diff --git a/.cproject b/.cproject
index f14a6cda202e8ed90ad22bc2eec27057b9692d4a..3a590a0c23a6f5a487d90bc8c0148b8325d90ffe 100644
--- a/.cproject
+++ b/.cproject
@@ -153,20 +153,20 @@
</storageModule>
<storageModule moduleId="org.eclipse.cdt.make.core.buildtargets"/>
<storageModule moduleId="org.eclipse.cdt.internal.ui.text.commentOwnerProjectMappings"/>
+ <storageModule moduleId="org.eclipse.cdt.core.LanguageSettingsProviders"/>
<storageModule moduleId="scannerConfiguration">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
+ <scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600;cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600.;cdt.managedbuild.tool.gnu.c.compiler.macosx.base.1651719834;cdt.managedbuild.tool.gnu.c.compiler.input.485220512">
+ <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
+ </scannerConfigBuildInfo>
<scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.45089428;cdt.managedbuild.toolchain.gnu.macosx.base.45089428.834509647;cdt.managedbuild.tool.gnu.c.compiler.macosx.base.44819609;cdt.managedbuild.tool.gnu.c.compiler.input.44052800">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
</scannerConfigBuildInfo>
<scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.45089428;cdt.managedbuild.toolchain.gnu.macosx.base.45089428.834509647;cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.1362645889;cdt.managedbuild.tool.gnu.cpp.compiler.input.2060403592">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP"/>
</scannerConfigBuildInfo>
- <scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600;cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600.;cdt.managedbuild.tool.gnu.c.compiler.macosx.base.1651719834;cdt.managedbuild.tool.gnu.c.compiler.input.485220512">
- <autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
- </scannerConfigBuildInfo>
<scannerConfigBuildInfo instanceId="cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600;cdt.managedbuild.toolchain.gnu.macosx.base.45089428.1343516600.;cdt.managedbuild.tool.gnu.cpp.compiler.macosx.base.1382053189;cdt.managedbuild.tool.gnu.cpp.compiler.input.913383985">
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP"/>
</scannerConfigBuildInfo>
</storageModule>
- <storageModule moduleId="org.eclipse.cdt.core.LanguageSettingsProviders"/>
</cproject>
diff --git a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW DWBA Formfactor.launch b/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW DWBA Formfactor.launch
deleted file mode 100644
index ba2c97ca0cf674625fed56568913d8eaa3e6e4ef..0000000000000000000000000000000000000000
--- a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW DWBA Formfactor.launch
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.cdt.launch.applicationLaunchType">
-<intAttribute key="org.eclipse.cdt.launch.ATTR_BUILD_BEFORE_LAUNCH_ATTR" value="0"/>
-<stringAttribute key="org.eclipse.cdt.launch.COREFILE_PATH" value=""/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_ARGUMENTS" value="dwba"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_NAME" value="/Users/herck/Development/git/GISASFW/App/App"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_ATTR" value="GISASFW"/>
-<booleanAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_AUTO_ATTR" value="false"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_ID_ATTR" value=""/>
-<booleanAttribute key="org.eclipse.cdt.launch.use_terminal" value="true"/>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/GISASFW"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="/Users/herck/Development/git/GISASFW/lib:/opt/local/lib/root"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
-</listAttribute>
-</launchConfiguration>
diff --git a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Diffuse.launch b/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Diffuse.launch
deleted file mode 100644
index 7c6526ed0d2296b5064858d00ed014b1149e4c82..0000000000000000000000000000000000000000
--- a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Diffuse.launch
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.cdt.launch.applicationLaunchType">
-<intAttribute key="org.eclipse.cdt.launch.ATTR_BUILD_BEFORE_LAUNCH_ATTR" value="0"/>
-<stringAttribute key="org.eclipse.cdt.launch.COREFILE_PATH" value=""/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_ARGUMENTS" value="diffuse"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_NAME" value="/Users/herck/Development/git/GISASFW/App/App"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_ATTR" value="GISASFW"/>
-<booleanAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_AUTO_ATTR" value="false"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_ID_ATTR" value=""/>
-<booleanAttribute key="org.eclipse.cdt.launch.use_terminal" value="true"/>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/GISASFW"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="/Users/herck/Development/git/GISASFW/lib:/opt/local/lib/root"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
-</listAttribute>
-</launchConfiguration>
diff --git a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Formfactor.launch b/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Formfactor.launch
deleted file mode 100644
index c0f5397733d0e8210225757c048ab297d0e0ba95..0000000000000000000000000000000000000000
--- a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Formfactor.launch
