Merge branch 'v3'

.config.mk.ci.clang

@@ -5,7 +5,7 @@ CXX = clang++
 
  DEBUG += -g                # Adds debug symbols
 
-LOGGING += -D INFO_                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
+LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour but might 
 
 #=================================================================================================
 # External libraries

.config.mk.ci.gcc

@@ -7,8 +7,6 @@ STRICT_WARNINGS = TRUE
 
  DEBUG += -g                # Adds debug symbols
 
-LOGGING += -D INFO_                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
-
 #=================================================================================================
 # External libraries
 #=================================================================================================
@@ -16,7 +14,4 @@ BLAS_LIBRARIES = -lopenblas -lgfortran                    # Openblas, serial
 LAPACK_LIBRARIES = -llapacke -llapack                     # Standard Lapack + Lapacke libraries
 SUITESPARSE = -lcholmod  -lspqr
 
-
-# custom include paths
-# OTHER += -I /path/to/include
-
+OTHER += -I /usr/include/python2.7/ -lboost_python -I/usr/lib64/python2.7/site-packages/numpy/core/include/ -lpython2.7 -fno-var-tracking-assignments
\ No newline at end of file

.config.mk.ci.gcc.nocheck

@@ -6,13 +6,13 @@ CXX = g++
 STRICT_WARNINGS = TRUE
 
 HIGH_OPTIMIZATION = TRUE          # Activates -O3 -march=native and some others
-DEBUG += -D DISABLE_RUNTIME_CHECKS_    # Disable all runtime checks
-DEBUG += -D REPLACE_ALLOCATOR
+DEBUG += -D XERUS_DISABLE_RUNTIME_CHECKS    # Disable all runtime checks
+DEBUG += -D XERUS_REPLACE_ALLOCATOR
 
  DEBUG += -g                # Adds debug symbols
 
 
-LOGGING += -D INFO_                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
+LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour bu
 
 #=================================================================================================
 # External libraries

.gitignore

@@ -13,12 +13,19 @@
 
 !*.mk
 !Makefile
+!.gitignore
 
 !*.sh
 
+!*.rb
+!*.py
+
 !*.md
 !*.xml
 !*.dox
+!*.css
+!*.js
+!*.yml
 
 # ...even if they are in subdirectories
 !*/
@@ -26,6 +33,5 @@
 # However we really want to ignore
 lapacke/*
 build/*
-doc/latex/*
 doc/html/*
 config.mk

.gitlab-ci.yml

@@ -3,8 +3,10 @@ stages:
 - test_gcc
 - build_gcc_nocheck
 - test_gcc_nocheck
+- build_python
 - build_clang
 - test_clang
+- build_homepage
 
 job_make_gcc:
   stage: build_gcc
@@ -23,6 +25,11 @@ job_test_gcc_nocheck:
   stage: test_gcc_nocheck
   script: "cp ../XerusTest .; ./XerusTest all"
 
+job_build_python:
+  stage: build_python
+  script: "g++ --version; cp .config.mk.ci.gcc config.mk; make python"
+  when: always
+
 job_make_clang:
   stage: build_clang
   script: "clang++ --version; cp .config.mk.ci.clang config.mk; make XerusTest; cp XerusTest ../"
@@ -32,3 +39,10 @@ job_test_clang:
   stage: test_clang
   script: "cp ../XerusTest .; ./XerusTest all"
 
+job_build_homepage:
+  stage: build_homepage
+  script: "make doc; scp -rv doc/html xerusweb:libxerus.org-443/html"
+  when: always
+  only: 
+    - master
+  allow_failure: true

ChangeLog.md

@@ -2,6 +2,17 @@
 
 Potentially breaking changes are marked with an exclamation point '!' at the begin of their description.
 
