * @param lhs :: Left-hand side HKLFilter operand.
+ * @param rhs :: Right-hand side HKLFilter operand.
+ * @return HKLFilterOr with two wrapped filters.
+ */
+const HKLFilter_const_sptr operator|(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs) {
+ return boost::make_shared<HKLFilterOr>(lhs, rhs);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/HKLGenerator.cpp b/Framework/Geometry/src/Crystal/HKLGenerator.cpp
new file mode 100644
index 00000000000..0156cd97045
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/HKLGenerator.cpp
@@ -0,0 +1,96 @@
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+/// Constructs a generator that creates all indices from hklMin to hklMax.
+HKLGenerator::HKLGenerator(const Kernel::V3D &hklMin, const Kernel::V3D &hklMax)
+ : m_hklMin(hklMin), m_hklMax(hklMax), m_size(getSize(m_hklMin, m_hklMax)),
+ m_begin(getBeginIterator()), m_end(getEndIterator()) {}
+
+/// Constructs a generator that creates all indices from -hklMinMax to
+/// hklMinMax.
+HKLGenerator::HKLGenerator(const Kernel::V3D &hklMinMax)
+ : m_hklMin(hklMinMax * -1), m_hklMax(hklMinMax),
+ m_size(getSize(m_hklMin, m_hklMax)), m_begin(getBeginIterator()),
+ m_end(getEndIterator()) {}
+
+/// Constructs a generator that creates all indices from -h,-k,-l to h,k,l.
+HKLGenerator::HKLGenerator(int hMinMax, int kMinMax, int lMinMax) {
+ m_hklMax = V3D(hMinMax, kMinMax, lMinMax);
+ m_hklMin = m_hklMax * -1;
+ m_size = getSize(m_hklMin, m_hklMax);
+
+ m_begin = getBeginIterator();
+ m_end = getEndIterator();
+}
+
+/// Constructs a generator that creates all indices for the given cell up to
+/// dMin.
+HKLGenerator::HKLGenerator(const UnitCell &unitCell, double dMin) {
+ m_hklMax = V3D(unitCell.a() / dMin, unitCell.b() / dMin, unitCell.c() / dMin);
+ m_hklMin = m_hklMax * -1;
+ m_size = getSize(m_hklMin, m_hklMax);
+
+ m_begin = getBeginIterator();
+ m_end = getEndIterator();
+}
+
+/// Returns the number of indices between min and max.
+size_t HKLGenerator::getSize(const V3D &min, const V3D &max) const {
+ V3D diff = (max - min) + V3D(1, 1, 1);
+ return static_cast<size_t>(diff.X() * diff.Y() * diff.Z());
+}
+
+/// Constructs an iterator that points to the beginning of the sequence.
+HKLGenerator::const_iterator HKLGenerator::getBeginIterator() const {
+ return HKLGenerator::const_iterator(m_hklMin, m_hklMax);
+}
+
+/// Constructs an iterator that points to an HKL one past the maximum.
+HKLGenerator::const_iterator HKLGenerator::getEndIterator() const {
+ return HKLGenerator::const_iterator(getEndHKL());
+}
+
+/// Returns the HKL "one past the maximum".
+V3D HKLGenerator::getEndHKL() const {
+ return V3D(m_hklMax.X() + 1, m_hklMin.Y(), m_hklMin.Z());
+}
+
+/// Return an iterator with min = max = current.
+HKLGenerator::const_iterator::const_iterator(const V3D ¤t)
+ : m_h(static_cast<int>(current.X())), m_k(static_cast<int>(current.Y())),
+ m_l(static_cast<int>(current.Z())), m_hkl(current), m_hMin(m_h),
+ m_hMax(m_h), m_kMin(m_k), m_kMax(m_k), m_lMin(m_l), m_lMax(m_l) {}
+
+/// Return an iterator that can move from min to max, with current = min
+HKLGenerator::const_iterator::const_iterator(const V3D &hklMin,
+ const V3D &hklMax)
+ : m_h(static_cast<int>(hklMin.X())), m_k(static_cast<int>(hklMin.Y())),
+ m_l(static_cast<int>(hklMin.Z())), m_hkl(hklMin), m_hMin(m_h),
+ m_hMax(static_cast<int>(hklMax.X())), m_kMin(m_k),
+ m_kMax(static_cast<int>(hklMax.Y())), m_lMin(m_l),
+ m_lMax(static_cast<int>(hklMax.Z())) {}
+
+/// Increments HKL, l moves fastest, h moves slowest, wrapping around at the max
+/// for each index.
+void HKLGenerator::const_iterator::increment() {
+ ++m_l;
+
+ if (m_l > m_lMax) {
+ m_l = m_lMin;
+
+ ++m_k;
+ if (m_k > m_kMax) {
+ m_k = m_kMin;
+ ++m_h;
+ }
+ }
+
+ m_hkl = V3D(m_h, m_k, m_l);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp b/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp
new file mode 100644
index 00000000000..59fd597ef21
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/ReflectionGenerator.cpp
@@ -0,0 +1,146 @@
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+/// Small helper functor to calculate d-Values from a unit cell.
+class LatticeSpacingCalculator {
+public:
+ LatticeSpacingCalculator(const UnitCell &cell) : m_cell(cell) {}
+
+ double operator()(const V3D &hkl) { return m_cell.d(hkl); }
+
+private:
+ UnitCell m_cell;
+};
+
+/// Constructor
+ReflectionGenerator::ReflectionGenerator(
+ const CrystalStructure &crystalStructure,
+ ReflectionConditionFilter defaultFilter)
+ : m_crystalStructure(crystalStructure),
+ m_sfCalculator(StructureFactorCalculatorFactory::create<
+ StructureFactorCalculatorSummation>(m_crystalStructure)),
+ m_defaultHKLFilter(getReflectionConditionFilter(defaultFilter)) {}
+
+/// Returns the internally stored crystal structure
+const CrystalStructure &ReflectionGenerator::getCrystalStructure() const {
+ return m_crystalStructure;
+}
+
+/// Returns a DRangeFilter from the supplied d-limits and the internally stored
+/// cell.
+HKLFilter_const_sptr ReflectionGenerator::getDRangeFilter(double dMin,
+ double dMax) const {
+ return boost::make_shared<const HKLFilterDRange>(m_crystalStructure.cell(),
+ dMin, dMax);
+}
+
+/// Returns a reflection condition HKLFilter based on the supplied enum.
+HKLFilter_const_sptr ReflectionGenerator::getReflectionConditionFilter(
+ ReflectionConditionFilter filter) {
+ switch (filter) {
+ case ReflectionConditionFilter::Centering:
+ return boost::make_shared<const HKLFilterCentering>(
+ m_crystalStructure.centering());
+ break;
+ case ReflectionConditionFilter::SpaceGroup:
+ return boost::make_shared<const HKLFilterSpaceGroup>(
+ m_crystalStructure.spaceGroup());
+ break;
+ case ReflectionConditionFilter::StructureFactor:
+ return boost::make_shared<const HKLFilterStructureFactor>(m_sfCalculator);
+ default:
+ return HKLFilter_const_sptr();
+ }
+}
+
+/// Returns a list of HKLs within the specified d-limits using the default
+/// reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getHKLs(double dMin, double dMax) const {
+ return getHKLs(dMin, dMax, m_defaultHKLFilter);
+}
+
+/// Returns a list of HKLs within the specified d-limits using the specified
+/// filter. If the pointer is null, it's ignored.
+std::vector<Kernel::V3D> ReflectionGenerator::getHKLs(
+ double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const {
+ HKLGenerator generator(m_crystalStructure.cell(), dMin);
+
+ HKLFilter_const_sptr filter = getDRangeFilter(dMin, dMax);
+ if (reflectionConditionFilter) {
+ filter = filter & reflectionConditionFilter;
+ }
+
+ std::vector<V3D> hkls;
+ hkls.reserve(generator.size());
+
+ std::remove_copy_if(generator.begin(), generator.end(),
+ std::back_inserter(hkls), (~filter)->fn());
+ return hkls;
+}
+
+/// Returns a list of symetrically independent HKLs within the specified
+/// d-limits using the default reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getUniqueHKLs(double dMin,
+ double dMax) const {
+ return getUniqueHKLs(dMin, dMax, m_defaultHKLFilter);
+}
+
+/// Returns a list of symetrically independent HKLs within the specified
+/// d-limits using the specified reflection condition filter.
