Changes in / [d223d5:b6da28]


Ignore:
Files:
33 added
44 deleted
155 edited

Legend:

Unmodified
Added
Removed

  • Makefile.am

    rd223d5 rb6da28  
    11ACLOCAL_AMFLAGS = -I m4
    22SUBDIRS = src src/unittests doc tests
    3 
    4 AUTOMAKE_OPTIONS = subdir-objects
    53
    64EXTRA_DIST = autogen.sh

  • configure.ac

    rd223d5 rb6da28  
    66AC_CONFIG_AUX_DIR(config)
    77AC_CONFIG_SRCDIR([src/builder.cpp])
    8 AC_CONFIG_HEADER([config.h libmolecuilder_config.h])
    9 AC_CONFIG_MACRO_DIR([m4])
     8AC_CONFIG_HEADER([config.h])
    109
    1110AM_INIT_AUTOMAKE(dist-bzip2 parallel-tests)
    … …  
    1514AC_PROG_CXX
    1615AC_PROG_CC
    17 # obselete by LT_INIT
    18 #AC_PROG_RANLIB
     16AC_PROG_RANLIB
    1917AC_PROG_INSTALL
    2018AC_CHECK_PROG([LATEX],[latex],[latex],[:])
    … …  
    2523AM_MISSING_PROG([DOXYGEN], [doxygen])
    2624
    27 LT_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
    33 AC_SUBST([MOLECUILDER_SO_VERSION], [1:2:0])
    34 AC_SUBST([MOLECUILDER_API_VERSION], [1.0])
    35 
    3625# Checks for libraries.
    37 AC_CHECK_LIB(m, sqrt, , AC_MSG_ERROR([compatible libc math library not found]))
     26AC_CHECK_LIB(m, sqrt, ,AC_MSG_ERROR([compatible libc math library not found]))
    3827
    3928# Boost libraries
    … …  
    121110        doc/molecuilder.xml])
    122111AC_CONFIG_FILES([
    123   molecuilder-${MOLECUILDER_API_VERSION}.pc:molecuilder.pc.in])
    124 AC_CONFIG_FILES([
    125112        Makefile
    126113        doc/Makefile
    127114        src/Makefile
    128115        src/Actions/Makefile
    129   src/Exceptions/Makefile
    130   src/Helpers/Makefile
    131   src/LinearAlgebra/Makefile
    132   src/Parser/Makefile
    133116        src/UIElements/Makefile
    134117        src/unittests/Makefile])

  • m4/gwqt4.m4

    rd223d5 rb6da28  
    147147        QT_LIBS="$QT_LIB"
    148148        if test $QT_IS_STATIC = yes ; then
    149             QT_LIBS="$QT_LIBS -lXext -lX11 -lm -lSM -lICE"
     149            QT_LIBS="$QT_LIBS -L$x_libraries -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 -lXext -lX11 -lm -lSM -lICE -ldl"
     156            QT_LIBS="$QT_LIBS -L$x_libraries -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 -lXext -lX11 -lm -lSM -lICE"
     164            QT_LIBS="$QT_LIBS -L$x_libraries -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 -lXext -lX11 -lm -lSM -lICE -lresolv -lsocket -lnsl"
     171            QT_LIBS="$QT_LIBS -L$x_libraries -lXext -lX11 -lm -lSM -lICE -lresolv -lsocket -lnsl"
    172172        fi
    173173        ;;

  • src/Actions/Action.cpp

    rd223d5 rb6da28  
    1818#include "UIElements/UIFactory.hpp"
    1919
    20 #include "Helpers/Log.hpp"
    21 #include "Helpers/Verbose.hpp"
     20#include "log.hpp"
     21#include "verbose.hpp"
    2222
    2323using namespace std;

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    rd223d5 rb6da28  
    1414#include "molecule.hpp"
    1515#include "linkedcell.hpp"
    16 #include "Helpers/Log.hpp"
    17 #include "Helpers/Verbose.hpp"
     16#include "log.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929const char AnalysisMolecularVolumeAction::NAME[] = "molecular-volume";

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    rd223d5 rb6da28  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "LinearAlgebra/Vector.hpp"
     20#include "vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "Actions/ValueStorage.hpp"
     30#include "UIElements/ValueStorage.hpp"
    3131
    3232const char AnalysisPairCorrelationAction::NAME[] = "pair-correlation";

  • src/Actions/AnalysisAction/PointCorrelationAction.cpp

    rd223d5 rb6da28  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "LinearAlgebra/Vector.hpp"
     20#include "vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "Actions/ValueStorage.hpp"
     30#include "UIElements/ValueStorage.hpp"
    3131
    3232const char AnalysisPointCorrelationAction::NAME[] = "point-correlation";

  • src/Actions/AnalysisAction/PointCorrelationAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313#include <vector>
    1414#include <string>

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515
    1616#include <iostream>
    … …  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "Actions/ValueStorage.hpp"
     23#include "UIElements/ValueStorage.hpp"
    2424
    2525const char AnalysisPrincipalAxisSystemAction::NAME[] = "principal-axis-system";

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    rd223d5 rb6da28  
    1313#include "boundary.hpp"
    1414#include "linkedcell.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "element.hpp"
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "LinearAlgebra/Vector.hpp"
     20#include "vector.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "Actions/ValueStorage.hpp"
     30#include "UIElements/ValueStorage.hpp"
    3131
    3232const char AnalysisSurfaceCorrelationAction::NAME[] = "surface-correlation";

  • src/Actions/AtomAction/AddAction.cpp

    rd223d5 rb6da28  
    1212#include "atom.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "LinearAlgebra/Vector.hpp"
    17 #include "Helpers/Verbose.hpp"
     16#include "vector.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929const char AtomAddAction::NAME[] = "add-atom";

  • src/Actions/AtomAction/AddAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313
    1414class element;

  • src/Actions/AtomAction/ChangeElementAction.cpp

    rd223d5 rb6da28  
    1212#include "atom.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "LinearAlgebra/Vector.hpp"
    16 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "vector.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "Actions/ValueStorage.hpp"
     26#include "UIElements/ValueStorage.hpp"
    2727
    2828const char AtomChangeElementAction::NAME[] = "change-element";

  • src/Actions/AtomAction/RemoveAction.cpp

    rd223d5 rb6da28  
    1212#include "atom.hpp"
    1313#include "Descriptors/AtomDescriptor.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "Actions/ValueStorage.hpp"
     26#include "UIElements/ValueStorage.hpp"
    2727
    2828const char AtomRemoveAction::NAME[] = "remove-atom";

  • src/Actions/CmdAction/BondLengthTableAction.cpp

    rd223d5 rb6da28  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727const char CommandLineBondLengthTableAction::NAME[] = "bond-table";

  • src/Actions/CmdAction/ElementDbAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "Helpers/Log.hpp"
     13#include "log.hpp"
    1414#include "periodentafel.hpp"
    15 #include "Helpers/Verbose.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727const char CommandLineElementDbAction::NAME[] = "element-db";

  • src/Actions/CmdAction/FastParsingAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626// memento to remember the state when undoing

  • src/Actions/CmdAction/VerboseAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/CmdAction/VerboseAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
    13 #include "Helpers/Verbose.hpp"
     12#include "log.hpp"
     13#include "verbose.hpp"
    1414
    1515#include <iostream>
    … …  
    2020#include "UIElements/UIFactory.hpp"
    2121#include "UIElements/Dialog.hpp"
    22 #include "Actions/ValueStorage.hpp"
     22#include "UIElements/ValueStorage.hpp"
    2323
    2424// memento to remember the state when undoing

  • src/Actions/CmdAction/VersionAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/CmdAction/VersionAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "version.h"
    1312
    1413#include <iostream>
    … …  
    1918#include "UIElements/UIFactory.hpp"
    2019#include "UIElements/Dialog.hpp"
    21 #include "Actions/ValueStorage.hpp"
     20#include "UIElements/ValueStorage.hpp"
    2221
    2322const char CommandLineVersionAction::NAME[] = "version";

  • src/Actions/ErrorAction.cpp

    rd223d5 rb6da28  
    1111
    1212#include "Actions/ErrorAction.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "Helpers/Assert.hpp"
    1616

  • src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

    rd223d5 rb6da28  
    1313#include "bondgraph.hpp"
    1414#include "config.hpp"
    15 #include "Helpers/Log.hpp"
     15#include "log.hpp"
    1616#include "molecule.hpp"
    1717#include "Descriptors/MoleculeDescriptor.hpp"
    1818#include "Descriptors/MoleculeIdDescriptor.hpp"
    1919#include "stackclass.hpp"
    20 #include "Helpers/Verbose.hpp"
     20#include "verbose.hpp"
    2121#include "World.hpp"
    2222
    … …  
    2828#include "UIElements/UIFactory.hpp"
    2929#include "UIElements/Dialog.hpp"
    30 #include "Actions/ValueStorage.hpp"
     30#include "UIElements/ValueStorage.hpp"
    3131
    3232const char FragmentationDepthFirstSearchAction::NAME[] = "depth-first-search";