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.cdt.launch.applicationLaunchType">
-<intAttribute key="org.eclipse.cdt.launch.ATTR_BUILD_BEFORE_LAUNCH_ATTR" value="0"/>
-<stringAttribute key="org.eclipse.cdt.launch.COREFILE_PATH" value=""/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_ARGUMENTS" value="formfactor"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_NAME" value="/Users/herck/Development/git/GISASFW/App/App"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_ATTR" value="GISASFW"/>
-<booleanAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_AUTO_ATTR" value="false"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_ID_ATTR" value=""/>
-<booleanAttribute key="org.eclipse.cdt.launch.use_terminal" value="true"/>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/GISASFW"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="/Users/herck/Development/git/GISASFW/lib:/opt/local/lib/root"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
-</listAttribute>
-</launchConfiguration>
diff --git a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Fresnel.launch b/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Fresnel.launch
deleted file mode 100644
index 80a990b6ba304465f532d6aabdd73e719df79c90..0000000000000000000000000000000000000000
--- a/.metadata/.plugins/org.eclipse.debug.core/.launches/GISASFW Fresnel.launch
+++ /dev/null
@@ -1,39 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.cdt.launch.applicationLaunchType">
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.AUTO_SOLIB" value="true"/>
-<listAttribute key="org.eclipse.cdt.dsf.gdb.AUTO_SOLIB_LIST"/>
-<stringAttribute key="org.eclipse.cdt.dsf.gdb.DEBUG_NAME" value="gdb"/>
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.DEBUG_ON_FORK" value="false"/>
-<stringAttribute key="org.eclipse.cdt.dsf.gdb.GDB_INIT" value=".gdbinit"/>
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.NON_STOP" value="false"/>
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.REVERSE" value="false"/>
-<listAttribute key="org.eclipse.cdt.dsf.gdb.SOLIB_PATH"/>
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.UPDATE_THREADLIST_ON_SUSPEND" value="false"/>
-<booleanAttribute key="org.eclipse.cdt.dsf.gdb.internal.ui.launching.LocalApplicationCDebuggerTab.DEFAULTS_SET" value="true"/>
-<intAttribute key="org.eclipse.cdt.launch.ATTR_BUILD_BEFORE_LAUNCH_ATTR" value="0"/>
-<stringAttribute key="org.eclipse.cdt.launch.COREFILE_PATH" value=""/>
-<stringAttribute key="org.eclipse.cdt.launch.DEBUGGER_ID" value="gdb"/>
-<stringAttribute key="org.eclipse.cdt.launch.DEBUGGER_START_MODE" value="run"/>
-<booleanAttribute key="org.eclipse.cdt.launch.DEBUGGER_STOP_AT_MAIN" value="true"/>
-<stringAttribute key="org.eclipse.cdt.launch.DEBUGGER_STOP_AT_MAIN_SYMBOL" value="main"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_ARGUMENTS" value="fresnel"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROGRAM_NAME" value="/Users/herck/Development/git/GISASFW/App/App"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_ATTR" value="GISASFW"/>
-<booleanAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_AUTO_ATTR" value="false"/>
-<stringAttribute key="org.eclipse.cdt.launch.PROJECT_BUILD_CONFIG_ID_ATTR" value=""/>
-<booleanAttribute key="org.eclipse.cdt.launch.use_terminal" value="true"/>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/GISASFW"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="/Users/herck/Development/git/GISASFW/lib:/opt/local/lib/root"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
-<listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
-</listAttribute>
-<stringAttribute key="org.eclipse.dsf.launch.MEMORY_BLOCKS" value="<?xml version="1.0" encoding="UTF-8" standalone="no"?> <memoryBlockExpressionList context="reserved-for-future-use"> <gdbmemoryBlockExpression address="4363286528" label="0x104127800"/> </memoryBlockExpressionList> "/>
-</launchConfiguration>
diff --git a/.settings/org.eclipse.cdt.core.prefs b/.settings/org.eclipse.cdt.core.prefs
index e9636c6db4e5c17722dfc7124b612a52d763f04a..7b2358a59ea3351fba40219075cdf19577acb8ea 100644
--- a/.settings/org.eclipse.cdt.core.prefs
+++ b/.settings/org.eclipse.cdt.core.prefs
@@ -1,6 +1,6 @@
eclipse.preferences.version=1
environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/DYLD_LIBRARY_PATH/delimiter=\:
environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/DYLD_LIBRARY_PATH/operation=replace
-environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/DYLD_LIBRARY_PATH/value=${workspace_loc\:/GISASFW/lib}
+environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/DYLD_LIBRARY_PATH/value=${workspace_loc\:/BornAgain/lib}
environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/append=true
environment/project/cdt.managedbuild.toolchain.gnu.macosx.base.45089428/appendContributed=true
diff --git a/App/App.pro b/App/App.pro
index 288e81fd60049b8d9ed64946f4f57c025783b317..11ba003261b52e5d811d25a874e3fc07aaf814cd 100644
--- a/App/App.pro
+++ b/App/App.pro
@@ -77,6 +77,7 @@ SOURCES += \
src/TestPerformance.cpp \
src/TestRootTree.cpp \
src/TestRoughness.cpp \
+ src/TestSpecularMatrix.cpp \
src/TestToySimulation.cpp \
src/TreeEventStructure.cpp \
src/main.cpp
@@ -141,6 +142,7 @@ HEADERS += \
inc/TestPerformance.h \
inc/TestRootTree.h \
inc/TestRoughness.h \
