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Last change on this file since 0275ad was 3f9eba, checked in by Frederik Heber <heber@…>, 14 years ago

New classes for random number generation.

we use boost::random as a basis. It implements a lot of pseudo-random engines and various distributions. However, everything is templated and there are no base classes to store prototypes of the instances in a map. We need these such that we are able to offer the user at run-time every choice possible.
Hence, we need to encapsulate all engines, distributions and (engine, distribution) tuples: RandomNumber..._Encapsulation classes.
each with an abstract base class as the interface: RandomNumber... classes.
RandomNumberGeneratorFactory is then a singleton that contains all the Maps and tables:
- from string (user input is string) to enum (storing enum is more efficient that a lengthy string)
- from enum to instance (of the abstract class).
RandomNumberGeneratorFactory is a singleton to allow for global control of what kind of numbers are generated, hence there are also two new Actions:
- SetRandomNumbersDistributionAction
- SetRandomNumbersEngineAction to specify which (engine,distribution) tuple to use. There are two new regression tests for these Actions.
The user in the end only uses two classes: RandomNumberGeneratorFactory and RandomNumberGenerator. The first only for obtaining a specific variant of the latter and the latter to generate the numbers (operator() is passed on to boost::variate_generator::operator()).
There is a unit test on the RandomNumberGeneratorFactory that checks some of the table entries and whether one of the RandomNumberGenerator is working (uniform_smallint so far).

Details:

As there are ~25 engines and ~15 distributions this makes an enormous amount of possible combinations. To automatically construct these, we use some stuff from boost::preprocessor in order to generate enums, tables and maps automatically just from a sequence of the typenames.
we have be-friended the unit test a lot to allow for easier testing, e.g. we need access to internal ..._type to test whether their type is correct.
cleanUp() purges the instance of RandomNumberGeneratorFactory.
in RandomNumber..._Encapsulation::name() functions are only used for the unit tests.
this all resides in its own subfolder RandomNumbers. So far, it is completely independent of everything else.

