Changes in / [822f01:e588312]


Ignore:
Files:
46 added
33 deleted
161 edited

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Unmodified
Added
Removed

  • Makefile.am

    r822f01 re588312  
    11ACLOCAL_AMFLAGS = -I m4
    22SUBDIRS = src src/unittests doc tests
     3
     4AUTOMAKE_OPTIONS = subdir-objects
    35
    46EXTRA_DIST = autogen.sh

  • configure.ac

    r822f01 re588312  
    66AC_CONFIG_AUX_DIR(config)
    77AC_CONFIG_SRCDIR([src/builder.cpp])
    8 AC_CONFIG_HEADER([config.h])
     8AC_CONFIG_HEADER([config.h libmolecuilder_config.h])
     9AC_CONFIG_MACRO_DIR([m4])
    910
    1011AM_INIT_AUTOMAKE(dist-bzip2 parallel-tests)
    … …  
    1415AC_PROG_CXX
    1516AC_PROG_CC
    16 AC_PROG_RANLIB
     17# obselete by LT_INIT
     18#AC_PROG_RANLIB
    1719AC_PROG_INSTALL
    1820AC_CHECK_PROG([LATEX],[latex],[latex],[:])
    … …  
    2325AM_MISSING_PROG([DOXYGEN], [doxygen])
    2426
     27LT_INIT([disable-static])
     28
     29# Define these substitions here to keep all version information in one place.
     30# For information on how to properly maintain the library version information,
     31# refer to the libtool manual, section "Updating library version information":
     32# http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
     33AC_SUBST([MOLECUILDER_SO_VERSION], [1:2:0])
     34AC_SUBST([MOLECUILDER_API_VERSION], [1.0])
     35
    2536# Checks for libraries.
    26 AC_CHECK_LIB(m, sqrt, ,AC_MSG_ERROR([compatible libc math library not found]))
     37AC_CHECK_LIB(m, sqrt, , AC_MSG_ERROR([compatible libc math library not found]))
    2738
    2839# Boost libraries
    … …  
    110121        doc/molecuilder.xml])
    111122AC_CONFIG_FILES([
     123  molecuilder-${MOLECUILDER_API_VERSION}.pc:molecuilder.pc.in])
     124AC_CONFIG_FILES([
    112125        Makefile
    113126        doc/Makefile
    114127        src/Makefile
    115128        src/Actions/Makefile
     129  src/Exceptions/Makefile
     130  src/Helpers/Makefile
     131  src/LinearAlgebra/Makefile
     132  src/Parser/Makefile
    116133        src/UIElements/Makefile
    117134        src/unittests/Makefile])

  • m4/gwqt4.m4

    r822f01 re588312  
    147147        QT_LIBS="$QT_LIB"
    148148        if test $QT_IS_STATIC = yes ; then
    149             QT_LIBS="$QT_LIBS -L$x_libraries -lXext -lX11 -lm -lSM -lICE"
     149            QT_LIBS="$QT_LIBS -lXext -lX11 -lm -lSM -lICE"
    150150        fi
    151151        ;;
    … …  
    154154        QT_LIBS="$QT_LIB"
    155155        if test $QT_IS_STATIC = yes ; then
    156             QT_LIBS="$QT_LIBS -L$x_libraries -lXext -lX11 -lm -lSM -lICE -ldl"
     156            QT_LIBS="$QT_LIBS -lXext -lX11 -lm -lSM -lICE -ldl"
    157157        fi
    158158        ;;
    … …  
    162162        QT_LIBS="$QT_LIB"
    163163        if test $QT_IS_STATIC = yes ; then
    164             QT_LIBS="$QT_LIBS -L$x_libraries -lXext -lX11 -lm -lSM -lICE"
     164            QT_LIBS="$QT_LIBS -lXext -lX11 -lm -lSM -lICE"
    165165        fi
    166166        ;;
    … …  
    169169        QT_LIBS="$QT_LIB"
    170170        if test $QT_IS_STATIC = yes ; then
    171             QT_LIBS="$QT_LIBS -L$x_libraries -lXext -lX11 -lm -lSM -lICE -lresolv -lsocket -lnsl"
     171            QT_LIBS="$QT_LIBS -lXext -lX11 -lm -lSM -lICE -lresolv -lsocket -lnsl"
    172172        fi
    173173        ;;

  • src/Actions/Action.cpp

    r822f01 re588312  
    1818#include "UIElements/UIFactory.hpp"
    1919
    20 #include "log.hpp"
    21 #include "verbose.hpp"
     20#include "Helpers/Log.hpp"
     21#include "Helpers/Verbose.hpp"
    2222
    2323using namespace std;

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    r822f01 re588312  
    1414#include "molecule.hpp"
    1515#include "linkedcell.hpp"
    16 #include "log.hpp"
    17 #include "verbose.hpp"
     16#include "Helpers/Log.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929const char AnalysisMolecularVolumeAction::NAME[] = "molecular-volume";

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    r822f01 re588312  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "vector.hpp"
     20#include "LinearAlgebra/Vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "UIElements/ValueStorage.hpp"
     30#include "Actions/ValueStorage.hpp"
    3131
    3232const char AnalysisPairCorrelationAction::NAME[] = "pair-correlation";

  • src/Actions/AnalysisAction/PointCorrelationAction.cpp

    r822f01 re588312  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "vector.hpp"
     20#include "LinearAlgebra/Vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "UIElements/ValueStorage.hpp"
     30#include "Actions/ValueStorage.hpp"
    3131
    3232const char AnalysisPointCorrelationAction::NAME[] = "point-correlation";

  • src/Actions/AnalysisAction/PointCorrelationAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
     13#include <vector>
     14#include <string>
    1315
    1416class element;

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515
    1616#include <iostream>
    … …  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "UIElements/ValueStorage.hpp"
     23#include "Actions/ValueStorage.hpp"
    2424
    2525const char AnalysisPrincipalAxisSystemAction::NAME[] = "principal-axis-system";

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    r822f01 re588312  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "vector.hpp"
     20#include "LinearAlgebra/Vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "UIElements/ValueStorage.hpp"
     30#include "Actions/ValueStorage.hpp"
    3131
    3232const char AnalysisSurfaceCorrelationAction::NAME[] = "surface-correlation";

  • src/Actions/AtomAction/AddAction.cpp

    r822f01 re588312  
    1212#include "atom.hpp"
    1313#include "element.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "vector.hpp"
    17 #include "verbose.hpp"
     16#include "LinearAlgebra/Vector.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929const char AtomAddAction::NAME[] = "add-atom";

  • src/Actions/AtomAction/AddAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
    1313
    1414class element;

  • src/Actions/AtomAction/ChangeElementAction.cpp

    r822f01 re588312  
    1212#include "atom.hpp"
    1313#include "element.hpp"
    14 #include "log.hpp"
    15 #include "vector.hpp"
    16 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "LinearAlgebra/Vector.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "UIElements/ValueStorage.hpp"
     26#include "Actions/ValueStorage.hpp"
    2727
    2828const char AtomChangeElementAction::NAME[] = "change-element";

  • src/Actions/AtomAction/RemoveAction.cpp

    r822f01 re588312  
    1212#include "atom.hpp"
    1313#include "Descriptors/AtomDescriptor.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "UIElements/ValueStorage.hpp"
     26#include "Actions/ValueStorage.hpp"
    2727
    2828const char AtomRemoveAction::NAME[] = "remove-atom";

  • src/Actions/CmdAction/BondLengthTableAction.cpp

    r822f01 re588312  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727const char CommandLineBondLengthTableAction::NAME[] = "bond-table";

  • src/Actions/CmdAction/ElementDbAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "log.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "periodentafel.hpp"
    15 #include "verbose.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727const char CommandLineElementDbAction::NAME[] = "element-db";

  • src/Actions/CmdAction/FastParsingAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626// memento to remember the state when undoing

  • src/Actions/CmdAction/VerboseAction.cpp

    r822f01 re588312  
    1010#include "Actions/CmdAction/VerboseAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
    13 #include "verbose.hpp"
     12#include "Helpers/Log.hpp"
     13#include "Helpers/Verbose.hpp"
    1414
    1515#include <iostream>
    … …  
    2020#include "UIElements/UIFactory.hpp"
    2121#include "UIElements/Dialog.hpp"
    22 #include "UIElements/ValueStorage.hpp"
     22#include "Actions/ValueStorage.hpp"
    2323
    2424// memento to remember the state when undoing

  • src/Actions/CmdAction/VersionAction.cpp

    r822f01 re588312  
    1010#include "Actions/CmdAction/VersionAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
     12#include "version.h"
    1213
    1314#include <iostream>
    … …  
    1819#include "UIElements/UIFactory.hpp"
    1920#include "UIElements/Dialog.hpp"
    20 #include "UIElements/ValueStorage.hpp"
     21#include "Actions/ValueStorage.hpp"
    2122
    2223const char CommandLineVersionAction::NAME[] = "version";

  • src/Actions/ErrorAction.cpp

    r822f01 re588312  
    1111
    1212#include "Actions/ErrorAction.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "Helpers/Assert.hpp"
    1616

  • src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

    r822f01 re588312  
    1313#include "bondgraph.hpp"
    1414#include "config.hpp"
    15 #include "log.hpp"
     15#include "Helpers/Log.hpp"
    1616#include "molecule.hpp"
    1717#include "Descriptors/MoleculeDescriptor.hpp"
    1818#include "Descriptors/MoleculeIdDescriptor.hpp"
    1919#include "stackclass.hpp"
    20 #include "verbose.hpp"
     20#include "Helpers/Verbose.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "UIElements/ValueStorage.hpp"
     30#include "Actions/ValueStorage.hpp"
    3131
    3232const char FragmentationDepthFirstSearchAction::NAME[] = "depth-first-search";

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    r822f01 re588312  
    1313#include "bondgraph.hpp"
    1414#include "config.hpp"
    15 #include "log.hpp"
     15#include "Helpers/Log.hpp"
    1616#include "molecule.hpp"
    1717#include "Descriptors/MoleculeDescriptor.hpp"
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929
    3030const char FragmentationFragmentationAction::NAME[] = "fragment-mol";

  • src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

    r822f01 re588312  
    1212#include "atom.hpp"
    1313#include "config.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    1616#include "Descriptors/MoleculeDescriptor.hpp"
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";