+std::vector<V3D> ReflectionGenerator::getUniqueHKLs(
+ double dMin, double dMax,
+ HKLFilter_const_sptr reflectionConditionFilter) const {
+ HKLGenerator generator(m_crystalStructure.cell(), dMin);
+
+ HKLFilter_const_sptr filter = getDRangeFilter(dMin, dMax);
+ if (reflectionConditionFilter) {
+ filter = filter & reflectionConditionFilter;
+ }
+
+ std::vector<V3D> hkls;
+ hkls.reserve(generator.size());
+
+ PointGroup_sptr pg = m_crystalStructure.spaceGroup()->getPointGroup();
+
+ for (auto hkl = generator.begin(); hkl != generator.end(); ++hkl) {
+ if (filter->isAllowed(*hkl)) {
+ hkls.push_back(pg->getReflectionFamily(*hkl));
+ }
+ }
+
+ std::sort(hkls.begin(), hkls.end());
+ hkls.erase(std::unique(hkls.begin(), hkls.end()), hkls.end());
+
+ return hkls;
+}
+
+/// Returns a list of d-values that correspond to the supplied hkl list, using
+/// the unit cell of the stored crystal structure.
+std::vector<double>
+ReflectionGenerator::getDValues(const std::vector<V3D> &hkls) const {
+ std::vector<double> dValues;
+ dValues.reserve(hkls.size());
+
+ std::transform(hkls.begin(), hkls.end(), std::back_inserter(dValues),
+ LatticeSpacingCalculator(m_crystalStructure.cell()));
+
+ return dValues;
+}
+
+/// Returns a list of squared structure factor amplitudes corresponding to the
+/// supplied list of HKLs.
+std::vector<double>
+ReflectionGenerator::getFsSquared(const std::vector<V3D> &hkls) const {
+ return m_sfCalculator->getFsSquared(hkls);
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp b/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp
new file mode 100644
index 00000000000..df4cb44ed97
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/StructureFactorCalculator.cpp
@@ -0,0 +1,83 @@
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+#include <boost/bind.hpp>
+
+namespace Mantid {
+namespace Geometry {
+
+StructureFactorCalculator::StructureFactorCalculator() {}
+
+/**
+ * Sets the crystal structure for which to calculate structure factors
+ *
+ * Additionally StructureFactorCalculator::crystalStructureSetHook() is called
+ * with the CrystalStructure. This function may be re-implemented
+ * by concrete structure factor calculators to perform other necessary actions
+ * that involve the crystal structure (for example extracting and storing
+ * members of it).
+ *
+ * @param crystalStructure :: Crystal structure for calculations.
+ */
+void StructureFactorCalculator::setCrystalStructure(
+ const CrystalStructure &crystalStructure) {
+ crystalStructureSetHook(crystalStructure);
+}
+
+/// Returns F^2 for the given HKL, calling StructureFactorCalculator::getF().
+double StructureFactorCalculator::getFSquared(const Kernel::V3D &hkl) const {
+ StructureFactor sf = getF(hkl);
+
+ return sf.real() * sf.real() + sf.imag() * sf.imag();
+}
+
+/**
+ * Returns structure factors for each HKL in the container
+ *
+ * The default implementation uses StructureFactorCalculator::getF() to get
+ * the structure factor for each HKL. This behavior can be overriden in
+ * sub-classes for example to implement this in a more efficient way.
+ *
+ * @param hkls :: Vector of HKLs.
+ * @return :: Vector of structure factors for the given HKLs.
+ */
+std::vector<StructureFactor>
+StructureFactorCalculator::getFs(const std::vector<Kernel::V3D> &hkls) const {
+ std::vector<StructureFactor> structureFactors(hkls.size());
+
+ std::transform(hkls.begin(), hkls.end(), structureFactors.begin(),
+ boost::bind(&StructureFactorCalculator::getF, this, _1));
+
+ return structureFactors;
+}
+
+/**
+ * Returns structure factors for each HKL in the container
+ *
+ * The default implementation uses StructureFactorCalculator::getFSquared() with
+ * each HKL. This behavior can be overriden in
+ * sub-classes for example to implement this in a more efficient way.
+ *
+ * @param hkls :: Vector of HKLs.
+ * @return :: Vector of squared structure factors for the given HKLs.
+ */
+std::vector<double> StructureFactorCalculator::getFsSquared(
+ const std::vector<Kernel::V3D> &hkls) const {
+ std::vector<double> fSquareds(hkls.size());
+
+ std::transform(
+ hkls.begin(), hkls.end(), fSquareds.begin(),
+ boost::bind(&StructureFactorCalculator::getFSquared, this, _1));
+
+ return fSquareds;
+}
+
+/// This function is called from
+/// StructureFactorCalculator::setCrystalStructure() and can be overriden to
+/// perform additional actions.
+void StructureFactorCalculator::crystalStructureSetHook(
+ const CrystalStructure &crystalStructure) {
+ UNUSED_ARG(crystalStructure)
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp b/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp
new file mode 100644
index 00000000000..eabc22952cb
--- /dev/null
+++ b/Framework/Geometry/src/Crystal/StructureFactorCalculatorSummation.cpp
@@ -0,0 +1,82 @@
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+#include "MantidGeometry/Crystal/BraggScattererInCrystalStructure.h"
+
+#include <iomanip>
+
+namespace Mantid {
+namespace Geometry {
+
+using namespace Kernel;
+
+StructureFactorCalculatorSummation::StructureFactorCalculatorSummation()
+ : StructureFactorCalculator(),
+ m_unitCellScatterers(CompositeBraggScatterer::create()) {}
+
+/// Returns the structure factor obtained from the stored scatterers.
+StructureFactor
+StructureFactorCalculatorSummation::getF(const Kernel::V3D &hkl) const {
+ return m_unitCellScatterers->calculateStructureFactor(hkl);
+}
+
+/// Calls updateUnitCellScatterers() to rebuild the complete list of scatterers.
+void StructureFactorCalculatorSummation::crystalStructureSetHook(
+ const CrystalStructure &crystalStructure) {
+ updateUnitCellScatterers(crystalStructure);
+}
+
+/**
+ * Rebuilds the internal list of scatterers
+ *
+ * This method extracts two items from the supplied CrystalStructure object, the
+ * list of scatterers in the asymmetric unit and the space group. Then it
+ * generates all equivalent positions and creates a complete list of scatterers.
+ *
+ * @param crystalStructure :: CrystalStructure for structure factor calculation.
+ */
+void StructureFactorCalculatorSummation::updateUnitCellScatterers(
+ const CrystalStructure &crystalStructure) {
+ m_unitCellScatterers->removeAllScatterers();
+
+ CompositeBraggScatterer_sptr scatterersInAsymmetricUnit =
+ crystalStructure.getScatterers();
+ SpaceGroup_const_sptr spaceGroup = crystalStructure.spaceGroup();
+
+ if (spaceGroup) {
+ std::vector<BraggScatterer_sptr> braggScatterers;
+ braggScatterers.reserve(scatterersInAsymmetricUnit->nScatterers() *
+ spaceGroup->order());
+
+ for (size_t i = 0; i < scatterersInAsymmetricUnit->nScatterers(); ++i) {
+ BraggScattererInCrystalStructure_sptr current =
+ boost::dynamic_pointer_cast<BraggScattererInCrystalStructure>(
+ scatterersInAsymmetricUnit->getScatterer(i));
+
+ if (current) {
+ std::vector<V3D> positions =
+ spaceGroup->getEquivalentPositions(current->getPosition());
+
+ for (auto pos = positions.begin(); pos != positions.end(); ++pos) {
+ BraggScatterer_sptr clone = current->clone();
+ clone->setProperty("Position", getV3DasString(*pos));
+
+ braggScatterers.push_back(clone);
+ }
+ }
+ }
+
+ m_unitCellScatterers->setScatterers(braggScatterers);
+ }
+}
+
+/// Return V3D as string without losing precision.