  • src/Actions/FragmentationAction/FragmentationAction.cpp

    rd223d5 rb6da28  
    1313#include "bondgraph.hpp"
    1414#include "config.hpp"
    15 #include "Helpers/Log.hpp"
     15#include "log.hpp"
    1616#include "molecule.hpp"
    1717#include "Descriptors/MoleculeDescriptor.hpp"
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929
    3030const char FragmentationFragmentationAction::NAME[] = "fragment-mol";

  • src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

    rd223d5 rb6da28  
    1212#include "atom.hpp"
    1313#include "config.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    1616#include "Descriptors/MoleculeDescriptor.hpp"
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";

  • src/Actions/Makefile.am

    rd223d5 rb6da28  
    66AM_LDFLAGS = $(CPPUNIT_LIBS) -ldl
    77AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
     8
     9noinst_LIBRARIES = libMolecuilderActions.a
     10libMolecuilderActions_a_SOURCES = ${ACTIONSSOURCE} ${ACTIONSHEADER}
    811
    912ACTIONSSOURCE = \
    … …  
    1720  ${TESSELATIONACTIONSOURCE} \
    1821  ${WORLDACTIONSOURCE} \
    19   MapOfActions.cpp \
    20   ValueStorage.cpp
     22  MapOfActions.cpp
    2123
    2224ACTIONSHEADER = \
    … …  
    3133  ${WORLDACTIONHEADER} \
    3234  MapOfActions.hpp \
    33   ValueStorage.hpp \
    3435  Values.hpp
    3536 
    … …  
    167168  WorldAction/SetOutputFormatsAction.hpp               
    168169
    169 
    170 lib_LTLIBRARIES = libMolecuilderActions-@MOLECUILDER_API_VERSION@.la
    171 libMolecuilderActions_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
    172 libMolecuilderActions_libs = ../Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la
    173 nobase_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.
    183 libMolecuilderActions_@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.
    188 libMolecuilderActions_@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.
    201 libMolecuilderActions_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
    202 nodist_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.
    208 pkgconfigdir = $(libdir)/pkgconfig
    209 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
    210 
    211170unity.cpp:
    212171        echo "" >  unity.cpp; \

  • src/Actions/MapOfActions.cpp

    rd223d5 rb6da28  
    2626#include "CommandLineParser.hpp"
    2727#include "element.hpp"
    28 #include "Helpers/Log.hpp"
    29 #include "LinearAlgebra/Matrix.hpp"
     28#include "log.hpp"
     29#include "Matrix.hpp"
    3030#include "molecule.hpp"
    3131#include "periodentafel.hpp"
    32 #include "LinearAlgebra/Vector.hpp"
    33 #include "Helpers/Verbose.hpp"
     32#include "vector.hpp"
     33#include "verbose.hpp"
    3434
    3535#include "Actions/ActionRegistry.hpp"

  • src/Actions/MoleculeAction/BondFileAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/MoleculeAction/BondFileAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727

  • src/Actions/MoleculeAction/ChangeNameAction.cpp

    rd223d5 rb6da28  
    2020#include "UIElements/UIFactory.hpp"
    2121#include "UIElements/Dialog.hpp"
    22 #include "Actions/ValueStorage.hpp"
     22#include "UIElements/ValueStorage.hpp"
    2323
    2424/****** MoleculeChangeNameAction *****/

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    rd223d5 rb6da28  
    1515#include "config.hpp"
    1616#include "molecule.hpp"
    17 #include "Helpers/Verbose.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929
    3030/****** MoleculeFillWithMoleculeAction *****/

  • src/Actions/MoleculeAction/FillWithMoleculeAction.hpp

    rd223d5 rb6da28  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
    13 #include "LinearAlgebra/Vector.hpp"
     13#include "vector.hpp"
    1414
    1515class MoleculeListClass;

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

    rd223d5 rb6da28  
    1212#include "atom.hpp"
    1313#include "defs.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727/****** MoleculeRotateToPrincipalAxisSystemAction *****/

  • src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

    rd223d5 rb6da28  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929
    3030/****** MoleculeSaveAdjacencyAction *****/

  • src/Actions/MoleculeAction/SaveBondsAction.cpp

    rd223d5 rb6da28  
    1212#include "bondgraph.hpp"
    1313#include "config.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929
    3030/****** MoleculeSaveBondsAction *****/

  • src/Actions/MoleculeAction/SaveTemperatureAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727/****** MoleculeSaveTemperatureAction *****/

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    rd223d5 rb6da28  
    1212#include "boundary.hpp"
    1313#include "config.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727/****** MoleculeSuspendInWaterAction *****/

  • src/Actions/MoleculeAction/TranslateAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/MoleculeAction/TranslateAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    14 #include "LinearAlgebra/Vector.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "vector.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "Actions/ValueStorage.hpp"
     26#include "UIElements/ValueStorage.hpp"
    2727
    2828/****** MoleculeTranslateAction *****/

  • src/Actions/MoleculeAction/TranslateAction.hpp

    rd223d5 rb6da28  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
    13 #include "LinearAlgebra/Vector.hpp"
     13#include "vector.hpp"
    1414
    1515class MoleculeListClass;

  • src/Actions/MoleculeAction/VerletIntegrationAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727/****** MoleculeVerletIntegrationAction *****/

  • src/Actions/ParserAction/LoadXyzAction.cpp

    rd223d5 rb6da28  
    1414#include "Parser/XyzParser.hpp"
    1515#include "atom.hpp"
    16 #include "Helpers/Log.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    18 #include "Helpers/Verbose.hpp"
     18#include "verbose.hpp"
    1919#include "World.hpp"
    2020
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929
    3030/****** ParserLoadXyzAction *****/

  • src/Actions/ParserAction/SaveXyzAction.cpp

    rd223d5 rb6da28  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "Actions/ValueStorage.hpp"
     23#include "UIElements/ValueStorage.hpp"
    2424
    2525

  • src/Actions/SelectionAction/AllAtomsAction.cpp

    rd223d5 rb6da28  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/AllMoleculesAction.cpp

    rd223d5 rb6da28  
    1212#include "Descriptors/MoleculeDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/AtomByIdAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/MoleculeByIdAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/NotAllAtomsAction.cpp

    rd223d5 rb6da28  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/NotAllMoleculesAction.cpp

    rd223d5 rb6da28  
    1212#include "Descriptors/MoleculeDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727

  • src/Actions/SelectionAction/NotAtomByIdAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626

  • src/Actions/SelectionAction/NotMoleculeByIdAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "molecule.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626

  • src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

    rd223d5 rb6da28  
    1313#include "config.hpp"
    1414#include "linkedcell.hpp"
    15 #include "Helpers/Log.hpp"
     15#include "log.hpp"
    1616#include "molecule.hpp"
    17 #include "Helpers/Verbose.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929/****** TesselationConvexEnvelopeAction *****/

  • src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp

    rd223d5 rb6da28  
    1212#include "boundary.hpp"
    1313#include "linkedcell.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "Actions/ValueStorage.hpp"
     26#include "UIElements/ValueStorage.hpp"
    2727
    2828/****** TesselationNonConvexEnvelopeAction *****/

  • src/Actions/WorldAction/AddEmptyBoundaryAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "LinearAlgebra/Vector.hpp"
     13#include "log.hpp"
     14#include "vector.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626#include "Helpers/Assert.hpp"
    2727

  • src/Actions/WorldAction/AddEmptyBoundaryAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313
    1414void WorldAddEmptyBoundary(Vector &boundary);

  • src/Actions/WorldAction/BoundInBoxAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/WorldAction/BoundInBoxAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    1414#include "World.hpp"
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626const char WorldBoundInBoxAction::NAME[] = "bound-in-box";

  • src/Actions/WorldAction/CenterInBoxAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "Box.hpp"
    13 #include "Helpers/Log.hpp"
     13#include "log.hpp"
    1414#include "molecule.hpp"
    1515#include "World.hpp"
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626const char WorldCenterInBoxAction::NAME[] = "center-in-box";

  • src/Actions/WorldAction/CenterOnEdgeAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "LinearAlgebra/Vector.hpp"
     13#include "log.hpp"
     14#include "vector.hpp"
    1515#include "World.hpp"
    16 #include "LinearAlgebra/Matrix.hpp"
     16#include "Matrix.hpp"
    1717
    1818#include <iostream>
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626#include "Helpers/Assert.hpp"
    2727

  • src/Actions/WorldAction/ChangeBoxAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/WorldAction/ChangeBoxAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
    13 #include "Helpers/Verbose.hpp"
     12#include "log.hpp"
     13#include "verbose.hpp"
    1414#include "World.hpp"
    1515#include "Box.hpp"
    16 #include "LinearAlgebra/Matrix.hpp"
     16#include "Matrix.hpp"
    1717
    1818#include <iostream>
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727const char WorldChangeBoxAction::NAME[] = "change-box";

  • src/Actions/WorldAction/InputAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/WorldAction/InputAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "molecule.hpp"
    1414#include "Parser/FormatParserStorage.hpp"
    1515#include "Parser/PcpParser.hpp"
    16 #include "Helpers/Verbose.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818
    … …  
    2424#include "UIElements/UIFactory.hpp"
    2525#include "UIElements/Dialog.hpp"
    26 #include "Actions/ValueStorage.hpp"
     26#include "UIElements/ValueStorage.hpp"
    2727
    2828const char WorldInputAction::NAME[] = "input";

  • src/Actions/WorldAction/OutputAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "Parser/ChangeTracker.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626const char WorldOutputAction::NAME[] = "output";

