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root/OpenMD/trunk/CMakeLists.txt
Revision: 2012
Committed: Wed Aug 13 17:18:37 2014 UTC (10 years, 9 months ago) by gezelter
Content type: text/plain
File size: 28557 byte(s)
Log Message: 
Added mdShrink utility

File Contents

# User Rev Content
1 chuckv 1466 # Top level cmake script for OpenMD.
2 gezelter 1694 project(OpenMD CXX)
3     cmake_minimum_required(VERSION 2.8.5)
4 chuckv 1466
5 gezelter 1668 SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules")
6    
7     if (NOT CMAKE_BUILD_TYPE)
8     set(CMAKE_BUILD_TYPE "Release")
9     endif()
10    
11 gezelter 1767 IF(WIN32)
12     ADD_DEFINITIONS(/D _CRT_SECURE_NO_WARNINGS)
13     ENDIF(WIN32)
14    
15 gezelter 1694 find_package(MPI)
16     if (NOT MPI_CXX_FOUND)
17     message(STATUS "========== OpenMD Parallel Information ==========")
18     message(STATUS )
19     message(STATUS "No MPI compiler found. Perhaps you want to set one explicitly?")
20     message(STATUS "To override the default compiler, set the environment variable")
21     message(STATUS " export CXX=/full/path/to/mpic++")
22     message(STATUS "in bash or ksh or sh. In csh or tcsh, use:")
23     message(STATUS " setenv CXX /full/path/to/mpic++")
24     message(STATUS "before running the cmake command.")
25     message(STATUS )
26     message(STATUS "=================================================")
27     endif()
28     IF ( MPI_CXX_FOUND )
29     INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH})
30     ENDIF()
31    
32 gezelter 1668 include(CheckCXXCompilerFlag)
33 gezelter 1694 include(CheckIncludeFileCXX)
34     include(CheckCXXSymbolExists)
35 gezelter 1668
36 chuckv 1466 # OpenMD version number.
37 chuckv 1496 set (VERSION_MAJOR "2")
38 gezelter 1979 set (VERSION_MINOR "2")
39 chuckv 1496 set (VERSION_TINY "0")
40 gezelter 1668 option(SINGLE_PRECISION "Build Single precision (float) version" OFF)
41    
42 gezelter 1647 IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
43 gezelter 1790 IF(WIN32)
44     SET(CMAKE_INSTALL_PREFIX "C:/Program Files (x86)/openmd"
45     CACHE PATH "OpenMD install prefix" FORCE)
46     ELSE(WIN32)
47     SET(CMAKE_INSTALL_PREFIX "/usr/local/openmd"
48     CACHE PATH "OpenMD install prefix" FORCE)
49     ENDIF(WIN32)
50 gezelter 1647 ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
51 gezelter 1790 ADD_DEFINITIONS( -DFRC_PATH=${CMAKE_INSTALL_PREFIX}/forceFields )
52 chuckv 1466
53 gezelter 1647 # ---------- Setup output Directories -------------------------
54     SET (CMAKE_LIBRARY_OUTPUT_DIRECTORY
55     ${PROJECT_BINARY_DIR}/lib
56     CACHE PATH
57     "Single directory for all shared libraries"
58     )
59     # --------- Setup the Executable output Directory -------------
60     SET (CMAKE_RUNTIME_OUTPUT_DIRECTORY
61     ${PROJECT_BINARY_DIR}/bin
62     CACHE PATH
63     "Single directory for all Executables."
64     )
65     # --------- Setup the static library directory -------------
66     SET (CMAKE_ARCHIVE_OUTPUT_DIRECTORY
67     ${PROJECT_BINARY_DIR}/lib
68     CACHE PATH
69     "Single directory for all static libraries."