  • src/Actions/Makefile.am

    r822f01 re588312  
    66AM_LDFLAGS = $(CPPUNIT_LIBS) -ldl
    77AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    8 
    9 noinst_LIBRARIES = libMolecuilderActions.a
    10 libMolecuilderActions_a_SOURCES = ${ACTIONSSOURCE} ${ACTIONSHEADER}
    118
    129ACTIONSSOURCE = \
    … …  
    2017  ${TESSELATIONACTIONSOURCE} \
    2118  ${WORLDACTIONSOURCE} \
    22   MapOfActions.cpp
     19  MapOfActions.cpp \
     20  ValueStorage.cpp
    2321
    2422ACTIONSHEADER = \
    … …  
    3331  ${WORLDACTIONHEADER} \
    3432  MapOfActions.hpp \
     33  ValueStorage.hpp \
    3534  Values.hpp
    3635 
    … …  
    168167  WorldAction/SetOutputFormatsAction.hpp               
    169168
     169
     170lib_LTLIBRARIES = libMolecuilderActions-@MOLECUILDER_API_VERSION@.la
     171libMolecuilderActions_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
     172libMolecuilderActions_libs = ../Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la
     173nobase_libMolecuilderActions_include_HEADERS = ${ACTIONSHEADER}
     174
     175## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
     176## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
     177## will therefore be treated as if it were literally part of the target name,
     178## and the variable name derived from that.
     179## The file extension .cc is recognized by Automake, and makes it produce
     180## rules which invoke the C++ compiler to produce a libtool object file (.lo)
     181## from each source file.  Note that it is not necessary to list header files
     182## which are already listed elsewhere in a _HEADERS variable assignment.
     183libMolecuilderActions_@MOLECUILDER_API_VERSION@_la_SOURCES = ${ACTIONSSOURCE}
     184
     185## Instruct libtool to include ABI version information in the generated shared
     186## library file (.so).  The library ABI version is defined in configure.ac, so
     187## that all version information is kept in one place.
     188libMolecuilderActions_@MOLECUILDER_API_VERSION@_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
     189
     190## The generated configuration header is installed in its own subdirectory of
     191## $(libdir).  The reason for this is that the configuration information put
     192## into this header file describes the target platform the installed library
     193## has been built for.  Thus the file must not be installed into a location
     194## intended for architecture-independent files, as defined by the Filesystem
     195## Hierarchy Standard (FHS).
     196## The nodist_ prefix instructs Automake to not generate rules for including
     197## the listed files in the distribution on 'make dist'.  Files that are listed
     198## in _HEADERS variables are normally included in the distribution, but the
     199## configuration header file is generated at configure time and should not be
     200## shipped with the source tarball.
     201libMolecuilderActions_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
     202nodist_libMolecuilderActions_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
     203
     204## Install the generated pkg-config file (.pc) into the expected location for
     205## architecture-dependent package configuration information.  Occasionally,
     206## pkg-config files are also used for architecture-independent data packages,
     207## in which case the correct install location would be $(datadir)/pkgconfig.
     208pkgconfigdir = $(libdir)/pkgconfig
     209pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
     210
    170211unity.cpp:
    171212        echo "" >  unity.cpp; \

  • src/Actions/MapOfActions.cpp

    r822f01 re588312  
    2626#include "CommandLineParser.hpp"
    2727#include "element.hpp"
    28 #include "log.hpp"
    29 #include "Matrix.hpp"
     28#include "Helpers/Log.hpp"
     29#include "LinearAlgebra/Matrix.hpp"
    3030#include "molecule.hpp"
    3131#include "periodentafel.hpp"
    32 #include "vector.hpp"
    33 #include "verbose.hpp"
     32#include "LinearAlgebra/Vector.hpp"
     33#include "Helpers/Verbose.hpp"
    3434
    3535#include "Actions/ActionRegistry.hpp"

  • src/Actions/MapOfActions.hpp

    r822f01 re588312  
    1010
    1111#include <boost/program_options.hpp>
     12#include <boost/lexical_cast.hpp>
    1213
    1314#include <map>

  • src/Actions/MoleculeAction/BondFileAction.cpp

    r822f01 re588312  
    1010#include "Actions/MoleculeAction/BondFileAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727

  • src/Actions/MoleculeAction/ChangeNameAction.cpp

    r822f01 re588312  
    2020#include "UIElements/UIFactory.hpp"
    2121#include "UIElements/Dialog.hpp"
    22 #include "UIElements/ValueStorage.hpp"
     22#include "Actions/ValueStorage.hpp"
    2323
    2424/****** MoleculeChangeNameAction *****/

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    r822f01 re588312  
    1515#include "config.hpp"
    1616#include "molecule.hpp"
    17 #include "verbose.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929
    3030/****** MoleculeFillWithMoleculeAction *****/

  • src/Actions/MoleculeAction/FillWithMoleculeAction.hpp

    r822f01 re588312  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
    13 #include "vector.hpp"
     13#include "LinearAlgebra/Vector.hpp"
    1414
    1515class MoleculeListClass;

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

    r822f01 re588312  
    1212#include "atom.hpp"
    1313#include "defs.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    r822f01 re588312  
    1010#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727/****** MoleculeRotateToPrincipalAxisSystemAction *****/

  • src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

    r822f01 re588312  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929
    3030/****** MoleculeSaveAdjacencyAction *****/

  • src/Actions/MoleculeAction/SaveBondsAction.cpp

    r822f01 re588312  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929
    3030/****** MoleculeSaveBondsAction *****/

  • src/Actions/MoleculeAction/SaveTemperatureAction.cpp

    r822f01 re588312  
    1010#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727/****** MoleculeSaveTemperatureAction *****/

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    r822f01 re588312  
    1212#include "boundary.hpp"
    1313#include "config.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727/****** MoleculeSuspendInWaterAction *****/

  • src/Actions/MoleculeAction/TranslateAction.cpp

    r822f01 re588312  
    1010#include "Actions/MoleculeAction/TranslateAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    14 #include "vector.hpp"
    15 #include "verbose.hpp"
     14#include "LinearAlgebra/Vector.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "UIElements/ValueStorage.hpp"
     26#include "Actions/ValueStorage.hpp"
    2727
    2828/****** MoleculeTranslateAction *****/

  • src/Actions/MoleculeAction/TranslateAction.hpp

    r822f01 re588312  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
    13 #include "vector.hpp"
     13#include "LinearAlgebra/Vector.hpp"
    1414
    1515class MoleculeListClass;

  • src/Actions/MoleculeAction/VerletIntegrationAction.cpp

    r822f01 re588312  
    1010#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727/****** MoleculeVerletIntegrationAction *****/

  • src/Actions/ParserAction/LoadXyzAction.cpp

    r822f01 re588312  
    1414#include "Parser/XyzParser.hpp"
    1515#include "atom.hpp"
    16 #include "log.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    18 #include "verbose.hpp"
     18#include "Helpers/Verbose.hpp"
    1919#include "World.hpp"
    2020
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929
    3030/****** ParserLoadXyzAction *****/

  • src/Actions/ParserAction/SaveXyzAction.cpp

    r822f01 re588312  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "UIElements/ValueStorage.hpp"
     23#include "Actions/ValueStorage.hpp"
    2424
    2525

  • src/Actions/SelectionAction/AllAtomsAction.cpp

    r822f01 re588312  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/AllMoleculesAction.cpp

    r822f01 re588312  
    1212#include "Descriptors/MoleculeDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/AtomByIdAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/MoleculeByIdAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/NotAllAtomsAction.cpp

    r822f01 re588312  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/NotAllMoleculesAction.cpp

    r822f01 re588312  
    1212#include "Descriptors/MoleculeDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/NotAtomByIdAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/NotMoleculeByIdAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626

  • src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

    r822f01 re588312  
    1313#include "config.hpp"
    1414#include "linkedcell.hpp"
    15 #include "log.hpp"
     15#include "Helpers/Log.hpp"
    1616#include "molecule.hpp"
    17 #include "verbose.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929/****** TesselationConvexEnvelopeAction *****/

  • src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

    r822f01 re588312  
    1212#include "boundary.hpp"
    1313#include "linkedcell.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "UIElements/ValueStorage.hpp"
     26#include "Actions/ValueStorage.hpp"
    2727
    2828/****** TesselationNonConvexEnvelopeAction *****/

  • src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
    14 #include "vector.hpp"
     13#include "Helpers/Log.hpp"
     14#include "LinearAlgebra/Vector.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626#include "Helpers/Assert.hpp"
    2727

  • src/Actions/WorldAction/AddEmptyBoundaryAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
    1313
    1414void WorldAddEmptyBoundary(Vector &boundary);

  • src/Actions/WorldAction/BoundInBoxAction.cpp

    r822f01 re588312  
    1010#include "Actions/WorldAction/BoundInBoxAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    1414#include "World.hpp"
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626const char WorldBoundInBoxAction::NAME[] = "bound-in-box";

  • src/Actions/WorldAction/CenterInBoxAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "Box.hpp"
    13 #include "log.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "molecule.hpp"
    1515#include "World.hpp"
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626const char WorldCenterInBoxAction::NAME[] = "center-in-box";

  • src/Actions/WorldAction/CenterOnEdgeAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
    14 #include "vector.hpp"
     13#include "Helpers/Log.hpp"
     14#include "LinearAlgebra/Vector.hpp"
    1515#include "World.hpp"
    16 #include "Matrix.hpp"
     16#include "LinearAlgebra/Matrix.hpp"
    1717
    1818#include <iostream>
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626#include "Helpers/Assert.hpp"
    2727

  • src/Actions/WorldAction/ChangeBoxAction.cpp

    r822f01 re588312  
    1010#include "Actions/WorldAction/ChangeBoxAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
    13 #include "verbose.hpp"
     12#include "Helpers/Log.hpp"
     13#include "Helpers/Verbose.hpp"
    1414#include "World.hpp"
    1515#include "Box.hpp"
    16 #include "Matrix.hpp"
     16#include "LinearAlgebra/Matrix.hpp"
    1717
    1818#include <iostream>
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727const char WorldChangeBoxAction::NAME[] = "change-box";

  • src/Actions/WorldAction/InputAction.cpp

    r822f01 re588312  
    1010#include "Actions/WorldAction/InputAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "molecule.hpp"
    1414#include "Parser/FormatParserStorage.hpp"
    1515#include "Parser/PcpParser.hpp"
    16 #include "verbose.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "UIElements/ValueStorage.hpp"
     26#include "Actions/ValueStorage.hpp"
    2727
    2828const char WorldInputAction::NAME[] = "input";

  • src/Actions/WorldAction/OutputAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "Parser/ChangeTracker.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626const char WorldOutputAction::NAME[] = "output";

  • src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

    r822f01 re588312  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "log.hpp"
     14#include "Helpers/Log.hpp"
    1515#include "molecule.hpp"
    16 #include "vector.hpp"
    17 #include "verbose.hpp"
     16#include "LinearAlgebra/Vector.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929const char WorldRemoveSphereOfAtomsAction::NAME[] = "remove-sphere";