+std::string
+StructureFactorCalculatorSummation::getV3DasString(const V3D &point) const {
+ std::ostringstream posStream;
+ posStream << std::setprecision(17);
+ posStream << point;
+
+ return posStream.str();
+}
+
+} // namespace Geometry
+} // namespace Mantid
diff --git a/Framework/Geometry/test/BasicHKLFiltersTest.h b/Framework/Geometry/test/BasicHKLFiltersTest.h
new file mode 100644
index 00000000000..7295290c09a
--- /dev/null
+++ b/Framework/Geometry/test/BasicHKLFiltersTest.h
@@ -0,0 +1,146 @@
+#ifndef MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_
+#define MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+
+#include <strstream>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+using ::testing::_;
+using ::testing::Return;
+using ::testing::Mock;
+
+class BasicHKLFiltersTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static BasicHKLFiltersTest *createSuite() {
+ return new BasicHKLFiltersTest();
+ }
+ static void destroySuite(BasicHKLFiltersTest *suite) { delete suite; }
+
+ void testHKLFilterDRangeConstructors() {
+ UnitCell cell(10., 10., 10.);
+
+ TS_ASSERT_THROWS_NOTHING(HKLFilterDRange dFilter(cell, 1.0));
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, -1.0), std::range_error);
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 0.0), std::range_error);
+
+ TS_ASSERT_THROWS_NOTHING(HKLFilterDRange dFilter(cell, 1.0, 2.0));
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 1.0, 0.5), std::range_error);
+ TS_ASSERT_THROWS(HKLFilterDRange dFilter(cell, 1.0, -0.5),
+ std::range_error);
+ }
+
+ void testHKLFilterDRangeDescription() {
+ UnitCell cell(10., 10., 10.);
+
+ std::ostringstream reference;
+ reference << "(" << 1.0 << " <= d <= " << 10.0 << ")";
+
+ HKLFilterDRange dFilter(cell, 1.0);
+ TS_ASSERT_EQUALS(dFilter.getDescription(), reference.str());
+ }
+
+ void testHKLFilterDRangeIsAllowed() {
+ UnitCell cell(10., 10., 10.);
+ HKLFilterDRange dFilter(cell, 1.0, 9.0);
+
+ TS_ASSERT(dFilter.isAllowed(V3D(1, 2, 3)));
+
+ TS_ASSERT(dFilter.isAllowed(V3D(2, 0, 0)));
+ TS_ASSERT(!dFilter.isAllowed(V3D(1, 0, 0)));
+
+ TS_ASSERT(dFilter.isAllowed(V3D(10, 0, 0)));
+ TS_ASSERT(!dFilter.isAllowed(V3D(11, 0, 0)));
+ }
+
+ void testHKLFilterSpaceGroupConstructor() {
+ SpaceGroup_const_sptr invalid;
+ TS_ASSERT_THROWS(HKLFilterSpaceGroup sgFilter(invalid), std::runtime_error);
+
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+ TS_ASSERT_THROWS_NOTHING(HKLFilterSpaceGroup sgFilter(sg));
+ }
+
+ void testHKLFilterSpaceGroupDescription() {
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+
+ HKLFilterSpaceGroup sgFilter(sg);
+
+ TS_ASSERT_EQUALS(sgFilter.getDescription(),
+ "(Space group: " + sg->hmSymbol() + ")");
+ }
+
+ void testHKLFilterSpaceGroupIsAllowed() {
+ SpaceGroup_const_sptr sg =
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m");
+
+ HKLFilterSpaceGroup sgFilter(sg);
+
+ TS_ASSERT(!sgFilter.isAllowed(V3D(1, 0, 0)));
+ TS_ASSERT(!sgFilter.isAllowed(V3D(1, 1, 0)));
+ TS_ASSERT(sgFilter.isAllowed(V3D(1, 1, 1)));
+
+ TS_ASSERT(!sgFilter.isAllowed(V3D(2, 0, 0)));
+ TS_ASSERT(!sgFilter.isAllowed(V3D(3, 0, 0)));
+ TS_ASSERT(sgFilter.isAllowed(V3D(4, 0, 0)));
+ }
+
+ void testHKLFilterStructureFactorConstructor() {
+ StructureFactorCalculator_sptr invalid;
+ TS_ASSERT_THROWS(HKLFilterStructureFactor sfFilter(invalid),
+ std::runtime_error);
+
+ StructureFactorCalculator_sptr mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+ TS_ASSERT_THROWS_NOTHING(HKLFilterStructureFactor sfFilter(mock));
+ TS_ASSERT_THROWS_NOTHING(HKLFilterStructureFactor sfFilter(mock, 12.0));
+ }
+
+ void testHKLFilterStructureFactorDescription() {
+ std::ostringstream reference;
+ reference << "(F^2 > " << 1.0 << ")";
+
+ StructureFactorCalculator_sptr mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+ HKLFilterStructureFactor sfFilter(mock, 1.0);
+ TS_ASSERT_EQUALS(sfFilter.getDescription(), reference.str());
+ }
+
+ void testHKLFilterStructureFactorIsAllowed() {
+ boost::shared_ptr<MockStructureFactorCalculator> mock =
+ boost::make_shared<MockStructureFactorCalculator>();
+
+ EXPECT_CALL(*mock, getFSquared(_))
+ .WillOnce(Return(2.0))
+ .WillOnce(Return(0.5))
+ .WillOnce(Return(1.0));
+
+ HKLFilterStructureFactor sfFilter(mock, 1.0);
+ TS_ASSERT(sfFilter.isAllowed(V3D(1, 1, 1)));
+ TS_ASSERT(!sfFilter.isAllowed(V3D(1, 1, 1)));
+ TS_ASSERT(!sfFilter.isAllowed(V3D(1, 1, 1)));
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(mock.get()))
+ }
+
+private:
+ class MockStructureFactorCalculator : public StructureFactorCalculator {
+ public:
+ MOCK_CONST_METHOD1(getF, StructureFactor(const V3D &));
+ MOCK_CONST_METHOD1(getFSquared, double(const V3D &));
+ };
+};
+
+#endif /* MANTID_GEOMETRY_BASICHKLFILTERSTEST_H_ */
diff --git a/Framework/Geometry/test/HKLFilterTest.h b/Framework/Geometry/test/HKLFilterTest.h
new file mode 100644
index 00000000000..c0ef32dde75
--- /dev/null
+++ b/Framework/Geometry/test/HKLFilterTest.h
@@ -0,0 +1,209 @@
+#ifndef MANTID_GEOMETRY_HKLFILTERTEST_H_
+#define MANTID_GEOMETRY_HKLFILTERTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/HKLFilter.h"
+#include "MantidKernel/V3D.h"
+
+#include <boost/make_shared.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+using ::testing::_;
+using ::testing::Return;
+using ::testing::Mock;
+
+class HKLFilterTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static HKLFilterTest *createSuite() { return new HKLFilterTest(); }
+ static void destroySuite(HKLFilterTest *suite) { delete suite; }
+
+ void testFn() {
+ MockHKLFilter filter;
+ EXPECT_CALL(filter, isAllowed(_))
+ .Times(2)
+ .WillOnce(Return(true))
+ .WillRepeatedly(Return(false));
+
+ std::function<bool(const V3D &)> f = filter.fn();
+
+ TS_ASSERT_EQUALS(f(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(f(V3D(1, 1, 1)), false);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&filter));
+ }
+
+ void testUnaryLogicOperation() {
+ HKLFilter_const_sptr filter = boost::make_shared<MockHKLFilter>();
+
+ TS_ASSERT_THROWS_NOTHING(MockHKLFilterUnaryLogicOperation op(filter));
+
+ MockHKLFilterUnaryLogicOperation op(filter);
+ TS_ASSERT_EQUALS(op.getOperand(), filter);
+
+ HKLFilter_const_sptr invalid;
+ TS_ASSERT_THROWS(MockHKLFilterUnaryLogicOperation op(invalid),
+ std::runtime_error);
+ }
+
+ void testBinaryLogicOperation() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ TS_ASSERT_THROWS_NOTHING(MockHKLFilterBinaryLogicOperation op(lhs, rhs));
+
+ MockHKLFilterBinaryLogicOperation op(lhs, rhs);
+ TS_ASSERT_EQUALS(op.getLHS(), lhs);
+ TS_ASSERT_EQUALS(op.getRHS(), rhs);
+
+ HKLFilter_const_sptr invalid;
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(invalid, rhs),
+ std::runtime_error);
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(lhs, invalid),
+ std::runtime_error);
+ TS_ASSERT_THROWS(MockHKLFilterBinaryLogicOperation op(invalid, invalid),
+ std::runtime_error);
+ }
+
+ void testHKLFilterNot() {
+ boost::shared_ptr<const MockHKLFilter> filter(new MockHKLFilter);
+
+ EXPECT_CALL(*filter, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ HKLFilterNot notFilter(filter);
+
+ TS_ASSERT_EQUALS(notFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(notFilter.isAllowed(V3D(1, 1, 1)), true);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(filter).get()));
+ }
+
+ void testHKLFilterNotOperator() {
+ HKLFilter_const_sptr filter = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr notFilter = ~filter;
+
+ boost::shared_ptr<const HKLFilterNot> notFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterNot>(notFilter);
+ TS_ASSERT(notFilterCasted);
+
+ TS_ASSERT_EQUALS(notFilterCasted->getOperand(), filter);
+ }
+
+ void testHKLFilterAnd() {
+ boost::shared_ptr<const MockHKLFilter> lhs(new MockHKLFilter);