70     )
71    
72 gezelter 1636 FIND_PACKAGE(Subversion)
73     IF ( Subversion_FOUND AND EXISTS ${PROJECT_SOURCE_DIR}/.svn )
74     Subversion_WC_INFO(${PROJECT_SOURCE_DIR} Project)
75 gezelter 1694 MESSAGE(STATUS "Current revision is ${Project_WC_REVISION}")
76 gezelter 1636 Subversion_WC_LOG(${PROJECT_SOURCE_DIR} Project)
77     SET(SVN_REV ${Project_WC_REVISION})
78 gezelter 1652 SET(GENERATELOGS "${PROJECT_SOURCE_DIR}/doc/svn2cl")
79     ADD_CUSTOM_TARGET(ChangeLog
80     COMMAND ${GENERATELOGS} "--group-by-day" "--include-rev"
81     "--linelen=78" "--output=${PROJECT_BINARY_DIR}/ChangeLog" "${PROJECT_SOURCE_DIR}"
82     )
83 gezelter 1836 ELSE()
84     SET(SVN_REV Release)
85 gezelter 1636 ENDIF()
86    
87 gezelter 1694 check_include_file_cxx(conio.h HAVE_CONIO_H)
88     check_cxx_symbol_exists(strncasecmp "string.h" HAVE_STRNCASECMP)
89 gezelter 1668
90 chuckv 1466 # Optional libraries: If we can find these, we will build with them
91     # Look for OpenBabel libraries
92 chuckv 1496 find_package(OpenBabel2)
93     IF(OPENBABEL2_FOUND)
94     SET(USE_OPENBABEL)
95     include_directories(${OPENBABEL2_INCLUDE_DIR})
96 gezelter 1694 # link libraries are added only for targets that need them.
97 gezelter 1695 ELSE(OPENBABEL2_FOUND)
98 gezelter 1705 MESSAGE(STATUS "No OpenBabel found - will not build atom2md")
99 chuckv 1496 ENDIF(OPENBABEL2_FOUND)
100    
101 gezelter 1743 find_package(Eigen3)
102     if(EIGEN3_FOUND)
103     add_definitions(-DHAVE_EIGEN -DHAVE_EIGEN3)
104     include_directories(${EIGEN3_INCLUDE_DIR})
105     else()
106     find_package(Eigen2) # find and setup Eigen2
107     if(EIGEN2_FOUND)
108     add_definitions (-DHAVE_EIGEN)
109     include_directories(${EIGEN2_INCLUDE_DIR})
110     endif()
111     endif()
112    
113 chuckv 1466 #Look for QHULL Libraries
114 gezelter 1879 SET(QHULL_USE_STATIC 1)
115 gezelter 1694 find_package(Qhull)
116 chuckv 1496 IF(QHULL_FOUND)
117     SET(HAVE_QHULL 1)
118 chuckv 1500 include_directories(${QHULL_INCLUDE_DIR})
119 chuckv 1496 LINK_LIBRARIES(${QHULL_LIBRARIES})
120 gezelter 1695 ELSE(QHULL_FOUND)
121 gezelter 1705 MESSAGE(STATUS "No Qhull found - will be missing some features")
122 chuckv 1496 ENDIF(QHULL_FOUND)
123 chuckv 1466
124 chuckv 1496 # zlib stuff
125     find_package(ZLIB)
126     if(ZLIB_FOUND)
127     SET(HAVE_LIBZ 1)
128     add_definitions(-DHAVE_LIBZ)
129     include_directories(${ZLIB_INCLUDE_DIR})
130     LINK_LIBRARIES(${ZLIB_LIBRARIES})
131 gezelter 1695 ELSE(ZLIB_FOUND)
132 gezelter 1705 MESSAGE(STATUS "No zlib found - will be missing compressed dump files")
133 chuckv 1496 endif(ZLIB_FOUND)
134    
135 gezelter 1695 #FFTW3
136 gezelter 1694 IF(SINGLE_PRECISION)
137     find_package(FFTW3 COMPONENTS single)
138     else()
139     find_package(FFTW3 COMPONENTS double)
140     endif(SINGLE_PRECISION)
141     if (FFTW3_FOUND)
142     include_directories (${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR} ${FFTW3_INCLUDE_DIR})
143 chuckv 1496 SET(HAVE_LIBFFTW 1)
144 gezelter 1668 SET(HAVE_FFTW3_H 1)
