diff --git a/Core/Algorithms/inc/DWBADiffuseReflection.h b/Core/Algorithms/inc/DWBADiffuseReflection.h
index c17e1c8f84a2d4c535f30de914c3cf3e32a2f536..37a8df1632f06f8eb6e33db29ac2aa2a6546dffe 100644
--- a/Core/Algorithms/inc/DWBADiffuseReflection.h
+++ b/Core/Algorithms/inc/DWBADiffuseReflection.h
@@ -28,7 +28,8 @@ class DWBADiffuseReflection : public ISimulation
public:
DWBADiffuseReflection();
- void execute(const MultiLayer &sample, const kvector_t &ki, const kvector_t &kf);
+ void execute(const MultiLayer &sample,
+ const kvector_t &ki, const kvector_t &kf);
void setSample(const MultiLayer &sample) {m_sample = &sample; }
@@ -37,6 +38,7 @@ class DWBADiffuseReflection : public ISimulation
double getDiffuseCrosscorr() const { return m_diffuse_crosscorr; }
void setKvectors(const kvector_t &ki, const kvector_t &kf);
+
private:
void diffuse_autocorr();
diff --git a/Core/Algorithms/inc/DWBASimulation.h b/Core/Algorithms/inc/DWBASimulation.h
index 7d4c8d5fba40c14b6a1983f12cd09126f0cdbef5..e3d04f808b423a96b112904522cda8bb62dece24 100644
--- a/Core/Algorithms/inc/DWBASimulation.h
+++ b/Core/Algorithms/inc/DWBASimulation.h
@@ -22,30 +22,28 @@
#include "ThreadInfo.h"
#include "Types.h"
-//! Calculates scattering cross sections in DWBA
+//! Base class for different simulations, using DWBA.
class DWBASimulation : public ISimulation
{
public:
- DWBASimulation()
- : m_alpha_i(0), m_thread_info(), mp_simulation(0) {}
+ DWBASimulation() : m_alpha_i(0), m_thread_info(), mp_simulation(0) {}
virtual ~DWBASimulation() { delete mp_simulation; }
//! Initialize the simulation with the parameters from simulation
- virtual void init(const Simulation &simulation);
+ virtual void init(const Simulation& simulation);
//! Set thread information for masking
- virtual void setThreadInfo(const ThreadInfo &thread_info) {
- m_thread_info = thread_info;
- }
+ virtual void setThreadInfo(const ThreadInfo& thread_info)
+ { m_thread_info = thread_info; }
//! return output data containing calculated intensity
- const OutputData<double> &getDWBAIntensity() const
+ const OutputData<double>& getDWBAIntensity() const
{ return m_dwba_intensity; }
//! add intensity to current dwba intensity
- void addDWBAIntensity(const OutputData<double > &data_to_add)
+ void addDWBAIntensity(const OutputData<double>& data_to_add)
{ m_dwba_intensity += data_to_add; }
//! clone DWBA simulation
@@ -69,7 +67,7 @@ class DWBASimulation : public ISimulation
const iterator end() { return m_dwba_intensity.end(); }
//! return a read-only iterator that points to the one past last element
- const const_iterator end() const { return m_dwba_intensity.end(); }
+ const const_iterator end() const { return m_dwba_intensity.end(); }
protected:
OutputData<double> m_dwba_intensity;
diff --git a/Core/Algorithms/inc/DiffuseDWBASimulation.h b/Core/Algorithms/inc/DiffuseDWBASimulation.h
index 38a79e6ec5664c4bcd686aaa73d4d1ff6515ba76..e6da8b69fd24ec6d6c70c2c0c56f0e5040d7ad27 100644
