source: src/Makefile.am@ c77ac8

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 c77ac8 was c42e60, checked in by Frederik Heber <heber@…>, 14 years ago

Two new descriptors: AtomOfMoleculeSelection, MoleculeOfAtomSelection. Rewrote associated SelectionActions.

That is, the SelectionActions are meant to use one selection and turn the
other accordingly. It is a sort of exchange between the two. I can convert
a selection of atoms to molecules and vica versa, but this "mapping" is NOT
injective but always surjective.

Testchange:

  • Selection/Atoms/testsuite-selection-atoms-of-molecule.at: Due to the absent parameter now, we first select the molecule by id and then ...
  • Property mode set to 100644
File size: 13.4 KB
Line 
1# PLEASE adhere to the alphabetical ordering in this Makefile!
2# Also indentation by a single tab
3
4SUBDIRS = Actions Exceptions Helpers LinearAlgebra Parser UIElements
5
6AM_CPPFLAGS = ${BOOST_CPPFLAGS}
7
8ATOMSOURCE = \
9 atom.cpp \
10 AtomicInfo.cpp \
11 atom_atominfo.cpp \
12 atom_bondedparticle.cpp \
13 atom_bondedparticleinfo.cpp \
14 atom_graphnode.cpp \
15 atom_graphnodeinfo.cpp \
16 atom_particleinfo.cpp \
17 atom_trajectoryparticle.cpp \
18 atom_trajectoryparticleinfo.cpp
19ATOMHEADER = \
20 atom.hpp \
21 AtomicInfo.hpp \
22 atom_atominfo.hpp \
23 atom_bondedparticle.hpp \
24 atom_bondedparticleinfo.hpp \
25 atom_graphnode.hpp \
26 atom_graphnodeinfo.hpp \
27 atom_particleinfo.hpp \
28 atom_trajectoryparticle.hpp \
29 atom_trajectoryparticleinfo.hpp
30
31ANALYSISSOURCE = \
32 analysis_bonds.cpp \
33 analysis_correlation.cpp
34ANALYSISHEADER = \
35 analysis_bonds.hpp \
36 analysis_correlation.hpp
37
38ACTIONSSOURCE = \
39 Actions/Action.cpp \
40 Actions/ActionHistory.cpp \
41 Actions/ActionRegistry.cpp \
42 Actions/ActionSequence.cpp \
43 Actions/ActionTraits.cpp \
44 Actions/ErrorAction.cpp \
45 Actions/MakroAction.cpp \
46 Actions/ManipulateAtomsProcess.cpp \
47 Actions/MethodAction.cpp \
48 Actions/OptionRegistry.cpp \
49 Actions/OptionTrait.cpp \
50 Actions/Process.cpp
51
52ACTIONSHEADER = \
53 Actions/Action.hpp \
54 Actions/ActionHistory.hpp \
55 Actions/ActionRegistry.hpp \
56 Actions/ActionSequence.hpp \
57 Actions/ActionTraits.hpp \
58 Actions/Calculation.hpp \
59 Actions/Calculation_impl.hpp \
60 Actions/ErrorAction.hpp \
61 Actions/MakroAction.hpp \
62 Actions/ManipulateAtomsProcess.hpp \
63 Actions/MethodAction.hpp \
64 Actions/OptionRegistry.hpp \
65 Actions/OptionTrait.hpp \
66 Actions/Process.hpp
67
68
69PATTERNSOURCE = \
70 Patterns/Observer.cpp
71PATTERNHEADER = \
72 Patterns/Cacheable.hpp \
73 Patterns/Observer.hpp \
74 Patterns/Singleton.hpp
75
76SHAPESOURCE = \
77 Shapes/BaseShapes.cpp \
78 Shapes/Shape.cpp \
79 Shapes/ShapeOps.cpp
80SHAPEHEADER = \
81 Shapes/BaseShapes.hpp \
82 Shapes/Shape.hpp \
83 Shapes/ShapeOps.hpp
84
85
86DESCRIPTORSOURCE = \
87 Descriptors/AtomDescriptor.cpp \
88 Descriptors/AtomIdDescriptor.cpp \
89 Descriptors/AtomOfMoleculeSelectionDescriptor.cpp \
90 Descriptors/AtomSelectionDescriptor.cpp \
91 Descriptors/AtomShapeDescriptor.cpp \
92 Descriptors/AtomTypeDescriptor.cpp \
93 Descriptors/MoleculeDescriptor.cpp \
94 Descriptors/MoleculeFormulaDescriptor.cpp \
95 Descriptors/MoleculeIdDescriptor.cpp \
96 Descriptors/MoleculeNameDescriptor.cpp \
97 Descriptors/MoleculeOfAtomSelectionDescriptor.cpp \
98 Descriptors/MoleculeOrderDescriptor.cpp \
99 Descriptors/MoleculePtrDescriptor.cpp \