  • src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp

    rd223d5 rb6da28  
    1212#include "Descriptors/AtomDescriptor.hpp"
    1313#include "atom.hpp"
    14 #include "Helpers/Log.hpp"
     14#include "log.hpp"
    1515#include "molecule.hpp"
    16 #include "LinearAlgebra/Vector.hpp"
    17 #include "Helpers/Verbose.hpp"
     16#include "vector.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929const char WorldRemoveSphereOfAtomsAction::NAME[] = "remove-sphere";

  • src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313
    1414

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
     13#include "log.hpp"
    1414#include "molecule.hpp"
    15 #include "LinearAlgebra/Vector.hpp"
    16 #include "LinearAlgebra/Matrix.hpp"
    17 #include "Helpers/Verbose.hpp"
     15#include "vector.hpp"
     16#include "Matrix.hpp"
     17#include "verbose.hpp"
    1818#include "World.hpp"
    1919#include "Box.hpp"
    … …  
    2626#include "UIElements/UIFactory.hpp"
    2727#include "UIElements/Dialog.hpp"
    28 #include "Actions/ValueStorage.hpp"
     28#include "UIElements/ValueStorage.hpp"
    2929#include "Descriptors/MoleculeDescriptor.hpp"
    3030#include "Descriptors/MoleculePtrDescriptor.hpp"

  • src/Actions/WorldAction/RepeatBoxAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313
    1414void WorldRepeatBox(Vector &Repeater);

  • src/Actions/WorldAction/ScaleBoxAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "atom.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "LinearAlgebra/Vector.hpp"
    15 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "vector.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717#include "Box.hpp"
    18 #include "LinearAlgebra/Matrix.hpp"
     18#include "Matrix.hpp"
    1919
    2020#include <iostream>
    … …  
    2525#include "UIElements/UIFactory.hpp"
    2626#include "UIElements/Dialog.hpp"
    27 #include "Actions/ValueStorage.hpp"
     27#include "UIElements/ValueStorage.hpp"
    2828
    2929const char WorldScaleBoxAction::NAME[] = "scale-box";

  • src/Actions/WorldAction/ScaleBoxAction.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Actions/Action.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
     12#include "vector.hpp"
    1313
    1414void WorldScaleBox(Vector &Scaler);

  • src/Actions/WorldAction/SetDefaultNameAction.cpp

    rd223d5 rb6da28  
    1010#include "Actions/WorldAction/SetDefaultNameAction.hpp"
    1111#include "Actions/ActionRegistry.hpp"
    12 #include "Helpers/Log.hpp"
    13 #include "Helpers/Verbose.hpp"
     12#include "log.hpp"
     13#include "verbose.hpp"
    1414#include "World.hpp"
    1515
    … …  
    2121#include "UIElements/UIFactory.hpp"
    2222#include "UIElements/Dialog.hpp"
    23 #include "Actions/ValueStorage.hpp"
     23#include "UIElements/ValueStorage.hpp"
    2424
    2525

  • src/Actions/WorldAction/SetGaussianBasisAction.cpp

    rd223d5 rb6da28  
    1111#include "Actions/ActionRegistry.hpp"
    1212#include "config.hpp"
    13 #include "Helpers/Log.hpp"
    14 #include "Helpers/Verbose.hpp"
     13#include "log.hpp"
     14#include "verbose.hpp"
    1515#include "World.hpp"
    1616
    … …  
    2222#include "UIElements/UIFactory.hpp"
    2323#include "UIElements/Dialog.hpp"
    24 #include "Actions/ValueStorage.hpp"
     24#include "UIElements/ValueStorage.hpp"
    2525
    2626

  • src/Actions/WorldAction/SetOutputFormatsAction.cpp

    rd223d5 rb6da28  
    1212#include "Parser/ChangeTracker.hpp"
    1313#include "Parser/FormatParserStorage.hpp"
    14 #include "Helpers/Log.hpp"
    15 #include "Helpers/Verbose.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
    1616#include "World.hpp"
    1717
    … …  
    2323#include "UIElements/UIFactory.hpp"
    2424#include "UIElements/Dialog.hpp"
    25 #include "Actions/ValueStorage.hpp"
     25#include "UIElements/ValueStorage.hpp"
    2626
    2727const char WorldSetOutputFormatsAction::NAME[] = "set-output";

  • src/Box.cpp

    rd223d5 rb6da28  
    1414#include <cstdlib>
    1515
    16 #include "LinearAlgebra/Matrix.hpp"
    17 #include "LinearAlgebra/Vector.hpp"
    18 #include "LinearAlgebra/Plane.hpp"
     16#include "Matrix.hpp"
     17#include "vector.hpp"
     18#include "Plane.hpp"
    1919
    2020#include "Helpers/Assert.hpp"

  • src/Box.hpp

    rd223d5 rb6da28  
    1515#include <list>
    1616#include <vector>
    17 #include "LinearAlgebra/VectorSet.hpp"
     17#include "VectorSet.hpp"
    1818
    1919/**

  • src/CommandLineParser.cpp

    rd223d5 rb6da28  
    1515#include "Patterns/Singleton_impl.hpp"
    1616#include "CommandLineParser.hpp"
    17 #include "Helpers/Log.hpp"
    18 #include "Helpers/Verbose.hpp"
     17#include "log.hpp"
     18#include "verbose.hpp"
    1919
    2020using namespace std;

  • src/ConfigFileBuffer.cpp

    rd223d5 rb6da28  
    77
    88#include "ConfigFileBuffer.hpp"
    9 #include "Helpers/helpers.hpp"
     9#include "helpers.hpp"
    1010#include "lists.hpp"
    11 #include "Helpers/Verbose.hpp"
    12 #include "Helpers/Log.hpp"
     11#include "verbose.hpp"
     12#include "log.hpp"
    1313#include "World.hpp"
    1414

  • src/Descriptors/AtomSelectionDescriptor.cpp

    rd223d5 rb6da28  
    99#include "Descriptors/AtomSelectionDescriptor_impl.hpp"
    1010
    11 #include "Helpers/helpers.hpp"
     11#include "helpers.hpp"
    1212
    1313AtomSelectionDescriptor_impl::AtomSelectionDescriptor_impl(){}

  • src/Descriptors/MoleculeSelectionDescriptor.cpp

    rd223d5 rb6da28  
    99#include "Descriptors/MoleculeSelectionDescriptor_impl.hpp"
    1010
    11 #include "Helpers/helpers.hpp"
     11#include "helpers.hpp"
    1212
    1313MoleculeSelectionDescriptor_impl::MoleculeSelectionDescriptor_impl(){}

  • src/Descriptors/SelectiveIterator_impl.hpp

    rd223d5 rb6da28  
    99#define SELECTIVEITERATOR_IMPL_HPP_
    1010
    11 #include "Helpers/helpers.hpp"
     11#include "helpers.hpp"
    1212
    1313template<class _Target,

  • src/Formula.hpp

    rd223d5 rb6da28  
    1616
    1717#include "types.hpp"
    18 #include "Helpers/helpers.hpp"
     18#include "helpers.hpp"
    1919
    2020class element;

  • src/Helpers/MemDebug.hpp

    rd223d5 rb6da28  
    101101
    102102#else
    103 
    104 #include <iosfwd>
    105 
    106103// memory debugging was disabled
    107104
    108105namespace Memory {
    109   inline void getState(){};
     106  inline void getState(){}
    110107
    111108  inline void dumpMemory(std::ostream&){};

  • src/Legacy/oldmenu.cpp

    rd223d5 rb6da28  
    2020#include "element.hpp"
    2121#include "ellipsoid.hpp"
    22 #include "Helpers/helpers.hpp"
     22#include "helpers.hpp"
    2323#include "leastsquaremin.hpp"
    2424#include "linkedcell.hpp"
    25 #include "Helpers/Log.hpp"
     25#include "log.hpp"
    2626#include "memoryusageobserverunittest.hpp"
    2727#include "molecule.hpp"
    2828#include "periodentafel.hpp"
    2929#include "vector_ops.hpp"
    30 #include "LinearAlgebra/Plane.hpp"
    31 #include "LinearAlgebra/Line.hpp"
     30#include "Plane.hpp"
     31#include "Line.hpp"
    3232
    3333#include "UIElements/UIFactory.hpp"