--- a/Core/Algorithms/inc/DiffuseDWBASimulation.h
+++ b/Core/Algorithms/inc/DiffuseDWBASimulation.h
@@ -23,14 +23,15 @@ class DiffuseDWBASimulation: public LayerDWBASimulation
{
public:
DiffuseDWBASimulation()
- : m_refractive_index(1.0, 0.0), m_surface_density(1.0) {}
+ : m_refractive_index(1., 0.), m_surface_density(1.) {}
virtual ~DiffuseDWBASimulation() {}
virtual void run();
size_t getSize() const { return m_np_infos.size(); }
void addParticleInfo(DiffuseParticleInfo *p_info);
void setRefractiveIndex(complex_t n) { m_refractive_index = n; }
- void setSurfaceDensity(double surface_density) { m_surface_density = surface_density; }
+ void setSurfaceDensity(double surface_density)
+ { m_surface_density = surface_density; }
void rescaleAbundances(double factor);
protected:
@@ -39,14 +40,15 @@ class DiffuseDWBASimulation: public LayerDWBASimulation
SafePointerVector<DiffuseParticleInfo> m_np_infos;
struct DiffuseFormFactorTerm {
DiffuseFormFactorTerm()
- : m_form_factors(), m_probabilities(), m_factor(0.0) {}
+ : m_form_factors(), m_probabilities(), m_factor(0.) {}
~DiffuseFormFactorTerm();
- std::vector<IFormFactor *> m_form_factors;
+ std::vector<IFormFactor*> m_form_factors;
std::vector<double> m_probabilities;
double m_factor;
};
- void initDiffuseFormFactorTerms(std::vector<DiffuseFormFactorTerm *>& terms,
- size_t nbr_heights, size_t samples_per_particle);
+ void initDiffuseFormFactorTerms(
+ std::vector<DiffuseFormFactorTerm *>& terms,
+ size_t nbr_heights, size_t samples_per_particle);
};
#endif /* DIFFUSEDWBASIMULATION_H_ */
diff --git a/Core/Algorithms/inc/ISimulation.h b/Core/Algorithms/inc/ISimulation.h
index ace40605c185b66a21974a7dd4504d78b586a68c..2c98f75c9a448a105015b1688c7d08fd099a00d1 100644
--- a/Core/Algorithms/inc/ISimulation.h
+++ b/Core/Algorithms/inc/ISimulation.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file Algorithms/inc/ISimulation.h
-//! @brief Defines class ISimulation.
+//! @brief Defines interface class ISimulation.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
@@ -18,12 +18,18 @@
#include "ICloneable.h"
+//! Interface class, encapsulating different simulations.
+
class ISimulation : public ICloneable
{
public:
- virtual ~ISimulation() { }
- ISimulation *clone() const { throw NotImplementedException("ISimulation::clone() -> Error: not implemented exception."); }
- virtual void run() { }
+ virtual ~ISimulation() {}
+ ISimulation *clone() const
+ {
+ throw NotImplementedException("ISimulation::clone() -> "
+ "Error: not implemented exception.");
+ }
+ virtual void run() {}
};
#endif // ISIMULATION_H
diff --git a/Core/Algorithms/inc/LayerDWBASimulation.h b/Core/Algorithms/inc/LayerDWBASimulation.h
index ef6b03073e61c5941162de1b4d18da701ccfe58d..a322279568aa42c788f09cf1315fd9d0c7abaab3 100644
--- a/Core/Algorithms/inc/LayerDWBASimulation.h
+++ b/Core/Algorithms/inc/LayerDWBASimulation.h
@@ -19,7 +19,7 @@
#include "DWBASimulation.h"
#include "IDoubleToComplexFunction.h"
-//! ?