+ EXPECT_CALL(*lhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true));
+
+ boost::shared_ptr<const MockHKLFilter> rhs(new MockHKLFilter);
+ EXPECT_CALL(*rhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ HKLFilterAnd andFilter(lhs, rhs);
+
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(andFilter.isAllowed(V3D(1, 1, 1)), false);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(lhs).get()));
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(rhs).get()));
+ }
+
+ void testHKLFilterAndOperator() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr andFilter = lhs & rhs;
+
+ boost::shared_ptr<const HKLFilterAnd> andFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterAnd>(andFilter);
+
+ TS_ASSERT(andFilterCasted);
+
+ TS_ASSERT_EQUALS(andFilterCasted->getLHS(), lhs);
+ TS_ASSERT_EQUALS(andFilterCasted->getRHS(), rhs);
+ }
+
+ void testHKLFilterOr() {
+ boost::shared_ptr<const MockHKLFilter> lhs(new MockHKLFilter);
+ EXPECT_CALL(*lhs, isAllowed(_))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true))
+ .WillOnce(Return(false));
+
+ boost::shared_ptr<const MockHKLFilter> rhs(new MockHKLFilter);
+ EXPECT_CALL(*rhs, isAllowed(_))
+ .WillOnce(Return(false))
+ .WillOnce(Return(true));
+
+ HKLFilterOr orFilter(lhs, rhs);
+
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), false);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+ TS_ASSERT_EQUALS(orFilter.isAllowed(V3D(1, 1, 1)), true);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(lhs).get()));
+ TS_ASSERT(Mock::VerifyAndClearExpectations(
+ boost::const_pointer_cast<MockHKLFilter>(rhs).get()));
+ }
+
+ void testHKLFilterOrOperator() {
+ HKLFilter_const_sptr lhs = boost::make_shared<MockHKLFilter>();
+ HKLFilter_const_sptr rhs = boost::make_shared<MockHKLFilter>();
+
+ HKLFilter_const_sptr orFilter = lhs | rhs;
+
+ boost::shared_ptr<const HKLFilterOr> orFilterCasted =
+ boost::dynamic_pointer_cast<const HKLFilterOr>(orFilter);
+
+ TS_ASSERT(orFilterCasted);
+
+ TS_ASSERT_EQUALS(orFilterCasted->getLHS(), lhs);
+ TS_ASSERT_EQUALS(orFilterCasted->getRHS(), rhs);
+ }
+
+private:
+ class MockHKLFilter : public HKLFilter {
+ public:
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+
+ class MockHKLFilterUnaryLogicOperation : public HKLFilterUnaryLogicOperation {
+ public:
+ MockHKLFilterUnaryLogicOperation(const HKLFilter_const_sptr &filter)
+ : HKLFilterUnaryLogicOperation(filter) {}
+
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+
+ class MockHKLFilterBinaryLogicOperation
+ : public HKLFilterBinaryLogicOperation {
+ public:
+ MockHKLFilterBinaryLogicOperation(const HKLFilter_const_sptr &lhs,
+ const HKLFilter_const_sptr &rhs)
+ : HKLFilterBinaryLogicOperation(lhs, rhs) {}
+
+ MOCK_CONST_METHOD0(getDescription, std::string());
+ MOCK_CONST_METHOD1(isAllowed, bool(const V3D &));
+ };
+};
+#endif /* MANTID_GEOMETRY_HKLFILTERTEST_H_ */
diff --git a/Framework/Geometry/test/HKLGeneratorTest.h b/Framework/Geometry/test/HKLGeneratorTest.h
new file mode 100644
index 00000000000..f6cffd236d4
--- /dev/null
+++ b/Framework/Geometry/test/HKLGeneratorTest.h
@@ -0,0 +1,98 @@
+#ifndef MANTID_GEOMETRY_HKLGENERATORTEST_H_
+#define MANTID_GEOMETRY_HKLGENERATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include "MantidGeometry/Crystal/HKLGenerator.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class HKLGeneratorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static HKLGeneratorTest *createSuite() { return new HKLGeneratorTest(); }
+ static void destroySuite(HKLGeneratorTest *suite) { delete suite; }
+
+ void test_HKLGeneratorReturnsCorrectSizeSymmetricInt() {
+ HKLGenerator gen(2, 2, 2);
+
+ TS_ASSERT_EQUALS(gen.size(), 125);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeSymmetricV3D() {
+ HKLGenerator gen(V3D(2, 2, 2));
+
+ TS_ASSERT_EQUALS(gen.size(), 125);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeAsymmetricV3D() {
+ HKLGenerator gen(V3D(-2, -1, -5), V3D(3, 4, -2));
+
+ TS_ASSERT_EQUALS(gen.size(), 144);
+ }
+
+ void test_HKLGeneratorReturnsCorrectSizeOne() {
+ HKLGenerator gen(V3D(-2, -1, -5), V3D(-2, -1, -5));
+ TS_ASSERT_EQUALS(gen.size(), 1);
+ }
+
+ void test_beginIterator() {
+ HKLGenerator gen(V3D(-2, -2, -3), V3D(1, 1, 0));
+
+ HKLGenerator::const_iterator it = gen.begin();
+ TS_ASSERT_EQUALS(*it, V3D(-2, -2, -3));
+ }
+
+ void test_endIterator() {
+ HKLGenerator gen(V3D(-2, -2, -3), V3D(1, 1, 0));
+
+ HKLGenerator::const_iterator it = gen.end();
+ TS_ASSERT_EQUALS(*it, V3D(2, -2, -3));
+ }
+
+ void test_iterator_dereference() {
+ HKLGenerator::const_iterator it;
+ TS_ASSERT_EQUALS(*it, V3D(0, 0, 0));
+ }
+
+ void test_comparison() {
+ HKLGenerator::const_iterator it1(V3D(-2, -3, 1));
+ HKLGenerator::const_iterator it2(V3D(-2, -3, 1));
+ HKLGenerator::const_iterator it3(V3D(-2, -3, 0));
+
+ TS_ASSERT_EQUALS(it1, it2);
+ TS_ASSERT_DIFFERS(it1, it3);
+ }
+
+ void test_iterator_increment() {
+ HKLGenerator::const_iterator defaultIterator;
+ TS_ASSERT_THROWS_NOTHING(++defaultIterator);
+ }
+
+ void test_iterator_dereference_range() {
+ HKLGenerator::const_iterator it(V3D(-1, -1, -1), V3D(1, 1, 1));
+ TS_ASSERT_EQUALS(*it, V3D(-1, -1, -1));
+ ++it;
+ TS_ASSERT_EQUALS(*it, V3D(-1, -1, 0));
+ }
+
+ void test_hkl_range() {
+ HKLGenerator::const_iterator it(V3D(-1, -1, -1), V3D(1, 1, 1));
+ HKLGenerator::const_iterator end(V3D(2, -1, -1));
+
+ std::vector<V3D> hkls;
+ std::copy(it, end, std::back_inserter(hkls));
+
+ TS_ASSERT_EQUALS(hkls.size(), 27);
+ TS_ASSERT_EQUALS(hkls[0], V3D(-1, -1, -1));
+ TS_ASSERT_EQUALS(hkls[1], V3D(-1, -1, 0));
+ TS_ASSERT_EQUALS(hkls[2], V3D(-1, -1, 1));
+ TS_ASSERT_EQUALS(hkls[3], V3D(-1, 0, -1));
+ TS_ASSERT_EQUALS(hkls[26], V3D(1, 1, 1));
+
+ TS_ASSERT_EQUALS(std::distance(it, end), 27);
+ }
+};
+
+#endif /* MANTID_GEOMETRY_HKLGENERATORTEST_H_ */
diff --git a/Framework/Geometry/test/ReflectionGeneratorTest.h b/Framework/Geometry/test/ReflectionGeneratorTest.h
new file mode 100644
index 00000000000..9c3da2883aa
--- /dev/null
+++ b/Framework/Geometry/test/ReflectionGeneratorTest.h
@@ -0,0 +1,126 @@
+#ifndef MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_
+#define MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidGeometry/Crystal/BasicHKLFilters.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class ReflectionGeneratorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static ReflectionGeneratorTest *createSuite() {
+ return new ReflectionGeneratorTest();
+ }
+ static void destroySuite(ReflectionGeneratorTest *suite) { delete suite; }
+
+ void test_getUniqueHKLs() {
+ double dMin = 0.55;
+ double dMax = 4.0;
+
+ ReflectionGenerator generator(
+ CrystalStructure("4.126 4.126 4.126", "P m -3 m", "Si 0 0 0 1.0 0.01"),
+ ReflectionConditionFilter::Centering);
+
+ TS_ASSERT_THROWS_NOTHING(generator.getUniqueHKLs(dMin, dMax));
+
+ std::vector<V3D> peaks = generator.getUniqueHKLs(dMin, dMax);
+
+ TS_ASSERT_EQUALS(peaks.size(), 68);
+ TS_ASSERT_EQUALS(peaks[0], V3D(1, 1, 0));
+ TS_ASSERT_EQUALS(peaks[11], V3D(3, 2, 0));
+ TS_ASSERT_EQUALS(peaks[67], V3D(7, 2, 1));
+
+ // make d-value list and check that peaks are within limits
+ std::vector<double> peaksD = generator.getDValues(peaks);
+
+ std::sort(peaksD.begin(), peaksD.end());
+
+ TS_ASSERT_LESS_THAN_EQUALS(dMin, peaksD.front());
+ TS_ASSERT_LESS_THAN_EQUALS(peaksD.back(), dMax);
+ }
+
+ void test_getHKLs() {
+ double dMin = 0.55;
+ double dMax = 4.0;
+
+ // make a structure with P-1
+ ReflectionGenerator generator(
+ CrystalStructure("4.126 4.126 4.126", "P -1", "Si 0 0 0 1.0 0.01"),
+ ReflectionConditionFilter::Centering);
+
+ std::vector<V3D> unique = generator.getUniqueHKLs(dMin, dMax);
+ std::vector<V3D> peaks = generator.getHKLs(dMin, dMax);
+
+ // Because of symmetry -1, each reflection has multiplicity 2.
