Adjusted relative paths of CMakeLists.txt

.gitignore

@@ -26,3 +26,4 @@ cmake/CMakeFiles/
 *.dat
 *.ipynb_checkpoints
 *.idea
+*.vscode

CHANGELOG.md

@@ -5,6 +5,7 @@
 * Fixed r term in source distribution for SNR and Pulsar
 * Fixed wrong mass inheritance for secondaries other than nuclei or electron/positron
 * Fixed wrong generation of interval ranges in ObserverTimeEvolution
+* Improved CMakeLists.txt to better work as submodule on other cpp based projects
 
 ### New features:
 

cmake/FindGooglePerfTools.cmake

@@ -7,7 +7,7 @@
 #  STACKTRACE_LIBRARIES, where to find the stacktrace library.
 #  PROFILER_LIBRARIES, where to find the profiler library.
 
-FIND_PATH(GOOGLE_PERFTOOLS_INCLUDE_DIR google/heap-profiler.h)
+FIND_PATH(GOOGLE_PERFTOOLS_INCLUDE_DIR NAMES google/heap-profiler.h gperftools/heap-profiler.h)
 
 SET(TCMALLOC_NAMES ${TCMALLOC_NAMES} tcmalloc)
 FIND_LIBRARY(TCMALLOC_LIBRARY  NAMES ${TCMALLOC_NAMES})

doc/pages/Cpp-projects.md

@@ -1,49 +1,49 @@
 ## Using CRPropa from C++
 Although is highly recommended to use and [to extend](Extending CRPropa) CRPropa with the default Python binding, there is also a possibility to use it within a C++ code when Python or SWIG are not available or desirable.
 
-To include CRPropa classes and definitions it is sufficient to include ``crpropa/CRPropa.h``, example:
+To include CRPropa classes and definitions it is sufficient to include ``CRPropa.h``, example:
 
 ```c++
-#include "crpropa/CRPropa.h"
+#include "CRPropa.h"
 
 using namespace crpropa;
 
 int main(void) {
 
-        ModuleList sim;
-        sim.add(new SimplePropagation(1*kpc, 10*Mpc));
-        sim.add(new Redshift());
-        sim.add(new PhotoPionProduction(CMB));
-        sim.add(new PhotoPionProduction(IRB));
-        sim.add(new PhotoDisintegration(CMB));
-        sim.add(new PhotoDisintegration(IRB));
-        sim.add(new NuclearDecay());
-        sim.add(new ElectronPairProduction(CMB));
-        sim.add(new ElectronPairProduction(IRB));
-        sim.add(new MinimumEnergy(1*EeV));
-
-        ref_ptr<Observer> obs = new Observer();
-        obs->add(new Observer1D());
-        obs->onDetection(new TextOutput("events.txt", Output::Event1D));
-        obs->onDetection(new TextOutput());
-        sim.add(obs);
-
-        ref_ptr<Source> source = new Source();
-        source->add(new SourceUniform1D(1*Mpc, 1000*Mpc));
-        source->add(new SourceRedshift1D());
-
-        ref_ptr<SourceComposition> composition =
-            new SourceComposition(1*EeV, 100*EeV, -1);
-        composition->add(1,  1,  1);
-        composition->add(4,  2,  1);
-        composition->add(14, 7,  1);
-        composition->add(56, 26, 1);
-        source->add(composition);
-
-        sim.setShowProgress(true);
-        sim.run(source, 2000, true);
-
-        return 0;
+	ModuleList sim;
+	sim.add(new SimplePropagation(1*kpc, 10*Mpc));
+	sim.add(new Redshift());
+	sim.add(new PhotoPionProduction(new CMB()));
+	sim.add(new PhotoPionProduction(new IRB_Kneiske04()));
+	sim.add(new PhotoDisintegration(new CMB()));
+	sim.add(new PhotoDisintegration(new IRB_Kneiske04()));
+	sim.add(new NuclearDecay());
+	sim.add(new ElectronPairProduction(new CMB()));
+	sim.add(new ElectronPairProduction(new IRB_Kneiske04()));
+	sim.add(new MinimumEnergy(1*EeV));
+
+	ref_ptr<Observer> obs = new Observer();
+	obs->add(new Observer1D());
+	obs->onDetection(new TextOutput("events.txt", Output::Event1D));
+	obs->onDetection(new TextOutput());
+	sim.add(obs);
+
+	ref_ptr<Source> source = new Source();
+	source->add(new SourceUniform1D(1*Mpc, 1000*Mpc));
+	source->add(new SourceRedshift1D());
+
+	ref_ptr<SourceComposition> composition =
+		new SourceComposition(1*EeV, 100*EeV, -1);
+	composition->add(1,  1,  1);
+	composition->add(4,  2,  1);
+	composition->add(14, 7,  1);
+	composition->add(56, 26, 1);
+	source->add(composition);
+
+	sim.setShowProgress(true);
+	sim.run(source.get(), 2000, true);
+
+	return 0;
 }
 ```
 

doc/pages/Installation.md

@@ -38,12 +38,12 @@ The following packages are provided with the source code and do not need to be i
     mkdir build
     cd build
     cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/.local
-    make
-    make install
+    cmake --build .
+    cmake --install .
     ```
 