+* 2017-05-29 v3.0.0
+ * Python wrapper now stable.
+ * ! REQUIRE macro now logs as error instead of fatal error.
+ * ! All macros and preprocessor defines now use the XERUS_ prefix. The config.mk file changed accordingly.
+ * ! TT::find_largest_entry and TT::dyadic_product left the TT scope.
+ * ! Tensor::modify_diag_elements renamed to Tensor::modify_diagonal_entries for naming consistency.
+ * Much faster solve of matrix equations Ax=b by exploiting symmetry and definiteness where possible. This directly speeds up the ALS as well.
+ * Added Tensor.one_norm() and one_norm(Tensor) to calculate the one norm of a Tensor.
+ * New documentation ('make doc') and homepage.
+ * Some minor bugfixes and performance improvements.
+
 * 2016-06-23 v2.4.0
  * Introduced nomeclature 'mode'. Marked all functions that will be renamed / removed in v3.0.0 as deprecated.
  * Added an experimental python wrapper when 'OTHER += -DXERUS_EXPERIMENTAL_PYTHON_WRAPPER' is defined in the config file.
@@ -18,7 +29,7 @@ Potentially breaking changes are marked with an exclamation point '!' at the beg
  * Bug fix in the handling of fixed indices in TensorNetworks.
  * Several static member function now warn if their return type is not used.
  * Initial support for compilation with the intel ICC.
- 
+
 * 2016-03-11 v2.2.1
  * Added support for 32bit systems.
 

VERSION

-2.4.0
+3.0.0

benchmark.cxx

 // Xerus - A General Purpose Tensor Library
-// Copyright (C) 2014-2016 Benjamin Huber and Sebastian Wolf. 
+// Copyright (C) 2014-2017 Benjamin Huber and Sebastian Wolf. 
 // 
 // Xerus is free software: you can redistribute it and/or modify
 // it under the terms of the GNU Affero General Public License as published
@@ -28,8 +28,7 @@
 
 #include "include/xerus.h"
 
-std::random_device rd;
-std::mt19937_64 rnd(rd());
+std::mt19937_64 rnd = xerus::misc::randomEngine;
 std::normal_distribution<double> normalDist(0,1);
 
 using namespace xerus;
@@ -61,12 +60,12 @@ struct LeastSquaresProblem {
 		return TTOperator::identity(dim);
 	}
 	virtual TTTensor get_x() const {
-		TTTensor x = TTTensor::random(dimensions, x_ranks, rnd, normalDist);
+		TTTensor x = TTTensor::random(dimensions, x_ranks, normalDist);
 		x /= frob_norm(x);
 		return x;
 	};
 	virtual TTTensor get_b() const {
-		TTTensor b = TTTensor::random(dimensions, b_ranks, rnd, normalDist);
+		TTTensor b = TTTensor::random(dimensions, b_ranks, normalDist);
 		b /= frob_norm(b);
 		return b;
 	};
@@ -98,7 +97,7 @@ namespace ls {
 		TTOperator get_a() const override {
 			std::vector<size_t> dim(dimensions);
 			dim.insert(dim.end(), dimensions.begin(), dimensions.end());
-			TTOperator A = TTOperator::random(dim, a_ranks, rnd, normalDist);
+			TTOperator A = TTOperator::random(dim, a_ranks, normalDist);
 			A /= frob_norm(A);
 			return A;
 		}
@@ -119,7 +118,7 @@ namespace ls {
 		TTOperator get_a() const override {
 			std::vector<size_t> dim(dimensions);
 			dim.insert(dim.end(), dimensions.begin(), dimensions.end());
-			TTOperator A = TTOperator::random(dim, a_ranks, rnd, normalDist);
+			TTOperator A = TTOperator::random(dim, a_ranks, normalDist);
 			Index i,j,k;
 			A(i,j) = A(i,k) * A(j,k);
 			A /= frob_norm(A);
@@ -175,7 +174,7 @@ std::vector<LeastSquaresProblem> leastSquaresProblems{
 
 std::string generate_profile_name() {
 	std::string profileName;
-#ifdef TEST_COVERAGE_
+#ifdef XERUS_TEST_COVERAGE
 	static_assert(false, "test coverage checking nonsensical with benchmark run");
 #endif
 	