+ TS_ASSERT_EQUALS(peaks.size(), 2 * unique.size());
+ }
+
+ void test_getDValues() {
+ std::vector<V3D> hkls;
+ hkls.push_back(V3D(1, 0, 0));
+ hkls.push_back(V3D(0, 1, 0));
+ hkls.push_back(V3D(0, 0, 1));
+
+ ReflectionGenerator generator(
+ CrystalStructure("2 3 5", "P -1", "Si 0 0 0 1.0 0.01"));
+ std::vector<double> dValues = generator.getDValues(hkls);
+
+ TS_ASSERT_EQUALS(dValues.size(), hkls.size());
+ TS_ASSERT_EQUALS(dValues[0], 2.0);
+ TS_ASSERT_EQUALS(dValues[1], 3.0);
+ TS_ASSERT_EQUALS(dValues[2], 5.0);
+ }
+
+ void test_getUniqueHKLsStructureFactor() {
+ CrystalStructure si("5.43 5.43 5.43", "F m -3 m",
+ "Si 0.3 0.3 0.3 1.0 0.05");
+
+ ReflectionGenerator generator(si,
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hklsCentering = generator.getUniqueHKLs(
+ 0.6, 10.0, boost::make_shared<HKLFilterCentering>(si.centering()));
+
+ std::vector<V3D> hklsStructureFactors = generator.getUniqueHKLs(0.6, 10.0);
+
+ TS_ASSERT_EQUALS(hklsCentering.size(), hklsStructureFactors.size());
+
+ for (size_t i = 0; i < hklsCentering.size(); ++i) {
+ TS_ASSERT_EQUALS(hklsCentering[i], hklsStructureFactors[i]);
+ }
+ }
+
+ void test_getUniqueHKLsHexagonal() {
+ ReflectionGenerator generator(
+ CrystalStructure("3.2094 3.2094 5.2108 90.0 90.0 120.0", "P 63/m m c",
+ "Mg 1/3 2/3 1/4 1.0 0.005"),
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.5, 10.0);
+
+ TS_ASSERT_EQUALS(hkls.size(), 88);
+
+ std::vector<double> dValues = generator.getDValues(hkls);
+ for (size_t i = 0; i < hkls.size(); ++i) {
+ TS_ASSERT_LESS_THAN(0.5, dValues[i]);
+ }
+ }
+
+ void test_getUniqueHKLsTrigonal() {
+ ReflectionGenerator generator(
+ CrystalStructure("4.759355 4.759355 12.99231 90.0 90.0 120.0", "R -3 c",
+ "Al 0 0 0.35217 1.0 0.005; O 0.69365 0 1/4 1.0 0.005"),
+ ReflectionConditionFilter::StructureFactor);
+
+ std::vector<V3D> hkls = generator.getUniqueHKLs(0.885, 10.0);
+
+ TS_ASSERT_EQUALS(hkls.size(), 44);
+ }
+};
+
+#endif /* MANTID_GEOMETRY_REFLECTIONGENERATORTEST_H_ */
diff --git a/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h b/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h
new file mode 100644
index 00000000000..a1ce3c9670a
--- /dev/null
+++ b/Framework/Geometry/test/StructureFactorCalculatorSummationTest.h
@@ -0,0 +1,75 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidGeometry/Crystal/StructureFactorCalculatorSummation.h"
+
+#include "MantidGeometry/Crystal/BraggScattererFactory.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+
+class StructureFactorCalculatorSummationTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static StructureFactorCalculatorSummationTest *createSuite() {
+ return new StructureFactorCalculatorSummationTest();
+ }
+ static void destroySuite(StructureFactorCalculatorSummationTest *suite) {
+ delete suite;
+ }
+
+ void testEquivalentPositionsAreUsed() {
+ // Approximate crystal structure of Silicon
+ CrystalStructure si = getCrystalStructure();
+
+ StructureFactorCalculatorSummation calculator;
+ calculator.setCrystalStructure(si);
+
+ // {1 0 0} reflections are not allowed because of F centering
+ TS_ASSERT_LESS_THAN(calculator.getFSquared(V3D(1, 0, 0)), 1e-9);
+
+ // {2 2 2} is forbidden because of Si on special position
+ TS_ASSERT_LESS_THAN(calculator.getFSquared(V3D(2, 2, 2)), 1e-9);
+
+ // With space group P-1, those are allowed.
+ si.setSpaceGroup(SpaceGroupFactory::Instance().createSpaceGroup("P -1"));
+
+ calculator.setCrystalStructure(si);
+ // {1 0 0} reflections are not allowed because of F centering
+ TS_ASSERT_LESS_THAN(1e-9, calculator.getFSquared(V3D(1, 0, 0)));
+
+ // {2 2 2} is forbidden because of Si on special position
+ TS_ASSERT_LESS_THAN(1e-9, calculator.getFSquared(V3D(2, 2, 2)));
+ }
+
+ void testCreateWithFactory() {
+ CrystalStructure si = getCrystalStructure();
+
+ StructureFactorCalculator_sptr calculator =
+ StructureFactorCalculatorFactory::create<
+ StructureFactorCalculatorSummation>(si);
+
+ // same reflections as in testEquivalentPositionsAreUsed
+ TS_ASSERT_LESS_THAN(calculator->getFSquared(V3D(1, 0, 0)), 1e-9);
+ TS_ASSERT_LESS_THAN(calculator->getFSquared(V3D(2, 2, 2)), 1e-9);
+ }
+
+private:
+ CrystalStructure getCrystalStructure() {
+ CompositeBraggScatterer_sptr scatterers = CompositeBraggScatterer::create();
+ scatterers->addScatterer(BraggScattererFactory::Instance().createScatterer(
+ "IsotropicAtomBraggScatterer", "Element=Si;Position=[0,0,0];U=0.05"));
+
+ CrystalStructure si(
+ UnitCell(5.43, 5.43, 5.43),
+ SpaceGroupFactory::Instance().createSpaceGroup("F d -3 m"), scatterers);
+
+ return si;
+ }
+};
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORSUMMATIONTEST_H_ */
diff --git a/Framework/Geometry/test/StructureFactorCalculatorTest.h b/Framework/Geometry/test/StructureFactorCalculatorTest.h
new file mode 100644
index 00000000000..72421449f71
--- /dev/null
+++ b/Framework/Geometry/test/StructureFactorCalculatorTest.h
@@ -0,0 +1,107 @@
+#ifndef MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_
+#define MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_
+
+#include <cxxtest/TestSuite.h>
+#include <gtest/gtest.h>
+#include <gmock/gmock.h>
+
+#include "MantidGeometry/Crystal/StructureFactorCalculator.h"
+#include "MantidGeometry/Crystal/SpaceGroupFactory.h"
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using ::testing::Mock;
+using ::testing::_;
+using ::testing::Return;
+
+class StructureFactorCalculatorTest : public CxxTest::TestSuite {
+public:
+ // This pair of boilerplate methods prevent the suite being created statically
+ // This means the constructor isn't called when running other tests
+ static StructureFactorCalculatorTest *createSuite() {
+ return new StructureFactorCalculatorTest();
+ }
+ static void destroySuite(StructureFactorCalculatorTest *suite) {
+ delete suite;
+ }
+
+ void testCrystalStructureSetHookIsCalled() {
+ CrystalStructure cs(UnitCell(1, 2, 3),
+ SpaceGroupFactory::Instance().createSpaceGroup("P -1"),
+ CompositeBraggScatterer::create());
+
+ MockStructureFactorCalculator calculator;
+ EXPECT_CALL(calculator, crystalStructureSetHook(_)).Times(1);
+
+ calculator.setCrystalStructure(cs);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFSquared() {
+ MockStructureFactorCalculator calculator;
+
+ EXPECT_CALL(calculator, getF(_))
+ .WillRepeatedly(Return(StructureFactor(2.21, 3.1)));
+
+ // Check that the square of 2.21 + i * 3.1 is returned
+ TS_ASSERT_DELTA(calculator.getFSquared(V3D()), 14.4941, 1e-15);
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFs() {
+ MockStructureFactorCalculator calculator;
+
+ int numHKLs = 10;
+ EXPECT_CALL(calculator, getF(_))
+ .Times(numHKLs)
+ .WillRepeatedly(Return(StructureFactor(2.0, 2.0)));
+
+ std::vector<V3D> hkls(numHKLs);
+ std::vector<StructureFactor> sfs = calculator.getFs(hkls);
+
+ TS_ASSERT_EQUALS(sfs.size(), hkls.size());
+
+ for (auto sf = sfs.begin(); sf != sfs.end(); ++sf) {
+ TS_ASSERT_EQUALS(*sf, StructureFactor(2.0, 2.0));
+ }
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+ void testGetFsSquared() {
+ MockStructureFactorCalculator calculator;
+
+ int numHKLs = 10;
+ EXPECT_CALL(calculator, getF(_))
+ .Times(numHKLs)
+ .WillRepeatedly(Return(StructureFactor(2.0, 2.0)));
+
+ std::vector<V3D> hkls(numHKLs);
+ std::vector<double> sfsSquared = calculator.getFsSquared(hkls);
+
+ TS_ASSERT_EQUALS(sfsSquared.size(), hkls.size());
+
+ for (auto sf = sfsSquared.begin(); sf != sfsSquared.end(); ++sf) {
+ TS_ASSERT_EQUALS(*sf, 8.0);
+ }
+
+ TS_ASSERT(Mock::VerifyAndClearExpectations(&calculator));
+ }
+
+private:
+ /* This MockStructureFactorCalculator helps to test whether the
+ * default implementations of the virtual methods work correctly.