145 gezelter 1694 INCLUDE_DIRECTORIES(${FFTW3_INCLUDE_DIR})
146     LINK_LIBRARIES(${FFTW3_LIBRARIES})
147 gezelter 1695 ELSE(FFTW3_FOUND)
148 gezelter 1705 MESSAGE(STATUS "No fftw3 found - will be missing some analysis modules")
149 gezelter 1694 endif (FFTW3_FOUND)
150 chuckv 1496
151 gezelter 1694
152 gezelter 1651 # add a target to generate API documentation with Doxygen
153     find_package(Doxygen)
154     if(DOXYGEN_FOUND)
155     configure_file("${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in" "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile" @ONLY)
156     add_custom_target(doc
157     ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile"
158     WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doc"
159     COMMENT "Generating API documentation with Doxygen" VERBATIM
160     )
161     endif(DOXYGEN_FOUND)
162 chuckv 1496
163 gezelter 1639 FIND_PACKAGE(Perl)
164     IF(PERL_FOUND)
165     SET(PERL ${PERL_EXECUTABLE})
166     ELSE(PERL_FOUND)
167 gezelter 1695 MESSAGE(STATUS "Failed to find perl - some scripts will not be made")
168 gezelter 1639 ENDIF(PERL_FOUND)
169    
170 gezelter 1695 SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation
171     locations")
172    
173 gezelter 1639 FIND_PACKAGE(PythonInterp)
174     IF(PYTHON_EXECUTABLE)
175     SET(PYTHON ${PYTHON_EXECUTABLE})
176     ELSE(PYTHON_EXECUTABLE)
177 gezelter 1695 MESSAGE(STATUS "Failed to find python - some scripts will not be made")
178 gezelter 1639 ENDIF(PYTHON_EXECUTABLE)
179    
180 chuckv 1496 configure_file (
181     "${PROJECT_SOURCE_DIR}/src/config.h.cmake"
182 gezelter 1655 "${PROJECT_BINARY_DIR}/config.h"
183     )
184 gezelter 1976 configure_file(
185     "${PROJECT_SOURCE_DIR}/src/utils/Revision.cpp.in"
186     "${PROJECT_BINARY_DIR}/Revision.cpp"
187     )
188    
189 gezelter 1655 include_directories("${PROJECT_BINARY_DIR}" "${PROJECT_SOURCE_DIR}/src")
190 chuckv 1496
191 chuckv 1466 #Add executables for build
192 gezelter 1639 set (PROGRAMS
193     openmd
194     openmd_MPI
195     Dump2XYZ
196     simpleBuilder
197     StaticProps
198     DynamicProps
199     randomBuilder
200     nanoparticleBuilder
201     thermalizer
202 gezelter 1879 recenter
203 gezelter 1639 atom2md
204     Hydro)
205 chuckv 1466
206 gezelter 1639 set(SOURCE
207 gezelter 1976 "${PROJECT_BINARY_DIR}/Revision.cpp"
208 gezelter 1639 src/antlr/ANTLRUtil.cpp
209     src/antlr/ASTFactory.cpp
210     src/antlr/ASTNULLType.cpp
211     src/antlr/ASTRefCount.cpp
212     src/antlr/BaseAST.cpp
213     src/antlr/BitSet.cpp
214     src/antlr/CommonAST.cpp
215     src/antlr/CommonASTWithHiddenTokens.cpp
216     src/antlr/CommonHiddenStreamToken.cpp
217     src/antlr/CommonToken.cpp
218     src/antlr/LLkParser.cpp
219     src/antlr/MismatchedCharException.cpp
220     src/antlr/MismatchedTokenException.cpp
221     src/antlr/NoViableAltException.cpp
222     src/antlr/NoViableAltForCharException.cpp
223     src/antlr/Parser.cpp
224     src/antlr/RecognitionException.cpp
225     src/antlr/String.cpp
226     src/antlr/Token.cpp
227     src/antlr/TokenRefCount.cpp