100 Descriptors/MoleculeSelectionDescriptor.cpp
101
102
103DESCRIPTORHEADER = \
104 Descriptors/AtomDescriptor.hpp \
105 Descriptors/AtomIdDescriptor.hpp \
106 Descriptors/AtomOfMoleculeSelectionDescriptor.hpp \
107 Descriptors/AtomSelectionDescriptor.hpp \
108 Descriptors/AtomShapeDescriptor.hpp \
109 Descriptors/AtomTypeDescriptor.hpp \
110 Descriptors/MoleculeDescriptor.hpp \
111 Descriptors/MoleculeFormulaDescriptor.hpp \
112 Descriptors/MoleculeIdDescriptor.hpp \
113 Descriptors/MoleculeNameDescriptor.hpp \
114 Descriptors/MoleculeOfAtomSelectionDescriptor.hpp \
115 Descriptors/MoleculeOrderDescriptor.hpp \
116 Descriptors/MoleculePtrDescriptor.hpp \
117 Descriptors/MoleculeSelectionDescriptor.hpp
118
119DESCRIPTORIMPLHEADER = \
120 Descriptors/AtomDescriptor_impl.hpp \
121 Descriptors/AtomIdDescriptor_impl.hpp \
122 Descriptors/AtomOfMoleculeSelectionDescriptor_impl.hpp \
123 Descriptors/AtomSelectionDescriptor_impl.hpp \
124 Descriptors/AtomShapeDescriptor_impl.hpp \
125 Descriptors/AtomTypeDescriptor_impl.hpp \
126 Descriptors/MoleculeDescriptor_impl.hpp \
127 Descriptors/MoleculeFormulaDescriptor_impl.hpp \
128 Descriptors/MoleculeIdDescriptor_impl.hpp \
129 Descriptors/MoleculeNameDescriptor_impl.hpp \
130 Descriptors/MoleculeOfAtomSelectionDescriptor_impl.hpp \
131 Descriptors/MoleculeOrderDescriptor_impl.hpp \
132 Descriptors/MoleculePtrDescriptor_impl.hpp \
133 Descriptors/MoleculeSelectionDescriptor_impl.hpp
134
135THERMOSTATSOURCE = \
136 Thermostats/Berendsen.cpp \
137 Thermostats/GaussianThermostat.cpp \
138 Thermostats/Langevin.cpp \
139 Thermostats/NoseHoover.cpp \
140 Thermostats/NoThermostat.cpp \
141 Thermostats/Thermostat.cpp \
142 Thermostats/Woodcock.cpp
143
144THERMOSTATHEADER = \
145 Thermostats/Berendsen.hpp \
146 Thermostats/GaussianThermostat.hpp \
147 Thermostats/Langevin.hpp \
148 Thermostats/NoseHoover.hpp \
149 Thermostats/NoThermostat.hpp \
150 Thermostats/Thermostat.hpp \
151 Thermostats/Woodcock.hpp
152
153TESSELATIONSOURCE = \
154 BoundaryLineSet.cpp \
155 BoundaryPointSet.cpp \
156 BoundaryPolygonSet.cpp \
157 BoundaryTriangleSet.cpp \
158 CandidateForTesselation.cpp \
159 PointCloud.cpp \
160 tesselation.cpp \
161 tesselationhelpers.cpp \
162 TesselPoint.cpp
163
164TESSELATIONHEADER = \
165 BoundaryLineSet.hpp \
166 BoundaryPointSet.hpp \
167 BoundaryPolygonSet.hpp \
168 BoundaryTriangleSet.hpp \
169 CandidateForTesselation.hpp \
170 PointCloud.hpp \
171 tesselation.hpp \
172 tesselationhelpers.hpp \
173 TesselPoint.hpp
174
175MOLECUILDERSOURCE = \
176 ${ANALYSISSOURCE} \
177 ${ACTIONSSOURCE} \
178 ${ATOMSOURCE} \
179 ${PATTERNSOURCE} \
180 ${SHAPESOURCE} \
181 ${DESCRIPTORSOURCE} \
182 ${THERMOSTATSOURCE} \
183 ${TESSELATIONSOURCE} \
184 bond.cpp \
185 bondgraph.cpp \
186 boundary.cpp \
187 Box.cpp \
188 config.cpp \
189 ConfigFileBuffer.cpp \
190 element.cpp \
191 elements_db.cpp \
192 ellipsoid.cpp \
193 Formula.cpp \
194 graph.cpp \
195 linkedcell.cpp \
196 moleculelist.cpp \
197 molecule.cpp \
198 molecule_dynamics.cpp \
199 molecule_fragmentation.cpp \
200 molecule_geometry.cpp \
201 molecule_graph.cpp \
202 molecule_pointcloud.cpp \
203 parser.cpp \
204 periodentafel.cpp \
205 ThermoStatContainer.cpp \
206 triangleintersectionlist.cpp \
207 UIElements/UIFactory.cpp \
208 World.cpp
209
210MOLECUILDERHEADER = \
211 ${ANALYSISHEADER} \
212 ${ACTIONSHEADER} \
213 ${ATOMHEADER} \
214 ${PATTERNHEADER} \
215 ${SHAPEHEADER} \
216 ${DESCRIPTORHEADER} \