+ inc/TestSpecularMatrix.h \
inc/TestToySimulation.h \
inc/TreeEventStructure.h \
inc/Version.h \
diff --git a/App/inc/TestPerformance.h b/App/inc/TestPerformance.h
index b1a90edc7e885425f4c4f498018dd01ca9ccec05..b456a8adfa72dc7792518b224e935f46e90f94f4 100644
--- a/App/inc/TestPerformance.h
+++ b/App/inc/TestPerformance.h
@@ -1,5 +1,5 @@
// ************************************************************************** //
-//
+//
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file App/inc/TestPerformance.h
@@ -75,6 +75,18 @@ class PerfTest_FresnelCoeff : public IFunctionalTest
ISample *m_sample;
};
+//! @class PerfTest_SpecularMatrix
+//! measurement of the performance in specular matrix calculation
+class PerfTest_SpecularMatrix : public IFunctionalTest
+{
+ public:
+ PerfTest_SpecularMatrix() : IFunctionalTest("SpecularMatrix"), m_sample(0){}
+ virtual ~PerfTest_SpecularMatrix() { }
+ void initialise(ProgramOptions *p_options);
+ void execute();
+ ISample *m_sample;
+};
+
//! @class PerfTest_Pyramid
//! measurement of the performance in pyramid form factor calculations
class PerfTest_Pyramid : public IFunctionalTest
diff --git a/App/inc/TestSpecularMatrix.h b/App/inc/TestSpecularMatrix.h
new file mode 100644
index 0000000000000000000000000000000000000000..17f26bfb7d698824172fd708a1852ef4a3287e05
--- /dev/null
+++ b/App/inc/TestSpecularMatrix.h
@@ -0,0 +1,51 @@
+// ************************************************************************** //
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file App/inc/TestSpecularMatrix.h
+//! @brief Defines class TestSpecularMatrix.
+//!
+//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//! @authors Scientific Computing Group at MLZ Garching
+//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
+//
+// ************************************************************************** //
+
+#ifndef TESTSPECULARMATRIX_H_
+#define TESTSPECULARMATRIX_H_
+
+#include "IFunctionalTest.h"
+#include "SpecularMatrix.h"
+#include "MultiLayer.h"
+#include "OutputData.h"
+
+//! Returns amplitudes for different wave components using the matrix formalism
+//! for several typical multilayer samples and produce validation plots
+
+class TestSpecularMatrix : public IFunctionalTest
+{
+ public:
+ TestSpecularMatrix();
+
+ void execute();
+
+ private:
+ //! Returns amplitudes vs. alpha_i for several standard samples
+ void test_standard_samples();
+ //! draw results of the test
+ void draw_standard_samples();
+
+ //! Returns amplitudes vs. alpha_i for set of roughnesses
+// void test_roughness_set();
+ //! draw result of the test
+// void draw_roughness_set();
+
+ MultiLayer *mp_sample; //!< pointer to multilayer sample
+ OutputData<SpecularMatrix::MultiLayerCoeff_t > *mp_coeffs; //!< output data structure
+};
+
+
+
+#endif /* TESTSPECULARMATRIX_H_ */
diff --git a/App/src/FunctionalTestFactory.cpp b/App/src/FunctionalTestFactory.cpp
index 4ce7b9451045305d1cae33fad25a3fa13fc21754..b554fffdc4f0d7003eb81b4eee4f78599d730ffc 100644
--- a/App/src/FunctionalTestFactory.cpp
+++ b/App/src/FunctionalTestFactory.cpp
@@ -48,6 +48,7 @@
#include "TestPerformance.h"
#include "TestRootTree.h"
#include "TestRoughness.h"
+#include "TestSpecularMatrix.h"
#include "TestToySimulation.h"
#include "TBenchmark.h"
@@ -298,5 +299,9 @@ void RegisterFunctionalTests(FunctionalTestFactory *p_test_factory)
"FormFactors",
IFactoryCreateFunction<TestFormFactors, IFunctionalTest>,
"functional test: FormFactors");
+ p_test_factory->registerItem(
+ "specularmatrix",
+ IFactoryCreateFunction<TestSpecularMatrix, IFunctionalTest>,
+ "functional test: specular reflectivity with matrix formalism");
}
diff --git a/App/src/TestPerformance.cpp b/App/src/TestPerformance.cpp
index dc6b0a58d86523d7692af191800d30e427763497..ca49bee1f3a7ddc76137fcc9f8ab7ae8458d1bb6 100644
--- a/App/src/TestPerformance.cpp
+++ b/App/src/TestPerformance.cpp
@@ -1,5 +1,5 @@
// ************************************************************************** //
-//
+//
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file App/src/TestPerformance.cpp
@@ -32,6 +32,7 @@
#include <sstream>
#include <iomanip>
#include <time.h>
+#include "SpecularMatrix.h"
TestPerformance::TestPerformance()
{
@@ -40,6 +41,7 @@ TestPerformance::TestPerformance()
m_tests.push_back( new PerformanceTestInfo(new PerfTest_Pyramid(), 20) );
m_tests.push_back( new PerformanceTestInfo(new PerfTest_RotatedPyramid(), 20) );
m_tests.push_back( new PerformanceTestInfo(new PerfTest_MesoCrystal(), 2) );
+ m_tests.push_back( new PerformanceTestInfo(new PerfTest_SpecularMatrix(), 200000) );
std::cout << "TestPerformance::TestPerformance() -> Info. Preparing to run " << m_tests.size() << " performance tests." << std::endl;
}
@@ -115,7 +117,7 @@ void TestPerformance::write_performance()
file << std::left << Utils::AdjustStringLength(m_performance_info["sysinfo"],23) << get_delimeter();
for(performance_tests_t::iterator it=m_tests.begin(); it!= m_tests.end(); ++it) {
std::string test_name = (*it)->m_test->getName();
- file << std::left << Utils::AdjustStringLength(m_performance_info[test_name],7) << get_delimeter();
+ file << std::left << Utils::AdjustStringLength(m_performance_info[test_name],11) << get_delimeter();
}
file<<std::endl;
@@ -179,6 +181,28 @@ void PerfTest_FresnelCoeff::execute()
FresnelCalculator.execute(*ml, kvec, coeffs);
}
+//! Start PerfTest_SpecularMatrix.
