From 80c6b98eaa393c88fc07de532e36b23de6ba7b09 Mon Sep 17 00:00:00 2001
From: Walter Van Herck <w.van.herck@fz-juelich.de>
Date: Thu, 28 Nov 2013 16:04:06 +0100
Subject: [PATCH] Remove transformation from FormFactorCrystal; transform
Lattice and LatticeBasis instead of q for form factor calculations; rotate
mesoformfactor also
---
Core/FormFactors/inc/FormFactorCrystal.h | 4 --
Core/FormFactors/src/FormFactorCrystal.cpp | 38 +++++---------
Core/Geometry/inc/ITransform3D.h | 24 ---------
Core/PythonAPI/src/Crystal.pypp.cpp | 49 ++++++++++++++-----
Core/PythonAPI/src/FormFactorCrystal.pypp.cpp | 10 ----
.../src/IClusteredParticles.pypp.cpp | 23 +++++++++
Core/Samples/inc/Crystal.h | 14 ++++--
Core/Samples/inc/IClusteredParticles.h | 12 +++--
Core/Samples/inc/Lattice.h | 5 ++
Core/Samples/inc/LatticeBasis.h | 3 ++
Core/Samples/src/Crystal.cpp | 30 ++++++++----
Core/Samples/src/Lattice.cpp | 10 +++-
Core/Samples/src/LatticeBasis.cpp | 22 +++++++++
Core/Samples/src/MesoCrystal.cpp | 2 +-
14 files changed, 149 insertions(+), 97 deletions(-)
diff --git a/Core/FormFactors/inc/FormFactorCrystal.h b/Core/FormFactors/inc/FormFactorCrystal.h
index 874aeb587e3..b614ec314d3 100644
--- a/Core/FormFactors/inc/FormFactorCrystal.h
+++ b/Core/FormFactors/inc/FormFactorCrystal.h
@@ -48,8 +48,6 @@ public:
virtual double getVolume() const;
- void setTransformation(const Geometry::PTransform3D& P_transform);
-
private:
void calculateLargestReciprocalDistance();
@@ -60,8 +58,6 @@ private:
IFormFactor *mp_meso_form_factor;
const IMaterial *mp_ambient_material;
double m_max_rec_length;
- Geometry::PTransform3D mP_transform;
- Geometry::PTransform3D mP_inverse_transform;
};
#endif /* FORMFACTORCRYSTAL_H_ */
diff --git a/Core/FormFactors/src/FormFactorCrystal.cpp b/Core/FormFactors/src/FormFactorCrystal.cpp
index 55d60da591e..97e8f9ddcb6 100644
--- a/Core/FormFactors/src/FormFactorCrystal.cpp
+++ b/Core/FormFactors/src/FormFactorCrystal.cpp
@@ -19,16 +19,22 @@ FormFactorCrystal::FormFactorCrystal(
const Crystal& p_crystal,
const IFormFactor& meso_crystal_form_factor,
const IMaterial *p_material, complex_t wavevector_scattering_factor)
-: m_lattice(p_crystal.getLattice())
+: m_lattice(p_crystal.getTransformedLattice())
, m_wavevector_scattering_factor(wavevector_scattering_factor)
, mp_ambient_material(p_material)
, m_max_rec_length(0.0)
{
setName("FormFactorCrystal");
- mp_lattice_basis = p_crystal.createBasis();
+ mp_lattice_basis = p_crystal.createTransformedBasis();
mp_basis_form_factor = mp_lattice_basis->createFormFactor(
m_wavevector_scattering_factor);
- mp_meso_form_factor = meso_crystal_form_factor.clone();
+ if (p_crystal.getTransform().get()) {
+ mp_meso_form_factor = new FormFactorDecoratorTransformation(
+ meso_crystal_form_factor.clone(),
+ p_crystal.getTransform() );
+ } else {
+ mp_meso_form_factor = meso_crystal_form_factor.clone();
+ }
setAmbientMaterial(mp_ambient_material);
calculateLargestReciprocalDistance();
}
@@ -47,9 +53,6 @@ FormFactorCrystal* FormFactorCrystal::clone() const
*mp_meso_form_factor, mp_ambient_material,
m_wavevector_scattering_factor);
result->setName(getName());
- if (mP_transform.get()) {
- result->setTransformation(mP_transform);
- }
return result;
}
@@ -72,13 +75,7 @@ complex_t FormFactorCrystal::evaluate(const cvector_t& k_i,