+ * Furthermore it is used to confirm that crystalStructureSetHook
+ * is called appropriately.
+ */
+ class MockStructureFactorCalculator : public StructureFactorCalculator {
+ public:
+ MOCK_CONST_METHOD1(getF, StructureFactor(const V3D &hkl));
+ MOCK_METHOD1(crystalStructureSetHook,
+ void(const CrystalStructure &crystalStructure));
+ };
+};
+
+#endif /* MANTID_GEOMETRY_STRUCTUREFACTORCALCULATORTEST_H_ */
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp
new file mode 100644
index 00000000000..daf4587a81d
--- /dev/null
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/CrystalStructure.cpp
@@ -0,0 +1,38 @@
+#include "MantidGeometry/Crystal/CrystalStructure.h"
+#include "MantidGeometry/Crystal/IsotropicAtomBraggScatterer.h"
+#include <boost/python/class.hpp>
+#include <boost/python/make_constructor.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using namespace boost::python;
+
+namespace {
+SpaceGroup_sptr getSpaceGroup(CrystalStructure &self) {
+ return boost::const_pointer_cast<SpaceGroup>(self.spaceGroup());
+}
+
+std::vector<std::string> getScatterers(CrystalStructure &self) {
+ CompositeBraggScatterer_sptr scatterers = self.getScatterers();
+
+ std::vector<std::string> scattererStrings;
+ scattererStrings.reserve(scatterers->nScatterers());
+
+ for (size_t i = 0; i < scatterers->nScatterers(); ++i) {
+ scattererStrings.push_back(
+ getIsotropicAtomBraggScattererString(scatterers->getScatterer(i)));
+ }
+
+ return scattererStrings;
+}
+}
+
+void export_CrystalStructure() {
+ class_<CrystalStructure>("CrystalStructure", no_init)
+ .def(init<const std::string &, const std::string &, const std::string &>(
+ (arg("unitCell"), arg("spaceGroup"), arg("scatterers"))))
+ .def("getUnitCell", &CrystalStructure::cell)
+ .def("getSpaceGroup", &getSpaceGroup)
+ .def("getScatterers", &getScatterers);
+}
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp
new file mode 100644
index 00000000000..83882c117af
--- /dev/null
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/ReflectionGenerator.cpp
@@ -0,0 +1,77 @@
+#include "MantidGeometry/Crystal/ReflectionGenerator.h"
+#include "MantidPythonInterface/kernel/Converters/PySequenceToVector.h"
+#include <boost/python/class.hpp>
+#include <boost/python/enum.hpp>
+#include <boost/python/list.hpp>
+
+using namespace Mantid::Geometry;
+using namespace Mantid::Kernel;
+using namespace Mantid::PythonInterface;
+using namespace boost::python;
+
+namespace {
+boost::python::list getListFromV3DVector(const std::vector<V3D> &hkls) {
+ boost::python::list hklList;
+ for (auto it = hkls.begin(); it != hkls.end(); ++it) {
+ hklList.append(*it);
+ }
+ return hklList;
+}
+
+boost::python::list getHKLsDefaultFilter(ReflectionGenerator &self, double dMin,
+ double dMax) {
+ return getListFromV3DVector(self.getHKLs(dMin, dMax));
+}
+
+boost::python::list getHKLsUsingFilter(ReflectionGenerator &self, double dMin,
+ double dMax,
+ ReflectionConditionFilter filter) {
+ return getListFromV3DVector(
+ self.getHKLs(dMin, dMax, self.getReflectionConditionFilter(filter)));
+}
+
+boost::python::list getUniqueHKLsDefaultFilter(ReflectionGenerator &self,
+ double dMin, double dMax) {
+ return getListFromV3DVector(self.getUniqueHKLs(dMin, dMax));
+}
+
+boost::python::list getUniqueHKLsUsingFilter(ReflectionGenerator &self,
+ double dMin, double dMax,
+ ReflectionConditionFilter filter) {
+ return getListFromV3DVector(self.getUniqueHKLs(
+ dMin, dMax, self.getReflectionConditionFilter(filter)));
+}
+
+std::vector<double> getDValues(ReflectionGenerator &self,
+ const boost::python::object &hkls) {
+ Converters::PySequenceToVector<V3D> converter(hkls);
+
+ return self.getDValues(converter());
+}
+
+std::vector<double> getFsSquared(ReflectionGenerator &self,
+ const boost::python::object &hkls) {
+ Converters::PySequenceToVector<V3D> converter(hkls);
+
+ return self.getFsSquared(converter());
+}
+}
+
+void export_ReflectionGenerator() {
+ enum_<ReflectionConditionFilter>("ReflectionConditionFilter")
+ .value("None", ReflectionConditionFilter::None)
+ .value("Centering", ReflectionConditionFilter::Centering)
+ .value("SpaceGroup", ReflectionConditionFilter::SpaceGroup)
+ .value("StructureFactor", ReflectionConditionFilter::StructureFactor)
+ .export_values();
+
+ class_<ReflectionGenerator>("ReflectionGenerator", no_init)
+ .def(init<const CrystalStructure &, optional<ReflectionConditionFilter>>(
+ (arg("crystalStructure"), arg("defaultFilter"))))
+ .def("getHKLs", &getHKLsDefaultFilter)
+ .def("getHKLsUsingFilter", &getHKLsUsingFilter)
+ .def("getUniqueHKLs", &getUniqueHKLsDefaultFilter)
+ .def("getUniqueHKLsUsingFilter", &getUniqueHKLsUsingFilter)
+ .def("getDValues", &getDValues)
+ .def("getFsSquared", &getFsSquared);
+}
diff --git a/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py b/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py
new file mode 100644
index 00000000000..147d8e1e232
--- /dev/null
+++ b/Framework/PythonInterface/test/python/mantid/geometry/CrystalStructureTest.py
@@ -0,0 +1,59 @@
+# pylint: disable=no-init,invalid-name,too-many-public-methods,broad-except
+import unittest
+from mantid.geometry import CrystalStructure
+
+
+class CrystalStructureTest(unittest.TestCase):
+ def test_creation(self):
+ # Some valid constructions
+ self.assertTrue(self.createCrystalStructureOrRaise("5.43 5.43 5.43", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01"))
+ self.assertTrue(self.createCrystalStructureOrRaise("5.43 5.43 5.43", "C m m m", "Al 1/3 0.454 1/12 1.0 0.01;\n"
+ "Si 2/3 0.121 1/8"))
+ self.assertTrue(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43 90 90 120", "R -3 c", "Al 1/3 0.454 1/12 1.0 0.01;\n"
+ "Si 2/3 0.121 1/8"))
+
+ # Invalid unit cell specification
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43 90.0", "C m m m", "Al 1/3 0.454 1/12 1.0 0.01"))
+
+ # Invalid space group
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43", "INVALID", "Al 1/3 0.454 1/12 1.0 0.01"))
+
+ # Invalid atom specification
+ self.assertFalse(
+ self.createCrystalStructureOrRaise("5.43 5.43 5.43", "C m c e", "Al 1/3 0"))
+
+ def createCrystalStructureOrRaise(self, unitCell, spaceGroup, atomStrings):
+ try:
+ CrystalStructure(unitCell, spaceGroup, atomStrings)
+ return True
+ except Exception:
+ return False
+
+ def test_UnitCell(self):
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
+ cell = structure.getUnitCell()
+
+ self.assertEqual(cell.a(), 5.43)
+ self.assertEqual(cell.b(), 5.42)
+ self.assertEqual(cell.c(), 5.41)
+
+ def test_SpaceGroup(self):
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", "Al 1/3 0.454 1/12 1.0 0.01")
+ spaceGroup = structure.getSpaceGroup()
+
+ self.assertEqual(spaceGroup.getHMSymbol(), "F d -3 m")
+
+ def test_scatterers(self):
+ initialString = "Al 1/3 0.454 1/12 1 0.01;Si 0.1 0.2 0.3 0.99 0.1"
+
+ structure = CrystalStructure("5.43 5.42 5.41", "F d -3 m", initialString)
+ scatterers = structure.getScatterers()
+
+ self.assertEqual(';'.join(scatterers), initialString)
+
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py b/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py
new file mode 100644
index 00000000000..4c942f8a7cc
--- /dev/null
+++ b/Framework/PythonInterface/test/python/mantid/geometry/ReflectionGeneratorTest.py
@@ -0,0 +1,69 @@
+# pylint: disable=no-init,invalid-name,too-many-public-methods
+import unittest
+from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+from mantid.kernel import V3D
+import numpy as np
+
+
+class CrystalStructureTest(unittest.TestCase):
+ crystalStructure = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.02")
+
+ def test_create(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ generator = ReflectionGenerator(self.crystalStructure, ReflectionConditionFilter.Centering)
+
+ def test_getHKLs(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getHKLs(1.0, 10.0)