217 ${DESCRIPTORIMPLHEADER} \
218 ${THERMOSTATHEADER} \
219 ${TESSELATIONHEADER} \
220 bond.hpp \
221 bondgraph.hpp \
222 boundary.hpp \
223 Box.hpp \
224 config.hpp \
225 ConfigFileBuffer.hpp \
226 element.hpp \
227 elements_db.hpp \
228 ellipsoid.hpp \
229 Formula.hpp \
230 graph.hpp \
231 linkedcell.hpp \
232 lists.hpp \
233 molecule.hpp \
234 parser.hpp \
235 periodentafel.hpp \
236 ThermoStatContainer.hpp \
237 triangleintersectionlist.hpp \
238 UIElements/UIFactory.hpp \
239 World.hpp
240
241lib_LTLIBRARIES = libMolecuilder-@MOLECUILDER_API_VERSION@.la
242libMolecuilder_includedir = $(includedir)/molecuilder-$(MOLECUILDER_API_VERSION)/Actions/
243libMolecuilder_LIBS = \
244 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
245 ${BOOST_PROGRAM_OPTIONS_LIB}
246
247# UIElements/libMolecuilderUI.a \
248 Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
249 Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
250 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
251 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
252 $(BOOST_LIB) \
253 ${BOOST_THREAD_LIB}
254
255nobase_libMolecuilder_include_HEADERS = ${MOLECUILDERHEADER}
256
257## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
258## target. Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
259## will therefore be treated as if it were literally part of the target name,
260## and the variable name derived from that.
261## The file extension .cc is recognized by Automake, and makes it produce
262## rules which invoke the C++ compiler to produce a libtool object file (.lo)
263## from each source file. Note that it is not necessary to list header files
264## which are already listed elsewhere in a _HEADERS variable assignment.
265libMolecuilder_@MOLECUILDER_API_VERSION@_la_SOURCES = ${MOLECUILDERSOURCE} $(srcdir)/version.c
266
267## Instruct libtool to include ABI version information in the generated shared
268## library file (.so). The library ABI version is defined in configure.ac, so
269## that all version information is kept in one place.
270libMolecuilder_@MOLECUILDER_API_VERSION@_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
271
272## The generated configuration header is installed in its own subdirectory of
273## $(libdir). The reason for this is that the configuration information put
274## into this header file describes the target platform the installed library
275## has been built for. Thus the file must not be installed into a location
276## intended for architecture-independent files, as defined by the Filesystem
277## Hierarchy Standard (FHS).
278## The nodist_ prefix instructs Automake to not generate rules for including
279## the listed files in the distribution on 'make dist'. Files that are listed
280## in _HEADERS variables are normally included in the distribution, but the
281## configuration header file is generated at configure time and should not be
282## shipped with the source tarball.
283libMolecuilder_libincludedir = $(libdir)/molecuilder-$(MOLECUILDER_API_VERSION)/include
284nodist_libMolecuilder_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
285
286## Install the generated pkg-config file (.pc) into the expected location for
287## architecture-dependent package configuration information. Occasionally,
288## pkg-config files are also used for architecture-independent data packages,
289## in which case the correct install location would be $(datadir)/pkgconfig.