-2. A set of unit tests can be run with ```make test```. If the tests are
-   successful continue with ```make install``` to install CRPropa at the
+2. A set of unit tests can be run with ```ctest```. If the tests are
+   successful continue with ```cmake --install .``` to install CRPropa at the
    specified path, or leave it in the build directory.  Make sure the
    environment variables are set accordingly: e.g. for an installation under
    $HOME/.local and using Python 3 set
@@ -54,7 +54,7 @@ The following packages are provided with the source code and do not need to be i
     export PKG_CONFIG_PATH=$HOME/.local/lib/pkgconfig:$PKG_CONFIG_PATH
     ```
 
-However, we highly recommend to use a virtualenv setup to install CRPropa!
+However, we highly recommend to use a virtualenv or conda setup to install CRPropa!
 
 
 ### Installation in python virtualenv
@@ -117,11 +117,11 @@ worthwhile effort afterwards.
     mkdir build
     cd build
     CMAKE_PREFIX_PATH=$CRPROPA_DIR cmake -DCMAKE_INSTALL_PREFIX=$CRPROPA_DIR ..
-    make
-    make install
+    cmake --build .
+    cmake --install .
     ```
 
-5. A set of unit tests can be run with ```make test```. 
+5. A set of unit tests can be run with ```ctest```. 
 
 6. (optional) Check the installation.
     ```python

include/crpropa/module/TextOutput.h

@@ -70,6 +70,12 @@ class TextOutput: public Output {
 	 @param collector	object of type ParticleCollector that will store the information
 	 */
 	static void load(const std::string &filename, ParticleCollector *collector);
+	/** Loads a stream to a particle collector.
+	 This is useful for analysis involving, e.g., magnetic lenses.
+	 @param in	stream containing the data to be loaded in the same format TextOutput outputs the data
+	 @param collector	object of type ParticleCollector that will store the information
+	 */
+	static void load(std::istream &in, ParticleCollector *collector);
 	std::string getDescription() const;
 
 	void dumpIndexList(std::vector<int> indicies);

src/Common.cpp

@@ -58,6 +58,18 @@ std::string getDataPath(std::string filename) {
 		}
 	}
 
+#ifdef CRPROPA_BINARY_DIR
+	{
+		std::string _path = CRPROPA_BINARY_DIR "/data";
+		if (is_directory(_path)) {
+			dataPath = _path;
+			KISS_LOG_INFO
+			<< "getDataPath: use binary path, " << dataPath << std::endl;
+			return concat_path(dataPath, filename);
+		}
+	}
+#endif
+
 	dataPath = "data";
 	KISS_LOG_INFO << "getDataPath: use default, " << dataPath << std::endl;
 	return removeNullCharacter(concat_path(dataPath, filename));

src/magneticField/turbulentField/PlaneWaveTurbulence.cpp

@@ -59,7 +59,7 @@
 
 #ifdef ENABLE_FAST_WAVES
 #include <immintrin.h>
-#include <memory.h>
+#include <memory>
 #endif
 
 namespace crpropa {

src/module/TextOutput.cpp

@@ -291,29 +291,35 @@ void TextOutput::process(Candidate *c) const {
 }
 
 void TextOutput::load(const std::string &filename, ParticleCollector *collector){
-
-	std::string line;
 	std::istream *in;
 	std::ifstream infile(filename.c_str());
-
-	Output output;
-	double lengthScale = output.getLengthScale();
-	double timeScale = output.getTimeScale();
-	double energyScale = output.getEnergyScale();
 
 	if (!infile.good())
 		throw std::runtime_error("crpropa::TextOutput: could not open file " + filename);
 	in = &infile;
-	
-	if (kiss::ends_with(filename, ".gz")){
+
+		if (kiss::ends_with(filename, ".gz")){
 #ifdef CRPROPA_HAVE_ZLIB
 		in = new zstream::igzstream(*in);
 #else
 		throw std::runtime_error("CRPropa was built without Zlib compression!");
 #endif
 	}
 
-	while (std::getline(*in, line)) {
+	load(*in, collector);
+	infile.close();
+}
+
+void TextOutput::load(std::istream &in, ParticleCollector *collector){
+
+	std::string line;
+
+	Output output;
+	double lengthScale = output.getLengthScale();
+	double timeScale = output.getTimeScale();
+	double energyScale = output.getEnergyScale();
+
+	while (std::getline(in, line)) {
 		std::stringstream stream(line);
 		if (stream.peek() == '#')
 			continue;
@@ -360,7 +366,6 @@ void TextOutput::load(const std::string &filename, ParticleCollector *collector)
 
 		collector->process(c);
 	}
-	infile.close();
 }
 
 std::string TextOutput::getDescription() const {