  • src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
    1313
    1414

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "molecule.hpp"
    15 #include "vector.hpp"
    16 #include "Matrix.hpp"
    17 #include "verbose.hpp"
     15#include "LinearAlgebra/Vector.hpp"
     16#include "LinearAlgebra/Matrix.hpp"
     17#include "Helpers/Verbose.hpp"
    1818#include "World.hpp"
    1919#include "Box.hpp"
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "UIElements/ValueStorage.hpp"
     28#include "Actions/ValueStorage.hpp"
    2929#include "Descriptors/MoleculeDescriptor.hpp"
    3030#include "Descriptors/MoleculePtrDescriptor.hpp"

  • src/Actions/WorldAction/RepeatBoxAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
    1313
    1414void WorldRepeatBox(Vector &Repeater);

  • src/Actions/WorldAction/ScaleBoxAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "log.hpp"
    14 #include "vector.hpp"
    15 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "LinearAlgebra/Vector.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717#include "Box.hpp"
    18 #include "Matrix.hpp"
     18#include "LinearAlgebra/Matrix.hpp"
    1919
    2020#include <iostream>
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "UIElements/ValueStorage.hpp"
     27#include "Actions/ValueStorage.hpp"
    2828
    2929const char WorldScaleBoxAction::NAME[] = "scale-box";

  • src/Actions/WorldAction/ScaleBoxAction.hpp

    r822f01 re588312  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "vector.hpp"
     12#include "LinearAlgebra/Vector.hpp"
    1313
    1414void WorldScaleBox(Vector &Scaler);

  • src/Actions/WorldAction/SetDefaultNameAction.cpp

    r822f01 re588312  
    1010#include "Actions/WorldAction/SetDefaultNameAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "log.hpp"
    13 #include "verbose.hpp"
     12#include "Helpers/Log.hpp"
     13#include "Helpers/Verbose.hpp"
    1414#include "World.hpp"
    1515
    … …  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "UIElements/ValueStorage.hpp"
     23#include "Actions/ValueStorage.hpp"
    2424
    2525

  • src/Actions/WorldAction/SetGaussianBasisAction.cpp

    r822f01 re588312  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "log.hpp"
    14 #include "verbose.hpp"
     13#include "Helpers/Log.hpp"
     14#include "Helpers/Verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "UIElements/ValueStorage.hpp"
     24#include "Actions/ValueStorage.hpp"
    2525
    2626

  • src/Actions/WorldAction/SetOutputFormatsAction.cpp

    r822f01 re588312  
    1212#include "Parser/ChangeTracker.hpp"
    1313#include "Parser/FormatParserStorage.hpp"
    14 #include "log.hpp"
    15 #include "verbose.hpp"
     14#include "Helpers/Log.hpp"
     15#include "Helpers/Verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "UIElements/ValueStorage.hpp"
     25#include "Actions/ValueStorage.hpp"
    2626
    2727const char WorldSetOutputFormatsAction::NAME[] = "set-output";

  • src/Box.cpp

    r822f01 re588312  
    1414#include <cstdlib>
    1515
    16 #include "Matrix.hpp"
    17 #include "vector.hpp"
    18 #include "Plane.hpp"
     16#include "LinearAlgebra/Matrix.hpp"
     17#include "LinearAlgebra/Vector.hpp"
     18#include "LinearAlgebra/Plane.hpp"
    1919
    2020#include "Helpers/Assert.hpp"

  • src/Box.hpp

    r822f01 re588312  
    1515#include <list>
    1616#include <vector>
    17 #include "VectorSet.hpp"
     17#include "LinearAlgebra/VectorSet.hpp"
    1818
    1919/**

  • src/CommandLineParser.cpp

    r822f01 re588312  
    1515#include "Patterns/Singleton_impl.hpp"
    1616#include "CommandLineParser.hpp"
    17 #include "log.hpp"
    18 #include "verbose.hpp"
     17#include "Helpers/Log.hpp"
     18#include "Helpers/Verbose.hpp"
    1919
    2020using namespace std;

  • src/ConfigFileBuffer.cpp

    r822f01 re588312  
    77
    88#include "ConfigFileBuffer.hpp"
    9 #include "helpers.hpp"
     9#include "Helpers/helpers.hpp"
    1010#include "lists.hpp"
    11 #include "verbose.hpp"
    12 #include "log.hpp"
     11#include "Helpers/Verbose.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "World.hpp"
    1414

  • src/Descriptors/AtomSelectionDescriptor.cpp

    r822f01 re588312  
    99#include "Descriptors/AtomSelectionDescriptor_impl.hpp"
    1010
    11 #include "helpers.hpp"
     11#include "Helpers/helpers.hpp"
    1212
    1313AtomSelectionDescriptor_impl::AtomSelectionDescriptor_impl(){}

  • src/Descriptors/MoleculeSelectionDescriptor.cpp

    r822f01 re588312  
    99#include "Descriptors/MoleculeSelectionDescriptor_impl.hpp"
    1010
    11 #include "helpers.hpp"
     11#include "Helpers/helpers.hpp"
    1212
    1313MoleculeSelectionDescriptor_impl::MoleculeSelectionDescriptor_impl(){}

  • src/Descriptors/SelectiveIterator_impl.hpp

    r822f01 re588312  
    99#define SELECTIVEITERATOR_IMPL_HPP_
    1010
    11 #include "helpers.hpp"
     11#include "Helpers/helpers.hpp"
    1212
    1313template<class _Target,

  • src/Formula.hpp

    r822f01 re588312  
    1616
    1717#include "types.hpp"
    18 #include "helpers.hpp"
     18#include "Helpers/helpers.hpp"
    1919
    2020class element;

  • src/Helpers/MemDebug.hpp

    r822f01 re588312  
    101101
    102102#else
     103
     104#include <iosfwd>
     105
    103106// memory debugging was disabled
    104107
    105108namespace Memory {
    106   inline void getState(){}
     109  inline void getState(){};
    107110
    108111  inline void dumpMemory(std::ostream&){};

  • src/Legacy/oldmenu.cpp

    r822f01 re588312  
    2020#include "element.hpp"
    2121#include "ellipsoid.hpp"
    22 #include "helpers.hpp"
     22#include "Helpers/helpers.hpp"
    2323#include "leastsquaremin.hpp"
    2424#include "linkedcell.hpp"
    25 #include "log.hpp"
     25#include "Helpers/Log.hpp"
    2626#include "memoryusageobserverunittest.hpp"
    2727#include "molecule.hpp"
    2828#include "periodentafel.hpp"
    2929#include "vector_ops.hpp"
    30 #include "Plane.hpp"
    31 #include "Line.hpp"
     30#include "LinearAlgebra/Plane.hpp"
     31#include "LinearAlgebra/Line.hpp"
    3232
    3333#include "UIElements/UIFactory.hpp"