290pkgconfigdir = $(libdir)/pkgconfig
291pkgconfig_DATA = $(top_builddir)/molecuilder-$(MOLECUILDER_API_VERSION).pc
292
293
294BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_FILESYSTEM_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_THREAD_LIB)
295INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
296
297noinst_LIBRARIES = libmenu.a
298bin_PROGRAMS = molecuilder molecuildergui joiner analyzer SubspaceFactorizer
299EXTRA_PROGRAMS = unity
300
301molecuilderdir = ${bindir}
302
303libmenu_a_SOURCES = ${UISOURCE} ${UIHEADER}
304
305molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
306
307SubspaceFactorizer_CXXFLAGS = $(BOOST_CPPFLAGS)
308SubspaceFactorizer_SOURCES = SubspaceFactorizer.cpp
309SubspaceFactorizer_LDADD = \
310 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
311 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
312 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
313 $(GSLLIB) \
314 $(BOOST_LIB)
315
316molecuilder_CXXFLAGS = $(BOOST_CPPFLAGS)
317#molecuilder_CXXFLAGS += -DNO_CACHING
318molecuilder_LDFLAGS = $(BOOST_LIB)
319molecuilder_SOURCES = builder.cpp
320molecuilder_LDADD = \
321 UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
322 Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
323 libMolecuilder-@MOLECUILDER_API_VERSION@.la \
324 Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
325 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
326 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
327 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
328 $(BOOST_LIB)
329
330#Stuff for building the GUI using Qt
331molecuildergui_SOURCES = builder.cpp
332molecuildergui_CXXFLAGS = $(BOOST_CPPFLAGS) -DUSE_GUI_QT
333molecuildergui_LDFLAGS = $(BOOST_LIB)
334
335unity_SOURCES = unity.cpp
336unity_LDADD = $(BOOST_LIB)
337
338molecuildergui_LDADD = \
339 UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
340 UIElements/libMolecuilderQtUI-@MOLECUILDER_API_VERSION@.la \
341 Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
342 libMolecuilder-@MOLECUILDER_API_VERSION@.la \
343 Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
344 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
345 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
346 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
347 $(BOOST_LIB) \
348 ${GUI_LIBS}
349
350joiner_SOURCES = joiner.cpp datacreator.cpp datacreator.hpp periodentafel.hpp
351joiner_LDADD = \
352 UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
353 Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
354 libMolecuilder-@MOLECUILDER_API_VERSION@.la \
355 Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
356 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
357 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
358 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
359 $(BOOST_LIB)
360
361analyzer_SOURCES = analyzer.cpp datacreator.cpp periodentafel.hpp datacreator.hpp
362analyzer_LDADD = \
363 UIElements/libMolecuilderUI-@MOLECUILDER_API_VERSION@.la \
364 Actions/libMolecuilderActions-@MOLECUILDER_API_VERSION@.la \
365 libMolecuilder-@MOLECUILDER_API_VERSION@.la \
366 Parser/libMolecuilderParser-@MOLECUILDER_API_VERSION@.la \
367 LinearAlgebra/libMolecuilderLinearAlgebra-@MOLECUILDER_API_VERSION@.la \
368 Exceptions/libMolecuilderExceptions-@MOLECUILDER_API_VERSION@.la \
369 Helpers/libMolecuilderHelpers-@MOLECUILDER_API_VERSION@.la \
370 $(BOOST_LIB)
371
372#EXTRA_DIST = ${molecuilder_DATA}
373
374FORCE:
375$(srcdir)/.git-version: FORCE
376 @if (test -d $(top_srcdir)/.git && cd $(srcdir) \
377 && { git describe --dirty --always || git describe; } ) > .git-version-t 2>/dev/null \
378 && ! diff .git-version-t $(srcdir)/.git-version >/dev/null 2>&1; then \
379 mv -f .git-version-t $(srcdir)/.git-version; \
380 else \
381 rm -f .git-version-t; \
382 fi
383
384EXTRA_DIST = $(srcdir)/.git-version
385
386$(srcdir)/version.c: $(srcdir)/.git-version
387 echo "const char *MOLECUILDERVERSION = \"$(PACKAGE_NAME) version "`cat $(srcdir)/.git-version`"\";" > $@
388
389
390unity.cpp: ${MOLECUILDERSOURCE} ${MOLECUILDERHEADER}
391 echo "#include \"$(srcdir)/Helpers/MemDebug.cpp\"" > unity.cpp; \
392 list='$(MOLECUILDERSOURCE)'; for file in $$list; do \
393 echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
394 done; \
395 subdirs='$(SUBDIRS)';for directory in $$subdirs; do\
396 olddir=$$PWD;\
397 cd $$directory && make unity.cpp;\
398 cd $$olddir;\
399 echo "#include \"$$directory/unity.cpp\"" >> unity.cpp;\
400 done;\
401 echo "#include \"$(srcdir)/builder.cpp\"" >> unity.cpp;
402 echo "#include \"$(srcdir)/version.c\"" >> unity.cpp;
403
404MOSTLYCLEANFILES = unity.cpp
405
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