+//! Base class for LayerDecoratorDWBASimulation, DiffuseDWBASimulation.
class LayerDWBASimulation : public DWBASimulation
{
@@ -27,14 +27,22 @@ class LayerDWBASimulation : public DWBASimulation
LayerDWBASimulation();
virtual ~LayerDWBASimulation();
- LayerDWBASimulation *clone() const { throw NotImplementedException("ISimulation::clone() -> Error: not implemented exception."); }
+ LayerDWBASimulation *clone() const
+ {
+ throw NotImplementedException(
+ "ISimulation::clone() -> Error: not implemented exception.");
+ }
void setKzFunction(const IDoubleToComplexMap &kz_function);
- void setReflectionTransmissionFunction(const IDoubleToPairOfComplexMap &rt_map);
- void setKzAndRTFunctions(const IDoubleToComplexMap &kz_function, const IDoubleToPairOfComplexMap &rt_map);
+ void setReflectionTransmissionFunction(
+ const IDoubleToPairOfComplexMap &rt_map);
+ void setKzAndRTFunctions(const IDoubleToComplexMap &kz_function,
+ const IDoubleToPairOfComplexMap &rt_map);
protected:
- Bin1DCVector getKfBin(double wavelength, const Bin1D &alpha_bin, const Bin1D &phi_bin) const;
+ Bin1DCVector getKfBin(double wavelength,
+ const Bin1D &alpha_bin,
+ const Bin1D &phi_bin) const;
IDoubleToComplexMap *mp_kz_function;
IDoubleToPairOfComplexMap *mp_RT_function;
};
diff --git a/Core/Algorithms/inc/MultiLayerDWBASimulation.h b/Core/Algorithms/inc/MultiLayerDWBASimulation.h
index 4c43ec74c1c42c0d495f7f34a193e08d88a697e1..6d11a3ca948c9eb3bc6e5a4a23dfc3051c214fd3 100644
--- a/Core/Algorithms/inc/MultiLayerDWBASimulation.h
+++ b/Core/Algorithms/inc/MultiLayerDWBASimulation.h
@@ -32,7 +32,11 @@ class MultiLayerDWBASimulation : public DWBASimulation
MultiLayerDWBASimulation(const MultiLayer *p_multi_layer);
virtual ~MultiLayerDWBASimulation();
- MultiLayerDWBASimulation *clone() const { throw NotImplementedException("MultiLayerDWBASimulation::clone() -> Error: not implemented"); }
+ MultiLayerDWBASimulation *clone() const
+ {
+ throw NotImplementedException(
+ "MultiLayerDWBASimulation::clone() -> Error: not implemented");
+ }
virtual void init(const Simulation &simulation);
@@ -40,6 +44,7 @@ class MultiLayerDWBASimulation : public DWBASimulation
virtual void setThreadInfo(const ThreadInfo &thread_info);
virtual void run();
+
protected:
std::set<double> getAlphaList() const;
std::map<size_t, LayerDWBASimulation*> m_layer_dwba_simulation_map;
diff --git a/Core/Algorithms/inc/MultiLayerRoughnessDWBASimulation.h b/Core/Algorithms/inc/MultiLayerRoughnessDWBASimulation.h
index cc7f812ed2b787e12b045b791a293aa4525c034d..99dfd9fe5c826709b76314cd0c49a14c279f8827 100644
--- a/Core/Algorithms/inc/MultiLayerRoughnessDWBASimulation.h
+++ b/Core/Algorithms/inc/MultiLayerRoughnessDWBASimulation.h
@@ -30,19 +30,28 @@ class MultiLayerRoughnessDWBASimulation : public DWBASimulation