+
+ self.assertEqual(len(hkls), 138)
+
+ # default is filtering by space group reflection condition
+ self.assertTrue(V3D(2, 2, 2) in hkls)
+ self.assertFalse(V3D(1, 0, 0) in hkls)
+
+ def test_getHKLsUsingFilter(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)
+
+ self.assertEqual(len(hkls), 130)
+
+ # The 222 is gone now
+ self.assertFalse(V3D(2, 2, 2) in hkls)
+
+ def test_getUniqueHKLs(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLs(1.0, 10.0)
+
+ self.assertEqual(len(hkls), 9)
+
+ self.assertTrue(V3D(2, 2, 2) in hkls)
+ self.assertFalse(V3D(1, 0, 0) in hkls)
+
+ def test_getUniqueHKLsUsingFilter(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLsUsingFilter(1.0, 10.0, ReflectionConditionFilter.StructureFactor)
+
+ self.assertEqual(len(hkls), 8)
+ self.assertFalse(V3D(2, 2, 2) in hkls)
+
+ def test_getDValues(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = [V3D(1, 0, 0), V3D(1, 1, 1)]
+
+ dValues = generator.getDValues(hkls)
+
+ self.assertEqual(len(hkls), len(dValues))
+ self.assertAlmostEqual(dValues[0], 5.431, places=10)
+ self.assertAlmostEqual(dValues[1], 5.431 / np.sqrt(3.), places=10)
+
+ def test_getFsSquared(self):
+ generator = ReflectionGenerator(self.crystalStructure)
+ hkls = generator.getUniqueHKLs(1.0, 10.0)
+
+ fsSquared = generator.getFsSquared(hkls)
+
+ self.assertEqual(len(fsSquared), len(hkls))
+
+if __name__ == '__main__':
+ unittest.main()
diff --git a/docs/source/concepts/CrystalStructureAndReflections.rst b/docs/source/concepts/CrystalStructureAndReflections.rst
new file mode 100644
index 00000000000..443dd594566
--- /dev/null
+++ b/docs/source/concepts/CrystalStructureAndReflections.rst
@@ -0,0 +1,293 @@
+.. _Crystal structure and reflections:
+
+Crystal structure and reflections
+=================================
+
+This document describes how crystal structure data can be processed and used in Mantid. For the understanding of the
+concepts of :ref:`symmetry <Symmetry groups>` and :ref:`space groups <Point and space groups>` in Mantid it may be
+useful to read those introductory articles before proceeding with this document. While there is a short introduction
+into theoretical aspects this page is not a replacement for proper introductory text books on the subject where all
+these principles are explained in great detail and on a much more general basis.
+
+Theoretical aspects
+~~~~~~~~~~~~~~~~~~~
+
+Crystal structures
+------------------
+
+A crystal is modelled as an infinitely repeating three-dimensional arrangement of scatterers, usually atoms. Due to
+the periodic nature of crystals, the entire object can be described by specifying the repeated unit and how
+it is repeated. These information are called "crystal structure" and comprise three components:
+
+ 1. Lattice (describes the periodicity of the structure)
+ 2. Basis (distribution of scatterers in the unit cell)
+ 3. Space group (describes the symmetry of the arrangement of scatterers)
+
+The description of the basis depends on the model's level of detail. In the simplest case it could be a list of
+point scatterers that are fully characterized by three coordinates (x, y and z in terms of the lattice vectors) and
+a scattering length. In reality however, the scatterers are usually atoms that fluctuate about their average position
+due to thermal agitation. A basic way to model this motion is to assume it to be an isotropic phenomenon, allowing the
+description with one single parameter that quantifies the radius of a sphere in which the scatterer oscillates
+harmonically. This so called Debye-Waller-factor will be introduced later on.
+
+Another important parameter for a basic description of the basis is the so called occupancy. It describes the fraction
+of the total number of scatterer-positions that is actually occupied. A common example where this is required are
+unordered binary metal mixtures where the same position in the crystal structure is partly filled with two different
+atoms in a randomly distributed manner.
+
+To summarize, a very basic model of the basis comprises a list of scatterers that are in turn characterized by
+six parameters:
+
+ 1. Scattering length (known for each element)
+ 2. Fractional coordinate x
+ 3. Fractional coordinate y
+ 4. Fractional coordinate z
+ 5. Occupancy of the site
+ 6. Isotropic thermal displacement parameter
+
+Knowledge of the space group makes it possible to derive all scatterers in the entire unit cell. The symmetry operations
+of the space group map each scatterer-position onto a set of equivalent positions that are consequently occupied by the
+same type of scatterer as well. Since the unit cell is repeated infinitely in all three directions of space, it is
+enough to describe one unit cell. Finally, the lattice is described by six parameters as well, the lengths of the three
+lattice vectors (usually given in :math:`\mathrm{\AA{}}`) and the three angles (in degree) between these vectors.
+
+Reflections and structure factors
+---------------------------------
+
+In a diffraction experiment the periodic arrangement of atoms is probed using radiation, in this case in the form of
+neutrons, of an appropriate wavelength (on the same scale of interatomic distances, typically between 0.5 and
+5 :math:`\mathrm{\AA{}}`). The incident beam interacts with the scatterers and in certain orientations the beam is
+"reflected" by a flock of lattice planes, a phenomenon which is described by Bragg's law:
+
+.. math::
+ 2d\sin\theta = \lambda
+
+In this equation :math: `d` is the spacing between the lattice planes, :math:`\theta` is the angle of the incoming beam
+and the lattice plane normal and lambda is the wavelength of the radiation. In an experiment theta and lambda are
+usually limited, thus they are limiting the range of interplanar spacings that can be probed. In Bragg's law the lattice
+plane families are only described by one parameter, the interplanar distance. But each lattice plane family also has an
+orientation in space which can be described by the plane's normal vector. Usually the vector is given in terms of the
+reciprocal lattice of the structure, where it is reduced to three integers H, K, L, the so called Miller indices. With
+knowledge of the :ref:`unit cell <Lattice>` (and thus the :math:`\mathbf{B}`-matrix), the interplanar spacing can also
+be computed like this:
+
+.. math::
+ d = \frac{1}{\left|\mathbf{B}\cdot\mathbf{h}\right|}
+
+The parameters taken into account so far determine the geometric characteristics of Bragg-reflections, i.e. their
+position on a detector and their time of flight. But besides these, each reflection also has an intensity. The
+intensity is proportional to the squared structure factor, which depends on the kind and arrangement of scatterers in
+the unit cell. The structure factor is a complex number and can be calculated for a certain HKL by summing the
+contributions of all N atoms j in the unit cell:
+
+.. math::
+ F_{\mathbf{h}} = \sum\limits_{j}^{N}b_j\exp\left(2\pi i \mathbf{h} \cdot \mathbf{x}_j\right)
+
+In the above equation :math:`b` is the scattering length, :math:`\mathbf{h}` is the Miller index triplet HKL and
+:math:`\mathbf{x}` contains the fractional coordinates of the j-th atom. To take into account isotropic thermal
+motion of atoms, the term is multiplied with the Debye-Waller factor:
+
+.. math::
+ F_{\mathbf{h}} = \sum\limits_{j}^{N}b_j\exp\left(2\pi i \mathbf{h} \cdot \mathbf{x}_j\right)
+ \exp\left(-2\pi^2 U/d_{\mathbf{h}}^2\right)
+
+Here, :math:`U` is the isotropic atomic displacement parameter, usually given in :math:`\mathrm{\AA{}}^2` and
+:math:`d` is the lattice spacing discussed above. There are other, more complex models to describe the movement of
+atoms, taking into account anisotropic movement and also anharmonic effects.