+
+void PerfTest_SpecularMatrix::initialise(ProgramOptions *p_options)
+{
+ IFunctionalTest::initialise(p_options);
+ if(m_sample) delete m_sample;
+ m_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample("SimpleMultilayer"));
+}
+
+//! Run PerfTest_SpecularMatrix.
+
+void PerfTest_SpecularMatrix::execute()
+{
+ static double alpha_i = -0.3;
+ kvector_t kvec;
+ kvec.setLambdaAlphaPhi(1.54*Units::angstrom, -alpha_i, 0.0);
+ SpecularMatrix::MultiLayerCoeff_t coeffs;
+ SpecularMatrix matrixCalculator;
+ MultiLayer *ml = dynamic_cast<MultiLayer *>(m_sample);
+ matrixCalculator.execute(*ml, kvec, coeffs);
+}
+
//! Start PerfTest_Pyramid.
void PerfTest_Pyramid::initialise(ProgramOptions *p_options)
diff --git a/App/src/TestSpecularMatrix.cpp b/App/src/TestSpecularMatrix.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b994dc636c257c39fcfacedf800a110b3675f73c
--- /dev/null
+++ b/App/src/TestSpecularMatrix.cpp
@@ -0,0 +1,192 @@
+// ************************************************************************** //
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file App/src/TestSpecularMatrix.cpp
+//! @brief Implements class TestSpecularMatrix.
+//!
+//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//! @authors Scientific Computing Group at MLZ Garching
+//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
+//
+// ************************************************************************** //
+
+#include "TestSpecularMatrix.h"
+
+#include "SampleFactory.h"
+#include "Units.h"
+#include "TCanvas.h"
+#include "TGraph.h"
+#include "DrawHelper.h"
+#include "TH1F.h"
+#include "TLegend.h"
+
+
+TestSpecularMatrix::TestSpecularMatrix()
+: mp_sample(0)
+, mp_coeffs(0)
+{
+ std::cout << "TestSpecularMatrix::TestSpecularMatrix() -> Info." << std::endl;
+}
+
+void TestSpecularMatrix::execute()
+{
+ std::cout << "TestSpecularMatrix::execute() -> Info." << std::endl;
+
+ // calculate amplitudes for several standard multi-layer samples
+ test_standard_samples();
+}
+
+void TestSpecularMatrix::test_standard_samples()
+{
+ std::vector<std::string > snames;
+ snames.push_back("MultilayerOffspecTestcase1a");
+
+ // loop over standard samples defined in SampleFactory and StandardSamples
+ for(size_t i_sample=0; i_sample<snames.size(); i_sample++){
+ mp_sample = dynamic_cast<MultiLayer *>(SampleFactory::createSample(snames[i_sample]));
+
+ mp_coeffs = new OutputData<SpecularMatrix::MultiLayerCoeff_t >;
+ mp_coeffs->addAxis(std::string("alpha_i"), 2000, 0.0*Units::degree, 2.0*Units::degree);
+ OutputData<SpecularMatrix::MultiLayerCoeff_t >::iterator it = mp_coeffs->begin();
+ while (it != mp_coeffs->end()) {
+ double alpha_i = mp_coeffs->getValueOfAxis("alpha_i", it.getIndex());
+ kvector_t kvec;
+ kvec.setLambdaAlphaPhi(1.54*Units::angstrom, -alpha_i, 0.0);
+
+ SpecularMatrix::MultiLayerCoeff_t coeffs;
+ SpecularMatrix matrixCalculator;
+ matrixCalculator.execute(*mp_sample, kvec, coeffs);
+
+ *it = coeffs;
+ ++it;
+
+ } // alpha_i
+
+ draw_standard_samples();
+
+ delete mp_sample;
+ delete mp_coeffs;
+ } // i_sample
+}
+
+void TestSpecularMatrix::draw_standard_samples()
+{
+ static int ncall = 0;
+
+ size_t nlayers = mp_sample->getNumberOfLayers();
+
+ // graphics for R,T coefficients in layers as a function of alpha_i
+ size_t ncoeffs = 2;
+ enum key_coeffs { kCoeffR, kCoeffT};
+ const char *coeffs_title[]={" |R| "," |T| "};
+ int coeffs_color[] = {kBlue, kRed};
+
+ std::vector<std::vector<TGraph *> > gr_coeff; // [nlayers][ncoeffs]
+ gr_coeff.resize(nlayers);
+ for(size_t i_layer=0; i_layer<nlayers; i_layer++) {
+ gr_coeff[i_layer].resize(ncoeffs,0);