  • src/Makefile.am

    rd223d5 rb6da28  
    22# Also indentation by a single tab
    33
    4 SUBDIRS = Actions Exceptions Helpers LinearAlgebra Parser UIElements
    5 
     4SUBDIRS = Actions UIElements
     5
     6# this includes source files that need to be present at multiple points
     7HELPERSOURCE =  \
     8  Helpers/Assert.cpp \
     9  Helpers/MemDebug.cpp
     10 
     11BASESOURCE = \
     12  ${HELPERSOURCE} \
     13  Space.cpp \
     14  vector.cpp
     15 
     16BASEHEADER = \
     17  ${HELPERHEADER} \
     18  Space.hpp \
     19  vector.hpp
     20                       
    621ATOMSOURCE = \
    722  atom.cpp \
    … …  
    2540  atom_trajectoryparticleinfo.hpp
    2641
     42LINALGSOURCE = \
     43  gslmatrix.cpp \
     44  gslvector.cpp \
     45  linearsystemofequations.cpp
     46                           
     47LINALGHEADER = \
     48  gslmatrix.hpp \
     49  gslvector.hpp \
     50  linearsystemofequations.hpp
     51                           
    2752ANALYSISSOURCE = \
    2853  analysis_bonds.cpp \
    … …  
    5681  Actions/MethodAction.hpp \
    5782  Actions/Process.hpp
     83
     84EXCEPTIONSOURCE = \
     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                                 
     95EXCEPTIONHEADER = \
     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
     106PARSERSOURCE = \
     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
     115PARSERHEADER = \
     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
    58123
    59124PATTERNSOURCE = \
    … …  
    120185QTUI_DEFS =
    121186
    122 MOLECUILDERSOURCE = \
     187SOURCE = \
    123188  ${ANALYSISSOURCE} \
    124189  ${ACTIONSSOURCE} \
    125190  ${ATOMSOURCE} \
     191  ${EXCEPTIONSOURCE} \
    126192  ${PATTERNSOURCE} \
    127193  ${PARSERSOURCE} \
    … …  
    138204  elements_db.cpp \
    139205  ellipsoid.cpp \
     206  errorlogger.cpp \
    140207  Formula.cpp \
    141208  graph.cpp \
     209  helpers.cpp \
     210  info.cpp \
    142211  leastsquaremin.cpp \
     212  Line.cpp \
    143213  linkedcell.cpp \
     214  log.cpp \
     215  logger.cpp \
     216  Matrix.cpp \
    144217  moleculelist.cpp \
    145218  molecule.cpp \
    … …  
    151224  parser.cpp \
    152225  periodentafel.cpp \
     226  Plane.cpp \
    153227  tesselation.cpp \
    154228  tesselationhelpers.cpp \
    … …  
    157231  UIElements/UIFactory.cpp \
    158232  vector_ops.cpp \
     233  verbose.cpp \
    159234  World.cpp
    160235
    161 MOLECUILDERHEADER = \
     236HEADER = \
    162237  ${ANALYSISHEADER} \
    163238  ${ACTIONSHEADER} \
    164239  ${ATOMHEADER} \
     240  ${EXCEPTIONHEADER} \
    165241  ${PARSERHEADER} \
    166242  ${PATTERNHEADER} \
    … …  
    178254  elements_db.hpp \
    179255  ellipsoid.hpp \
     256  errorlogger.hpp \
    180257  Formula.hpp \
    181258  graph.hpp \
     259  helpers.hpp \
     260  info.hpp \
    182261  leastsquaremin.hpp \
     262  Line.hpp \
    183263  linkedcell.hpp \
    184264  lists.hpp \
     265  log.hpp \
     266  logger.hpp \
     267  Matrix.hpp \
    185268  molecule.hpp \
    186269  molecule_template.hpp \
    187270  parser.hpp \
    188271  periodentafel.hpp \
     272  Plane.hpp \
    189273  stackclass.hpp \
    190274  tesselation.hpp \
    … …  
    193277  triangleintersectionlist.hpp \
    194278  UIElements/UIFactory.hpp \
     279  verbose.hpp \
    195280  vector_ops.hpp \
    196281  World.hpp
    197282
    198 lib_LTLIBRARIES = libMolecuilder-@MOLECUILDER_API_VERSION@.la
    199 libMolecuilder_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
    200 libMolecuilder_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 
    212 nobase_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.
    222 libMolecuilder_@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.
    227 libMolecuilder_@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.
    240 libMolecuilder_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
    241 nodist_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.
    247 pkgconfigdir = $(libdir)/pkgconfig
    248 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
    249 
     283# the following files are no longer used:
     284#  memoryallocator.hpp \
     285#  memoryallocator.cpp \
     286#  memoryusageobserver.hpp \
     287#  memoryusageobserver.cpp
    250288
    251289BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    … …  
    253291INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    254292
    255 noinst_LIBRARIES = libmenu.a
     293noinst_LIBRARIES = libmolecuilderbase.a libmolecuilder.a libgslwrapper.a libmenu.a libparser.a
    256294bin_PROGRAMS = molecuilder molecuildergui joiner analyzer
    257295EXTRA_PROGRAMS = unity
    … …  
    259297molecuilderdir = ${bindir}
    260298
     299libmolecuilderbase_a_SOURCES = ${BASESOURCE} ${BASEHEADER}
     300libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
    261301libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
     302libparser_a_SOURCES = ${PARSERSOURCE} ${PARSERHEADER}
     303libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    262304
    263305molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    … …  
    266308#molecuilder_CXXFLAGS += -DNO_CACHING
    267309molecuilder_LDFLAGS = $(BOOST_LIB)
    268 molecuilder_SOURCES = builder.cpp
    269 molecuilder_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 
     310molecuilder_SOURCES = ${LEGACYSOURCE} builder.cpp
     311molecuilder_SOURCES += $(srcdir)/version.c
     312molecuilder_LDADD = UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilderbase.a libmolecuilder.a libparser.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    281313
    282314#Stuff for building the GUI using QT
    283 molecuildergui_SOURCES = ${QTUISOURCE} builder.cpp
     315molecuildergui_SOURCES = ${QTUISOURCE} ${LEGACYSOURCE} builder.cpp
     316molecuildergui_SOURCES += $(srcdir)/version.c
    284317molecuildergui_CXXFLAGS = ${QT_CXXFLAGS} ${GLU_CXXFLAGS} -DUSE_GUI_QT
    285318molecuildergui_LDFLAGS = $(BOOST_LIB) ${QT_LDFLAGS} ${GLU_LDFLAGS}
    286 
    287 unity_SOURCES = unity.cpp
     319molecuildergui_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
     321joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
     322joiner_LDADD = libmolecuilder.a libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     323
     324analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
     325analyzer_LDADD = libmolecuilder.a libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     326
     327unity_SOURCES = unity.cpp $(srcdir)/version.c
    288328unity_LDADD = $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    289 
    290 molecuildergui_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 
    303 joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
    304 joiner_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 
    313 analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp
    314 analyzer_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}
    322329
    323330#Rules needed for QT4
    … …  
    335342        done;
    336343
     344unity.cpp: ${LINALGSOURCE} ${LINALGHEADER} ${SOURCE} ${HEADER}
     345        echo "" >  unity.cpp; \
     346        list='$(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 $$list; do \
     353          echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
     354        done; \
     355        subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
     356                olddir=$$PWD;\
     357                cd $$directory && make unity.cpp;\
     358                cd $$olddir;\
     359                echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
     360        done;\
     361        echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
     362
     363MOSTLYCLEANFILES = allmocs.moc.cpp unity.cpp
     364       
    337365#EXTRA_DIST = ${molecuilder_DATA}
    338366
    … …  
    353381
    354382
    355 unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
    356         echo "" >  unity.cpp; \
    357         list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
    358           echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
    359         done; \
    360         subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
    361                 olddir=$$PWD;\
    362                 cd $$directory && make unity.cpp;\
    363                 cd $$olddir;\
    364                 echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
    365         done;\
    366         echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
    367         echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;
    368 
    369 MOSTLYCLEANFILES = allmocs.moc.cpp unity.cpp
    370        

  • src/Parser/FormatParserStorage.cpp

    rd223d5 rb6da28  
    1717#include "Parser/XyzParser.hpp"
    1818
    19 #include "Helpers/Log.hpp"
    20 #include "Helpers/Verbose.hpp"
     19#include "log.hpp"
     20#include "verbose.hpp"
    2121
    2222#include "Helpers/Assert.hpp"

  • src/Parser/MpqcParser.cpp

    rd223d5 rb6da28  
    1111#include "config.hpp"
    1212#include "element.hpp"
    13 #include "Helpers/Log.hpp"
     13#include "log.hpp"
    1414#include "periodentafel.hpp"
    15 #include "LinearAlgebra/Vector.hpp"
    16 #include "Helpers/Verbose.hpp"
     15#include "vector.hpp"
     16#include "verbose.hpp"
    1717#include "World.hpp"
    1818

  • src/Parser/PcpParser.cpp

    rd223d5 rb6da28  
    1414#include "element.hpp"
    1515#include "Helpers/Assert.hpp"
    16 #include "Helpers/Log.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    1818#include "PcpParser.hpp"
    1919#include "periodentafel.hpp"
    2020#include "ThermoStatContainer.hpp"
    21 #include "Helpers/Verbose.hpp"
     21#include "verbose.hpp"
    2222#include "World.hpp"
    23 #include "LinearAlgebra/Matrix.hpp"
     23#include "Matrix.hpp"
    2424#include "Box.hpp"
    2525

  • src/Shapes/BaseShapes.cpp

    rd223d5 rb6da28  
    99#include "Shapes/BaseShapes_impl.hpp"
    1010
    11 #include "LinearAlgebra/Vector.hpp"
     11#include "vector.hpp"
    1212
    1313bool Sphere_impl::isInside(const Vector &point){

  • src/Shapes/ShapeOps_impl.hpp

    rd223d5 rb6da28  
    1010
    1111#include "Shapes/Shape_impl.hpp"
    12 #include "LinearAlgebra/Vector.hpp"
    13 #include "LinearAlgebra/Matrix.hpp"
     12#include "vector.hpp"
     13#include "Matrix.hpp"
    1414
    1515class Resize_impl :  public Shape_impl

  • src/ThermoStatContainer.cpp

    rd223d5 rb6da28  
    1010#include "ConfigFileBuffer.hpp"
    1111#include "config.hpp"
    12 #include "Helpers/Log.hpp"
     12#include "log.hpp"
    1313#include "ThermoStatContainer.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515
    1616/** Constructor for class ThermoStatContainer.