@@ -200,13 +199,13 @@ std::string generate_profile_name() {
 #ifdef USE_LTO
 	profileName += "_lto";
 #endif
-#ifdef DISABLE_RUNTIME_CHECKS_
+#ifdef XERUS_DISABLE_RUNTIME_CHECKS
 	profileName += "_noChecks";
 #endif
-#ifdef REPLACE_ALLOCATOR
+#ifdef XERUS_REPLACE_ALLOCATOR
 	profileName += "_replaceAlloc";
 #endif
-#ifdef PERFORMANCE_ANALYSIS
+#ifdef XERUS_PERFORMANCE_ANALYSIS
 	profileName += "_perfAnalysis";
 #endif
 	return profileName;

config.mk.default

@@ -7,6 +7,14 @@ CXX = g++
 # CXX = clang++
 
 
+#=================================================================================================
+# Library Options
+#=================================================================================================
+# Xerus offers python bindings through boost python, which can be build in a seperate library object
+# xerus.so
+# BUILD_PYTHON_BINDINGS = TRUE
+
+
 #=================================================================================================
 # Optimization
 #=================================================================================================
@@ -35,62 +43,57 @@ COMPILE_THREADS = 8						# Number of threads to use during link time optimizatio
 # The Xerus library performs a number of runtime checks to ensure a valid input to all routines.
 # While not recommended these runtime checks can be completly disabled by uncommenting the following
 # line. This slighlty improves the performance.
-# DEBUG += -D DISABLE_RUNTIME_CHECKS_	# Disable all runtime checks
-
-
-# In the default configuration xerus will throw exceptions if it encounters invalid inputs
-# or (hopefully never) suffers an internal error. For some debugging purposes however it is
-# more convinient to instruct xerus to directly exit in such cases.
-# NO_XERUS_EXCEPTIONS = TRUE			# Disable the use of exceptions by the xerus library
+# DEBUG += -D XERUS_DISABLE_RUNTIME_CHECKS	# Disable all runtime checks
 
 
 # With the following option the callstack that is returned by get_call_stack (and thus all fatal errors)
 # includes NO function names, source-filenames and line numbers.
 # NOTE: activate this to remove the dependence on the binutils libraries -lbfd -liberty -lz and -ldl
-# NO_FANCY_CALLSTACK = TRUE				# Show simple callstacks only
+# XERUS_NO_FANCY_CALLSTACK = TRUE				# Show simple callstacks only
 
 
 # When performing tests it is useful to ensure that all of the code in covered. This is ensured by
 # a set of macros including REQUIRE_TEST to mark lines that need to be tested. With the following
 # definition this coverage is tested.
-# DEBUG += -D TEST_COVERAGE_			# Enable coverage tests
+# DEBUG += -D XERUS_TEST_COVERAGE			# Enable coverage tests
 
 
 # Xerus uses many small objects (Indices, vectors of dimensions etc.) for which the standard allocator
 # is not very efficient. With the following option, an experimental replacement allocator will be 
 # included in the library, which will _globally_ replace the 'new' and 'delete' operators in your program.
 # Note also, that the replacement allocator is not (yet) thread safe!
-# DEBUG += -D REPLACE_ALLOCATOR
+# DEBUG += -D XERUS_REPLACE_ALLOCATOR
 
 
 # You can add all kind of debuging options. In the following are some examples
  DEBUG += -g							# Adds debug symbols
+# DEBUG += -D _GLIBCXX_ASSERTIONS			# Activate GLIBCXX assertions
  
 # Sanitization 
 # DEBUG += -fsanitize=undefined			# GCC only
 # DEBUG += -fsanitize=memory			# Clang only
 # DEBUG += -fsanitize=address			# find out of bounds access
+# DEBUG += -pg							# adds profiling code for the 'gprof' analyzer
 
 
 # Xerus has a buildin logging system to provide runtime information. Here you can adjust the logging level used by the library.
-# LOGGING += -D DEBUG_                  # Debug infomation, can significantly slow down the library.
-LOGGING += -D INFO_                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
-# LOGGING += -D WARNING_                # Informations that is linked to unexpected behaviour which indicates incorrect use of the library but are no errors as such.
-# LOGGING += -D ERROR_                  # Information about errors that occourt, assumedly by incorrect use of the library. 
-# LOGGING += -D CRITICAL_               # Information abount internal errors within the library.
+# LOGGING += -D XERUS_LOG_DEBUG                  # Debug infomation, can significantly slow down the library.
+LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
+# LOGGING += -D XERUS_LOG_WARNING                # Informations that is linked to unexpected behaviour which indicates incorrect use of the library but are no errors as such.
+# LOGGING += -D XERUS_LOG_ERROR                  # Information about errors that occourt, assumedly by incorrect use of the library. 
 