228     src/antlr/TokenStreamBasicFilter.cpp
229     src/antlr/TokenStreamHiddenTokenFilter.cpp
230     src/antlr/TokenStreamRewriteEngine.cpp
231     src/antlr/TokenStreamSelector.cpp
232     src/antlr/TreeParser.cpp
233     src/brains/BlockSnapshotManager.cpp
234     src/brains/DataStorage.cpp
235 gezelter 1725 src/brains/ForceField.cpp
236 gezelter 1639 src/brains/MoleculeCreator.cpp
237     src/brains/PairList.cpp
238     src/brains/Register.cpp
239     src/brains/SimSnapshotManager.cpp
240     src/brains/Snapshot.cpp
241     src/brains/Stats.cpp
242 gezelter 1748 src/constraints/Shake.cpp
243 gezelter 1639 src/constraints/Rattle.cpp
244     src/hydrodynamics/Ellipsoid.cpp
245     src/hydrodynamics/HydroProp.cpp
246     src/hydrodynamics/Sphere.cpp
247     src/integrators/DLM.cpp
248 gezelter 1766 src/flucq/FluctuatingChargeLangevin.cpp
249 gezelter 1743 src/flucq/FluctuatingChargeParameters.cpp
250 gezelter 1731 src/flucq/FluctuatingChargeNVT.cpp
251 gezelter 1743 src/flucq/FluctuatingChargePropagator.cpp
252 gezelter 1639 src/integrators/Integrator.cpp
253     src/integrators/IntegratorFactory.cpp
254     src/integrators/LangevinDynamics.cpp
255     src/integrators/LDForceManager.cpp
256     src/integrators/NgammaT.cpp
257 gezelter 2011 src/integrators/NPA.cpp
258 gezelter 1639 src/integrators/NPAT.cpp
259     src/integrators/NPrT.cpp
260     src/integrators/NPT.cpp
261     src/integrators/NPTf.cpp
262     src/integrators/NPTi.cpp
263     src/integrators/NPTsz.cpp
264     src/integrators/NPTxyz.cpp
265     src/integrators/NVE.cpp
266     src/integrators/NVT.cpp
267     src/integrators/VelocityVerletIntegrator.cpp
268     src/io/AtomTypesSectionParser.cpp
269     src/io/BaseAtomTypesSectionParser.cpp
270     src/io/BendTypesSectionParser.cpp
271     src/io/BondTypesSectionParser.cpp
272     src/io/ChargeAtomTypesSectionParser.cpp
273     src/io/DirectionalAtomTypesSectionParser.cpp
274     src/io/EAMAtomTypesSectionParser.cpp
275 gezelter 1710 src/io/FluctuatingChargeAtomTypesSectionParser.cpp
276 gezelter 1639 src/io/ForceFieldOptions.cpp
277     src/io/GayBerneAtomTypesSectionParser.cpp
278     src/io/Globals.cpp
279     src/io/InversionTypesSectionParser.cpp
280     src/io/LennardJonesAtomTypesSectionParser.cpp
281     src/io/MultipoleAtomTypesSectionParser.cpp
282     src/io/NonBondedInteractionsSectionParser.cpp
283     src/io/OptionSectionParser.cpp
284     src/io/ParamConstraint.cpp
285 gezelter 1710 src/io/PolarizableAtomTypesSectionParser.cpp
286 gezelter 1639 src/io/SCAtomTypesSectionParser.cpp
287     src/io/SectionParser.cpp
288     src/io/SectionParserManager.cpp
289     src/io/ShapeAtomTypesSectionParser.cpp
290     src/io/StickyAtomTypesSectionParser.cpp
291     src/io/StickyPowerAtomTypesSectionParser.cpp
292     src/io/TorsionTypesSectionParser.cpp
293     src/io/ZConsReader.cpp
294     src/lattice/CubicLattice.cpp
295     src/lattice/FCCLattice.cpp
296     src/lattice/Lattice.cpp
297     src/lattice/LatticeFactory.cpp
298     src/lattice/shapedLattice.cpp
299     src/math/ChebyshevT.cpp