// construct a real reciprocal vector
cvector_t q_bin_lower = k_i - k_f_bin.m_q_lower;
cvector_t q_bin_upper = k_i - k_f_bin.m_q_upper;
- Bin1DCVector q_bin;
- if (mP_inverse_transform.get()) {
- q_bin = Bin1DCVector(mP_inverse_transform->transformed(q_bin_lower),
- mP_inverse_transform->transformed(q_bin_upper));
- } else {
- q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
- }
+ Bin1DCVector q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
cvector_t q = q_bin.getMidPoint();
kvector_t q_real(q.x().real(), q.y().real(), q.z().real());
@@ -115,13 +112,7 @@ Eigen::Matrix2cd FormFactorCrystal::evaluatePol(const cvector_t& k_i,
// construct a real reciprocal vector
cvector_t q_bin_lower = k_i - k_f_bin.m_q_lower;
cvector_t q_bin_upper = k_i - k_f_bin.m_q_upper;
- Bin1DCVector q_bin;
- if (mP_inverse_transform.get()) {
- q_bin = Bin1DCVector(mP_inverse_transform->transformed(q_bin_lower),
- mP_inverse_transform->transformed(q_bin_upper));
- } else {
- q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
- }
+ Bin1DCVector q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
cvector_t q = q_bin.getMidPoint();
kvector_t q_real(q.x().real(), q.y().real(), q.z().real());
@@ -157,13 +148,6 @@ double FormFactorCrystal::getVolume() const
return mp_meso_form_factor->getVolume();
}
-void FormFactorCrystal::setTransformation(
- const Geometry::PTransform3D& P_transform)
-{
- mP_transform = P_transform;
- mP_inverse_transform = mP_transform->inverse();
-}
-
void FormFactorCrystal::calculateLargestReciprocalDistance()
{
kvector_t a1 = m_lattice.getBasisVectorA();
diff --git a/Core/Geometry/inc/ITransform3D.h b/Core/Geometry/inc/ITransform3D.h
index 07a91420edf..733e93bbd3b 100644
--- a/Core/Geometry/inc/ITransform3D.h
+++ b/Core/Geometry/inc/ITransform3D.h
@@ -46,10 +46,6 @@ public:
transformed(const BasicVector3D<complex_t>& v) const
{ return v; }
-#ifndef GCCXML_SKIP_THIS
- Eigen::Matrix2cd transformed(const Eigen::Matrix2cd &m) const;
-#endif
-
friend std::ostream& operator<<(std::ostream& ostr, const ITransform3D& m)
{ m.print(ostr); return ostr; }
@@ -59,26 +55,6 @@ public:
}// namespace Geometry
-#ifndef GCCXML_SKIP_THIS
-inline Eigen::Matrix2cd Geometry::ITransform3D::transformed(
- const Eigen::Matrix2cd& m) const
-{
- Eigen::Matrix2cd result;
- complex_t im(0.0, 1.0);
- double a = std::real( (complex_t)(m(0,0) + m(1,1)) )/2.0;
- double bx = std::real( (complex_t)m(1,0) );
- double by = std::imag( (complex_t)m(1,0) );
- double bz = std::real( (complex_t)(m(0,0) - m(1,1)) )/2.0;
- BasicVector3D<double> b_v(bx, by, bz);
- BasicVector3D<double> b_v_t = transformed(b_v);
- result(0,0) = a + b_v_t.z();
- result(0,1) = b_v_t.x() - im*b_v_t.y();
- result(1,0) = b_v_t.x() + im*b_v_t.y();
- result(1,1) = a - b_v_t.z();
- return result;
-}
-#endif
-
#endif /* GEOMETRY_ITRANSFORM3D_H */
diff --git a/Core/PythonAPI/src/Crystal.pypp.cpp b/Core/PythonAPI/src/Crystal.pypp.cpp
index 30711aebcec..0c46992beb8 100644
--- a/Core/PythonAPI/src/Crystal.pypp.cpp
+++ b/Core/PythonAPI/src/Crystal.pypp.cpp
@@ -49,6 +49,18 @@ struct Crystal_wrapper : Crystal, bp::wrapper< Crystal > {
return Crystal::cloneInvertB( );
}
+ virtual ::Geometry::PTransform3D getTransform( ) const {
+ if( bp::override func_getTransform = this->get_override( "getTransform" ) )
+ return func_getTransform( );