  • src/UIElements/CommandLineUI/CommandLineDialog.cpp

    rd223d5 rb6da28  
    2323#include "CommandLineParser.hpp"
    2424#include "defs.hpp"
    25 #include "Helpers/Log.hpp"
    26 #include "LinearAlgebra/Matrix.hpp"
     25#include "log.hpp"
     26#include "Matrix.hpp"
    2727#include "periodentafel.hpp"
    28 #include "Helpers/Verbose.hpp"
     28#include "verbose.hpp"
    2929#include "World.hpp"
    3030#include "Box.hpp"
    … …  
    3333#include "element.hpp"
    3434#include "molecule.hpp"
    35 #include "LinearAlgebra/Vector.hpp"
     35#include "vector.hpp"
    3636
    3737using namespace std;

  • src/UIElements/Dialog.cpp

    rd223d5 rb6da28  
    99
    1010#include "Dialog.hpp"
    11 #include "Actions/ValueStorage.hpp"
    12 
    13 #include "Helpers/Verbose.hpp"
     11#include "ValueStorage.hpp"
     12
     13#include "verbose.hpp"
    1414#include "atom.hpp"
    1515#include "element.hpp"
    1616#include "molecule.hpp"
    17 #include "LinearAlgebra/Vector.hpp"
    18 #include "LinearAlgebra/Matrix.hpp"
     17#include "vector.hpp"
     18#include "Matrix.hpp"
    1919#include "Box.hpp"
    2020

  • src/UIElements/Dialog.hpp

    rd223d5 rb6da28  
    1414
    1515#include "Box.hpp"
    16 #include "LinearAlgebra/Vector.hpp"
     16#include "vector.hpp"
    1717
    1818class atom;

  • src/UIElements/Makefile.am

    rd223d5 rb6da28  
    55AM_LDFLAGS = $(CPPUNIT_LIBS) -ldl
    66AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
     7
     8noinst_LIBRARIES = libMolecuilderUI.a
     9libMolecuilderUI_a_SOURCES = ${UISOURCE} ${UIHEADER}
    710
    811VIEWSOURCE = \
    … …  
    4245  ${VIEWSOURCE} \
    4346  Dialog.cpp \
    44   MainWindow.cpp
     47  MainWindow.cpp \
     48  ValueStorage.cpp
    4549 
    4650UIHEADER = \
    … …  
    5155  ${VIEWHEADER} \
    5256  Dialog.hpp \
    53   MainWindow.hpp
     57  MainWindow.hpp \
     58  ValueStorage.hpp
    5459
    5560TEXTUISOURCE = \
    … …  
    7580  CommandLineUI/CommandLineWindow.hpp
    7681
    77 lib_LTLIBRARIES = libMolecuilderUI-@MOLECUILDER_API_VERSION@.la
    78 libMolecuilderUI_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
    79 libMolecuilderUI_LIBS = \
    80         Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la
    81 
    82 nobase_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.
    92 libMolecuilderUI_@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.
    97 libMolecuilderUI_@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.
    110 libMolecuilderUI_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
    111 nodist_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.
    117 pkgconfigdir = $(libdir)/pkgconfig
    118 pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
    119 
    12082unity.cpp:
    12183        echo "" >  unity.cpp; \

  • src/UIElements/QT4/QTDialog.cpp

    rd223d5 rb6da28  
    3535#include "Descriptors/AtomIdDescriptor.hpp"
    3636#include "Descriptors/MoleculeIdDescriptor.hpp"
    37 #include "LinearAlgebra/Matrix.hpp"
     37#include "Matrix.hpp"
    3838#include "Box.hpp"
    3939

  • src/UIElements/QT4/QTMainWindow.cpp

    rd223d5 rb6da28  
    2121#include "atom.hpp"
    2222#include "molecule.hpp"
    23 #include "Helpers/Verbose.hpp"
     23#include "verbose.hpp"
    2424#include "Actions/Action.hpp"
    2525#include "Actions/ActionRegistry.hpp"

  • src/UIElements/TextUI/TextDialog.cpp

    rd223d5 rb6da28  
    1919#include "World.hpp"
    2020#include "periodentafel.hpp"
    21 #include "Helpers/Log.hpp"
    22 #include "Helpers/Verbose.hpp"
     21#include "log.hpp"
     22#include "verbose.hpp"
    2323
    2424#include "atom.hpp"
    2525#include "element.hpp"
    2626#include "molecule.hpp"
    27 #include "LinearAlgebra/Vector.hpp"
    28 #include "LinearAlgebra/Matrix.hpp"
     27#include "vector.hpp"
     28#include "Matrix.hpp"
    2929#include "Box.hpp"
    3030

  • src/UIElements/TextUI/TextWindow.cpp

    rd223d5 rb6da28  
    2727
    2828#include "defs.hpp"
    29 #include "Helpers/Log.hpp"
    30 #include "Helpers/Verbose.hpp"
     29#include "log.hpp"
     30#include "verbose.hpp"
    3131
    3232// all needed due to config::SaveAll()

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

    rd223d5 rb6da28  
    1414#include "QTStatusBar.hpp"
    1515#include "World.hpp"
    16 #include "Helpers/helpers.hpp"
     16#include "helpers.hpp"
    1717#include "Actions/Process.hpp"
    1818

  • src/World.cpp

    rd223d5 rb6da28  
    2525#include "Helpers/Assert.hpp"
    2626#include "Box.hpp"
    27 #include "LinearAlgebra/Matrix.hpp"
     27#include "Matrix.hpp"
    2828#include "defs.hpp"
    2929

  • src/analysis_bonds.cpp

    rd223d5 rb6da28  
    1212#include "bond.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/Info.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     14#include "info.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    1818

  • src/analysis_correlation.cpp

    rd223d5 rb6da28  
    1313#include "analysis_correlation.hpp"
    1414#include "element.hpp"
    15 #include "Helpers/Info.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "info.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    1818#include "tesselation.hpp"
    1919#include "tesselationhelpers.hpp"
    2020#include "triangleintersectionlist.hpp"
    21 #include "LinearAlgebra/Vector.hpp"
    22 #include "LinearAlgebra/Matrix.hpp"
    23 #include "Helpers/Verbose.hpp"
     21#include "vector.hpp"
     22#include "Matrix.hpp"
     23#include "verbose.hpp"
    2424#include "World.hpp"
    2525#include "Box.hpp"

  • src/analysis_correlation.hpp

    rd223d5 rb6da28  
    2727
    2828#include "atom.hpp"
    29 #include "Helpers/Verbose.hpp"
     29#include "verbose.hpp"
    3030
    3131/****************************************** forward declarations *****************************/

  • src/analyzer.cpp

    rd223d5 rb6da28  
    1313
    1414#include "datacreator.hpp"
    15 #include "Helpers/helpers.hpp"
     15#include "helpers.hpp"
    1616#include "parser.hpp"
    1717#include "periodentafel.hpp"
    18 #include "Helpers/Verbose.hpp"
     18#include "verbose.hpp"
    1919
    2020// include config.h

  • src/atom.cpp

    rd223d5 rb6da28  
    1313#include "lists.hpp"
    1414#include "parser.hpp"
    15 #include "LinearAlgebra/Vector.hpp"
     15#include "vector.hpp"
    1616#include "World.hpp"
    1717#include "molecule.hpp"

  • src/atom_atominfo.hpp

    rd223d5 rb6da28  
    1919#endif
    2020
    21 #include "LinearAlgebra/Vector.hpp"
     21#include "vector.hpp"
    2222
    2323/****************************************** forward declarations *****************************/

  • src/atom_bondedparticle.cpp

    rd223d5 rb6da28  
    1313#include "element.hpp"
    1414#include "lists.hpp"
    15 #include "Helpers/Log.hpp"
    16 #include "Helpers/Verbose.hpp"
     15#include "log.hpp"
     16#include "verbose.hpp"
    1717
    1818/** Constructor of class BondedParticle.

  • src/atom_graphnode.cpp

    rd223d5 rb6da28  
    99
    1010#include "atom_graphnode.hpp"
    11 #include "Helpers/Log.hpp"
    12 #include "Helpers/Verbose.hpp"
     11#include "log.hpp"
     12#include "verbose.hpp"
    1313
    1414/** Constructor of class GraphNode.

  • src/atom_trajectoryparticle.cpp

    rd223d5 rb6da28  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/Info.hpp"
    15 #include "Helpers/Log.hpp"
     14#include "info.hpp"
     15#include "log.hpp"
    1616#include "parser.hpp"
    1717#include "ThermoStatContainer.hpp"
    18 #include "Helpers/Verbose.hpp"
     18#include "verbose.hpp"
    1919
    2020/** Constructor of class TrajectoryParticle.