300     src/math/ChebyshevU.cpp
301     src/math/CubicSpline.cpp
302     src/math/LegendrePolynomial.cpp
303     src/math/RealSphericalHarmonic.cpp
304     src/math/RMSD.cpp
305     src/math/SeqRandNumGen.cpp
306     src/math/SphericalHarmonic.cpp
307     src/math/Wigner3jm.cpp
308     src/mdParser/FilenameObserver.cpp
309 gezelter 1743 src/optimization/OptimizationFactory.cpp
310     src/optimization/Armijo.cpp
311     src/optimization/BFGS.cpp
312     src/optimization/ConjugateGradient.cpp
313     src/optimization/Constraint.cpp
314     src/optimization/EndCriteria.cpp
315     src/optimization/LineSearch.cpp
316     src/optimization/LineSearchBasedMethod.cpp
317     src/optimization/SteepestDescent.cpp
318     src/optimization/PotentialEnergyObjectiveFunction.cpp
319 gezelter 1746 src/optimization/MinimizerParameters.cpp
320 gezelter 1639 src/nonbonded/EAM.cpp
321     src/nonbonded/GB.cpp
322     src/nonbonded/InteractionManager.cpp
323     src/nonbonded/LJ.cpp
324     src/nonbonded/MAW.cpp
325     src/nonbonded/Morse.cpp
326     src/nonbonded/RepulsivePower.cpp
327     src/nonbonded/SC.cpp
328     src/nonbonded/Sticky.cpp
329     src/nonbonded/SwitchingFunction.cpp
330     src/primitives/Atom.cpp
331     src/primitives/Bend.cpp
332     src/primitives/DirectionalAtom.cpp
333     src/primitives/GhostBend.cpp
334     src/primitives/GhostTorsion.cpp
335     src/primitives/Inversion.cpp
336     src/primitives/Molecule.cpp
337     src/primitives/RigidBody.cpp
338     src/primitives/StuntDouble.cpp
339 gezelter 1954 src/primitives/ShortRangeInteraction.cpp
340 gezelter 1639 src/primitives/Torsion.cpp
341     src/primitives/UreyBradleyBend.cpp
342 jmarr 1780 src/perturbations/ElectricField.cpp
343 gezelter 1639 src/restraints/MolecularRestraint.cpp
344     src/restraints/ObjectRestraint.cpp
345     src/selection/HullFinder.cpp
346     src/selection/IndexFinder.cpp
347     src/selection/NameFinder.cpp
348     src/selection/SelectionCompiler.cpp
349     src/selection/SelectionEvaluator.cpp
350     src/selection/SelectionManager.cpp
351     src/selection/SelectionToken.cpp
352     src/selection/TokenMap.cpp
353 gezelter 1954 src/selection/SelectionSet.cpp
354 gezelter 1639 src/types/AtomStamp.cpp
355     src/types/AtomType.cpp
356     src/types/BendStamp.cpp
357     src/types/BondStamp.cpp
358     src/types/CharmmTorsionType.cpp
359     src/types/Component.cpp
360 gezelter 1979 src/types/ConstraintStamp.cpp
361 gezelter 1639 src/types/CutoffGroupStamp.cpp
362 gezelter 1710 src/types/DirectionalAdapter.cpp
363     src/types/EAMAdapter.cpp
364     src/types/FixedChargeAdapter.cpp
365     src/types/FluctuatingChargeAdapter.cpp
366 gezelter 1639 src/types/FragmentStamp.cpp
367 gezelter 1710 src/types/GayBerneAdapter.cpp
368 gezelter 1639 src/types/ImproperCosineInversionType.cpp
369     src/types/InversionStamp.cpp
370 gezelter 1710 src/types/LennardJonesAdapter.cpp
371 gezelter 1639 src/types/MoleculeStamp.cpp
372 gezelter 1710 src/types/MultipoleAdapter.cpp
373 gezelter 1639 src/types/NonBondedInteractionType.cpp