+ else{
+ return this->Crystal::getTransform( );
+ }
+ }
+
+ ::Geometry::PTransform3D default_getTransform( ) const {
+ return Crystal::getTransform( );
+ }
+
virtual void setTransform( ::Geometry::PTransform3D const & transform ) {
if( bp::override func_setTransform = this->get_override( "setTransform" ) )
func_setTransform( transform );
@@ -208,24 +220,15 @@ void register_Crystal_class(){
, bp::return_value_policy< bp::reference_existing_object >() );
}
- { //::Crystal::createBasis
+ { //::Crystal::createTransformedBasis
- typedef ::LatticeBasis * ( ::Crystal::*createBasis_function_type )( ) const;
+ typedef ::LatticeBasis * ( ::Crystal::*createTransformedBasis_function_type )( ) const;
Crystal_exposer.def(
- "createBasis"
- , createBasis_function_type( &::Crystal::createBasis )
+ "createTransformedBasis"
+ , createTransformedBasis_function_type( &::Crystal::createTransformedBasis )
, bp::return_value_policy< bp::manage_new_object >() );
- }
- { //::Crystal::getLattice
-
- typedef ::Lattice ( ::Crystal::*getLattice_function_type )( ) const;
-
- Crystal_exposer.def(
- "getLattice"
- , getLattice_function_type( &::Crystal::getLattice ) );
-
}
{ //::Crystal::getLatticeBasis
@@ -236,6 +239,26 @@ void register_Crystal_class(){
, getLatticeBasis_function_type( &::Crystal::getLatticeBasis )
, bp::return_value_policy< bp::reference_existing_object >() );
+ }
+ { //::Crystal::getTransform
+
+ typedef ::Geometry::PTransform3D ( ::Crystal::*getTransform_function_type )( ) const;
+ typedef ::Geometry::PTransform3D ( Crystal_wrapper::*default_getTransform_function_type )( ) const;
+
+ Crystal_exposer.def(
+ "getTransform"
+ , getTransform_function_type(&::Crystal::getTransform)
+ , default_getTransform_function_type(&Crystal_wrapper::default_getTransform) );
+
+ }
+ { //::Crystal::getTransformedLattice
+
+ typedef ::Lattice ( ::Crystal::*getTransformedLattice_function_type )( ) const;
+
+ Crystal_exposer.def(
+ "getTransformedLattice"
+ , getTransformedLattice_function_type( &::Crystal::getTransformedLattice ) );
+
}
{ //::Crystal::setDWFactor
diff --git a/Core/PythonAPI/src/FormFactorCrystal.pypp.cpp b/Core/PythonAPI/src/FormFactorCrystal.pypp.cpp
index 71e92a0fae3..3faf86f8d95 100644
--- a/Core/PythonAPI/src/FormFactorCrystal.pypp.cpp
+++ b/Core/PythonAPI/src/FormFactorCrystal.pypp.cpp
@@ -319,16 +319,6 @@ void register_FormFactorCrystal_class(){
, getVolume_function_type(&::FormFactorCrystal::getVolume)
, default_getVolume_function_type(&FormFactorCrystal_wrapper::default_getVolume) );
- }
- { //::FormFactorCrystal::setTransformation
-
- typedef void ( ::FormFactorCrystal::*setTransformation_function_type )( ::Geometry::PTransform3D const & ) ;
-
- FormFactorCrystal_exposer.def(
- "setTransformation"
- , setTransformation_function_type( &::FormFactorCrystal::setTransformation )
- , ( bp::arg("P_transform") ) );
-
}
{ //::IParameterized::areParametersChanged
diff --git a/Core/PythonAPI/src/IClusteredParticles.pypp.cpp b/Core/PythonAPI/src/IClusteredParticles.pypp.cpp
index 290c5a3f77b..0d91d238c2d 100644
--- a/Core/PythonAPI/src/IClusteredParticles.pypp.cpp
+++ b/Core/PythonAPI/src/IClusteredParticles.pypp.cpp
@@ -49,6 +49,18 @@ struct IClusteredParticles_wrapper : IClusteredParticles, bp::wrapper< IClustere
return IClusteredParticles::cloneInvertB( );
}