 # Per default the logs are printed to cerr. Uncomment the following line to print the log messages to the file error.log instead.
-# LOGGING += -D LOGFILE_				# Use error file instead of cerr
+# LOGGING += -D XERUS_LOGFILE				# Use error file instead of cerr
 
 # Print absolute times instead of relative to program time
-# LOGGING += -D LOG_ABSOLUTE_TIME
+# LOGGING += -D XERUS_LOG_ABSOLUTE_TIME
 
 # Uncomment the following line to save the last Logs in a circular buffer (without printing them) to allow detailed reports in case of errors.
 # Note that this can significatly slow down the library.
-# LOGGING += -D LOG_BUFFER_					# Activate the log buffer
+# LOGGING += -D XERUS_LOG_BUFFER					# Activate the log buffer
 
 # Add time measurments for the relevant low level function calls. This allow to use get_analysis() to get a listing on all called low level fucntions and the time spend on them.
-# LOGGING += -D PERFORMANCE_ANALYSIS 		# Enable performance analysis
+# LOGGING += -D XERUS_PERFORMANCE_ANALYSIS 		# Enable performance analysis
 
 
 #=================================================================================================
@@ -98,8 +101,9 @@ LOGGING += -D INFO_                     # Information that is not linked to any
 #=================================================================================================
 # Set the directories to install libxerus.
 
-INSTALL_LIB_PATH = /usr/local/lib64/		# Path where to install the libxerus.so shared library.
-INSTALL_HEADER_PATH = /usr/local/include/	# Path where to install the xerus header files.
+#INSTALL_LIB_PATH = /usr/local/lib64/		# Path where to install the libxerus.so shared library.
+#INSTALL_HEADER_PATH = /usr/local/include/	# Path where to install the xerus header files.
+#INSTALL_PYTHON_PATH = /usr/local/lib64/python2.7/site-packages/	# Path for the installation of the python bindings.
 
 
 #=================================================================================================
@@ -124,6 +128,8 @@ LAPACK_LIBRARIES = -llapacke -llapack							# Standard Lapack + Lapacke librarie
 # Uncomment or add the appropriate CXSparse library
 SUITESPARSE = -lcholmod -lspqr
 
+# Uncomment or add the appropriate boost python library
+BOOST_PYTHON = -lboost_python
 
 # Custom include paths
 # OTHER += -I /path/to/include

doc/Makefile

+# ------------------------------------------------------------------------------------------------------
+#				Default rule should be the help message
+# ------------------------------------------------------------------------------------------------------
+help:
+	@printf "Possible make targets are:\n \
+	\t\thelp \t\t -- Print this help.\n \
+	\t\tdoc \t\t -- Build the html documentation for the xerus library.\n \
+	\t\tserve \t\t -- Build the html documentation for the xerus library and offer it via 'jekyll serve'.\n \
+	\t\tclean \t\t -- Remove all documentation files.\n"
+
+doc:
+	-mkdir html
+	doxygen doxygen/Doxyfile
+	jekyll build --source jekyll/ --destination html/
+
+clean:
+	-rm -r html
+
+serve:
+	-mkdir html
+	doxygen doxygen/Doxyfile
+	jekyll serve --source jekyll/ --destination html/

doc/advanced.md

-# Notes for Advanced Users
-
-## Multi-Threading
-
-Please note, that `xerus` is only thread-safe up to 1024 threads at the time of this writing. This number is due to the internal handling of indices. To ensure that indices can 
-be compared and identified uniquely, they store a unique id of which the first 10 bits are reserved to denote the number of the current thread. With more than 1024 threads (when these
-10 bits overflow) it can thus lead to collisions and indices that were shared between threads and were meant to be seperate suddenly evaluate to be equal to all algorithms.
-
-

doc/Doxyfile → doc/doxygen/Doxyfile

@@ -51,7 +51,7 @@ PROJECT_BRIEF          = "a general purpose tensor library"
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           = xerus.svg
+PROJECT_LOGO           = doxygen/xerus.svg
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is
@@ -437,7 +437,7 @@ EXTRACT_PACKAGE        = YES
 # included in the documentation.
 # The default value is: NO.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -562,7 +562,7 @@ SORT_MEMBER_DOCS       = YES
 # this will also influence the order of the classes in the class list.
 # The default value is: NO.
 