MultiLayerRoughnessDWBASimulation(const MultiLayer *p_multi_layer);
virtual ~MultiLayerRoughnessDWBASimulation();
- MultiLayerRoughnessDWBASimulation *clone() const { throw NotImplementedException("MultiLayerRoughnessDWBASimulation::clone() -> Error: not implemented."); }
+ MultiLayerRoughnessDWBASimulation *clone() const
+ {
+ throw NotImplementedException(
+ "MultiLayerRoughnessDWBASimulation::clone() -> "
+ "Error: not implemented.");
+ }
virtual void run();
// set T and R functions for given layer
- void setReflectionTransmissionFunction(size_t i_layer, const IDoubleToPairOfComplexMap &RT_function);
+ void setReflectionTransmissionFunction(
+ size_t i_layer, const IDoubleToPairOfComplexMap &RT_function);
// evaluate
- virtual double evaluate(const cvector_t &k_i, const cvector_t &k_f, double alpha_i, double alpha_f);
+ virtual double evaluate(const cvector_t &k_i, const cvector_t &k_f,
+ double alpha_i, double alpha_f);
protected:
complex_t get_refractive_term(size_t ilayer) const;
- complex_t get_sum4terms(size_t ilayer, const cvector_t &k_i, const cvector_t &k_f, double alpha_i, double alpha_f);
+ complex_t get_sum4terms(size_t ilayer,
+ const cvector_t &k_i, const cvector_t &k_f,
+ double alpha_i, double alpha_f);
std::vector<IDoubleToPairOfComplexMap *> mp_RT_function;
MultiLayer *mp_multi_layer;
diff --git a/Core/Algorithms/inc/OpticalFresnel.h b/Core/Algorithms/inc/OpticalFresnel.h
index 89b9ee06cae6304bdb1b426e119947b0d7398f19..1bd49f71053af7c111e32032367ebf8fc059bb6f 100644
--- a/Core/Algorithms/inc/OpticalFresnel.h
+++ b/Core/Algorithms/inc/OpticalFresnel.h
@@ -26,7 +26,7 @@
class OpticalFresnel : public ISimulation
{
public:
- OpticalFresnel();
+ OpticalFresnel() : m_use_roughness(false) {}
//! reflection/transmission Fresnel coefficients
class FresnelCoeff {
diff --git a/Core/Algorithms/src/DWBASimulation.cpp b/Core/Algorithms/src/DWBASimulation.cpp
index 7a189340c4ad7435d54be45d8841500ae0ba968f..043f8eadb7d61e254820ca0f78b3dd38eedc535c 100644
--- a/Core/Algorithms/src/DWBASimulation.cpp
+++ b/Core/Algorithms/src/DWBASimulation.cpp
@@ -45,7 +45,8 @@ DWBASimulation *DWBASimulation::clone() const
p_result->m_ki = m_ki;
p_result->m_alpha_i = m_alpha_i;
p_result->m_thread_info = m_thread_info;
- if (mp_simulation) p_result->mp_simulation = mp_simulation->clone();
+ if (mp_simulation)
+ p_result->mp_simulation = mp_simulation->clone();
return p_result;
}
diff --git a/Core/Algorithms/src/DiffuseDWBASimulation.cpp b/Core/Algorithms/src/DiffuseDWBASimulation.cpp
index e0cdfd7b68925296007f267df31e6fb0d98007f1..806fabe168cbedf80587c6752fec849995f6e266 100644
--- a/Core/Algorithms/src/DiffuseDWBASimulation.cpp
+++ b/Core/Algorithms/src/DiffuseDWBASimulation.cpp
@@ -16,6 +16,8 @@
#include "DiffuseDWBASimulation.h"
#include "FormFactorDWBAConstZ.h"
+// Run a simulation.