Property mode set to 100644

File size: 11.4 KB

Line
1	# PLEASE adhere to the alphabetical ordering in this Makefile!
2	# Also indentation by a single tab
3
4	INCLUDES = -I$(top_srcdir)/src
5
6	AM_LDFLAGS = -ldl
7	AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
8
9	ACTIONSSOURCE = \
10	${ANALYSISACTIONSOURCE} \
11	${ATOMACTIONSOURCE} \
12	${CMDACTIONSOURCE} \
13	${FRAGMENTATIONACTIONSOURCE} \
14	${MOLECULEACTIONSOURCE} \
15	${PARSERACTIONSOURCE} \
16	${RANDONNUMBERSSOURCE} \
17	${SELECTIONATOMACTIONSOURCE} \
18	${SELECTIONMOLECULEACTIONSOURCE} \
19	${TESSELATIONACTIONSOURCE} \
20	${WORLDACTIONSOURCE} \
21	RedoAction.cpp \
22	UndoAction.cpp \
23	ValueStorage.cpp
24
25	ACTIONSHEADER = \
26	${ANALYSISACTIONHEADER} \
27	${ATOMACTIONHEADER} \
28	${CMDACTIONHEADER} \
29	${FRAGMENTATIONACTIONHEADER} \
30	${MOLECULEACTIONHEADER} \
31	${PARSERACTIONHEADER} \
32	${RANDONNUMBERSHEADER} \
33	${SELECTIONATOMACTIONHEADER} \
34	${SELECTIONMOLECULEACTIONHEADER} \
35	${TESSELATIONACTIONHEADER} \
36	${WORLDACTIONHEADER} \
37	ValueStorage.hpp \
38	Values.hpp
39
40	ANALYSISACTIONSOURCE = \
41	AnalysisAction/DipoleAngularCorrelationAction.cpp \
42	AnalysisAction/MolecularVolumeAction.cpp \
43	AnalysisAction/PairCorrelationAction.cpp \
44	AnalysisAction/PointCorrelationAction.cpp \
45	AnalysisAction/PrincipalAxisSystemAction.cpp \
46	AnalysisAction/SurfaceCorrelationAction.cpp
47	ANALYSISACTIONHEADER = \
48	AnalysisAction/DipoleAngularCorrelationAction.hpp \
49	AnalysisAction/MolecularVolumeAction.hpp \
50	AnalysisAction/PairCorrelationAction.hpp \
51	AnalysisAction/PointCorrelationAction.hpp \
52	AnalysisAction/PrincipalAxisSystemAction.hpp \
53	AnalysisAction/SurfaceCorrelationAction.hpp
54
55	ATOMACTIONSOURCE = \
56	AtomAction/AddAction.cpp \
57	AtomAction/ChangeElementAction.cpp \
58	AtomAction/RemoveAction.cpp \
59	AtomAction/RotateAroundOriginByAngleAction.cpp \
60	AtomAction/TranslateAction.cpp
61	ATOMACTIONHEADER = \
62	AtomAction/AddAction.hpp \
63	AtomAction/ChangeElementAction.hpp \
64	AtomAction/RemoveAction.cpp \
65	AtomAction/RotateAroundOriginByAngleAction.hpp \
66	AtomAction/TranslateAction.hpp
67
68	CMDACTIONSOURCE = \
69	CommandAction/BondLengthTableAction.cpp \
70	CommandAction/ElementDbAction.cpp \
71	CommandAction/FastParsingAction.cpp \
72	CommandAction/HelpAction.cpp \
73	CommandAction/VerboseAction.cpp \
74	CommandAction/VersionAction.cpp \
75	CommandAction/WarrantyAction.cpp
76	CMDACTIONHEADER = \
77	CommandAction/BondLengthTableAction.hpp \
78	CommandAction/ElementDbAction.hpp \
79	CommandAction/FastParsingAction.hpp \
80	CommandAction/HelpAction.hpp \
81	CommandAction/VerboseAction.hpp \
82	CommandAction/VersionAction.hpp \
83	CommandAction/WarrantyAction.hpp
84
85	FRAGMENTATIONACTIONSOURCE = \
86	FragmentationAction/ConstructBondGraphAction.cpp \
87	FragmentationAction/DepthFirstSearchAction.cpp \
88	FragmentationAction/FragmentationAction.cpp \
89	FragmentationAction/SubgraphDissectionAction.cpp
90	FRAGMENTATIONACTIONHEADER = \
91	FragmentationAction/ConstructBondGraphAction.hpp \
92	FragmentationAction/DepthFirstSearchAction.hpp \
93	FragmentationAction/FragmentationAction.hpp \
94	FragmentationAction/SubgraphDissectionAction.hpp
95
96	MOLECULEACTIONSOURCE = \
97	MoleculeAction/BondFileAction.cpp \
98	MoleculeAction/ChangeNameAction.cpp \
99	MoleculeAction/CopyAction.cpp \
100	MoleculeAction/FillWithMoleculeAction.cpp \
101	MoleculeAction/FillVoidWithMoleculeAction.cpp \
102	MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
103	MoleculeAction/LoadAction.cpp \
104	MoleculeAction/RotateAroundSelfByAngleAction.cpp \
105	MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
106	MoleculeAction/SaveAction.cpp \
107	MoleculeAction/SaveAdjacencyAction.cpp \
108	MoleculeAction/SaveBondsAction.cpp \
109	MoleculeAction/SaveTemperatureAction.cpp \
110	MoleculeAction/SuspendInWaterAction.cpp \
111	MoleculeAction/VerletIntegrationAction.cpp
112	MOLECULEACTIONHEADER = \
113	MoleculeAction/BondFileAction.hpp \
114	MoleculeAction/ChangeNameAction.hpp \
115	MoleculeAction/CopyAction.hpp \
116	MoleculeAction/FillWithMoleculeAction.hpp \