+ for(size_t i_coeff=0; i_coeff<ncoeffs; i_coeff++) {
+ gr_coeff[i_layer][i_coeff] = new TGraph();
+ }
+ }
+ TGraph *gr_absSum = new TGraph(); // |R_top|+|T_bottom|
+
+ OutputData<SpecularMatrix::MultiLayerCoeff_t >::const_iterator it = mp_coeffs->begin();
+ int i_point = 0;
+ while (it != mp_coeffs->end()) {
+ double alpha_i = mp_coeffs->getValueOfAxis("alpha_i", it.getIndex());
+ const SpecularMatrix::MultiLayerCoeff_t coeffs = *it++;
+
+ // Filling graphics for R,T as a function of alpha_i
+ for(size_t i_layer=0; i_layer<nlayers; ++i_layer ) {
+ gr_coeff[i_layer][kCoeffR]->SetPoint(i_point, Units::rad2deg(alpha_i), std::abs(coeffs[i_layer].R()) );
+ gr_coeff[i_layer][kCoeffT]->SetPoint(i_point, Units::rad2deg(alpha_i), std::abs(coeffs[i_layer].T()) );
+ }
+
+ // Filling graphics for |R|+|T| as a function of alpha_i taking R from the top and T from the bottom layers
+ int nlast = (int)nlayers - 1;
+ double sum;
+ if(coeffs[0].lambda.real()!=0.0) {
+ sum = std::norm(coeffs[0].R()) + std::norm(coeffs[nlast].T())*coeffs[nlast].lambda.real()/coeffs[0].lambda.real();
+ } else {
+ sum = 1.0;
+ std::cout << "Re(k_{z,0}) = 0 for alpha_i = " << alpha_i << std::endl;
+ std::cout << " and Re(k_{z,N+1}) = " << coeffs[nlast].lambda.real() << std::endl;
+ }
+ gr_absSum->SetPoint(i_point++, Units::rad2deg(alpha_i), sum);
+ }
+
+ // create name of canvas different for each new call of this method
+ std::ostringstream os;
+ os << (ncall++) << std::endl;
+ std::string cname = std::string("c1_test_Fresnel_sample")+os.str();
+ TCanvas *c1 = new TCanvas(cname.c_str(),"Fresnel Coefficients in Multilayer",1024,768);
+ DrawHelper::SetMagnifier(c1);
+
+ // estimate subdivision of canvas (we need place for 'nlayers' and for one sample picture)
+ int ndiv(2);
+ if( nlayers+1 > 4 ) ndiv = int(sqrt(nlayers+1)+1);
+ c1->Divide(ndiv,ndiv);
+
+ for(size_t i_layer=0; i_layer<nlayers; i_layer++) {
+ c1->cd((int)i_layer+1);
+ gPad->SetLogy();
+
+ // calculating histogram limits common for all graphs on given pad
+ double xmin(0), ymin(0), xmax(0), ymax(0);
+ for(size_t i_coeff=0; i_coeff<ncoeffs; i_coeff++){
+ double x1(0), y1(0), x2(0), y2(0);
+ gr_coeff[i_layer][kCoeffT]->ComputeRange(x1, y1, x2, y2);
+ if(x1 < xmin ) xmin= x1;
+ if(x2 > xmax ) xmax = x2;
+ if(y1 < ymin ) ymin = y1;
+ if(y2 > ymax ) ymax = y2;
+ }
+ TH1F h1ref("h1ref","h1ref",100, xmin, xmax);
+ h1ref.SetMinimum(1e-6);
+ h1ref.SetMaximum(10);
+ h1ref.SetStats(0);
+ h1ref.SetTitle("");
+ h1ref.GetXaxis()->SetTitle("angle, deg");
+ h1ref.GetYaxis()->SetTitle("|R|, |T|");
+ h1ref.DrawCopy();
+
+ TLegend *leg = new TLegend(0.725,0.7,0.89,0.88);
+ leg->SetTextSize(0.04);
+ leg->SetBorderSize(1);
+ leg->SetFillStyle(0);
+ std::ostringstream os;
+ os << " layer #" << i_layer;
+ leg->SetHeader(os.str().c_str());
+
+ for(size_t i_coeff=0; i_coeff<ncoeffs; i_coeff++) {
+ TGraph *gr = gr_coeff[i_layer][i_coeff];
+ gr->SetLineColor( coeffs_color[i_coeff] );
+ gr->SetMarkerColor( coeffs_color[i_coeff] );
+ gr->SetMarkerStyle(21);
+ gr->SetMarkerSize(0.2);
+ gr->Draw("pl same");
+ leg->AddEntry(gr, coeffs_title[i_coeff],"pl");
+ }
+ leg->Draw();
+ }
+ TGraph *gr = gr_absSum;
+ gr->SetMarkerStyle(21);
+ gr->SetMarkerSize(0.2);
+ gr->SetLineColor(kMagenta);
+ gr->SetMarkerColor(kMagenta);
+ gr->Draw("pl same");
+ TLegend *leg = new TLegend(0.625,0.6,0.89,0.69);
+ leg->SetTextSize(0.04);
+ leg->SetBorderSize(0);
+ leg->SetFillStyle(0);
+ leg->AddEntry(gr, "|R_top|+|T_bottom|","pl");
+ leg->Draw();
+
+ // drawing sample geometry
+ c1->cd((int)nlayers+1);
+ DrawHelper::DrawMultilayer(mp_sample);