-SORT_BRIEF_DOCS        = NO
+SORT_BRIEF_DOCS        = YES
 
 # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
 # (brief and detailed) documentation of class members so that constructors and
@@ -574,7 +574,7 @@ SORT_BRIEF_DOCS        = NO
 # detailed member documentation.
 # The default value is: NO.
 
-SORT_MEMBERS_CTORS_1ST = NO
+SORT_MEMBERS_CTORS_1ST = YES
 
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
 # of group names into alphabetical order. If set to NO the group names will
@@ -591,7 +591,7 @@ SORT_GROUP_NAMES       = NO
 # list.
 # The default value is: NO.
 
-SORT_BY_SCOPE_NAME     = NO
+SORT_BY_SCOPE_NAME     = YES
 
 # If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
 # type resolution of all parameters of a function it will reject a match between
@@ -687,7 +687,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            = 
+LAYOUT_FILE            = doxygen/DoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -708,7 +708,7 @@ CITE_BIB_FILES         =
 # messages are off.
 # The default value is: NO.
 
-QUIET                  = NO
+QUIET                  = YES
 
 # The WARNINGS tag can be used to turn on/off the warning messages that are
 # generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
@@ -740,7 +740,7 @@ WARN_IF_DOC_ERROR      = YES
 # parameter documentation, but not about the absence of documentation.
 # The default value is: NO.
 
-WARN_NO_PARAMDOC       = NO
+WARN_NO_PARAMDOC       = YES
 
 # The WARN_FORMAT tag determines the format of the warning messages that doxygen
 # can produce. The string should contain the $file, $line, and $text tags, which
@@ -768,8 +768,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = . \
-                         ../tutorials/ \
+INPUT                  = doxygen/ \
                          ../include/ \
                          ../include/xerus/ \
                          ../include/xerus/algorithms/ \
@@ -815,7 +814,7 @@ RECURSIVE              = NO
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = *.hxx
+EXCLUDE                = *.cxx
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -848,14 +847,14 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = ../tutorials/
+EXAMPLE_PATH           = 
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       = *
+EXAMPLE_PATTERNS       =
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
@@ -916,7 +915,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = mainpage.md
+USE_MDFILE_AS_MAINPAGE = doxygen/mainpage.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1045,7 +1044,7 @@ GENERATE_HTML          = YES
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = html/doxygen
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).
@@ -1072,7 +1071,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            = header.html
+HTML_HEADER            = doxygen/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1082,7 +1081,7 @@ HTML_HEADER            = header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            = footer.html
+HTML_FOOTER            = doxygen/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1094,7 +1093,7 @@ HTML_FOOTER            = footer.html
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        = stylesheet.css
+HTML_STYLESHEET        = doxygen/stylesheet.css
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
 # cascading style sheets that are included after the standard style sheets
@@ -1107,7 +1106,7 @@ HTML_STYLESHEET        = stylesheet.css
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  = DoxygenLayout.xml
+HTML_EXTRA_STYLESHEET  = doxygen/DoxygenLayout.xml
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1470,7 +1469,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = MathJax
+MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-MML-AM_CHTML
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
@@ -1580,7 +1579,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

doc/DoxygenLayout.xml → doc/doxygen/DoxygenLayout.xml

@@ -2,7 +2,8 @@
   <!-- Generated by doxygen 1.8.3 -->
   <!-- Navigation index tabs for HTML output -->
   <navindex>
-    <tab type="mainpage" visible="yes" title=""/>
+	<tab type="user" url="/" title="Xerus"/>  
+	<tab type="mainpage" visible="yes" title=""/>
     <tab type="pages" visible="yes" title="" intro=""/>
     <tab type="modules" visible="yes" title="" intro=""/>
     <tab type="namespaces" visible="yes" title="">
@@ -19,7 +20,8 @@
       <tab type="filelist" visible="yes" title="" intro=""/>
       <tab type="globals" visible="yes" title="" intro=""/>
     </tab>
-    <tab type="examples" visible="yes" title="" intro=""/>  
+    <tab type="user" url="/documentation.html" title="Documentation"/>  
+	<tab type="user" url="/examples.html" title="Examples"/>  
     <tab type="user" url="https://git.hemio.de/xerus/xerus" title="Git"/>
     <tab type="user" url="https://git.hemio.de/xerus/xerus/issues" title="Issue-Tracker"/>
   </navindex>