117	MoleculeAction/FillVoidWithMoleculeAction.hpp \
118	MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
119	MoleculeAction/LoadAction.cpp \
120	MoleculeAction/RotateAroundSelfByAngleAction.hpp \
121	MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
122	MoleculeAction/SaveAction.hpp \
123	MoleculeAction/SaveAdjacencyAction.hpp \
124	MoleculeAction/SaveBondsAction.hpp \
125	MoleculeAction/SaveTemperatureAction.hpp \
126	MoleculeAction/SuspendInWaterAction.hpp \
127	MoleculeAction/VerletIntegrationAction.hpp
128
129	RANDONNUMBERSSOURCE =\
130	RandomNumbersAction/SetRandomNumbersDistributionAction.cpp \
131	RandomNumbersAction/SetRandomNumbersEngineAction.cpp
132
133	RANDONNUMBERSHEADER =\
134	RandomNumbersAction/SetRandomNumbersDistributionAction.hpp \
135	RandomNumbersAction/SetRandomNumbersEngineAction.hpp
136
137	SELECTIONATOMACTIONSOURCE = \
138	SelectionAction/Atoms/AllAtomsAction.cpp \
139	SelectionAction/Atoms/AllAtomsInsideCuboidAction.cpp \
140	SelectionAction/Atoms/AllAtomsInsideSphereAction.cpp \
141	SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp \
142	SelectionAction/Atoms/AtomByElementAction.cpp \
143	SelectionAction/Atoms/AtomByIdAction.cpp \
144	SelectionAction/Atoms/ClearAllAtomsAction.cpp \
145	SelectionAction/Atoms/NotAllAtomsAction.cpp \
146	SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.cpp \
147	SelectionAction/Atoms/NotAllAtomsInsideSphereAction.cpp \
148	SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp \
149	SelectionAction/Atoms/NotAtomByElementAction.cpp \
150	SelectionAction/Atoms/NotAtomByIdAction.cpp
151	SELECTIONATOMACTIONHEADER = \
152	SelectionAction/Atoms/AllAtomsAction.hpp \
153	SelectionAction/Atoms/AllAtomsInsideCuboidAction.hpp \
154	SelectionAction/Atoms/AllAtomsInsideSphereAction.hpp \
155	SelectionAction/Atoms/AllAtomsOfMoleculeAction.hpp \
156	SelectionAction/Atoms/AtomByElementAction.hpp \
157	SelectionAction/Atoms/AtomByIdAction.hpp \
158	SelectionAction/Atoms/ClearAllAtomsAction.hpp \
159	SelectionAction/Atoms/NotAllAtomsAction.hpp \
160	SelectionAction/Atoms/NotAllAtomsInsideCuboidAction.hpp \
161	SelectionAction/Atoms/NotAllAtomsInsideSphereAction.hpp \
162	SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.hpp \
163	SelectionAction/Atoms/NotAtomByElementAction.hpp \
164	SelectionAction/Atoms/NotAtomByIdAction.hpp
165
166	SELECTIONMOLECULEACTIONSOURCE = \
167	SelectionAction/Molecules/AllMoleculesAction.cpp \
168	SelectionAction/Molecules/ClearAllMoleculesAction.cpp \
169	SelectionAction/Molecules/MoleculeByFormulaAction.cpp \
170	SelectionAction/Molecules/MoleculeByIdAction.cpp \
171	SelectionAction/Molecules/MoleculeByNameAction.cpp \
172	SelectionAction/Molecules/MoleculeByOrderAction.cpp \
173	SelectionAction/Molecules/MoleculeOfAtomAction.cpp \
174	SelectionAction/Molecules/NotAllMoleculesAction.cpp \
175	SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp \
176	SelectionAction/Molecules/NotMoleculeByIdAction.cpp \
177	SelectionAction/Molecules/NotMoleculeByNameAction.cpp \
178	SelectionAction/Molecules/NotMoleculeByOrderAction.cpp \
179	SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp
180	SELECTIONMOLECULEACTIONHEADER = \
181	SelectionAction/Molecules/AllMoleculesAction.hpp \
182	SelectionAction/Molecules/ClearAllMoleculesAction.hpp \
183	SelectionAction/Molecules/MoleculeByFormulaAction.hpp \
184	SelectionAction/Molecules/MoleculeByIdAction.hpp \
185	SelectionAction/Molecules/MoleculeByNameAction.hpp \
186	SelectionAction/Molecules/MoleculeByOrderAction.hpp \
187	SelectionAction/Molecules/MoleculeOfAtomAction.hpp \
188	SelectionAction/Molecules/NotAllMoleculesAction.hpp \
189	SelectionAction/Molecules/NotMoleculeByFormulaAction.hpp \
190	SelectionAction/Molecules/NotMoleculeByIdAction.hpp \
191	SelectionAction/Molecules/NotMoleculeByNameAction.hpp \
192	SelectionAction/Molecules/NotMoleculeByOrderAction.hpp \
193	SelectionAction/Molecules/NotMoleculeOfAtomAction.hpp
194
195	TESSELATIONACTIONSOURCE = \
196	TesselationAction/ConvexEnvelopeAction.cpp \
197	TesselationAction/NonConvexEnvelopeAction.cpp
198	TESSELATIONACTIONHEADER = \