+ virtual ::Geometry::PTransform3D getTransform( ) const {
+ if( bp::override func_getTransform = this->get_override( "getTransform" ) )
+ return func_getTransform( );
+ else{
+ return this->IClusteredParticles::getTransform( );
+ }
+ }
+
+ ::Geometry::PTransform3D default_getTransform( ) const {
+ return IClusteredParticles::getTransform( );
+ }
+
virtual void setAmbientMaterial( ::IMaterial const * p_ambient_material ){
bp::override func_setAmbientMaterial = this->get_override( "setAmbientMaterial" );
func_setAmbientMaterial( boost::python::ptr(p_ambient_material) );
@@ -212,6 +224,17 @@ void register_IClusteredParticles_class(){
, default_cloneInvertB_function_type(&IClusteredParticles_wrapper::default_cloneInvertB)
, bp::return_value_policy< bp::reference_existing_object >() );
+ }
+ { //::IClusteredParticles::getTransform
+
+ typedef ::Geometry::PTransform3D ( ::IClusteredParticles::*getTransform_function_type )( ) const;
+ typedef ::Geometry::PTransform3D ( IClusteredParticles_wrapper::*default_getTransform_function_type )( ) const;
+
+ IClusteredParticles_exposer.def(
+ "getTransform"
+ , getTransform_function_type(&::IClusteredParticles::getTransform)
+ , default_getTransform_function_type(&IClusteredParticles_wrapper::default_getTransform) );
+
}
{ //::IClusteredParticles::setAmbientMaterial
diff --git a/Core/Samples/inc/Crystal.h b/Core/Samples/inc/Crystal.h
index f1cf70b8f50..65a9a33c63f 100644
--- a/Core/Samples/inc/Crystal.h
+++ b/Core/Samples/inc/Crystal.h
@@ -43,11 +43,10 @@ public:
virtual IFormFactor *createTotalFormFactor(
const IFormFactor& meso_crystal_form_factor,
const IMaterial *p_ambient_material,
- complex_t wavevector_scattering_factor,
- const Geometry::PTransform3D& transform) const;
+ complex_t wavevector_scattering_factor) const;
- Lattice getLattice() const { return m_lattice; }
- LatticeBasis *createBasis() const { return mp_lattice_basis->clone(); }
+ Lattice getTransformedLattice() const;
+ LatticeBasis *createTransformedBasis() const;
const LatticeBasis *getLatticeBasis() const { return mp_lattice_basis; }
@@ -59,10 +58,17 @@ public:
//! Sets transformation.
virtual void setTransform(const Geometry::PTransform3D& transform);
+ //! Gets transformation
+ virtual Geometry::PTransform3D getTransform() const {
+ return mP_transform;
+ }
+
+
private:
Crystal(LatticeBasis *p_lattice_basis, const Lattice& lattice);
Lattice m_lattice;
+ Geometry::PTransform3D mP_transform;
LatticeBasis *mp_lattice_basis;
double m_dw_factor;
};
diff --git a/Core/Samples/inc/IClusteredParticles.h b/Core/Samples/inc/IClusteredParticles.h
index b799a4a0455..4864b336726 100644
--- a/Core/Samples/inc/IClusteredParticles.h
+++ b/Core/Samples/inc/IClusteredParticles.h
@@ -59,13 +59,11 @@ public:
virtual IFormFactor *createTotalFormFactor(
const IFormFactor& meso_crystal_form_factor,
const IMaterial *p_ambient_material,
- complex_t wavevector_scattering_factor,
- const Geometry::PTransform3D& transform) const
+ complex_t wavevector_scattering_factor) const
{
(void)meso_crystal_form_factor;
(void)p_ambient_material;
(void)wavevector_scattering_factor;
- (void)transform;
throw NotImplementedException(
"IClusteredParticles::createTotalFormFactor() "
"-> NotImplementedException");
@@ -80,7 +78,7 @@ public:
"-> NotImplementedException");
}
- //! Sets transformation.