  • src/Makefile.am

    r822f01 re588312  
    22# Also indentation by a single tab
    33
    4 SUBDIRS = Actions UIElements
    5 
    6 # this includes source files that need to be present at multiple points
    7 HELPERSOURCE =  \
    8   Helpers/Assert.cpp \
    9   Helpers/MemDebug.cpp
    10  
    11 BASESOURCE = \
    12   ${HELPERSOURCE} \
    13   Space.cpp \
    14   vector.cpp
    15  
    16 BASEHEADER = \
    17   ${HELPERHEADER} \
    18   Space.hpp \
    19   vector.hpp
    20                        
     4SUBDIRS = Actions Exceptions Helpers LinearAlgebra Parser UIElements
     5
    216ATOMSOURCE = \
    227  atom.cpp \
    … …  
    4025  atom_trajectoryparticleinfo.hpp
    4126
    42 LINALGSOURCE = \
    43   gslmatrix.cpp \
    44   gslvector.cpp \
    45   linearsystemofequations.cpp
    46                            
    47 LINALGHEADER = \
    48   gslmatrix.hpp \
    49   gslvector.hpp \
    50   linearsystemofequations.hpp
    51                            
    5227ANALYSISSOURCE = \
    5328  analysis_bonds.cpp \
    … …  
    8156  Actions/MethodAction.hpp \
    8257  Actions/Process.hpp
    83 
    84 EXCEPTIONSOURCE = \
    85   Exceptions/CustomException.cpp \
    86   Exceptions/IllegalTypeException.cpp \
    87   Exceptions/LinearDependenceException.cpp \
    88   Exceptions/MathException.cpp \
    89   Exceptions/MissingValueException.cpp \
    90   Exceptions/NotInvertibleException.cpp \
    91   Exceptions/ParseError.cpp \
    92   Exceptions/SkewException.cpp \
    93   Exceptions/ZeroVectorException.cpp
    94                                  
    95 EXCEPTIONHEADER = \
    96   Exceptions/CustomException.hpp \
    97   Exceptions/IllegalTypeException.hpp \
    98   Exceptions/LinearDependenceException.hpp \
    99   Exceptions/MathException.hpp \
    100   Exceptions/MissingValueException.hpp \
    101   Exceptions/NotInvertibleException.hpp \
    102   Exceptions/ParseError.hpp \
    103   Exceptions/SkewException.hpp \
    104   Exceptions/ZeroVectorException.hpp
    105 
    106 PARSERSOURCE = \
    107   Parser/ChangeTracker.cpp \
    108   Parser/FormatParser.cpp \
    109   Parser/FormatParserStorage.cpp \
    110   Parser/MpqcParser.cpp \
    111   Parser/PcpParser.cpp \
    112   Parser/TremoloParser.cpp \
    113   Parser/XyzParser.cpp
    114 
    115 PARSERHEADER = \
    116   Parser/ChangeTracker.hpp \
    117   Parser/FormatParser.hpp \
    118   Parser/FormatParserStorage.hpp \
    119   Parser/MpqcParser.hpp \
    120   Parser/PcpParser.hpp \
    121   Parser/TremoloParser.hpp \
    122   Parser/XyzParser.hpp
    12358
    12459PATTERNSOURCE = \
    … …  
    185120QTUI_DEFS =
    186121
    187 SOURCE = \
     122MOLECUILDERSOURCE = \
    188123  ${ANALYSISSOURCE} \
    189124  ${ACTIONSSOURCE} \
    190125  ${ATOMSOURCE} \
    191   ${EXCEPTIONSOURCE} \
    192126  ${PATTERNSOURCE} \
    193127  ${PARSERSOURCE} \
    … …  
    204138  elements_db.cpp \
    205139  ellipsoid.cpp \
    206   errorlogger.cpp \
    207140  Formula.cpp \
    208141  graph.cpp \
    209   helpers.cpp \
    210   info.cpp \
    211142  leastsquaremin.cpp \
    212   Line.cpp \
    213143  linkedcell.cpp \
    214   log.cpp \
    215   logger.cpp \
    216   Matrix.cpp \
    217144  moleculelist.cpp \
    218145  molecule.cpp \
    … …  
    224151  parser.cpp \
    225152  periodentafel.cpp \
    226   Plane.cpp \
    227153  tesselation.cpp \
    228154  tesselationhelpers.cpp \
    … …  
    231157  UIElements/UIFactory.cpp \
    232158  vector_ops.cpp \
    233   verbose.cpp \
    234159  World.cpp
    235160
    236 HEADER = \
     161MOLECUILDERHEADER = \
    237162  ${ANALYSISHEADER} \
    238163  ${ACTIONSHEADER} \
    239164  ${ATOMHEADER} \
    240   ${EXCEPTIONHEADER} \
    241165  ${PARSERHEADER} \
    242166  ${PATTERNHEADER} \
    … …  
    254178  elements_db.hpp \
    255179  ellipsoid.hpp \
    256   errorlogger.hpp \
    257180  Formula.hpp \
    258181  graph.hpp \
    259   helpers.hpp \
    260   info.hpp \
    261182  leastsquaremin.hpp \
    262   Line.hpp \
    263183  linkedcell.hpp \
    264184  lists.hpp \
    265   log.hpp \
    266   logger.hpp \
    267   Matrix.hpp \
    268185  molecule.hpp \
    269186  molecule_template.hpp \
    270187  parser.hpp \
    271188  periodentafel.hpp \
    272   Plane.hpp \
    273189  stackclass.hpp \
    274190  tesselation.hpp \
    … …  
    277193  triangleintersectionlist.hpp \
    278194  UIElements/UIFactory.hpp \
    279   verbose.hpp \
    280195  vector_ops.hpp \
    281196  World.hpp
    282197
    283 # the following files are no longer used:
    284 #  memoryallocator.hpp \
    285 #  memoryallocator.cpp \
    286 #  memoryusageobserver.hpp \
    287 #  memoryusageobserver.cpp
     198lib_LTLIBRARIES = libMolecuilder-@MOLECUILDER_API_VERSION@.la
     199libMolecuilder_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
     200libMolecuilder_LIBS = \
     201        LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     202        ${BOOST_PROGRAM_OPTIONS_LIB}
     203
     204#       UIElements/libMolecuilderUI.a \
     205        Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
     206        Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
     207        Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     208        Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     209        $(BOOST_LIB) \
     210        ${BOOST_THREAD_LIB}
     211
     212nobase_libMolecuilder_include_HEADERS = ${MOLECUILDERHEADER}
     213
     214## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
     215## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
     216## will therefore be treated as if it were literally part of the target name,
     217## and the variable name derived from that.
     218## The file extension .cc is recognized by Automake, and makes it produce
     219## rules which invoke the C++ compiler to produce a libtool object file (.lo)
     220## from each source file.  Note that it is not necessary to list header files
     221## which are already listed elsewhere in a _HEADERS variable assignment.
     222libMolecuilder_@MOLECUILDER_API_VERSION@_la_SOURCES = ${MOLECUILDERSOURCE} $(srcdir)/version.c
     223
     224## Instruct libtool to include ABI version information in the generated shared
     225## library file (.so).  The library ABI version is defined in configure.ac, so
     226## that all version information is kept in one place.
     227libMolecuilder_@MOLECUILDER_API_VERSION@_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
     228
     229## The generated configuration header is installed in its own subdirectory of
     230## $(libdir).  The reason for this is that the configuration information put
     231## into this header file describes the target platform the installed library
     232## has been built for.  Thus the file must not be installed into a location
     233## intended for architecture-independent files, as defined by the Filesystem
     234## Hierarchy Standard (FHS).
     235## The nodist_ prefix instructs Automake to not generate rules for including
     236## the listed files in the distribution on 'make dist'.  Files that are listed
     237## in _HEADERS variables are normally included in the distribution, but the
     238## configuration header file is generated at configure time and should not be
     239## shipped with the source tarball.
     240libMolecuilder_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
     241nodist_libMolecuilder_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
     242
     243## Install the generated pkg-config file (.pc) into the expected location for
     244## architecture-dependent package configuration information.  Occasionally,
     245## pkg-config files are also used for architecture-independent data packages,
     246## in which case the correct install location would be $(datadir)/pkgconfig.
     247pkgconfigdir = $(libdir)/pkgconfig
     248pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
     249
    288250
    289251BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    … …  
    291253INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    292254
    293 noinst_LIBRARIES = libmolecuilderbase.a libmolecuilder.a libgslwrapper.a libmenu.a libparser.a
     255noinst_LIBRARIES = libmenu.a
    294256bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
    295257EXTRA_PROGRAMS = unity
    … …  
    297259molecuilderdir = ${bindir}
    298260
    299 libmolecuilderbase_a_SOURCES = ${BASESOURCE} ${BASEHEADER}
    300 libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
    301261libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
    302 libparser_a_SOURCES = ${PARSERSOURCE} ${PARSERHEADER}
    303 libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    304262
    305263molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    … …  
    308266#molecuilder_CXXFLAGS += -DNO_CACHING
    309267molecuilder_LDFLAGS = $(BOOST_LIB)
    310 molecuilder_SOURCES = ${LEGACYSOURCE} builder.cpp
    311 molecuilder_SOURCES += $(srcdir)/version.c
    312 molecuilder_LDADD = UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilderbase.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     268molecuilder_SOURCES = builder.cpp
     269molecuilder_LDADD = \
     270        UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
     271        Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
     272        libMolecuilder-@MOLECUILDER_API_VERSION@.la \
     273        Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
     274        LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     275        Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     276        Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     277        $(BOOST_LIB) \
     278        ${BOOST_THREAD_LIB} \
     279        ${BOOST_PROGRAM_OPTIONS_LIB}
     280
    313281
    314282#Stuff for building the GUI using QT
    315 molecuildergui_SOURCES = ${QTUISOURCE} ${LEGACYSOURCE} builder.cpp
    316 molecuildergui_SOURCES += $(srcdir)/version.c
     283molecuildergui_SOURCES = ${QTUISOURCE} builder.cpp
    317284molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
    318285molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
    319 molecuildergui_LDADD = UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilderbase.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}  ${GUI_LIBS}
    320 
    321 joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    322 joiner_LDADD = libmolecuilder.a libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    323 
    324 analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
    325 analyzer_LDADD = libmolecuilder.a libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    326 
    327 unity_SOURCES = unity.cpp $(srcdir)/version.c
     286
     287unity_SOURCES = unity.cpp
    328288unity_LDADD = $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     289
     290molecuildergui_LDADD = \
     291        UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
     292        Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
     293        libMolecuilder-@MOLECUILDER_API_VERSION@.la \
     294        Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
     295        LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     296        Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     297        Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     298        $(BOOST_LIB) \
     299        ${BOOST_THREAD_LIB} \
     300        ${BOOST_PROGRAM_OPTIONS_LIB} \
     301        ${GUI_LIBS}
     302
     303joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
     304joiner_LDADD = \
     305        libMolecuilder-@MOLECUILDER_API_VERSION@.la \
     306        LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     307        Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     308        Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     309        $(BOOST_LIB) \
     310        ${BOOST_THREAD_LIB} \
     311        ${BOOST_PROGRAM_OPTIONS_LIB}
     312
     313analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp
     314analyzer_LDADD = \
     315        libMolecuilder-@MOLECUILDER_API_VERSION@.la \
     316        LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     317        Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     318        Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     319        $(BOOST_LIB) \
     320        ${BOOST_THREAD_LIB} \
     321        ${BOOST_PROGRAM_OPTIONS_LIB}
    329322
    330323#Rules needed for QT4
    … …  
    342335        done;
    343336
    344 unity.cpp: ${LINALGSOURCE} ${LINALGHEADER} ${SOURCE} ${HEADER}
     337#EXTRA_DIST = ${molecuilder_DATA}
     338
     339FORCE:
     340$(srcdir)/.git-version: FORCE
     341        @if (test -d $(top_srcdir)/.git && cd $(srcdir) \
     342             && { git describe --dirty --always || git describe; } ) > .git-version-t 2>/dev/null \
     343          && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
     344          mv -f .git-version-t $(srcdir)/.git-version; \
     345        else \
     346          rm -f .git-version-t; \
     347        fi
     348
     349EXTRA_DIST = $(srcdir)/.git-version
     350
     351$(srcdir)/version.c: $(srcdir)/.git-version
     352        echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
     353
     354
     355unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
    345356        echo "" >  unity.cpp; \
    346         list='$(BASESOURCE)'; for file in $$list; do \
    347           echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
    348         done; \
    349         list='$(LINALGSOURCE)'; for file in $$list; do \
    350           echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
    351         done; \
    352         list='$(SOURCE)'; for file in $$list; do \
     357        list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
    353358          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
    354359        done; \
    … …  
    360365        done;\
    361366        echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
     367        echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;
    362368
    363369MOSTLYCLEANFILES = allmocs.moc.cpp unity.cpp
    364370       
    365 #EXTRA_DIST = ${molecuilder_DATA}
    366 
    367 FORCE:
    368 $(srcdir)/.git-version: FORCE
    369         @if (test -d $(top_srcdir)/.git && cd $(srcdir) \
    370              && { git describe --dirty --always || git describe; } ) > .git-version-t 2>/dev/null \
    371           && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
    372           mv -f .git-version-t $(srcdir)/.git-version; \
    373         else \
    374           rm -f .git-version-t; \
    375         fi
    376 
    377 EXTRA_DIST = $(srcdir)/.git-version
    378 
    379 $(srcdir)/version.c: $(srcdir)/.git-version
    380         echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
    381 
    382 

  • src/Parser/FormatParserStorage.cpp

    r822f01 re588312  
    1717#include "Parser/XyzParser.hpp"
    1818
    19 #include "log.hpp"
    20 #include "verbose.hpp"
     19#include "Helpers/Log.hpp"
     20#include "Helpers/Verbose.hpp"
    2121
    2222#include "Helpers/Assert.hpp"

  • src/Parser/MpqcParser.cpp

    r822f01 re588312  
    1111#include "config.hpp"
    1212#include "element.hpp"
    13 #include "log.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "periodentafel.hpp"
    15 #include "vector.hpp"
    16 #include "verbose.hpp"
     15#include "LinearAlgebra/Vector.hpp"
     16#include "Helpers/Verbose.hpp"
    1717#include "World.hpp"
    1818

  • src/Parser/PcpParser.cpp

    r822f01 re588312  
    1414#include "element.hpp"
    1515#include "Helpers/Assert.hpp"
    16 #include "log.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    1818#include "PcpParser.hpp"
    1919#include "periodentafel.hpp"
    2020#include "ThermoStatContainer.hpp"
    21 #include "verbose.hpp"
     21#include "Helpers/Verbose.hpp"
    2222#include "World.hpp"
    23 #include "Matrix.hpp"
     23#include "LinearAlgebra/Matrix.hpp"
    2424#include "Box.hpp"
    2525

  • src/Patterns/Registry_impl.hpp

    r822f01 re588312  
    1515
    1616#include "Helpers/Assert.hpp"
    17 #include <iostream>
     17#include <iosfwd>
    1818
    1919/** Constructor for class Registry.