374 gezelter 1710 src/types/PolarizableAdapter.cpp
375 gezelter 1639 src/types/RestraintStamp.cpp
376     src/types/RigidBodyStamp.cpp
377     src/types/ShapeAtomType.cpp
378 gezelter 1710 src/types/StickyAdapter.cpp
379     src/types/SuttonChenAdapter.cpp
380 gezelter 1639 src/types/TorsionStamp.cpp
381     src/types/ZconsStamp.cpp
382     src/utils/ElementsTable.cpp
383     src/utils/MoLocator.cpp
384     src/utils/PropertyMap.cpp
385     src/utils/StringTokenizer.cpp
386     src/utils/StringUtils.cpp
387     src/utils/Trim.cpp
388     src/utils/Utility.cpp
389     src/utils/wildcards.cpp
390     src/visitors/AtomNameVisitor.cpp
391     src/visitors/AtomVisitor.cpp
392     src/visitors/CompositeVisitor.cpp
393     src/visitors/LipidTransVisitor.cpp
394     src/visitors/OtherVisitor.cpp
395     src/visitors/ReplacementVisitor.cpp
396     src/visitors/RigidBodyVisitor.cpp
397     src/visitors/ZconsVisitor.cpp
398 gezelter 1731 src/rnemd/RNEMDParameters.cpp
399 gezelter 1879 src/clusters/Icosahedron.cpp
400     src/clusters/Decahedron.cpp
401 gezelter 1639 )
402 chuckv 1466
403 gezelter 1639 set( PARALLEL_SOURCE
404 gezelter 1969 src/antlr/CharBuffer.cpp
405     src/antlr/CharScanner.cpp
406     src/antlr/InputBuffer.cpp
407     src/antlr/TokenBuffer.cpp
408     src/mdParser/MDLexer.cpp
409     src/mdParser/MDParser.cpp
410     src/mdParser/MDTreeParser.cpp
411 gezelter 1639 src/brains/ForceManager.cpp
412     src/brains/SimCreator.cpp
413     src/brains/SimInfo.cpp
414     src/brains/Thermo.cpp
415     src/constraints/ZconstraintForceManager.cpp
416 gezelter 1743 src/flucq/FluctuatingChargeConstraints.cpp
417     src/flucq/FluctuatingChargeObjectiveFunction.cpp
418 gezelter 1972 src/flucq/FluctuatingChargeForces.cpp
419 gezelter 1730 src/integrators/LangevinHullForceManager.cpp
420 gezelter 1731 src/rnemd/RNEMD.cpp
421 gezelter 1639 src/integrators/Velocitizer.cpp
422 gezelter 1981 src/io/ConstraintWriter.cpp
423 gezelter 1639 src/io/DumpReader.cpp
424     src/io/DumpWriter.cpp
425     src/io/RestReader.cpp
426     src/io/RestWriter.cpp
427     src/io/StatWriter.cpp
428     src/io/ZConsWriter.cpp
429     src/io/ifstrstream.cpp
430     src/math/ParallelRandNumGen.cpp
431 gezelter 1926 src/nonbonded/Electrostatic.cpp
432 gezelter 1639 src/parallel/ForceDecomposition.cpp
433     src/parallel/ForceMatrixDecomposition.cpp
434     src/restraints/RestraintForceManager.cpp
435     src/restraints/ThermoIntegrationForceManager.cpp
436 gezelter 1802 src/selection/DistanceFinder.cpp
437 gezelter 1639 src/utils/ProgressBar.cpp
438 gezelter 1668 src/utils/simError.cpp
439 gezelter 1802 src/utils/OpenMDBitSet.cpp
440 gezelter 1743 src/optimization/Problem.cpp
441 gezelter 1639 )
442    
443 gezelter 1767 IF(ZLIB_FOUND)
444     set(ZLIB_SOURCE
445     src/io/gzstream.cpp
446     )
447     ENDIF(ZLIB_FOUND)
448    
449 gezelter 1639 IF(QHULL_FOUND)
450     set(QHULL_SOURCE
451     src/integrators/LangevinHullDynamics.cpp
452     src/math/Triangle.cpp
453     )
454     set(QHULL_PARALLEL_SOURCE
455     src/integrators/LangevinHullForceManager.cpp