doc/doxygen/mainpage.md

+# xerus - a general purpose tensor library    {#mainpage}
+
+## Doxygen Documentation
+
+This is the (automatically generated) Doxygen documentation for the `xerus` library. It is the only complete documentation (ie.
+mentioning all classes and functions with at least a one-line description) but far less accessible than the documents of the
+[main documentation](/documentation.html) or even the [examples](/examples.html).
+
+It is advisable to use a modern IDE when working with any c++ source code, but in particular when using the `xerus` library. In 
+which case all of the information of this documentation should also be available from within your IDE as mouse-over text or similar.
+If your IDE does not provide this functionality consider switching to `kdevelop`, `clion` or a similarly advanced IDE.

doc/jekyll/.gitignore

+_site
+

doc/jekyll/_config.yml

+# Jekyll configuration
+
+name: Xerus Documentation
+description: Documentation for the xerus library.
+
+# baseurl will often be '', but for a project page on gh-pages, it needs to
+# be the project name.
+# *** IMPORTANT: If your local "jekyll serve" throws errors change this to '' or
+#     run it like so: jekyll serve --baseurl=''
+baseurl: ''
+
+permalink: /:title
+# paginate: 3
+
+highlighter: rouge
+# highlighter: coderay
+markdown: kramdown
+# gems: ['TabsConverter']
+
+# exclude: ['README.md', 'LICENSE']
+keep_files: ['doxygen']

doc/jekyll/_includes/examples/als.cpp

+#include <xerus.h>
+
+using namespace xerus;
+
+class InternalSolver {
+	const size_t d;
+	
+	std::vector<Tensor> leftAStack;
+	std::vector<Tensor> rightAStack;
+	
+	std::vector<Tensor> leftBStack;
+	std::vector<Tensor> rightBStack;
+	
+	TTTensor& x;
+	const TTOperator& A;
+	const TTTensor& b;
+	const double solutionsNorm;
+public:
+	size_t maxIterations;
+	
+	InternalSolver(const TTOperator& _A, TTTensor& _x, const TTTensor& _b) 
+		: d(_x.degree()), x(_x), A(_A), b(_b), solutionsNorm(frob_norm(_b)), maxIterations(1000)
+	{ 
+		leftAStack.emplace_back(Tensor::ones({1,1,1}));
+		rightAStack.emplace_back(Tensor::ones({1,1,1}));
+		leftBStack.emplace_back(Tensor::ones({1,1}));
+		rightBStack.emplace_back(Tensor::ones({1,1}));
+	}
+	
+	
+	void push_left_stack(const size_t _position) {
+		Index i1, i2, i3, j1 , j2, j3, k1, k2;
+		const Tensor &xi = x.get_component(_position);
+		const Tensor &Ai = A.get_component(_position);
+		const Tensor &bi = b.get_component(_position);
+		
+		Tensor tmpA, tmpB;
+		tmpA(i1, i2, i3) = leftAStack.back()(j1, j2, j3)
+				*xi(j1, k1, i1)*Ai(j2, k1, k2, i2)*xi(j3, k2, i3);
+		leftAStack.emplace_back(std::move(tmpA));
+		tmpB(i1, i2) = leftBStack.back()(j1, j2)
+				*xi(j1, k1, i1)*bi(j2, k1, i2);
+		leftBStack.emplace_back(std::move(tmpB));
+	}
+	
+	
+	void push_right_stack(const size_t _position) {
+		Index i1, i2, i3, j1 , j2, j3, k1, k2;
+		const Tensor &xi = x.get_component(_position);
+		const Tensor &Ai = A.get_component(_position);
+		const Tensor &bi = b.get_component(_position);
+		
+		Tensor tmpA, tmpB;
+		tmpA(i1, i2, i3) = xi(i1, k1, j1)*Ai(i2, k1, k2, j2)*xi(i3, k2, j3)
+				*rightAStack.back()(j1, j2, j3);
+		rightAStack.emplace_back(std::move(tmpA));
+		tmpB(i1, i2) = xi(i1, k1, j1)*bi(i2, k1, j2)
+				*rightBStack.back()(j1, j2);
+		rightBStack.emplace_back(std::move(tmpB));
+	}
+	
+	double calc_residual_norm() {
+		Index i,j;