  • src/Shapes/BaseShapes.cpp

    r822f01 re588312  
    99#include "Shapes/BaseShapes_impl.hpp"
    1010
    11 #include "vector.hpp"
     11#include "LinearAlgebra/Vector.hpp"
    1212
    1313bool Sphere_impl::isInside(const Vector &point){

  • src/Shapes/ShapeOps_impl.hpp

    r822f01 re588312  
    1010
    1111#include "Shapes/Shape_impl.hpp"
    12 #include "vector.hpp"
    13 #include "Matrix.hpp"
     12#include "LinearAlgebra/Vector.hpp"
     13#include "LinearAlgebra/Matrix.hpp"
    1414
    1515class Resize_impl :  public Shape_impl

  • src/ThermoStatContainer.cpp

    r822f01 re588312  
    1010#include "ConfigFileBuffer.hpp"
    1111#include "config.hpp"
    12 #include "log.hpp"
     12#include "Helpers/Log.hpp"
    1313#include "ThermoStatContainer.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515
    1616/** Constructor for class ThermoStatContainer.

  • src/UIElements/CommandLineUI/CommandLineDialog.cpp

    r822f01 re588312  
    2323#include "CommandLineParser.hpp"
    2424#include "defs.hpp"
    25 #include "log.hpp"
    26 #include "Matrix.hpp"
     25#include "Helpers/Log.hpp"
     26#include "LinearAlgebra/Matrix.hpp"
    2727#include "periodentafel.hpp"
    28 #include "verbose.hpp"
     28#include "Helpers/Verbose.hpp"
    2929#include "World.hpp"
    3030#include "Box.hpp"
    … …  
    3333#include "element.hpp"
    3434#include "molecule.hpp"
    35 #include "vector.hpp"
     35#include "LinearAlgebra/Vector.hpp"
    3636
    3737using namespace std;

  • src/UIElements/Dialog.cpp

    r822f01 re588312  
    99
    1010#include "Dialog.hpp"
    11 #include "ValueStorage.hpp"
    12 
    13 #include "verbose.hpp"
     11#include "Actions/ValueStorage.hpp"
     12
     13#include "Helpers/Verbose.hpp"
    1414#include "atom.hpp"
    1515#include "element.hpp"
    1616#include "molecule.hpp"
    17 #include "vector.hpp"
    18 #include "Matrix.hpp"
     17#include "LinearAlgebra/Vector.hpp"
     18#include "LinearAlgebra/Matrix.hpp"
    1919#include "Box.hpp"
    2020

  • src/UIElements/Dialog.hpp

    r822f01 re588312  
    1414
    1515#include "Box.hpp"
    16 #include "vector.hpp"
     16#include "LinearAlgebra/Vector.hpp"
    1717
    1818class atom;

  • src/UIElements/Makefile.am

    r822f01 re588312  
    55AM_LDFLAGS = $(CPPUNIT_LIBS) -ldl
    66AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    7 
    8 noinst_LIBRARIES = libMolecuilderUI.a
    9 libMolecuilderUI_a_SOURCES = ${UISOURCE} ${UIHEADER}
    107
    118VIEWSOURCE = \
    … …  
    4542  ${VIEWSOURCE} \
    4643  Dialog.cpp \
    47   MainWindow.cpp \
    48   ValueStorage.cpp
     44  MainWindow.cpp
    4945 
    5046UIHEADER = \
    … …  
    5551  ${VIEWHEADER} \
    5652  Dialog.hpp \
    57   MainWindow.hpp \
    58   ValueStorage.hpp
     53  MainWindow.hpp
    5954
    6055TEXTUISOURCE = \
    … …  
    8075  CommandLineUI/CommandLineWindow.hpp
    8176
     77lib_LTLIBRARIES = libMolecuilderUI-@MOLECUILDER_API_VERSION@.la
     78libMolecuilderUI_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
     79libMolecuilderUI_LIBS = \
     80        Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la
     81
     82nobase_libMolecuilderUI_include_HEADERS = ${UIHEADER}
     83
     84## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
     85## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
     86## will therefore be treated as if it were literally part of the target name,
     87## and the variable name derived from that.
     88## The file extension .cc is recognized by Automake, and makes it produce
     89## rules which invoke the C++ compiler to produce a libtool object file (.lo)
     90## from each source file.  Note that it is not necessary to list header files
     91## which are already listed elsewhere in a _HEADERS variable assignment.
     92libMolecuilderUI_@MOLECUILDER_API_VERSION@_la_SOURCES = ${UISOURCE}
     93
     94## Instruct libtool to include ABI version information in the generated shared
     95## library file (.so).  The library ABI version is defined in configure.ac, so
     96## that all version information is kept in one place.
     97libMolecuilderUI_@MOLECUILDER_API_VERSION@_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
     98
     99## The generated configuration header is installed in its own subdirectory of
     100## $(libdir).  The reason for this is that the configuration information put
     101## into this header file describes the target platform the installed library
     102## has been built for.  Thus the file must not be installed into a location
     103## intended for architecture-independent files, as defined by the Filesystem
     104## Hierarchy Standard (FHS).
     105## The nodist_ prefix instructs Automake to not generate rules for including
     106## the listed files in the distribution on 'make dist'.  Files that are listed
     107## in _HEADERS variables are normally included in the distribution, but the
     108## configuration header file is generated at configure time and should not be
     109## shipped with the source tarball.
     110libMolecuilderUI_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
     111nodist_libMolecuilderUI_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
     112
     113## Install the generated pkg-config file (.pc) into the expected location for
     114## architecture-dependent package configuration information.  Occasionally,
     115## pkg-config files are also used for architecture-independent data packages,
     116## in which case the correct install location would be $(datadir)/pkgconfig.
     117pkgconfigdir = $(libdir)/pkgconfig
     118pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
     119
    82120unity.cpp:
    83121        echo "" >  unity.cpp; \

  • src/UIElements/Menu/TextMenu.hpp

    r822f01 re588312  
    1010
    1111#include <list>
    12 #include <ostream>
     12#include <iosfwd>
    1313#include <string>
    1414

  • src/UIElements/QT4/QTDialog.cpp

    r822f01 re588312  
    77
    88#include "UIElements/QT4/QTDialog.hpp"
     9
     10#include <boost/lexical_cast.hpp>
    911
    1012#include <string>
    … …  
    3335#include "Descriptors/AtomIdDescriptor.hpp"
    3436#include "Descriptors/MoleculeIdDescriptor.hpp"
    35 #include "Matrix.hpp"
     37#include "LinearAlgebra/Matrix.hpp"
    3638#include "Box.hpp"
    3739

  • src/UIElements/QT4/QTMainWindow.cpp

    r822f01 re588312  
    2121#include "atom.hpp"
    2222#include "molecule.hpp"
    23 #include "verbose.hpp"
     23#include "Helpers/Verbose.hpp"
    2424#include "Actions/Action.hpp"
    2525#include "Actions/ActionRegistry.hpp"

  • src/UIElements/TextUI/TextDialog.cpp

    r822f01 re588312  
    1919#include "World.hpp"
    2020#include "periodentafel.hpp"
    21 #include "log.hpp"
    22 #include "verbose.hpp"
     21#include "Helpers/Log.hpp"
     22#include "Helpers/Verbose.hpp"
    2323
    2424#include "atom.hpp"
    2525#include "element.hpp"
    2626#include "molecule.hpp"
    27 #include "vector.hpp"
    28 #include "Matrix.hpp"
     27#include "LinearAlgebra/Vector.hpp"
     28#include "LinearAlgebra/Matrix.hpp"
    2929#include "Box.hpp"
     30
     31#include <boost/lexical_cast.hpp>
    3032
    3133using namespace std;

  • src/UIElements/TextUI/TextWindow.cpp

    r822f01 re588312  
    2727
    2828#include "defs.hpp"
    29 #include "log.hpp"
    30 #include "verbose.hpp"
     29#include "Helpers/Log.hpp"
     30#include "Helpers/Verbose.hpp"
    3131
    3232// all needed due to config::SaveAll()

  • src/UIElements/Views/QT4/QTStatusBar.cpp

    r822f01 re588312  
    1414#include "QTStatusBar.hpp"
    1515#include "World.hpp"
    16 #include "helpers.hpp"
     16#include "Helpers/helpers.hpp"
    1717#include "Actions/Process.hpp"
    1818

  • src/World.cpp

    r822f01 re588312  
    2525#include "Helpers/Assert.hpp"
    2626#include "Box.hpp"
    27 #include "Matrix.hpp"
     27#include "LinearAlgebra/Matrix.hpp"
    2828#include "defs.hpp"
    2929

  • src/analysis_bonds.cpp

    r822f01 re588312  
    1212#include "bond.hpp"
    1313#include "element.hpp"
    14 #include "info.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     14#include "Helpers/Info.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    1818

  • src/analysis_correlation.cpp

    r822f01 re588312  
    1313#include "analysis_correlation.hpp"
    1414#include "element.hpp"
    15 #include "info.hpp"
    16 #include "log.hpp"
     15#include "Helpers/Info.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    1818#include "tesselation.hpp"
    1919#include "tesselationhelpers.hpp"
    2020#include "triangleintersectionlist.hpp"
    21 #include "vector.hpp"
    22 #include "Matrix.hpp"
    23 #include "verbose.hpp"
     21#include "LinearAlgebra/Vector.hpp"
     22#include "LinearAlgebra/Matrix.hpp"
     23#include "Helpers/Verbose.hpp"
    2424#include "World.hpp"
    2525#include "Box.hpp"

  • src/analysis_correlation.hpp

    r822f01 re588312  
    2727
    2828#include "atom.hpp"
    29 #include "verbose.hpp"
     29#include "Helpers/Verbose.hpp"
    3030
    3131/****************************************** forward declarations *****************************/

  • src/analyzer.cpp

    r822f01 re588312  
    1313
    1414#include "datacreator.hpp"
    15 #include "helpers.hpp"
     15#include "Helpers/helpers.hpp"
    1616#include "parser.hpp"
    1717#include "periodentafel.hpp"
    18 #include "verbose.hpp"
     18#include "Helpers/Verbose.hpp"
    1919
    2020// include config.h

  • src/atom.cpp

    r822f01 re588312  
    1313#include "lists.hpp"
    1414#include "parser.hpp"
    15 #include "vector.hpp"
     15#include "LinearAlgebra/Vector.hpp"
    1616#include "World.hpp"
    1717#include "molecule.hpp"

  • src/atom_atominfo.hpp

    r822f01 re588312  
    1919#endif
    2020
    21 #include "vector.hpp"
     21#include "LinearAlgebra/Vector.hpp"
    2222
    2323/****************************************** forward declarations *****************************/

  • src/atom_bondedparticle.cpp

    r822f01 re588312  
    1313#include "element.hpp"
    1414#include "lists.hpp"
    15 #include "log.hpp"
    16 #include "verbose.hpp"
     15#include "Helpers/Log.hpp"
     16#include "Helpers/Verbose.hpp"
    1717
    1818/** Constructor of class BondedParticle.