456     src/math/ConvexHull.cpp
457     src/math/AlphaHull.cpp
458     )
459     ENDIF(QHULL_FOUND)
460    
461 gezelter 1767 IF(WIN32)
462     set(GETOPT_SOURCE
463 gezelter 1795 src/utils/wingetopt.cpp
464 gezelter 1767 )
465     ENDIF(WIN32)
466    
467     add_library(openmd_core STATIC ${SOURCE} ${QHULL_SOURCE} ${ZLIB_SOURCE} )
468 gezelter 1639 add_library(openmd_single STATIC ${PARALLEL_SOURCE} ${QHULL_PARALLEL_SOURCE} )
469    
470     IF(MPI_FOUND)
471     add_library(openmd_parallel STATIC ${PARALLEL_SOURCE} ${QHULL_PARALLEL_SOURCE} )
472     set_target_properties(openmd_parallel PROPERTIES
473     COMPILE_DEFINITIONS IS_MPI
474     )
475     ENDIF(MPI_FOUND)
476    
477     add_executable(openmd src/applications/openmd/openmd.cpp)
478     target_link_libraries(openmd openmd_single openmd_core openmd_single openmd_core)
479    
480     if (MPI_FOUND)
481     add_executable(openmd_MPI src/applications/openmd/openmd.cpp)
482     set_target_properties(openmd_MPI PROPERTIES
483     COMPILE_DEFINITIONS IS_MPI
484     )
485     target_link_libraries(openmd_MPI openmd_parallel openmd_core openmd_parallel openmd_core)
486 gezelter 1647 INSTALL(TARGETS
487     openmd_parallel openmd_MPI
488     RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
489     LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
490     ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
491     )
492 gezelter 1639 ENDIF (MPI_FOUND)
493    
494     set (DUMP2XYZSOURCE
495     src/applications/dump2Xyz/Dump2XYZ.cpp
496 gezelter 1655 src/applications/dump2Xyz/Dump2XYZCmd.cpp
497 gezelter 1639 )
498    
499     set (DYNAMICPROPSSOURCE
500     src/applications/dynamicProps/ActionCorrFunc.cpp
501     src/applications/dynamicProps/CrossTimeCorrFunc.cpp
502     src/applications/dynamicProps/DipoleCorrFunc.cpp
503     src/applications/dynamicProps/DirectionalRCorrFunc.cpp
504     src/applications/dynamicProps/DynamicProps.cpp
505     src/applications/dynamicProps/EnergyCorrFunc.cpp
506     src/applications/dynamicProps/FrameTimeCorrFunc.cpp
507 gezelter 2003 src/applications/dynamicProps/FreqFlucCorrFunc.cpp
508 gezelter 1639 src/applications/dynamicProps/LegendreCorrFunc.cpp
509 gezelter 1915 src/applications/dynamicProps/LegendreCorrFuncZ.cpp
510 gezelter 1934 src/applications/dynamicProps/cOHz.cpp
511 gezelter 1639 src/applications/dynamicProps/MomentumCorrFunc.cpp
512     src/applications/dynamicProps/ParticleTimeCorrFunc.cpp
513 gezelter 1954 src/applications/dynamicProps/InteractionTimeCorrFunc.cpp
514 gezelter 1639 src/applications/dynamicProps/RadialRCorrFunc.cpp
515     src/applications/dynamicProps/RCorrFunc.cpp
516 gezelter 1811 src/applications/dynamicProps/SelectionCorrFunc.cpp
517 gezelter 1639 src/applications/dynamicProps/StressCorrFunc.cpp
518     src/applications/dynamicProps/SystemDipoleCorrFunc.cpp
519     src/applications/dynamicProps/ThetaCorrFunc.cpp
520     src/applications/dynamicProps/TimeCorrFunc.cpp
521     src/applications/dynamicProps/VCorrFunc.cpp
522 gezelter 1954 src/applications/dynamicProps/BondCorrFunc.cpp
