source: src/Makefile.am@ 5f612ee

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 5f612ee was 5f612ee, checked in by Frederik Heber <heber@…>, 15 years ago

Merge branch 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

  • new molecule() replaced by World::getInstance().createMolecule()
  • new atom() replaced by World::getInstance().createAtom() where appropriate.
  • Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
  • DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
  • ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

  • Property mode set to 100644
File size: 6.3 KB
Line 
1ATOMSOURCE = atom.cpp atom_atominfo.cpp atom_bondedparticle.cpp atom_bondedparticleinfo.cpp atom_graphnode.cpp atom_graphnodeinfo.cpp atom_particleinfo.cpp atom_trajectoryparticle.cpp atom_trajectoryparticleinfo.cpp
2ATOMHEADER = atom.hpp atom_atominfo.hpp atom_bondedparticle.hpp atom_bondedparticleinfo.hpp atom_graphnode.hpp atom_graphnodeinfo.hpp atom_particleinfo.hpp atom_trajectoryparticle.hpp atom_trajectoryparticleinfo.hpp
3
4LINALGSOURCE = gslmatrix.cpp gslvector.cpp linearsystemofequations.cpp
5LINALGHEADER = gslmatrix.hpp gslvector.hpp linearsystemofequations.hpp
6
7ANALYSISSOURCE = analysis_bonds.cpp analysis_correlation.cpp
8ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
9
10ACTIONSSOURCE = Actions/Action.cpp \
11 Actions/ActionHistory.cpp \
12 Actions/ActionRegistry.cpp \
13 Actions/ActionSequence.cpp \
14 Actions/ErrorAction.cpp \
15 Actions/MakroAction.cpp \
16 Actions/ManipulateAtomsProcess.cpp \
17 Actions/MethodAction.cpp \
18 Actions/Process.cpp \
19 Actions/small_actions.cpp
20
21
22ACTIONSHEADER = Actions/Action.hpp \
23 Actions/ActionHistory.hpp \
24 Actions/ActionRegistry.hpp \
25 Actions/ActionSequence.hpp \
26 Actions/Calculation.hpp \
27 Actions/Calculation_impl.hpp \
28 Actions/ErrorAction.hpp \
29 Actions/MakroAction.hpp \
30 Actions/ManipulateAtomsProcess.hpp \
31 Actions/MethodAction.hpp \
32 Actions/Process.hpp \
33 Actions/small_actions.hpp
34
35
36
37PATTERNSOURCE = Patterns/Observer.cpp
38PATTERNHEADER = Patterns/Cacheable.hpp \
39 Patterns/Observer.hpp \
40 Patterns/Singleton.hpp
41
42VIEWSOURCE = Views/View.cpp Views/StringView.cpp Views/MethodStringView.cpp Views/StreamStringView.cpp
43VIEWHEADER = Views/View.hpp Views/StringView.hpp Views/MethodStringView.hpp Views/StreamStringView.hpp
44
45MENUSOURCE = Menu/Menu.cpp Menu/TextMenu.cpp Menu/MenuItem.cpp Menu/SubMenuItem.cpp Menu/ActionMenuItem.cpp Menu/SeperatorItem.cpp Menu/DisplayMenuItem.cpp
46MENUHEADER = Menu/Menu.hpp Menu/TextMenu.hpp Menu/MenuItem.hpp Menu/SubMenuItem.hpp Menu/ActionMenuItem.hpp Menu/SeperatorItem.hpp Menu/DisplayMenuItem.hpp
47
48UISOURCE = ${ACTIONSSOURCE} ${VIEWSOURCE} ${MENUSOURCE} UIElements/UIFactory.cpp UIElements/TextUIFactory.cpp UIElements/MainWindow.cpp UIElements/TextWindow.cpp UIElements/TextStatusIndicator.cpp UIElements/Dialog.cpp UIElements/TextDialog.cpp
49UIHEADER = ${ACTIONSHEADER} ${VIEWHEADER} ${MENUHEADER} UIElements/UIFactory.hpp UIElements/TextUIFactory.hpp UIElements/MainWindow.hpp UIElements/TextWindow.hpp UIElements/TextStatusIndicator.hpp UIElements/Dialog.hpp UIElements/TextDialog.hpp
50
51# all these files are only used for legacy reasons while the transition is in progress
52# they are only needed to keep the program usable at any point of the transition and will be
53# deleted once everything is fully refactored
54LEGACYSOURCE = Legacy/oldmenu.cpp
55LEGACYHEADER = Legacy/oldmenu.hpp
56