+
void DiffuseDWBASimulation::run()
{
std::vector<DiffuseFormFactorTerm*> diffuse_terms;
@@ -40,11 +42,11 @@ void DiffuseDWBASimulation::run()
}
Bin1DCVector k_f_bin = getKfBin(getWaveLength(), alpha_bin, phi_bin);
- double total_intensity = 0.0;
+ double total_intensity = 0;
for (size_t i=0; i<diffuse_terms.size(); ++i) {
DiffuseFormFactorTerm *p_diffuse_term = diffuse_terms[i];
- complex_t amplitude(0.0, 0.0);
- double intensity = 0.0;
+ complex_t amplitude(0., 0.);
+ double intensity = 0;
for (size_t j=0; j<p_diffuse_term->m_form_factors.size(); ++j) {
complex_t amp =
p_diffuse_term->m_form_factors[j]->evaluate(
@@ -60,7 +62,8 @@ void DiffuseDWBASimulation::run()
++it_intensity;
}
- for (size_t i=0; i<diffuse_terms.size(); ++i) delete diffuse_terms[i];
+ for (size_t i=0; i<diffuse_terms.size(); ++i)
+ delete diffuse_terms[i];
}
void DiffuseDWBASimulation::addParticleInfo(DiffuseParticleInfo *p_info)
@@ -70,18 +73,17 @@ void DiffuseDWBASimulation::addParticleInfo(DiffuseParticleInfo *p_info)
void DiffuseDWBASimulation::rescaleAbundances(double factor)
{
- size_t number_of_nps = m_np_infos.size();
- for (size_t np_index=0; np_index<number_of_nps; ++np_index) {
+ for (size_t np_index=0; np_index<m_np_infos.size(); ++np_index) {
m_np_infos[np_index]->scaleAbundance(factor);
}
}
void DiffuseDWBASimulation::initDiffuseFormFactorTerms(
- std::vector<DiffuseFormFactorTerm*>& terms, size_t nbr_heights,
+ std::vector<DiffuseFormFactorTerm*>& terms,
+ size_t nbr_heights,
size_t samples_per_particle)
{
- size_t number_of_nps = m_np_infos.size();
- for (size_t i=0; i<number_of_nps; ++i) {
+ for (size_t i=0; i<m_np_infos.size(); ++i) {
DiffuseParticleInfo *p_diff_info = m_np_infos[i];
Particle *p_particle = p_diff_info->getParticle()->clone();
double total_particle_density = p_diff_info->getNumberPerMeso();
@@ -94,11 +96,13 @@ void DiffuseDWBASimulation::initDiffuseFormFactorTerms(
(double)j*p_diff_info->getHeightRange()/(nbr_heights-1.0);
std::vector<IFormFactor*> form_factors;
p_diff_info->getParticle()->getSimpleFormFactor()->createDistributedFormFactors(
- form_factors, p_diffuse_term->m_probabilities, samples_per_particle);
+ form_factors, p_diffuse_term->m_probabilities,
+ samples_per_particle);
for (size_t ff_index=0; ff_index<form_factors.size(); ++ff_index) {
p_particle->setSimpleFormFactor(form_factors[ff_index]);
IFormFactor *ff_particle = p_particle->createFormFactor();
- FormFactorDWBAConstZ *p_dwba_z = new FormFactorDWBAConstZ(ff_particle, depth);
+ FormFactorDWBAConstZ *p_dwba_z =
+ new FormFactorDWBAConstZ(ff_particle, depth);
p_dwba_z->setReflectionTransmissionFunction(*mp_RT_function);
p_diffuse_term->m_form_factors.push_back(p_dwba_z);
diff --git a/Core/Algorithms/src/OpticalFresnel.cpp b/Core/Algorithms/src/OpticalFresnel.cpp
index be612b42084ac6e33fe7581968d04f22c6357f27..802d0b6fb0cfa8f61f0dc95b9a11521cf63cdf3a 100644
--- a/Core/Algorithms/src/OpticalFresnel.cpp
+++ b/Core/Algorithms/src/OpticalFresnel.cpp
@@ -18,10 +18,6 @@
#include "OpticalFresnel.h"
#include "Numeric.h"
-OpticalFresnel::OpticalFresnel() : m_use_roughness(false)
-{
-}
-
void OpticalFresnel::execute(const MultiLayer &sample, const kvector_t &kvec, MultiLayerCoeff_t &coeff)
{
coeff.clear();
@@ -104,8 +100,11 @@ void OpticalFresnel::calculateFresnelCoefficientsWithRoughness(const MultiLayer
coeff[i].r = (coeff[i].kz - coeff[i + 1].kz)
/ (coeff[i].kz + coeff[i + 1].kz);
} else {
- coeff[i].r = std::sinh(picoeff * sigma * (coeff[i].kz - coeff[i + 1].kz))