  • src/atom_trajectoryparticleinfo.hpp

    rd223d5 rb6da28  
    2020#include <vector>
    2121
    22 #include "LinearAlgebra/Vector.hpp"
    23 #include "LinearAlgebra/VectorSet.hpp"
     22#include "vector.hpp"
     23#include "VectorSet.hpp"
    2424
    2525/********************************************** declarations *******************************/

  • src/bond.cpp

    rd223d5 rb6da28  
    77#include "Helpers/MemDebug.hpp"
    88
    9 #include "Helpers/Verbose.hpp"
     9#include "verbose.hpp"
    1010#include "atom.hpp"
    1111#include "bond.hpp"

  • src/bondgraph.cpp

    rd223d5 rb6da28  
    1414#include "bondgraph.hpp"
    1515#include "element.hpp"
    16 #include "Helpers/Info.hpp"
    17 #include "Helpers/Verbose.hpp"
    18 #include "Helpers/Log.hpp"
     16#include "info.hpp"
     17#include "verbose.hpp"
     18#include "log.hpp"
    1919#include "molecule.hpp"
    2020#include "parser.hpp"
    2121#include "periodentafel.hpp"
    22 #include "LinearAlgebra/Vector.hpp"
     22#include "vector.hpp"
    2323
    2424/** Constructor of class BondGraph.

  • src/boundary.cpp

    rd223d5 rb6da28  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/helpers.hpp"
    15 #include "Helpers/Info.hpp"
     14#include "helpers.hpp"
     15#include "info.hpp"
    1616#include "linkedcell.hpp"
    17 #include "Helpers/Verbose.hpp"
    18 #include "Helpers/Log.hpp"
     17#include "verbose.hpp"
     18#include "log.hpp"
    1919#include "molecule.hpp"
    2020#include "tesselation.hpp"
    2121#include "tesselationhelpers.hpp"
    2222#include "World.hpp"
    23 #include "LinearAlgebra/Plane.hpp"
    24 #include "LinearAlgebra/Matrix.hpp"
     23#include "Plane.hpp"
     24#include "Matrix.hpp"
    2525#include "Box.hpp"
    2626

  • src/builder.cpp

    rd223d5 rb6da28  
    5959#include "CommandLineParser.hpp"
    6060#include "config.hpp"
    61 #include "Helpers/Log.hpp"
     61#include "log.hpp"
    6262#include "molecule.hpp"
    6363#include "periodentafel.hpp"
    … …  
    7272#include "UIElements/Dialog.hpp"
    7373#include "Menu/ActionMenuItem.hpp"
    74 #include "Helpers/Verbose.hpp"
     74#include "verbose.hpp"
    7575#include "World.hpp"
    7676

  • src/config.cpp

    rd223d5 rb6da28  
    1616#include "ConfigFileBuffer.hpp"
    1717#include "element.hpp"
    18 #include "Helpers/helpers.hpp"
    19 #include "Helpers/Info.hpp"
     18#include "helpers.hpp"
     19#include "info.hpp"
    2020#include "lists.hpp"
    21 #include "Helpers/Verbose.hpp"
    22 #include "Helpers/Log.hpp"
     21#include "verbose.hpp"
     22#include "log.hpp"
    2323#include "molecule.hpp"
    2424#include "molecule.hpp"
    … …  
    2626#include "ThermoStatContainer.hpp"
    2727#include "World.hpp"
    28 #include "LinearAlgebra/Matrix.hpp"
     28#include "Matrix.hpp"
    2929#include "Box.hpp"
    3030

  • src/datacreator.cpp

    rd223d5 rb6da28  
    1010
    1111#include "datacreator.hpp"
    12 #include "Helpers/helpers.hpp"
     12#include "helpers.hpp"
    1313#include "parser.hpp"
    14 #include "Helpers/Verbose.hpp"
     14#include "verbose.hpp"
    1515
    1616#include <iomanip>

  • src/ellipsoid.cpp

    rd223d5 rb6da28  
    1818#include "ellipsoid.hpp"
    1919#include "linkedcell.hpp"
    20 #include "Helpers/Log.hpp"
     20#include "log.hpp"
    2121#include "tesselation.hpp"
    22 #include "LinearAlgebra/Vector.hpp"
    23 #include "LinearAlgebra/Matrix.hpp"
    24 #include "Helpers/Verbose.hpp"
     22#include "vector.hpp"
     23#include "Matrix.hpp"
     24#include "verbose.hpp"
    2525
    2626/** Determines squared distance for a given point \a x to surface of ellipsoid.

  • src/graph.cpp

    rd223d5 rb6da28  
    1313#include "config.hpp"
    1414#include "graph.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    1818

  • src/joiner.cpp

    rd223d5 rb6da28  
    1313
    1414#include "datacreator.hpp"
    15 #include "Helpers/helpers.hpp"
     15#include "helpers.hpp"
    1616#include "parser.hpp"
    1717#include "periodentafel.hpp"
    18 #include "Helpers/Verbose.hpp"
     18#include "verbose.hpp"
    1919
    2020//============================== MAIN =============================

  • src/leastsquaremin.cpp

    rd223d5 rb6da28  
    1111
    1212#include "leastsquaremin.hpp"
    13 #include "LinearAlgebra/Vector.hpp"
     13#include "vector.hpp"
    1414
    1515/** Determines sum of squared distances of \a X to all \a **vectors.

  • src/linkedcell.cpp

    rd223d5 rb6da28  
    88
    99#include "atom.hpp"
    10 #include "Helpers/helpers.hpp"
     10#include "helpers.hpp"
    1111#include "linkedcell.hpp"
    12 #include "Helpers/Verbose.hpp"
    13 #include "Helpers/Log.hpp"
     12#include "verbose.hpp"
     13#include "log.hpp"
    1414#include "molecule.hpp"
    1515#include "tesselation.hpp"
    16 #include "LinearAlgebra/Vector.hpp"
     16#include "vector.hpp"
    1717
    1818// ========================================================= class LinkedCell ===========================================

  • src/linkedcell.hpp

    rd223d5 rb6da28  
    2424
    2525#include "defs.hpp"
    26 #include "LinearAlgebra/Vector.hpp"
     26#include "vector.hpp"
    2727
    2828/****************************************** forward declarations *****************************/

  • src/molecule.cpp

    rd223d5 rb6da28  
    2424#include "element.hpp"
    2525#include "graph.hpp"
    26 #include "Helpers/helpers.hpp"
     26#include "helpers.hpp"
    2727#include "leastsquaremin.hpp"
    2828#include "linkedcell.hpp"
    2929#include "lists.hpp"
    30 #include "Helpers/Log.hpp"
     30#include "log.hpp"
    3131#include "molecule.hpp"
    3232
    … …  
    3434#include "stackclass.hpp"
    3535#include "tesselation.hpp"
    36 #include "LinearAlgebra/Vector.hpp"
    37 #include "LinearAlgebra/Matrix.hpp"
     36#include "vector.hpp"
     37#include "Matrix.hpp"
    3838#include "World.hpp"
    3939#include "Box.hpp"
    40 #include "LinearAlgebra/Plane.hpp"
     40#include "Plane.hpp"
    4141#include "Exceptions/LinearDependenceException.hpp"
    4242

  • src/molecule_dynamics.cpp

    rd223d5 rb6da28  
    1212#include "config.hpp"
    1313#include "element.hpp"
    14 #include "Helpers/Info.hpp"
    15 #include "Helpers/Verbose.hpp"
    16 #include "Helpers/Log.hpp"
     14#include "info.hpp"
     15#include "verbose.hpp"
     16#include "log.hpp"
    1717#include "molecule.hpp"
    1818#include "parser.hpp"
    19 #include "LinearAlgebra/Plane.hpp"
     19#include "Plane.hpp"
    2020#include "ThermoStatContainer.hpp"
    2121

  • src/molecule_fragmentation.cpp

    rd223d5 rb6da28  
    1515#include "config.hpp"
    1616#include "element.hpp"
    17 #include "Helpers/helpers.hpp"
     17#include "helpers.hpp"
    1818#include "lists.hpp"
    19 #include "Helpers/Verbose.hpp"
    20 #include "Helpers/Log.hpp"
     19#include "verbose.hpp"
     20#include "log.hpp"
    2121#include "molecule.hpp"
    2222#include "periodentafel.hpp"
    2323#include "World.hpp"
    24 #include "LinearAlgebra/Matrix.hpp"
     24#include "Matrix.hpp"
    2525#include "Box.hpp"
    2626#include "stackclass.hpp"

  • src/molecule_geometry.cpp

    rd223d5 rb6da28  
    1616#include "config.hpp"
    1717#include "element.hpp"
    18 #include "Helpers/helpers.hpp"
     18#include "helpers.hpp"
    1919#include "leastsquaremin.hpp"
    20 #include "Helpers/Verbose.hpp"
    21 #include "Helpers/Log.hpp"
     20#include "verbose.hpp"
     21#include "log.hpp"
    2222#include "molecule.hpp"
    2323#include "World.hpp"
    24 #include "LinearAlgebra/Plane.hpp"
    25 #include "LinearAlgebra/Matrix.hpp"
     24#include "Plane.hpp"
     25#include "Matrix.hpp"
    2626#include "Box.hpp"
    2727#include <boost/foreach.hpp>