+}
diff --git a/BornAgain.pro b/BornAgain.pro
index 8dc7f80ec2c797baff81636c18f3f6a31c6b07a4..b3a2923311365bd85349b932a3dfdc792571e398 100644
--- a/BornAgain.pro
+++ b/BornAgain.pro
@@ -16,4 +16,4 @@ SUBDIRS += Tests/UnitTests/TestCore
TestCore.depends = ThirdParty/gtest
TestCore.depends = ThirdParty/gtest
-CONFIG += ordered # comiplation in lister order
+CONFIG += ordered # compilation in lister order
diff --git a/Core/Algorithms/inc/SpecularMatrix.h b/Core/Algorithms/inc/SpecularMatrix.h
new file mode 100644
index 0000000000000000000000000000000000000000..b0b988bbb0272eb5da9d93edf8269cbbc9591957
--- /dev/null
+++ b/Core/Algorithms/inc/SpecularMatrix.h
@@ -0,0 +1,75 @@
+// ************************************************************************** //
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file Algorithms/inc/SpecularMatrix.h
+//! @brief Defines class SpecularMatrix.
+//!
+//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//! @authors Scientific Computing Group at MLZ Garching
+//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
+//
+// ************************************************************************** //
+
+#ifndef SPECULARMATRIX_H_
+#define SPECULARMATRIX_H_
+
+#include "Types.h"
+#include "ISimulation.h"
+#include "MultiLayer.h"
+
+#include "Eigen/Core"
+
+//! Implements the matrix formalism for the calculation of wave amplitudes of
+//! the coherent wave solution in a multilayer
+
+class SpecularMatrix : public ISimulation
+{
+public:
+ SpecularMatrix() : m_use_roughness(false) { (void)m_use_roughness; }
+
+ //! layer coefficients for matrix formalism
+ class LayerMatrixCoeff {
+ public:
+ LayerMatrixCoeff() : lambda(0) {}
+ ~LayerMatrixCoeff() {}
+ complex_t R() const { return (phi_psi(1)+phi_psi(0)/lambda)/2.0; }
+ complex_t T() const { return (phi_psi(1)-phi_psi(0)/lambda)/2.0; }
+ // A - amplitude of initial wave, R, T - amplitudes of reflected and transmitted waves
+ complex_t lambda; // positive eigenvalue of transfer matrix
+ Eigen::Vector2cd phi_psi;
+ Eigen::Matrix2cd l;
+ Eigen::Matrix2cd l_accumulated;
+ };
+
+ //! multi layer coefficients for matrix formalism
+ class MultiLayerMatrixCoeff
+ {
+ public:
+ inline LayerMatrixCoeff& operator[](size_t i) { return m_data[i]; }
+ inline const LayerMatrixCoeff& operator[](size_t i) const { return m_data[i]; }
+ inline size_t size() const { return m_data.size(); }
+ inline void clear() { m_data.clear(); }
+ inline void resize(size_t size) { m_data.resize(size); }
+ complex_t R; // total reflection coefficient
+ Eigen::Matrix2cd L;
+ private:
+ std::vector<LayerMatrixCoeff > m_data;
+ };
+
+ typedef MultiLayerMatrixCoeff MultiLayerCoeff_t; // set of layer coefficients for matrix formalism
+
+ //! Returns Fresnel coefficients for given multi layer and kvector
+ void execute(const MultiLayer& sample, const kvector_t& k, MultiLayerCoeff_t& coeff);
+
+private:
+ bool m_use_roughness;
+
+ void calculateEigenvalues(const MultiLayer& sample, const kvector_t& k, MultiLayerCoeff_t& coeff) const;
+ void calculateTransferMatrices(const MultiLayer& sample, const kvector_t& k, MultiLayerCoeff_t& coeff) const;
+ void calculateBoundaryValues(MultiLayerCoeff_t& coeff) const;
+};
+
+#endif /* SPECULARMATRIX_H_ */
diff --git a/Core/Algorithms/src/OpticalFresnel.cpp b/Core/Algorithms/src/OpticalFresnel.cpp
index c1e136345c14e6a8d11ce3ddfda5140be2f69fc1..172dc5dd22264b98bff2d95d1b8669e93f190e8d 100644
--- a/Core/Algorithms/src/OpticalFresnel.cpp
+++ b/Core/Algorithms/src/OpticalFresnel.cpp
@@ -68,12 +68,14 @@ void OpticalFresnel::execute(const MultiLayer& sample, const kvector_t& kvec, Mu