  • src/atom_graphnode.cpp

    r822f01 re588312  
    99
    1010#include "atom_graphnode.hpp"
    11 #include "log.hpp"
    12 #include "verbose.hpp"
     11#include "Helpers/Log.hpp"
     12#include "Helpers/Verbose.hpp"
    1313
    1414/** Constructor of class GraphNode.

  • src/atom_trajectoryparticle.cpp

    r822f01 re588312  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "info.hpp"
    15 #include "log.hpp"
     14#include "Helpers/Info.hpp"
     15#include "Helpers/Log.hpp"
    1616#include "parser.hpp"
    1717#include "ThermoStatContainer.hpp"
    18 #include "verbose.hpp"
     18#include "Helpers/Verbose.hpp"
    1919
    2020/** Constructor of class TrajectoryParticle.

  • src/atom_trajectoryparticleinfo.hpp

    r822f01 re588312  
    2020#include <vector>
    2121
    22 #include "vector.hpp"
    23 #include "VectorSet.hpp"
     22#include "LinearAlgebra/Vector.hpp"
     23#include "LinearAlgebra/VectorSet.hpp"
    2424
    2525/********************************************** declarations *******************************/

  • src/bond.cpp

    r822f01 re588312  
    77#include "Helpers/MemDebug.hpp"
    88
    9 #include "verbose.hpp"
     9#include "Helpers/Verbose.hpp"
    1010#include "atom.hpp"
    1111#include "bond.hpp"

  • src/bondgraph.cpp

    r822f01 re588312  
    1414#include "bondgraph.hpp"
    1515#include "element.hpp"
    16 #include "info.hpp"
    17 #include "verbose.hpp"
    18 #include "log.hpp"
     16#include "Helpers/Info.hpp"
     17#include "Helpers/Verbose.hpp"
     18#include "Helpers/Log.hpp"
    1919#include "molecule.hpp"
    2020#include "parser.hpp"
    2121#include "periodentafel.hpp"
    22 #include "vector.hpp"
     22#include "LinearAlgebra/Vector.hpp"
    2323
    2424/** Constructor of class BondGraph.

  • src/boundary.cpp

    r822f01 re588312  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "helpers.hpp"
    15 #include "info.hpp"
     14#include "Helpers/helpers.hpp"
     15#include "Helpers/Info.hpp"
    1616#include "linkedcell.hpp"
    17 #include "verbose.hpp"
    18 #include "log.hpp"
     17#include "Helpers/Verbose.hpp"
     18#include "Helpers/Log.hpp"
    1919#include "molecule.hpp"
    2020#include "tesselation.hpp"
    2121#include "tesselationhelpers.hpp"
    2222#include "World.hpp"
    23 #include "Plane.hpp"
    24 #include "Matrix.hpp"
     23#include "LinearAlgebra/Plane.hpp"
     24#include "LinearAlgebra/Matrix.hpp"
    2525#include "Box.hpp"
    2626

  • src/builder.cpp

    r822f01 re588312  
    5959#include "CommandLineParser.hpp"
    6060#include "config.hpp"
    61 #include "log.hpp"
     61#include "Helpers/Log.hpp"
    6262#include "molecule.hpp"
    6363#include "periodentafel.hpp"
    … …  
    7272#include "UIElements/Dialog.hpp"
    7373#include "Menu/ActionMenuItem.hpp"
    74 #include "verbose.hpp"
     74#include "Helpers/Verbose.hpp"
    7575#include "World.hpp"
    7676

  • src/config.cpp

    r822f01 re588312  
    1616#include "ConfigFileBuffer.hpp"
    1717#include "element.hpp"
    18 #include "helpers.hpp"
    19 #include "info.hpp"
     18#include "Helpers/helpers.hpp"
     19#include "Helpers/Info.hpp"
    2020#include "lists.hpp"
    21 #include "verbose.hpp"
    22 #include "log.hpp"
     21#include "Helpers/Verbose.hpp"
     22#include "Helpers/Log.hpp"
    2323#include "molecule.hpp"
    2424#include "molecule.hpp"
    … …  
    2626#include "ThermoStatContainer.hpp"
    2727#include "World.hpp"
    28 #include "Matrix.hpp"
     28#include "LinearAlgebra/Matrix.hpp"
    2929#include "Box.hpp"
    3030

  • src/datacreator.cpp

    r822f01 re588312  
    1010
    1111#include "datacreator.hpp"
    12 #include "helpers.hpp"
     12#include "Helpers/helpers.hpp"
    1313#include "parser.hpp"
    14 #include "verbose.hpp"
     14#include "Helpers/Verbose.hpp"
    1515
    1616#include <iomanip>

  • src/ellipsoid.cpp

    r822f01 re588312  
    1818#include "ellipsoid.hpp"
    1919#include "linkedcell.hpp"
    20 #include "log.hpp"
     20#include "Helpers/Log.hpp"
    2121#include "tesselation.hpp"
    22 #include "vector.hpp"
    23 #include "Matrix.hpp"
    24 #include "verbose.hpp"
     22#include "LinearAlgebra/Vector.hpp"
     23#include "LinearAlgebra/Matrix.hpp"
     24#include "Helpers/Verbose.hpp"
    2525
    2626/** Determines squared distance for a given point \a x to surface of ellipsoid.

  • src/graph.cpp

    r822f01 re588312  
    1313#include "config.hpp"
    1414#include "graph.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    1818

  • src/joiner.cpp

    r822f01 re588312  
    1313
    1414#include "datacreator.hpp"
    15 #include "helpers.hpp"
     15#include "Helpers/helpers.hpp"
    1616#include "parser.hpp"
    1717#include "periodentafel.hpp"
    18 #include "verbose.hpp"
     18#include "Helpers/Verbose.hpp"
    1919
    2020//============================== MAIN =============================

  • src/leastsquaremin.cpp

    r822f01 re588312  
    1111
    1212#include "leastsquaremin.hpp"
    13 #include "vector.hpp"
     13#include "LinearAlgebra/Vector.hpp"
    1414
    1515/** Determines sum of squared distances of \a X to all \a **vectors.

  • src/linkedcell.cpp

    r822f01 re588312  
    88
    99#include "atom.hpp"
    10 #include "helpers.hpp"
     10#include "Helpers/helpers.hpp"
    1111#include "linkedcell.hpp"
    12 #include "verbose.hpp"
    13 #include "log.hpp"
     12#include "Helpers/Verbose.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "molecule.hpp"
    1515#include "tesselation.hpp"
    16 #include "vector.hpp"
     16#include "LinearAlgebra/Vector.hpp"
    1717
    1818// ========================================================= class LinkedCell ===========================================

  • src/linkedcell.hpp

    r822f01 re588312  
    2424
    2525#include "defs.hpp"
    26 #include "vector.hpp"
     26#include "LinearAlgebra/Vector.hpp"
    2727
    2828/****************************************** forward declarations *****************************/

  • src/molecule.cpp

    r822f01 re588312  
    2424#include "element.hpp"
    2525#include "graph.hpp"
    26 #include "helpers.hpp"
     26#include "Helpers/helpers.hpp"
    2727#include "leastsquaremin.hpp"
    2828#include "linkedcell.hpp"
    2929#include "lists.hpp"
    30 #include "log.hpp"
     30#include "Helpers/Log.hpp"
    3131#include "molecule.hpp"
    3232
    … …  
    3434#include "stackclass.hpp"
    3535#include "tesselation.hpp"
    36 #include "vector.hpp"
    37 #include "Matrix.hpp"
     36#include "LinearAlgebra/Vector.hpp"
     37#include "LinearAlgebra/Matrix.hpp"
    3838#include "World.hpp"
    3939#include "Box.hpp"
    40 #include "Plane.hpp"
     40#include "LinearAlgebra/Plane.hpp"
    4141#include "Exceptions/LinearDependenceException.hpp"
    4242

  • src/molecule_dynamics.cpp

    r822f01 re588312  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "info.hpp"
    15 #include "verbose.hpp"
    16 #include "log.hpp"
     14#include "Helpers/Info.hpp"
     15#include "Helpers/Verbose.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "molecule.hpp"
    1818#include "parser.hpp"
    19 #include "Plane.hpp"
     19#include "LinearAlgebra/Plane.hpp"
    2020#include "ThermoStatContainer.hpp"
    2121

  • src/molecule_fragmentation.cpp

    r822f01 re588312  
    1515#include "config.hpp"
    1616#include "element.hpp"
    17 #include "helpers.hpp"
     17#include "Helpers/helpers.hpp"
    1818#include "lists.hpp"
    19 #include "verbose.hpp"
    20 #include "log.hpp"
     19#include "Helpers/Verbose.hpp"
     20#include "Helpers/Log.hpp"
    2121#include "molecule.hpp"
    2222#include "periodentafel.hpp"
    2323#include "World.hpp"
    24 #include "Matrix.hpp"
     24#include "LinearAlgebra/Matrix.hpp"
    2525#include "Box.hpp"
    2626#include "stackclass.hpp"