  • src/molecule_graph.cpp

    rd223d5 rb6da28  
    1818#include "defs.hpp"
    1919#include "element.hpp"
    20 #include "Helpers/helpers.hpp"
    21 #include "Helpers/Info.hpp"
     20#include "helpers.hpp"
     21#include "info.hpp"
    2222#include "linkedcell.hpp"
    2323#include "lists.hpp"
    24 #include "Helpers/Verbose.hpp"
    25 #include "Helpers/Log.hpp"
     24#include "verbose.hpp"
     25#include "log.hpp"
    2626#include "molecule.hpp"
    2727#include "World.hpp"
    2828#include "Helpers/fast_functions.hpp"
    2929#include "Helpers/Assert.hpp"
    30 #include "LinearAlgebra/Matrix.hpp"
     30#include "Matrix.hpp"
    3131#include "Box.hpp"
    3232#include "stackclass.hpp"

  • src/molecule_pointcloud.cpp

    rd223d5 rb6da28  
    1010#include "atom.hpp"
    1111#include "config.hpp"
    12 #include "Helpers/Info.hpp"
     12#include "info.hpp"
    1313#include "molecule.hpp"
    1414

  • src/moleculelist.cpp

    rd223d5 rb6da28  
    2323#include "config.hpp"
    2424#include "element.hpp"
    25 #include "Helpers/helpers.hpp"
     25#include "helpers.hpp"
    2626#include "linkedcell.hpp"
    2727#include "lists.hpp"
    28 #include "Helpers/Verbose.hpp"
    29 #include "Helpers/Log.hpp"
     28#include "verbose.hpp"
     29#include "log.hpp"
    3030#include "molecule.hpp"
    3131#include "periodentafel.hpp"
    3232#include "Helpers/Assert.hpp"
    33 #include "LinearAlgebra/Matrix.hpp"
     33#include "Matrix.hpp"
    3434#include "Box.hpp"
    3535#include "stackclass.hpp"

  • src/parser.cpp

    rd223d5 rb6da28  
    1111#include <cstring>
    1212
    13 #include "Helpers/helpers.hpp"
     13#include "helpers.hpp"
    1414#include "parser.hpp"
    15 #include "Helpers/Verbose.hpp"
     15#include "verbose.hpp"
    1616
    1717// include config.h

  • src/periodentafel.cpp

    rd223d5 rb6da28  
    1717#include "element.hpp"
    1818#include "elements_db.hpp"
    19 #include "Helpers/helpers.hpp"
     19#include "helpers.hpp"
    2020#include "lists.hpp"
    21 #include "Helpers/Log.hpp"
     21#include "log.hpp"
    2222#include "periodentafel.hpp"
    23 #include "Helpers/Verbose.hpp"
     23#include "verbose.hpp"
    2424
    2525using namespace std;

  • src/stackclass.hpp

    rd223d5 rb6da28  
    1111#endif
    1212
    13 #include "Helpers/Verbose.hpp"
    14 #include "Helpers/Log.hpp"
     13#include "verbose.hpp"
     14#include "log.hpp"
    1515
    1616/****************************************** forward declarations *****************************/

  • src/tesselation.cpp

    rd223d5 rb6da28  
    1111#include <iomanip>
    1212
    13 #include "Helpers/helpers.hpp"
    14 #include "Helpers/Info.hpp"
     13#include "helpers.hpp"
     14#include "info.hpp"
    1515#include "linkedcell.hpp"
    16 #include "Helpers/Log.hpp"
     16#include "log.hpp"
    1717#include "tesselation.hpp"
    1818#include "tesselationhelpers.hpp"
    1919#include "triangleintersectionlist.hpp"
    20 #include "LinearAlgebra/Vector.hpp"
    21 #include "LinearAlgebra/Line.hpp"
     20#include "vector.hpp"
     21#include "Line.hpp"
    2222#include "vector_ops.hpp"
    23 #include "Helpers/Verbose.hpp"
    24 #include "LinearAlgebra/Plane.hpp"
     23#include "verbose.hpp"
     24#include "Plane.hpp"
    2525#include "Exceptions/LinearDependenceException.hpp"
    2626#include "Helpers/Assert.hpp"

  • src/tesselation.hpp

    rd223d5 rb6da28  
    2626
    2727#include "atom_particleinfo.hpp"
    28 #include "Helpers/helpers.hpp"
    29 #include "LinearAlgebra/Vector.hpp"
     28#include "helpers.hpp"
     29#include "vector.hpp"
    3030
    3131/****************************************** forward declarations *****************************/

  • src/tesselationhelpers.cpp

    rd223d5 rb6da28  
    1010#include <fstream>
    1111
    12 #include "Helpers/Info.hpp"
     12#include "info.hpp"
    1313#include "linkedcell.hpp"
    14 #include "LinearAlgebra/linearsystemofequations.hpp"
    15 #include "Helpers/Log.hpp"
     14#include "linearsystemofequations.hpp"
     15#include "log.hpp"
    1616#include "tesselation.hpp"
    1717#include "tesselationhelpers.hpp"
    18 #include "LinearAlgebra/Vector.hpp"
    19 #include "LinearAlgebra/Line.hpp"
     18#include "vector.hpp"
     19#include "Line.hpp"
    2020#include "vector_ops.hpp"
    21 #include "Helpers/Verbose.hpp"
    22 #include "LinearAlgebra/Plane.hpp"
    23 #include "LinearAlgebra/Matrix.hpp"
     21#include "verbose.hpp"
     22#include "Plane.hpp"
     23#include "Matrix.hpp"
    2424
    2525void GetSphere(Vector * const center, const Vector &a, const Vector &b, const Vector &c, const double RADIUS)

  • src/test/ActOnAlltest.hpp

    rd223d5 rb6da28  
    1212
    1313#include <list>
    14 #include "../LinearAlgebra/Vector.hpp"
     14#include "../vector.hpp"
    1515
    1616#define ListOfVectors list<Vector *>

  • src/triangleintersectionlist.cpp

    rd223d5 rb6da28  
    1515#include "triangleintersectionlist.hpp"
    1616
    17 #include "Helpers/Info.hpp"
     17#include "info.hpp"
    1818#include "tesselation.hpp"
    19 #include "LinearAlgebra/Vector.hpp"
    20 #include "Helpers/Verbose.hpp"
     19#include "vector.hpp"
     20#include "verbose.hpp"
    2121
    2222/** Constructor for class TriangleIntersectionList.

  • src/unittests/ActOnAllUnitTest.cpp

    rd223d5 rb6da28  
    1414#include "../test/ActOnAlltest.hpp"
    1515#include "ActOnAllUnitTest.hpp"
    16 #include "LinearAlgebra/Vector.hpp"
     16#include "vector.hpp"
    1717
    1818#ifdef HAVE_TESTRUNNER

  • src/unittests/BoxUnittest.cpp

    rd223d5 rb6da28  
    1616#endif /*HAVE_TESTRUNNER*/
    1717
    18 #include "LinearAlgebra/Vector.hpp"
    19 #include "LinearAlgebra/Matrix.hpp"
     18#include "vector.hpp"
     19#include "Matrix.hpp"
    2020#include "Box.hpp"
    2121#include "Helpers/Assert.hpp"

  • src/unittests/LineUnittest.cpp

    rd223d5 rb6da28  
    88#include "LineUnittest.hpp"
    99
    10 #include "LinearAlgebra/Vector.hpp"
     10#include "vector.hpp"
    1111#include "Exceptions/LinearDependenceException.hpp"
    1212#include "Exceptions/SkewException.hpp"

  • src/unittests/LineUnittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/Line.hpp"
     13#include "Line.hpp"
    1414
    1515class LineUnittest : public CppUnit::TestFixture