void OpticalFresnel::calculateKZ(const MultiLayer& sample, const kvector_t& kvec, MultiLayerCoeff_t& coeff) const
{
// z-component of reflected wave vector inside each layer
- // Q_{z,j}& = 2k_{z,j} = 2\cdot \sqrt{ k^2 n_j^2 - k_x^2 }
+ // k is the vacuum wave number
+ // Q_{z,j}& = 2k_{z,j} = 2\cdot \sqrt{ k^2 n_j^2 - k_x^2 n_0^2 }
+ // top layer refractive index:
+ complex_t rindex0 = sample.getLayer(0)->getRefractiveIndex();
+ complex_t rindex0_squared = rindex0*rindex0;
for(size_t i=0; i<coeff.size(); ++i) {
complex_t rindex = sample.getLayer(i)->getRefractiveIndex();
- //coeff[i].kz = std::sqrt( kvec.mag2()*rindex*rindex - kvec.magxy()*kvec.rho() );
- //coeff[i].kz = std::sqrt( kvec.mag2()*rindex*rindex - kvec.perp2() );
- coeff[i].kz = std::sqrt( kvec.mag2()*rindex*rindex - kvec.magxy2() );
+ coeff[i].kz = std::sqrt( kvec.mag2()*rindex*rindex - kvec.magxy2()*rindex0_squared );
}
}
@@ -158,7 +160,7 @@ void OpticalFresnel::calculateX2(const MultiLayer& sample, MultiLayerCoeff_t& co
for(int i=(int)coeff.size()-2; i>=0; --i) {
// first check for infinity
if(std::abs(coeff[i].r*coeff[i+1].X + complex_t(1,0)) < Numeric::double_epsilon) {
- throw DivisionByZeroException("Division by zer during calculation of X_i");
+ throw DivisionByZeroException("Division by zero during calculation of X_i");
}
double d = i==0 ? 0.0 : sample.getLayerThickness(i);
complex_t exp_factor;
diff --git a/Core/Algorithms/src/SpecularMatrix.cpp b/Core/Algorithms/src/SpecularMatrix.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..07b0c097f6b967e6269da7078c4ac09a2b936632
--- /dev/null
+++ b/Core/Algorithms/src/SpecularMatrix.cpp
@@ -0,0 +1,84 @@
+// ************************************************************************** //
+//
+// BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file Algorithms/src/SpecularMatrix.cpp
+//! @brief Implements class SpecularMatrix.
+//!
+//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
+//! @license GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2013
+//! @authors Scientific Computing Group at MLZ Garching
+//! @authors C. Durniak, G. Pospelov, W. Van Herck, J. Wuttke
+//
+// ************************************************************************** //
+
+
+#include "SpecularMatrix.h"
+
+void SpecularMatrix::execute(const MultiLayer& sample, const kvector_t& k,
+ MultiLayerCoeff_t& coeff)
+{
+ coeff.clear();
+ coeff.resize(sample.getNumberOfLayers());
+
+ calculateEigenvalues(sample, k, coeff);
+
+ calculateTransferMatrices(sample, k, coeff);
+
+ calculateBoundaryValues(coeff);
+}
+
+void SpecularMatrix::calculateEigenvalues(const MultiLayer& sample,
+ const kvector_t& k, MultiLayerCoeff_t& coeff) const
+{
+ double sinalpha = std::abs( k.cosTheta() );
+ double cosalpha2 = 1.0 - sinalpha*sinalpha;
+ complex_t rindex0 = sample.getLayer(0)->getRefractiveIndex();
+ complex_t r2cosalpha2 = rindex0*rindex0*cosalpha2;
+ for(size_t i=0; i<coeff.size(); ++i) {
+ complex_t rindex = sample.getLayer(i)->getRefractiveIndex();
+ coeff[i].lambda = std::sqrt(rindex*rindex - r2cosalpha2);
+ }
+}
+
+void SpecularMatrix::calculateTransferMatrices(const MultiLayer& sample,
+ const kvector_t& k, MultiLayerCoeff_t& coeff) const
+{
+ // Layer 0 gets identity matrix:
+ coeff[0].l.setIdentity();
+ coeff.L.setIdentity();
+ for(size_t i=1; i<coeff.size()-1; ++i) {
+ complex_t lambda = coeff[i].lambda;
+ complex_t kdlambda = k.mag()*sample.getLayer(i)->getThickness()*lambda;
+ complex_t cosine_term = std::cos(kdlambda);
+ complex_t sine_term =
+ ( std::abs(kdlambda) < Numeric::double_epsilon ) ?