  • src/molecule_geometry.cpp

    r822f01 re588312  
    1616#include "config.hpp"
    1717#include "element.hpp"
    18 #include "helpers.hpp"
     18#include "Helpers/helpers.hpp"
    1919#include "leastsquaremin.hpp"
    20 #include "verbose.hpp"
    21 #include "log.hpp"
     20#include "Helpers/Verbose.hpp"
     21#include "Helpers/Log.hpp"
    2222#include "molecule.hpp"
    2323#include "World.hpp"
    24 #include "Plane.hpp"
    25 #include "Matrix.hpp"
     24#include "LinearAlgebra/Plane.hpp"
     25#include "LinearAlgebra/Matrix.hpp"
    2626#include "Box.hpp"
    2727#include <boost/foreach.hpp>

  • src/molecule_graph.cpp

    r822f01 re588312  
    1818#include "defs.hpp"
    1919#include "element.hpp"
    20 #include "helpers.hpp"
    21 #include "info.hpp"
     20#include "Helpers/helpers.hpp"
     21#include "Helpers/Info.hpp"
    2222#include "linkedcell.hpp"
    2323#include "lists.hpp"
    24 #include "verbose.hpp"
    25 #include "log.hpp"
     24#include "Helpers/Verbose.hpp"
     25#include "Helpers/Log.hpp"
    2626#include "molecule.hpp"
    2727#include "World.hpp"
    2828#include "Helpers/fast_functions.hpp"
    2929#include "Helpers/Assert.hpp"
    30 #include "Matrix.hpp"
     30#include "LinearAlgebra/Matrix.hpp"
    3131#include "Box.hpp"
    3232#include "stackclass.hpp"

  • src/molecule_pointcloud.cpp

    r822f01 re588312  
    1010#include "atom.hpp"
    1111#include "config.hpp"
    12 #include "info.hpp"
     12#include "Helpers/Info.hpp"
    1313#include "molecule.hpp"
    1414

  • src/moleculelist.cpp

    r822f01 re588312  
    2323#include "config.hpp"
    2424#include "element.hpp"
    25 #include "helpers.hpp"
     25#include "Helpers/helpers.hpp"
    2626#include "linkedcell.hpp"
    2727#include "lists.hpp"
    28 #include "verbose.hpp"
    29 #include "log.hpp"
     28#include "Helpers/Verbose.hpp"
     29#include "Helpers/Log.hpp"
    3030#include "molecule.hpp"
    3131#include "periodentafel.hpp"
    3232#include "Helpers/Assert.hpp"
    33 #include "Matrix.hpp"
     33#include "LinearAlgebra/Matrix.hpp"
    3434#include "Box.hpp"
    3535#include "stackclass.hpp"

  • src/parser.cpp

    r822f01 re588312  
    1111#include <cstring>
    1212
    13 #include "helpers.hpp"
     13#include "Helpers/helpers.hpp"
    1414#include "parser.hpp"
    15 #include "verbose.hpp"
     15#include "Helpers/Verbose.hpp"
    1616
    1717// include config.h

  • src/periodentafel.cpp

    r822f01 re588312  
    1717#include "element.hpp"
    1818#include "elements_db.hpp"
    19 #include "helpers.hpp"
     19#include "Helpers/helpers.hpp"
    2020#include "lists.hpp"
    21 #include "log.hpp"
     21#include "Helpers/Log.hpp"
    2222#include "periodentafel.hpp"
    23 #include "verbose.hpp"
     23#include "Helpers/Verbose.hpp"
    2424
    2525using namespace std;

  • src/stackclass.hpp

    r822f01 re588312  
    1111#endif
    1212
    13 #include "verbose.hpp"
    14 #include "log.hpp"
     13#include "Helpers/Verbose.hpp"
     14#include "Helpers/Log.hpp"
    1515
    1616/****************************************** forward declarations *****************************/

  • src/tesselation.cpp

    r822f01 re588312  
    1111#include <iomanip>
    1212
    13 #include "helpers.hpp"
    14 #include "info.hpp"
     13#include "Helpers/helpers.hpp"
     14#include "Helpers/Info.hpp"
    1515#include "linkedcell.hpp"
    16 #include "log.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "tesselation.hpp"
    1818#include "tesselationhelpers.hpp"
    1919#include "triangleintersectionlist.hpp"
    20 #include "vector.hpp"
    21 #include "Line.hpp"
     20#include "LinearAlgebra/Vector.hpp"
     21#include "LinearAlgebra/Line.hpp"
    2222#include "vector_ops.hpp"
    23 #include "verbose.hpp"
    24 #include "Plane.hpp"
     23#include "Helpers/Verbose.hpp"
     24#include "LinearAlgebra/Plane.hpp"
    2525#include "Exceptions/LinearDependenceException.hpp"
    2626#include "Helpers/Assert.hpp"

  • src/tesselation.hpp

    r822f01 re588312  
    2626
    2727#include "atom_particleinfo.hpp"
    28 #include "helpers.hpp"
    29 #include "vector.hpp"
     28#include "Helpers/helpers.hpp"
     29#include "LinearAlgebra/Vector.hpp"
    3030
    3131/****************************************** forward declarations *****************************/

  • src/tesselationhelpers.cpp

    r822f01 re588312  
    1010#include <fstream>
    1111
    12 #include "info.hpp"
     12#include "Helpers/Info.hpp"
    1313#include "linkedcell.hpp"
    14 #include "linearsystemofequations.hpp"
    15 #include "log.hpp"
     14#include "LinearAlgebra/linearsystemofequations.hpp"
     15#include "Helpers/Log.hpp"
    1616#include "tesselation.hpp"
    1717#include "tesselationhelpers.hpp"
    18 #include "vector.hpp"
    19 #include "Line.hpp"
     18#include "LinearAlgebra/Vector.hpp"
     19#include "LinearAlgebra/Line.hpp"
    2020#include "vector_ops.hpp"
    21 #include "verbose.hpp"
    22 #include "Plane.hpp"
    23 #include "Matrix.hpp"
     21#include "Helpers/Verbose.hpp"
     22#include "LinearAlgebra/Plane.hpp"
     23#include "LinearAlgebra/Matrix.hpp"
    2424
    2525void GetSphere(Vector * const center, const Vector &a, const Vector &b, const Vector &c, const double RADIUS)

  • src/test/ActOnAlltest.hpp

    r822f01 re588312  
    1212
    1313#include <list>
    14 #include "../vector.hpp"
     14#include "../LinearAlgebra/Vector.hpp"
    1515
    1616#define ListOfVectors list<Vector *>

  • src/triangleintersectionlist.cpp

    r822f01 re588312  
    1515#include "triangleintersectionlist.hpp"
    1616
    17 #include "info.hpp"
     17#include "Helpers/Info.hpp"
    1818#include "tesselation.hpp"
    19 #include "vector.hpp"
    20 #include "verbose.hpp"
     19#include "LinearAlgebra/Vector.hpp"
     20#include "Helpers/Verbose.hpp"
    2121
    2222/** Constructor for class TriangleIntersectionList.

  • src/unittests/ActOnAllUnitTest.cpp

    r822f01 re588312  
    1414#include "../test/ActOnAlltest.hpp"
    1515#include "ActOnAllUnitTest.hpp"
    16 #include "vector.hpp"
     16#include "LinearAlgebra/Vector.hpp"
    1717
    1818#ifdef HAVE_TESTRUNNER

  • src/unittests/ActionSequenceTest.cpp

    r822f01 re588312  
    243243
    244244  CPPUNIT_ASSERT_EQUAL(true,wasCalled1->wasCalled());
    245   CPPUNIT_ASSERT_EQUAL(true,wasCalled1->wasCalled());
     245  CPPUNIT_ASSERT_EQUAL(true,wasCalled2->wasCalled());
    246246
    247247  ActionHistory::getInstance().undoLast();
    248248
    249249  CPPUNIT_ASSERT_EQUAL(false,wasCalled1->wasCalled());
    250   CPPUNIT_ASSERT_EQUAL(false,wasCalled1->wasCalled());
    251 
    252 }
    253 
    254 
     250  CPPUNIT_ASSERT_EQUAL(false,wasCalled2->wasCalled());
     251
     252}
     253
     254

  • src/unittests/BoxUnittest.cpp

    r822f01 re588312  
    1616#endif /*HAVE_TESTRUNNER*/
    1717
    18 #include "vector.hpp"
    19 #include "Matrix.hpp"
     18#include "LinearAlgebra/Vector.hpp"
     19#include "LinearAlgebra/Matrix.hpp"
    2020#include "Box.hpp"
    2121#include "Helpers/Assert.hpp"

  • src/unittests/LineUnittest.cpp

    r822f01 re588312  
    88#include "LineUnittest.hpp"
    99
    10 #include "vector.hpp"
     10#include "LinearAlgebra/Vector.hpp"
    1111#include "Exceptions/LinearDependenceException.hpp"
    1212#include "Exceptions/SkewException.hpp"

  • src/unittests/LineUnittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "Line.hpp"
     13#include "LinearAlgebra/Line.hpp"
    1414
    1515class LineUnittest : public CppUnit::TestFixture