199	TesselationAction/ConvexEnvelopeAction.hpp \
200	TesselationAction/NonConvexEnvelopeAction.hpp
201
202	WORLDACTIONSOURCE = \
203	WorldAction/AddEmptyBoundaryAction.cpp \
204	WorldAction/BoundInBoxAction.cpp \
205	WorldAction/CenterInBoxAction.cpp \
206	WorldAction/CenterOnEdgeAction.cpp \
207	WorldAction/ChangeBoxAction.cpp \
208	WorldAction/InputAction.cpp \
209	WorldAction/OutputAction.cpp \
210	WorldAction/RepeatBoxAction.cpp \
211	WorldAction/ScaleBoxAction.cpp \
212	WorldAction/SetDefaultNameAction.cpp \
213	WorldAction/SetGaussianBasisAction.cpp \
214	WorldAction/SetOutputFormatsAction.cpp
215	WORLDACTIONHEADER = \
216	WorldAction/AddEmptyBoundaryAction.hpp \
217	WorldAction/BoundInBoxAction.hpp \
218	WorldAction/CenterInBoxAction.hpp \
219	WorldAction/CenterOnEdgeAction.hpp \
220	WorldAction/ChangeBoxAction.hpp \
221	WorldAction/InputAction.hpp \
222	WorldAction/OutputAction.hpp \
223	WorldAction/RepeatBoxAction.hpp \
224	WorldAction/ScaleBoxAction.hpp \
225	WorldAction/SetDefaultNameAction.hpp \
226	WorldAction/SetGaussianBasisAction.hpp \
227	WorldAction/SetOutputFormatsAction.hpp
228
229
230	lib_LTLIBRARIES = libMolecuilderActions.la
231	libMolecuilderActions_la_includedir = $(includedir)/MoleCuilder/Actions/
232	libMolecuilderActions_la_LIBADD = \
233	../Parser/libMolecuilderParser.la \
234	../Shapes/libMolecuilderShapes.la \
235	${CodePatterns_LIBS}
236	# ../UIElements/libMolecuilderUI.la
237	nobase_libMolecuilderActions_la_include_HEADERS = ${ACTIONSHEADER}
238
239	## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
240	## target. Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
241	## will therefore be treated as if it were literally part of the target name,
242	## and the variable name derived from that.
243	## The file extension .cc is recognized by Automake, and makes it produce
244	## rules which invoke the C++ compiler to produce a libtool object file (.lo)
245	## from each source file. Note that it is not necessary to list header files
246	## which are already listed elsewhere in a _HEADERS variable assignment.
247	libMolecuilderActions_la_SOURCES = ${ACTIONSSOURCE}
248
249	## Instruct libtool to include ABI version information in the generated shared
250	## library file (.so). The library ABI version is defined in configure.ac, so
251	## that all version information is kept in one place.
252	libMolecuilderActions_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
253
254	## The generated configuration header is installed in its own subdirectory of
255	## $(libdir). The reason for this is that the configuration information put
256	## into this header file describes the target platform the installed library
257	## has been built for. Thus the file must not be installed into a location
258	## intended for architecture-independent files, as defined by the Filesystem
259	## Hierarchy Standard (FHS).
260	## The nodist_ prefix instructs Automake to not generate rules for including
261	## the listed files in the distribution on 'make dist'. Files that are listed
262	## in _HEADERS variables are normally included in the distribution, but the
263	## configuration header file is generated at configure time and should not be
264	## shipped with the source tarball.
265	#libMolecuilderActions_libincludedir = $(libdir)/MoleCuilder/include
266	#nodist_libMolecuilderActions_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
267
268	## Install the generated pkg-config file (.pc) into the expected location for
269	## architecture-dependent package configuration information. Occasionally,
270	## pkg-config files are also used for architecture-independent data packages,
271	## in which case the correct install location would be $(datadir)/pkgconfig.
272	#pkgconfigdir = $(libdir)/pkgconfig
273	#pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
274
275	unity.cpp:
276	echo "" > unity.cpp; \
277	list='$(ACTIONSSOURCE)'; for file in $$list; do \
278	echo "#include \"$(srcdir)/$$file\"" >> unity.cpp; \
279	done;
280
281	MOSTLYCLEANFILES = unity.cpp

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