- / std::sinh(picoeff * sigma * (coeff[i].kz + coeff[i + 1].kz));
+ coeff[i].r =
+ std::sinh(picoeff * sigma *
+ (coeff[i].kz - coeff[i + 1].kz)) /
+ std::sinh(picoeff * sigma *
+ (coeff[i].kz + coeff[i + 1].kz));
}
diff --git a/Core/Samples/inc/DiffuseParticleInfo.h b/Core/Samples/inc/DiffuseParticleInfo.h
index 75caff4280f83b9bdf493a53adb2741cc5b250b5..9d95e236a746a4fd10553c251a880ebcc1ccbcf3 100644
--- a/Core/Samples/inc/DiffuseParticleInfo.h
+++ b/Core/Samples/inc/DiffuseParticleInfo.h
@@ -31,7 +31,7 @@ class DiffuseParticleInfo: public ParticleInfo
//! scale abundance
void scaleAbundance(double factor) { m_abundance *= factor; }
- //! scale abundance
+ //! scale number of particles per containing mesocrystal
void scaleNumberPerMeso(double factor) { m_number_per_meso *= factor; }
//! set number of particles per containing mesocrystal
diff --git a/Core/Samples/inc/ParticleInfo.h b/Core/Samples/inc/ParticleInfo.h
index f9d0aedd3026d8a5e3b591b15602fe9666a9f98d..38c40c071e79f1e848c9444cbe523af8619cac22 100644
--- a/Core/Samples/inc/ParticleInfo.h
+++ b/Core/Samples/inc/ParticleInfo.h
@@ -20,7 +20,7 @@
#include "Particle.h"
#include "Transform3D.h"
-//! Holds additional information about particle (used in ParticleDecoration)
+//! Holds additional information about particle (used in ParticleDecoration).
class ParticleInfo : public ICompositeSample
{
@@ -48,7 +48,7 @@ class ParticleInfo : public ICompositeSample
}
//! Return depth.
- double getDepth() const { return m_depth;}
+ double getDepth() const { return m_depth; }
//! Set depth.
void setDepth(double depth) { m_depth = depth; }
@@ -60,7 +60,6 @@ class ParticleInfo : public ICompositeSample
void setAbundance(double abundance) { m_abundance = abundance; }
protected:
- //! register some class members for later access via parameter pool
virtual void init_parameters();
Particle *mp_particle;
diff --git a/pub/core/Doxyfile b/pub/core/Doxyfile
index fda5fa709f0a48917a1ea961909059c174c663f6..b28d87ef069c1ad16c1c5f372a5b1fb5a1d6e5cc 100644
--- a/pub/core/Doxyfile
+++ b/pub/core/Doxyfile
@@ -113,7 +113,7 @@ ALWAYS_DETAILED_SEC = NO
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
-INLINE_INHERITED_MEMB = NO
+INLINE_INHERITED_MEMB = YES
# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
# path before files name in the file list and in the header files. If set
@@ -1649,7 +1649,7 @@ CLASS_GRAPH = YES
# indirect implementation dependencies (inheritance, containment, and
# class references variables) of the class with other documented classes.
-COLLABORATION_GRAPH = NO
+COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
# will generate a graph for groups, showing the direct groups dependencies
@@ -1696,7 +1696,7 @@ INCLUDED_BY_GRAPH = YES
# the time of a run. So in most cases it will be better to enable call graphs
# for selected functions only using the \callgraph command.
-CALL_GRAPH = YES # TEMPORARY
+CALL_GRAPH = NO
# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
# doxygen will generate a caller dependency graph for every global function
@@ -1704,7 +1704,7 @@ CALL_GRAPH = YES # TEMPORARY
# the time of a run. So in most cases it will be better to enable caller
# graphs for selected functions only using the \callergraph command.
-CALLER_GRAPH = YES # TEMPORARY
+CALLER_GRAPH = NO
# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
# will generate a graphical hierarchy of all classes instead of a textual one.