+
+Implementation in Mantid
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The concepts described above are available through the Python interface of Mantid. Crystal structures are represented
+by a class that stores the three necessary pieces of information. Objects of that class can be created by supplying
+string representations of those three arguments.
+
+.. testcode:: ExCrystalStructureConstruction
+
+ from mantid.geometry import CrystalStructure
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+
+ unitCell = silicon.getUnitCell()
+ print 'Crystal structure of silicon:'
+ print ' Unit cell:', unitCell.a(), unitCell.b(), unitCell.c(), unitCell.alpha(), unitCell.beta(), unitCell.gamma()
+
+ spaceGroup = silicon.getSpaceGroup()
+ print ' Space group:', spaceGroup.getHMSymbol()
+ print ' Point group:', spaceGroup.getPointGroup().getHMSymbol()
+
+ scatterers = silicon.getScatterers()
+ print ' Total number of scatterers:', len(scatterers)
+
+ for i, scatterer in enumerate(scatterers):
+ print ' ' + str(i) + ':', scatterer
+
+The above script produces the following output:
+
+.. testoutput:: ExCrystalStructureConstruction
+
+ Crystal structure of silicon:
+ Unit cell: 5.431 5.431 5.431 90.0 90.0 90.0
+ Space group: F d -3 m
+ Point group: m-3m
+ Total number of scatterers: 1
+ 0: Si 0 0 0 1 0.05
+
+In general, the unit cell must be specified using either 3 or 6 space-separated floating point numbers, representing
+the three axis lengths and the three angles between them. The list of scatterers is required to be a semi-colon
+separated list of strings which contain the following information: Element symbol, x, y, z (fractional coordinates),
+occupancy (between 0 and 1) and isotropic atomic displacement parameter. The fractional coordinates can also be given
+as fractions (for example :math:`1/2` or :math:`1/3`) and for giving the coordinates in hexagonal or trigonal structures
+this is highly recommended as there may be precision problems with decimal numbers.
+
+While the CrystalStructure class is storing information, there is another class that makes use of these information to
+generate reflections and calculate structure factors. This class is called ReflectionGenerator and can be constructed
+from a CrystalStructure-object:
+
+.. testcode:: ExReflectionGeneratorConstruction
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator
+ from mantid.kernel import V3D
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLs(0.7, 3.0)
+
+ print 'There are', len(hkls), 'unique reflections for Si in the specified resolution range.'
+ print 'The reflection [222] is' + (' not' if not V3D(2, 2, 2) in hkls else '') + ' contained in the list.'
+
+.. testoutput:: ExReflectionGeneratorConstruction
+
+ There are 20 unique reflections for Si in the specified resolution range.
+ The reflection [222] is contained in the list.
+
+Checking the reflection conditions of space group :math:`Fd\bar{3}m` (origin choice 1) in the International Tables for
+Crystallography shows that if an atom is on the 8a position, additional conditions apply (:math:`h=2n+1` or
+:math:`h+k+l=4n` for general reflections). Using these additional conditions, the 222 reflection should in fact
+not be in the list. This can be verified by calculating structure factors for the list of reflections and check if
+there are very small values present.
+
+.. testcode:: ExReflectionGeneratorViolations
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator
+ import numpy as np
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLs(0.7, 3.0)
+
+ # Calculate structure factors for those HKLs
+ fSquared = generator.getFsSquared(hkls)
+
+ # Find HKLs with very small structure factors:
+ zeroFSquared = [(hkl, sf) for hkl, sf in zip(hkls, fSquared) if sf < 1e-9]
+
+ print 'HKL F^2'
+ for hkl, sf in zeroFSquared:
+ print hkl, ' ', np.round(sf, 2)
+
+The output of the above script should show three reflections with very small values for :math:`F^2`. Their indices
+violate the special conditions mentioned in the previous paragraph, so the reflections are actually extinct:
+
+.. testoutput:: ExReflectionGeneratorViolations
+
+ HKL F^2
+ [2,2,2] 0.0
+ [4,4,2] 0.0
+ [6,2,2] 0.0
+
+Those three reflections are included in the list of unique HKLs, because the standard method to determine whether a
+reflection is allowed or not uses the space group symmetry which only reflects the general conditions listed in ITA.
+It is however possible to exclude those reflections at the cost of more computations by making use of the structure
+factor calculation. This can either be done by passing an additional enum-value of the type ReflectionConditionFilter
+to the constructor of ReflectionGenerator or by passing it to the actual generator function:
+
+.. testcode:: ExReflectionGeneratorSF
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+ from mantid.kernel import V3D
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom, use structure factors for filtering
+ hkls = generator.getUniqueHKLsUsingFilter(0.7, 3.0, ReflectionConditionFilter.StructureFactor)
+
+ print 'There are', len(hkls), 'unique reflections for Si in the specified resolution range.'
+ print 'The reflection [222] is' + (' not' if not V3D(2, 2, 2) in hkls else '') + ' contained in the list.'
+
+With this option, the three reflections from the example above are missing and as an indicator, the [222] reflection
+is actually checked:
+
+.. testoutput:: ExReflectionGeneratorSF
+
+ There are 17 unique reflections for Si in the specified resolution range.
+ The reflection [222] is not contained in the list.
+
+Other options for filtering are Centering and None. If the latter one is used the reflections are only filtered
+according to their :math:`d`-value to fit the specified range.
+
+Another capability of ReflectionGenerator is the calculation of :math:`d`-values for a list of HKLs, very similar
+to the process for :math:`F^2`:
+
+.. testcode:: ExReflectionGeneratorCalculateD
+
+ from mantid.geometry import CrystalStructure, ReflectionGenerator, ReflectionConditionFilter
+ import numpy as np
+
+ silicon = CrystalStructure("5.431 5.431 5.431", "F d -3 m", "Si 0 0 0 1.0 0.05")
+ generator = ReflectionGenerator(silicon)
+
+ # Create list of unique reflections between 0.7 and 3.0 Angstrom
+ hkls = generator.getUniqueHKLsUsingFilter(0.7, 3.0, ReflectionConditionFilter.StructureFactor)
+
+ # Calculate d and F^2
+ dValues = generator.getDValues(hkls)
+ fSquared = generator.getFsSquared(hkls)
+
+ pg = silicon.getSpaceGroup().getPointGroup()
+
+ # Make list of tuples and sort by d-values, descending, include point group for multiplicity.
+ reflections = sorted([(hkl, d, fsq, len(pg.getEquivalents(hkl))) for hkl, d, fsq in zip(hkls, dValues, fSquared)],
+ key=lambda x: x[1], reverse=True)
+
+ print '{0:<8}{1:>8}{2:>8}{3:>4}'.format('HKL', 'd', 'F^2', 'M')
+ for reflection in reflections:
+ print '{0!s:<8}{1:>8.5f}{2:>8.2f}{3:>4}'.format(*reflection)
+
+This script will print a table with the reflections including their :math:`d`-value, :math:`F^2` and multiplicity due to point group
+symmetry:
+
+.. testoutput:: ExReflectionGeneratorCalculateD
+
+ HKL d F^2 M
+ [2,2,0] 1.92015 645.02 12
+ [3,1,1] 1.63751 263.85 24
+ [4,0,0] 1.35775 377.63 6
+ [3,3,1] 1.24596 154.47 24
+ [4,2,2] 1.10860 221.08 24
+ [3,3,3] 1.04520 90.43 8
+ [5,1,1] 1.04520 90.43 24
+ [4,4,0] 0.96007 129.43 12
+ [5,3,1] 0.91801 52.94 48
+ [6,2,0] 0.85872 75.78 24
+ [5,3,3] 0.82822 31.00 24
+ [4,4,4] 0.78390 44.36 8
+ [5,5,1] 0.76049 18.15 24
+ [7,1,1] 0.76049 18.15 24
+ [6,4,2] 0.72575 25.97 48
+ [5,5,3] 0.70706 10.62 24
+ [7,3,1] 0.70706 10.62 48
+
+Further reading
+~~~~~~~~~~~~~~~
+
+This concept page explains what's available in the Python interface. Some underlying parts may be interesting for C++
+developers, as the concepts of generating and filtering HKLs are pretty much hidden behind the ReflectionGenerator class
+in the Python interface. More detail is available in the generated C++ documentation.
+
+.. categories:: Concepts
--
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