  • src/unittests/Makefile.am

    rd223d5 rb6da28  
    4949noinst_PROGRAMS = $(TESTS) TestRunner
    5050
    51 GSLLIBS = \
    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}
    57 ALLLIBS = \
    58         ../Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
    59         ${PARSERLIBS} \
    60         ../libMolecuilder-@MOLECUILDER_API_VERSION@.la \
    61         ${GSLLIBS} \
    62         ${BOOST_PROGRAM_OPTIONS_LIB}
    63 PARSERLIBS = ../Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la
    64 UILIBS = ../UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la 
     51GSLLIBS = ../libgslwrapper.a ../libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
     52ALLLIBS = ../libmolecuilder.a ${GSLLIBS}
     53PARSERLIBS = ../libparser.a ${ALLLIBS}
     54UILIBS = ../UIElements/libMolecuilderUI.a ../Actions/libMolecuilderActions.a ${ALLLIBS} ${BOOST_PROGRAM_OPTIONS_LIB}
    6555
    6656TESTSOURCES = \
    … …  
    129119  MoleculeDescriptorTest.hpp \
    130120  periodentafelTest.hpp \
    131   ParserUnitTest.hpp \
    132121  PlaneUnittest.hpp \
    133122  ObserverTest.hpp \
    … …  
    140129 
    141130
    142 ActionSequenceTest_SOURCES = UnitTestMain.cpp ActionSequenceTest.cpp ActionSequenceTest.hpp
    143 ActionSequenceTest_LDADD = ${UILIBS} ${ALLLIBS}
     131ActionSequenceTest_SOURCES = UnitTestMain.cpp ActionSequenceTest.cpp ActionSequenceTest.hpp $(srcdir)/../version.c
     132ActionSequenceTest_LDADD = ${UILIBS}
    144133
    145134ActOnAllUnitTest_SOURCES = UnitTestMain.cpp ../test/ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp
    … …  
    180169
    181170GSLMatrixSymmetricUnitTest_SOURCES = UnitTestMain.cpp gslmatrixsymmetricunittest.cpp gslmatrixsymmetricunittest.hpp
    182 GSLMatrixSymmetricUnitTest_LDADD = ${ALLLIBS}
     171GSLMatrixSymmetricUnitTest_LDADD = ${GSLLIBS}
    183172
    184173GSLMatrixUnitTest_SOURCES = UnitTestMain.cpp gslmatrixunittest.cpp gslmatrixunittest.hpp
    185 GSLMatrixUnitTest_LDADD = ${ALLLIBS}
     174GSLMatrixUnitTest_LDADD = ${GSLLIBS}
    186175
    187176GSLVectorUnitTest_SOURCES = UnitTestMain.cpp gslvectorunittest.cpp gslvectorunittest.hpp
    188 GSLVectorUnitTest_LDADD = ${ALLLIBS}
     177GSLVectorUnitTest_LDADD = ${GSLLIBS}
    189178
    190179InfoUnitTest_SOURCES = UnitTestMain.cpp infounittest.cpp infounittest.hpp
    … …  
    206195LogUnitTest_LDADD = ${ALLLIBS}
    207196
    208 manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp
    209 manipulateAtomsTest_LDADD = ${UILIBS} ${ALLLIBS}
     197manipulateAtomsTest_SOURCES = UnitTestMain.cpp manipulateAtomsTest.cpp manipulateAtomsTest.hpp $(srcdir)/../version.c
     198manipulateAtomsTest_LDADD = ${UILIBS}
    210199
    211200MatrixUnittest_SOURCES = UnitTestMain.cpp MatrixUnittest.cpp MatrixUnittest.hpp
    … …  
    219208
    220209ParserUnitTest_SOURCES = UnitTestMain.cpp ParserUnitTest.cpp ParserUnitTest.hpp
    221 ParserUnitTest_LDADD = ${ALLLIBS}
     210ParserUnitTest_LDADD = ${PARSERLIBS}
    222211
    223212periodentafelTest_SOURCES = UnitTestMain.cpp periodentafelTest.cpp periodentafelTest.hpp
    … …  
    245234Tesselation_InOutsideUnitTest_LDADD = ${ALLLIBS}
    246235
    247 TestRunner_SOURCES = TestRunnerMain.cpp $(TESTSOURCES) $(TESTHEADERS)
    248 TestRunner_LDADD = ${UILIBS} ${ALLLIBS}
     236TestRunner_SOURCES = TestRunnerMain.cpp $(srcdir)/../version.c $(TESTSOURCES) $(TESTHEADERS)
     237TestRunner_LDADD = ../UIElements/libMolecuilderUI.a ../Actions/libMolecuilderActions.a ../libmolecuilder.a ../libparser.a ../libgslwrapper.a ../libmolecuilderbase.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    249238
    250239VectorUnitTest_SOURCES = UnitTestMain.cpp vectorunittest.cpp vectorunittest.hpp

  • src/unittests/MatrixUnittest.cpp

    rd223d5 rb6da28  
    1111
    1212#include "MatrixUnittest.hpp"
    13 #include "LinearAlgebra/Matrix.hpp"
    14 #include "LinearAlgebra/Vector.hpp"
     13#include "Matrix.hpp"
     14#include "vector.hpp"
    1515#include "Exceptions/NotInvertibleException.hpp"
    1616

  • src/unittests/PlaneUnittest.cpp

    rd223d5 rb6da28  
    1818#endif /*HAVE_TESTRUNNER*/
    1919
    20 #include "LinearAlgebra/Vector.hpp"
    21 #include "LinearAlgebra/Line.hpp"
     20#include "vector.hpp"
     21#include "Line.hpp"
    2222
    2323CPPUNIT_TEST_SUITE_REGISTRATION( PlaneUnittest );

  • src/unittests/PlaneUnittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/Plane.hpp"
     13#include "Plane.hpp"
    1414
    1515class PlaneUnittest : public CppUnit::TestFixture

  • src/unittests/ShapeUnittest.cpp

    rd223d5 rb6da28  
    1616#endif /*HAVE_TESTRUNNER*/
    1717
    18 #include "LinearAlgebra/Vector.hpp"
    1918#include "Shapes/Shape.hpp"
     19#include "vector.hpp"
    2020
    2121// Registers the fixture into the 'registry'

  • src/unittests/ShapeUnittest.hpp

    rd223d5 rb6da28  
    1414class Vector;
    1515
    16 #include "LinearAlgebra/Vector.hpp"
     16#include "vector.hpp"
    1717
    1818class ShapeUnittest : public CppUnit::TestFixture

  • src/unittests/bondgraphunittest.cpp

    rd223d5 rb6da28  
    2323#include "bondgraph.hpp"
    2424#include "element.hpp"
    25 #include "Helpers/Log.hpp"
     25#include "log.hpp"
    2626#include "molecule.hpp"
    2727#include "periodentafel.hpp"

  • src/unittests/gslmatrixsymmetricunittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/gslmatrix.hpp"
     13#include "gslmatrix.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/gslmatrixunittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/gslmatrix.hpp"
     13#include "gslmatrix.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/gslvectorunittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/gslvector.hpp"
     13#include "gslvector.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/infounittest.cpp

    rd223d5 rb6da28  
    1515#include <stdio.h>
    1616
    17 #include "Helpers/Info.hpp"
     17#include "info.hpp"
    1818#include "infounittest.hpp"
    19 #include "Helpers/Log.hpp"
     19#include "log.hpp"
    2020
    2121#ifdef HAVE_TESTRUNNER

  • src/unittests/linearsystemofequationsunittest.cpp

    rd223d5 rb6da28  
    1515
    1616#include "linearsystemofequationsunittest.hpp"
    17 #include "LinearAlgebra/Vector.hpp"
     17#include "vector.hpp"
    1818
    1919#ifdef HAVE_TESTRUNNER

  • src/unittests/linearsystemofequationsunittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/linearsystemofequations.hpp"
     13#include "linearsystemofequations.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/unittests/logunittest.cpp

    rd223d5 rb6da28  
    1111
    1212#include "logunittest.hpp"
    13 #include "Helpers/Log.hpp"
     13#include "log.hpp"
    1414#include "defs.hpp"
    15 #include "Helpers/Verbose.hpp"
     15#include "verbose.hpp"
    1616
    1717#ifdef HAVE_TESTRUNNER

  • src/unittests/memoryallocatorunittest.cpp

    rd223d5 rb6da28  
    1313#include "memoryallocatorunittest.hpp"
    1414#include "memoryusageobserver.hpp"
    15 #include "Helpers/helpers.hpp"
    16 #include "Helpers/Log.hpp"
     15#include "helpers.hpp"
     16#include "log.hpp"
    1717#include "defs.hpp"
    1818

  • src/unittests/stackclassunittest.cpp

    rd223d5 rb6da28  
    1313
    1414#include "stackclassunittest.hpp"
    15 #include "Helpers/Log.hpp"
     15#include "log.hpp"
    1616
    1717#ifdef HAVE_TESTRUNNER

  • src/unittests/tesselation_insideoutsideunittest.cpp

    rd223d5 rb6da28  
    1717#include "tesselation.hpp"
    1818#include "tesselation_insideoutsideunittest.hpp"
    19 #include "Helpers/Verbose.hpp"
     19#include "verbose.hpp"
    2020
    2121#ifdef HAVE_TESTRUNNER

  • src/unittests/vectorunittest.cpp

    rd223d5 rb6da28  
    1414
    1515#include "defs.hpp"
    16 #include "Helpers/Log.hpp"
    17 #include "LinearAlgebra/Vector.hpp"
     16#include "log.hpp"
     17#include "vector.hpp"
    1818#include "vector_ops.hpp"
    1919#include "vectorunittest.hpp"
    20 #include "LinearAlgebra/Plane.hpp"
     20#include "Plane.hpp"
    2121#include "Exceptions/LinearDependenceException.hpp"
    22 #include "LinearAlgebra/Matrix.hpp"
     22#include "Matrix.hpp"
    2323
    2424#ifdef HAVE_TESTRUNNER

  • src/unittests/vectorunittest.hpp

    rd223d5 rb6da28  
    1111#include <cppunit/extensions/HelperMacros.h>
    1212
    13 #include "LinearAlgebra/Vector.hpp"
     13#include "vector.hpp"
    1414
    1515/********************************************** Test classes **************************************/

  • src/vector_ops.cpp

    rd223d5 rb6da28  
    88#include "Helpers/MemDebug.hpp"
    99
    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"
     10#include "vector.hpp"
     11#include "Plane.hpp"
     12#include "log.hpp"
     13#include "verbose.hpp"
     14#include "gslmatrix.hpp"
    1515#include "leastsquaremin.hpp"
    16 #include "Helpers/Info.hpp"
     16#include "info.hpp"
    1717#include "Helpers/fast_functions.hpp"
    1818#include "Exceptions/LinearDependenceException.hpp"
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