+ //! Sets transformation
virtual void setTransform(const Geometry::PTransform3D& transform)
{
(void)transform;
@@ -89,6 +87,12 @@ public:
"-> NotImplementedException");
}
+ //! Gets transformation
+ virtual Geometry::PTransform3D getTransform() const
+ {
+ return Geometry::PTransform3D();
+ }
+
};
#endif /* ICLUSTEREDNANOPARTICLES_H_ */
diff --git a/Core/Samples/inc/Lattice.h b/Core/Samples/inc/Lattice.h
index f7504dcea3c..7165e6783c8 100644
--- a/Core/Samples/inc/Lattice.h
+++ b/Core/Samples/inc/Lattice.h
@@ -20,6 +20,7 @@
#include "ISelectionRule.h"
#include "TRange.h"
#include "FastVector.h"
+#include "ITransform3D.h"
#include <vector>
@@ -33,6 +34,10 @@ public:
Lattice(const Lattice& lattice);
~Lattice();
+ //! Create transformed lattice
+ Lattice createTransformedLattice(
+ const Geometry::PTransform3D& transform) const;
+
//! Initializes cached data
void initialize() const;
diff --git a/Core/Samples/inc/LatticeBasis.h b/Core/Samples/inc/LatticeBasis.h
index 62a2c08a379..8c11d287947 100644
--- a/Core/Samples/inc/LatticeBasis.h
+++ b/Core/Samples/inc/LatticeBasis.h
@@ -32,6 +32,9 @@ public:
//! Returns a clone with inverted magnetic fields
virtual LatticeBasis *cloneInvertB() const;
+ //! Creates a transformed version of itself
+ LatticeBasis *createTransformed() const;
+
//! Calls the ISampleVisitor's visit method
virtual void accept(ISampleVisitor *p_visitor) const {
p_visitor->visit(this);
diff --git a/Core/Samples/src/Crystal.cpp b/Core/Samples/src/Crystal.cpp
index 70f929ee722..8898dc7d686 100644
--- a/Core/Samples/src/Crystal.cpp
+++ b/Core/Samples/src/Crystal.cpp
@@ -52,21 +52,31 @@ Crystal* Crystal::cloneInvertB() const
IFormFactor* Crystal::createTotalFormFactor(
const IFormFactor& meso_crystal_form_factor,
const IMaterial *p_ambient_material,
- complex_t wavevector_scattering_factor,
- const Geometry::PTransform3D& P_transform) const
+ complex_t wavevector_scattering_factor) const
{
FormFactorCrystal *p_ff_crystal =
new FormFactorCrystal(*this, meso_crystal_form_factor,
p_ambient_material, wavevector_scattering_factor);
- if (P_transform.get()) {
- p_ff_crystal->setTransformation(P_transform);
- }
if (m_dw_factor>0.0) {
return new FormFactorDecoratorDebyeWaller(p_ff_crystal, m_dw_factor);
}
return p_ff_crystal;
}
+Lattice Crystal::getTransformedLattice() const
+{
+ if (mP_transform.get()) {
+ return m_lattice.createTransformedLattice(mP_transform);
+ } else {
+ return m_lattice;
+ }
+}
+
+LatticeBasis* Crystal::createTransformedBasis() const
+{
+ return mp_lattice_basis->createTransformed();
+}
+
std::vector<DiffuseParticleInfo*>* Crystal::createDiffuseParticleInfo(
const ParticleInfo& parent_info) const
{
@@ -95,6 +105,12 @@ std::vector<DiffuseParticleInfo*>* Crystal::createDiffuseParticleInfo(
return p_result;
}
+void Crystal::setTransform(const Geometry::PTransform3D& transform)
+{
+ mp_lattice_basis->setTransform(transform);