57DESCRIPTORSOURCE = Descriptors/AtomDescriptor.cpp \
58 Descriptors/AtomIdDescriptor.cpp \
59 Descriptors/AtomTypeDescriptor.cpp \
60 Descriptors/MoleculeDescriptor.cpp \
61 Descriptors/MoleculeIdDescriptor.cpp
62
63
64DESCRIPTORHEADER = Descriptors/AtomDescriptor.hpp \
65 Descriptors/AtomIdDescriptor.hpp \
66 Descriptors/AtomTypeDescriptor.hpp \
67 Descriptors/MoleculeDescriptor.hpp \
68 Descriptors/MoleculeIdDescriptor.hpp
69
70
71
72SOURCE = ${ANALYSISSOURCE} \
73 ${ATOMSOURCE} \
74 ${PATTERNSOURCE} \
75 ${UISOURCE} \
76 ${DESCRIPTORSOURCE} \
77 ${LEGACYSOURCE} \
78 bond.cpp \
79 bondgraph.cpp \
80 boundary.cpp \
81 config.cpp \
82 element.cpp \
83 ellipsoid.cpp \
84 errorlogger.cpp \
85 graph.cpp \
86 helpers.cpp \
87 Helpers/Assert.cpp \
88 info.cpp \
89 leastsquaremin.cpp \
90 linkedcell.cpp \
91 lists.cpp \
92 log.cpp \
93 logger.cpp \
94 memoryusageobserver.cpp \
95 moleculelist.cpp \
96 molecule.cpp \
97 molecule_dynamics.cpp \
98 molecule_fragmentation.cpp \
99 molecule_geometry.cpp \
100 molecule_graph.cpp \
101 molecule_pointcloud.cpp \
102 parser.cpp \
103 periodentafel.cpp \
104 tesselation.cpp \
105 tesselationhelpers.cpp \
106 triangleintersectionlist.cpp \
107 vector.cpp \
108 verbose.cpp \
109 World.cpp
110
111HEADER = \
112 ${ANALYSISHEADER} \
113 ${ATOMHEADER} \
114 ${PATTERNHEADER} \
115 ${UIHEADER} \
116 ${DESCRIPTORHEADER} \
117 ${LEGACYHEADER} \
118 bond.hpp \
119 bondgraph.hpp \
120 boundary.hpp \
121 config.hpp \
122 defs.hpp \
123 element.hpp \
124 ellipsoid.hpp \
125 errorlogger.hpp \
126 graph.hpp \
127 helpers.hpp \
128 info.hpp \
129 leastsquaremin.hpp \
130 linkedcell.hpp \
131 lists.hpp \
132 log.hpp \
133 logger.hpp \
134 memoryallocator.hpp \
135 memoryusageobserver.hpp \
136 molecule.hpp \
137 molecule_template.hpp \
138 parser.hpp \
139 periodentafel.hpp \
140 stackclass.hpp \
141 tesselation.hpp \
142 tesselationhelpers.hpp \
143 triangleintersectionlist.hpp \
144 vector.hpp \
145 verbose.hpp \
146 World.hpp
147
148BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
149INCLUDES = -I$(top_srcdir)/src/unittests
150
151noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
152bin_PROGRAMS = molecuilder joiner analyzer
153molecuilderdir = ${bindir}
154libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
155libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
156molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
157molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
158molecuilder_SOURCES = builder.cpp
159molecuilder_LDADD = libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
160joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
161joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
162analyzer_SOURCES = analyzer.cpp datacreator.cpp parser.cpp helpers.hpp periodentafel.hpp parser.hpp datacreator.hpp
163analyzer_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}
164
165#EXTRA_DIST = ${molecuilder_DATA}
166
167FORCE:
168$(srcdir)/.git-version: FORCE
169 @if (test -d $(top_srcdir)/../.git && cd $(srcdir) && git describe HEAD) > .git-version-t 2>/dev/null \
170 && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
171 mv -f .git-version-t $(srcdir)/.git-version; \
172 else \
173 rm -f .git-version-t; \
174 fi
175
176EXTRA_DIST = $(srcdir)/.git-version
177
178$(srcdir)/version.c: $(srcdir)/.git-version
179 echo "const char *ESPACKVersion = \"$(PACKAGE_NAME) -- git version: "`cat $(srcdir)/.git-version`"\";" > $@
180
181molecuilder_SOURCES += $(srcdir)/version.c
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