+ k.mag()*sample.getLayer(i)->getThickness() :
+ std::sin(kdlambda)/lambda;
+ coeff[i].l(0,0) = cosine_term;
+ coeff[i].l(0,1) = -complex_t(0.0, 1.0)*lambda*lambda*sine_term;
+ coeff[i].l(1,0) = -complex_t(0.0, 1.0)*sine_term;
+ coeff[i].l(1,1) = cosine_term;
+ coeff.L = coeff[i].l * coeff.L;
+ }
+ // Last layer also gets identity matrix:
+ size_t N = coeff.size();
+ coeff[N-1].l.setIdentity();
+}
+
+void SpecularMatrix::calculateBoundaryValues(MultiLayerCoeff_t& coeff) const
+{
+ complex_t lambda0 = coeff[0].lambda;
+ size_t N = coeff.size();
+ complex_t lambdaN = coeff[N-1].lambda;
+ complex_t denominator = (lambda0*coeff.L(0,0) + coeff.L(0,1) + lambdaN*(lambda0*coeff.L(1,0) + coeff.L(1,1)));
+ coeff.R = (lambda0*coeff.L(0,0) - coeff.L(0,1) + lambdaN*(lambda0*coeff.L(1,0) - coeff.L(1,1)))/denominator;
+ // Boundary values at bottom of top layer
+ // and top of first layer:
+ coeff[1].phi_psi(0) = coeff[0].phi_psi(0) = lambda0*(coeff.R - 1.0);
+ coeff[1].phi_psi(1) = coeff[0].phi_psi(1) = coeff.R + 1.0;
+ for(size_t i=2; i<coeff.size(); ++i) {
+ coeff[i].phi_psi = coeff[i-1].l*coeff[i-1].phi_psi;
+ }
+}
diff --git a/Core/Core.pro b/Core/Core.pro
index 4e5d541cffe1369f33ac43f3dfe163c017841c6e..fead580a35efa7d3b2d94a3051642c7d301187fa 100644
--- a/Core/Core.pro
+++ b/Core/Core.pro
@@ -72,6 +72,7 @@ SOURCES += \
Algorithms/src/ResolutionFunction2DSimple.cpp \
Algorithms/src/Simulation.cpp \
Algorithms/src/SizeSpacingCorrelationApproximationStrategy.cpp \
+ Algorithms/src/SpecularMatrix.cpp \
Algorithms/src/StrategyBuilder.cpp \
\
FormFactors/src/FormFactorBox.cpp \
@@ -219,6 +220,7 @@ HEADERS += \
Algorithms/inc/Simulation.h \
Algorithms/inc/SimulationParameters.h \
Algorithms/inc/SizeSpacingCorrelationApproximationStrategy.h \
+ Algorithms/inc/SpecularMatrix.h \
Algorithms/inc/StrategyBuilder.h \
Algorithms/inc/ThreadInfo.h \
\
diff --git a/dev-tools/log/perf_history.txt b/dev-tools/log/perf_history.txt
index d0d52e739f7ce8656e2bdc7681208d3f2f6533ed..cf9e623a2a2d08cbbf0147658288af16426caf3d 100644
--- a/dev-tools/log/perf_history.txt
+++ b/dev-tools/log/perf_history.txt
@@ -1,4 +1,4 @@
-# date and time | hostname | system information | FresnelCoeff Pyramid RotatedPyramid MesoCrystal
+# date and time | hostname | system information | FresnelCoeff Pyramid RotatedPyramid MesoCrystal Matrix Method
2012-07-24 18:21:18 | jcnsopc73 | macosx64, 2800 MHz | 82987.5 | 4.14079 | 3.89105 | 0.23391 |
2012-07-24 18:22:36 | jcnsopc73 | macosx64, 2800 MHz | 82987.5 | 4.14938 | 3.91389 | 0.23391 |
@@ -244,3 +244,5 @@
2013-04-08 20:48:26 | jcnsops73 | macosx64, 2800 MHz | 294118 | 21.978 | 22.7273 | 6.25 |
2013-04-08 20:48:32 | jcnsops73 | macosx64, 2800 MHz | 289855 | 22.2222 | 22.7273 | 6.06061 |
+# added performance method for matrix calculation of layer wave amplitudes
+2013-05-07 16:05:21 | jcnsopc74 | macosx64, 2800 MHz | 294118 | 11.976 | 11.976 | 3.63636 | 1.05263e+06 |
diff --git a/shared.pri b/shared.pri
index bfa23a29031ff9249b349ed23ce6fbb7d92c1d48..cfa5c631b8ecfd1b1dc77dfe640b314bd55873ce 100644
--- a/shared.pri
+++ b/shared.pri
@@ -33,6 +33,13 @@ INCLUDEPATH *= $${GSL_INCLUDE}
LIBS *= -L$${GSL_LIB}
LIBS += -lgsl -lgslcblas
+# --- checking eigen headers ---
+EIGEN_HEADERFILE = Eigen/Core
+EIGEN_HEADER_LOCATIONS = /opt/local/include /usr/local/include /usr/include
+for(dir, EIGEN_HEADER_LOCATIONS): isEmpty(EIGEN_INCLUDE): exists($${dir}/$${EIGEN_HEADERFILE}): EIGEN_INCLUDE = $${dir}
+isEmpty(EIGEN_INCLUDE): message("Can't find" $${EIGEN_HEADERFILE} "in" $${EIGEN_HEADER_LOCATIONS})
+INCLUDEPATH *= $${EIGEN_INCLUDE}
+
# --- checking fftw3 ---
FFTW3_HEADERFILE = fftw3.h
FFTW3_HEADER_LOCATIONS = /opt/local/include /usr/local/include /usr/include