+ mP_transform = transform;
+}
+
Crystal::Crystal(LatticeBasis* p_lattice_basis, const Lattice& lattice)
: m_lattice(lattice)
, m_dw_factor(0.0)
@@ -104,7 +120,3 @@ Crystal::Crystal(LatticeBasis* p_lattice_basis, const Lattice& lattice)
registerChild(mp_lattice_basis);
}
-void Crystal::setTransform(const Geometry::PTransform3D& transform)
-{
- mp_lattice_basis->setTransform(transform);
-}
diff --git a/Core/Samples/src/Lattice.cpp b/Core/Samples/src/Lattice.cpp
index 280f09146d2..434222116c5 100644
--- a/Core/Samples/src/Lattice.cpp
+++ b/Core/Samples/src/Lattice.cpp
@@ -55,6 +55,15 @@ Lattice::~Lattice()
delete mp_selection_rule;
}
+Lattice Lattice::createTransformedLattice(
+ const Geometry::PTransform3D& transform) const
+{
+ kvector_t a1 = transform->transformed(m_a1);
+ kvector_t a2 = transform->transformed(m_a2);
+ kvector_t a3 = transform->transformed(m_a3);
+ return Lattice(a1, a2, a3);
+}
+
void Lattice::initialize() const
{
computeReciprocalVectors();
@@ -234,4 +243,3 @@ void Lattice::computeInverseVectors(const kvector_t& v1, const kvector_t& v2,
gsl_matrix_free(p_inverseMatrix);
}
-
diff --git a/Core/Samples/src/LatticeBasis.cpp b/Core/Samples/src/LatticeBasis.cpp
index 4f72fb60450..6cc4ea07cf8 100644
--- a/Core/Samples/src/LatticeBasis.cpp
+++ b/Core/Samples/src/LatticeBasis.cpp
@@ -73,6 +73,27 @@ LatticeBasis* LatticeBasis::cloneInvertB() const
return p_new;
}
+LatticeBasis* LatticeBasis::createTransformed() const
+{
+ if (!mP_transform.get()) {
+ return clone();
+ }
+ LatticeBasis *p_new = new LatticeBasis();
+ std::vector<kvector_t> new_positions;
+ for (size_t index=0; index<m_particles.size(); ++index) {
+ new_positions.clear();
+ for (std::vector<kvector_t>::const_iterator it =
+ m_positions_vector[index].begin();
+ it !=m_positions_vector[index].end(); ++it) {
+ new_positions.push_back(mP_transform->transformed(*it));
+ }
+ p_new->addParticle(*m_particles[index], new_positions);
+ }
+ p_new->setName(getName());
+ p_new->setAmbientMaterial(this->mp_ambient_material);
+ return p_new;
+}
+
void LatticeBasis::addParticle(const Particle& particle,
std::vector<kvector_t > positions)
{
@@ -140,3 +161,4 @@ void LatticeBasis::addParticlePointer(Particle* p_particle,
m_particles.push_back(p_particle);
m_positions_vector.push_back(positions);
}
+
diff --git a/Core/Samples/src/MesoCrystal.cpp b/Core/Samples/src/MesoCrystal.cpp
index 17384aa802a..4a178ffeaeb 100644
--- a/Core/Samples/src/MesoCrystal.cpp
+++ b/Core/Samples/src/MesoCrystal.cpp
@@ -72,7 +72,7 @@ IFormFactor* MesoCrystal::createFormFactor(
{
return mp_particle_structure->createTotalFormFactor(
*mp_meso_form_factor, mp_ambient_material,
- wavevector_scattering_factor, mP_transform);
+ wavevector_scattering_factor);
}
void MesoCrystal::setTransform(const Geometry::PTransform3D& transform)
--
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