  • src/unittests/Makefile.am

    r822f01 re588312  
    4949noinst_PROGRAMS = $(TESTS) TestRunner
    5050
    51 GSLLIBS = ../libgslwrapper.a ../libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
    52 ALLLIBS = ../libmolecuilder.a ${GSLLIBS}
    53 PARSERLIBS = ../libparser.a ${ALLLIBS}
    54 UILIBS = ../UIElements/libMolecuilderUI.a ../Actions/libMolecuilderActions.a ${ALLLIBS} ${BOOST_PROGRAM_OPTIONS_LIB}
     51GSLLIBS = \
     52        ../LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
     53        ../Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
     54        ../Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
     55        $(BOOST_LIB) \
     56        ${BOOST_THREAD_LIB}
     57ALLLIBS = \
     58        ../Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
     59        ${PARSERLIBS} \
     60        ../libMolecuilder-@MOLECUILDER_API_VERSION@.la \
     61        ${GSLLIBS} \
     62        ${BOOST_PROGRAM_OPTIONS_LIB}
     63PARSERLIBS = ../Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la
     64UILIBS = ../UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la 
    5565
    5666TESTSOURCES = \
    … …  
    119129  MoleculeDescriptorTest.hpp \
    120130  periodentafelTest.hpp \
     131  ParserUnitTest.hpp \
    121132  PlaneUnittest.hpp \
    122133  ObserverTest.hpp \
    … …  
    129140 
    130141
    131 ActionSequenceTest_SOURCES = UnitTestMain.cpp ActionSequenceTest.cpp ActionSequenceTest.hpp $(srcdir)/../version.c
    132 ActionSequenceTest_LDADD = ${UILIBS}
     142ActionSequenceTest_SOURCES = UnitTestMain.cpp ActionSequenceTest.cpp ActionSequenceTest.hpp
     143ActionSequenceTest_LDADD = ${UILIBS} ${ALLLIBS}
    133144
    134145ActOnAllUnitTest_SOURCES = UnitTestMain.cpp ../test/ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp
    … …  
    169180
    170181GSLMatrixSymmetricUnitTest_SOURCES = UnitTestMain.cpp gslmatrixsymmetricunittest.cpp gslmatrixsymmetricunittest.hpp
    171 GSLMatrixSymmetricUnitTest_LDADD = ${GSLLIBS}
     182GSLMatrixSymmetricUnitTest_LDADD = ${ALLLIBS}
    172183
    173184GSLMatrixUnitTest_SOURCES = UnitTestMain.cpp gslmatrixunittest.cpp gslmatrixunittest.hpp
    174 GSLMatrixUnitTest_LDADD = ${GSLLIBS}
     185GSLMatrixUnitTest_LDADD = ${ALLLIBS}
    175186
    176187GSLVectorUnitTest_SOURCES = UnitTestMain.cpp gslvectorunittest.cpp gslvectorunittest.hpp
    177 GSLVectorUnitTest_LDADD = ${GSLLIBS}
     188GSLVectorUnitTest_LDADD = ${ALLLIBS}
    178189
    179190InfoUnitTest_SOURCES = UnitTestMain.cpp infounittest.cpp infounittest.hpp
    … …  
    195206LogUnitTest_LDADD = ${ALLLIBS}
    196207
    197 manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp $(srcdir)/../version.c
    198 manipulateAtomsTest_LDADD = ${UILIBS}
     208manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp
     209manipulateAtomsTest_LDADD = ${UILIBS} ${ALLLIBS}
    199210
    200211MatrixUnittest_SOURCES = UnitTestMain.cpp MatrixUnittest.cpp MatrixUnittest.hpp
    … …  
    208219
    209220ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp
    210 ParserUnitTest_LDADD = ${PARSERLIBS}
     221ParserUnitTest_LDADD = ${ALLLIBS}
    211222
    212223periodentafelTest_SOURCES = UnitTestMain.cpp periodentafelTest.cpp periodentafelTest.hpp
    … …  
    234245Tesselation_InOutsideUnitTest_LDADD = ${ALLLIBS}
    235246
    236 TestRunner_SOURCES = TestRunnerMain.cpp $(srcdir)/../version.c $(TESTSOURCES) $(TESTHEADERS)
    237 TestRunner_LDADD = ../UIElements/libMolecuilderUI.a ../Actions/libMolecuilderActions.a ../libmolecuilder.a ../libparser.a ../libgslwrapper.a ../libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     247TestRunner_SOURCES = TestRunnerMain.cpp $(TESTSOURCES) $(TESTHEADERS)
     248TestRunner_LDADD = ${UILIBS} ${ALLLIBS}
    238249
    239250VectorUnitTest_SOURCES = UnitTestMain.cpp vectorunittest.cpp vectorunittest.hpp

  • src/unittests/MatrixUnittest.cpp

    r822f01 re588312  
    1111
    1212#include "MatrixUnittest.hpp"
    13 #include "Matrix.hpp"
    14 #include "vector.hpp"
     13#include "LinearAlgebra/Matrix.hpp"
     14#include "LinearAlgebra/Vector.hpp"
    1515#include "Exceptions/NotInvertibleException.hpp"
    1616

  • src/unittests/PlaneUnittest.cpp

    r822f01 re588312  
    1818#endif /*HAVE_TESTRUNNER*/
    1919
    20 #include "vector.hpp"
    21 #include "Line.hpp"
     20#include "LinearAlgebra/Vector.hpp"
     21#include "LinearAlgebra/Line.hpp"
    2222
    2323CPPUNIT_TEST_SUITE_REGISTRATION( PlaneUnittest );

  • src/unittests/PlaneUnittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "Plane.hpp"
     13#include "LinearAlgebra/Plane.hpp"
    1414
    1515class PlaneUnittest : public CppUnit::TestFixture

  • src/unittests/ShapeUnittest.cpp

    r822f01 re588312  
    1616#endif /*HAVE_TESTRUNNER*/
    1717
     18#include "LinearAlgebra/Vector.hpp"
    1819#include "Shapes/Shape.hpp"
    19 #include "vector.cpp"
    2020
    2121// Registers the fixture into the 'registry'

  • src/unittests/ShapeUnittest.hpp

    r822f01 re588312  
    1414class Vector;
    1515
    16 #include "vector.hpp"
     16#include "LinearAlgebra/Vector.hpp"
    1717
    1818class ShapeUnittest : public CppUnit::TestFixture

  • src/unittests/bondgraphunittest.cpp

    r822f01 re588312  
    2323#include "bondgraph.hpp"
    2424#include "element.hpp"
    25 #include "log.hpp"
     25#include "Helpers/Log.hpp"
    2626#include "molecule.hpp"
    2727#include "periodentafel.hpp"

  • src/unittests/gslmatrixsymmetricunittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "gslmatrix.hpp"
     13#include "LinearAlgebra/gslmatrix.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/gslmatrixunittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "gslmatrix.hpp"
     13#include "LinearAlgebra/gslmatrix.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/gslvectorunittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "gslvector.hpp"
     13#include "LinearAlgebra/gslvector.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/infounittest.cpp

    r822f01 re588312  
    1515#include <stdio.h>
    1616
    17 #include "info.hpp"
     17#include "Helpers/Info.hpp"
    1818#include "infounittest.hpp"
    19 #include "log.hpp"
     19#include "Helpers/Log.hpp"
    2020
    2121#ifdef HAVE_TESTRUNNER

  • src/unittests/linearsystemofequationsunittest.cpp

    r822f01 re588312  
    1515
    1616#include "linearsystemofequationsunittest.hpp"
    17 #include "vector.hpp"
     17#include "LinearAlgebra/Vector.hpp"
    1818
    1919#ifdef HAVE_TESTRUNNER

  • src/unittests/linearsystemofequationsunittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "linearsystemofequations.hpp"
     13#include "LinearAlgebra/linearsystemofequations.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/logunittest.cpp

    r822f01 re588312  
    1111
    1212#include "logunittest.hpp"
    13 #include "log.hpp"
     13#include "Helpers/Log.hpp"
    1414#include "defs.hpp"
    15 #include "verbose.hpp"
     15#include "Helpers/Verbose.hpp"
    1616
    1717#ifdef HAVE_TESTRUNNER

  • src/unittests/memoryallocatorunittest.cpp

    r822f01 re588312  
    1313#include "memoryallocatorunittest.hpp"
    1414#include "memoryusageobserver.hpp"
    15 #include "helpers.hpp"
    16 #include "log.hpp"
     15#include "Helpers/helpers.hpp"
     16#include "Helpers/Log.hpp"
    1717#include "defs.hpp"
    1818

  • src/unittests/stackclassunittest.cpp

    r822f01 re588312  
    1313
    1414#include "stackclassunittest.hpp"
    15 #include "log.hpp"
     15#include "Helpers/Log.hpp"
    1616
    1717#ifdef HAVE_TESTRUNNER

  • src/unittests/tesselation_insideoutsideunittest.cpp

    r822f01 re588312  
    1717#include "tesselation.hpp"
    1818#include "tesselation_insideoutsideunittest.hpp"
    19 #include "verbose.hpp"
     19#include "Helpers/Verbose.hpp"
    2020
    2121#ifdef HAVE_TESTRUNNER

  • src/unittests/vectorunittest.cpp

    r822f01 re588312  
    1414
    1515#include "defs.hpp"
    16 #include "log.hpp"
    17 #include "vector.hpp"
     16#include "Helpers/Log.hpp"
     17#include "LinearAlgebra/Vector.hpp"
    1818#include "vector_ops.hpp"
    1919#include "vectorunittest.hpp"
    20 #include "Plane.hpp"
     20#include "LinearAlgebra/Plane.hpp"
    2121#include "Exceptions/LinearDependenceException.hpp"
    22 #include "Matrix.hpp"
     22#include "LinearAlgebra/Matrix.hpp"
    2323
    2424#ifdef HAVE_TESTRUNNER

  • src/unittests/vectorunittest.hpp

    r822f01 re588312  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "vector.hpp"
     13#include "LinearAlgebra/Vector.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/vector_ops.cpp

    r822f01 re588312  
    88#include "Helpers/MemDebug.hpp"
    99
    10 #include "vector.hpp"
    11 #include "Plane.hpp"
    12 #include "log.hpp"
    13 #include "verbose.hpp"
    14 #include "gslmatrix.hpp"
     10#include "LinearAlgebra/Vector.hpp"
     11#include "LinearAlgebra/Plane.hpp"
     12#include "Helpers/Log.hpp"
     13#include "Helpers/Verbose.hpp"
     14#include "LinearAlgebra/gslmatrix.hpp"
    1515#include "leastsquaremin.hpp"
    16 #include "info.hpp"
     16#include "Helpers/Info.hpp"
    1717#include "Helpers/fast_functions.hpp"
    1818#include "Exceptions/LinearDependenceException.hpp"

  • test_all.sh

    r822f01 re588312  
    111111  echo "Making";
    112112  if [ $noprocs -gt 1 ]; then
    113     make -j$noprocs all install >>$logfile 2>&1;
    114   else
    115     make all install >>$logfile 2>&1;
     113    make -j$noprocs all >>$logfile 2>&1;
     114  else
     115    make all >>$logfile 2>&1;
    116116  fi
    117117}

  • tests/Tesselations/Makefile.am

    r822f01 re588312  
    1 TESTS = 1_2-dimethoxyethane.test \
    2 1_2-dimethylbenzene.test \
    3 2-methylcyclohexanone.test \
    4 benzene.test \
    5 cholesterol.test \
    6 cycloheptane.test \
    7 dimethyl_bromomalonate.test \
    8 glucose.test \
    9 heptan.test \
    10 isoleucine.test \
    11 neohexane.test \
    12 N_N-dimethylacetamide.test \
    13 proline.test \
    14 putrescine.test \
    15 tartaric_acid.test
     1TESTS = \
     2        1_2-dimethoxyethane.test \
     3        1_2-dimethylbenzene.test \
     4        2-methylcyclohexanone.test \
     5        benzene.test \
     6        cholesterol.test \
     7        cycloheptane.test \
     8        dimethyl_bromomalonate.test \
     9        glucose.test \
     10        isoleucine.test \
     11        neohexane.test \
     12        N_N-dimethylacetamide.test \
     13        proline.test \
     14        putrescine.test \
     15        tartaric_acid.test
     16
     17#       heptan.test
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