523 gezelter 1655 src/applications/dynamicProps/DynamicPropsCmd.cpp
524 gezelter 1639 )
525    
526     set (HYDROSOURCE
527     src/applications/hydrodynamics/AnalyticalModel.cpp
528     src/applications/hydrodynamics/ApproximationModel.cpp
529     src/applications/hydrodynamics/BeadModel.cpp
530     src/applications/hydrodynamics/CompositeShape.cpp
531     src/applications/hydrodynamics/Hydro.cpp
532     src/applications/hydrodynamics/HydrodynamicsModel.cpp
533     src/applications/hydrodynamics/HydrodynamicsModelFactory.cpp
534     src/applications/hydrodynamics/RoughShell.cpp
535     src/applications/hydrodynamics/ShapeBuilder.cpp
536 gezelter 1655 src/applications/hydrodynamics/HydroCmd.cpp
537 gezelter 1639 )
538    
539     set (STATICPROPSSOURCE
540     src/applications/staticProps/AngleR.cpp
541     src/applications/staticProps/BondAngleDistribution.cpp
542     src/applications/staticProps/BondOrderParameter.cpp
543     src/applications/staticProps/BOPofR.cpp
544     src/applications/staticProps/DensityPlot.cpp
545     src/applications/staticProps/GofAngle2.cpp
546     src/applications/staticProps/GofR.cpp
547     src/applications/staticProps/GofRAngle.cpp
548     src/applications/staticProps/GofRZ.cpp
549     src/applications/staticProps/GofXyz.cpp
550     src/applications/staticProps/GofZ.cpp
551     src/applications/staticProps/Hxy.cpp
552 gezelter 1998 src/applications/staticProps/MultipoleSum.cpp
553 gezelter 1639 src/applications/staticProps/NanoLength.cpp
554     src/applications/staticProps/NanoVolume.cpp
555 gezelter 1994 src/applications/staticProps/NitrileFrequencyMap.cpp
556 gezelter 1639 src/applications/staticProps/ObjectCount.cpp
557     src/applications/staticProps/P2OrderParameter.cpp
558     src/applications/staticProps/pAngle.cpp
559     src/applications/staticProps/RadialDistrFunc.cpp
560     src/applications/staticProps/RhoR.cpp
561     src/applications/staticProps/RhoZ.cpp
562     src/applications/staticProps/RippleOP.cpp
563 gezelter 1879 src/applications/staticProps/RNEMDStats.cpp
564 gezelter 1639 src/applications/staticProps/SCDOrderParameter.cpp
565 gezelter 1879 src/applications/staticProps/SpatialStatistics.cpp
566 gezelter 1639 src/applications/staticProps/StaticProps.cpp
567     src/applications/staticProps/TetrahedralityParam.cpp
568 gezelter 1763 src/applications/staticProps/TetrahedralityParamZ.cpp
569 gezelter 1639 src/applications/staticProps/TwoDGofR.cpp
570 gezelter 1655 src/applications/staticProps/StaticPropsCmd.cpp
571 gezelter 1639 )
572    
573     set (NANOPARTICLEBUILDERSOURCE
574     src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp
575     src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp
576 gezelter 1655 src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp
577 gezelter 1639 )
578    
579 kstocke1 1701 set (NANORODBUILDERSOURCE
580     src/applications/nanoparticleBuilder/nanorodBuilder.cpp
581     src/applications/nanoparticleBuilder/shapedLatticeRod.cpp
582 gezelter 1879 src/applications/nanoparticleBuilder/shapedLatticeEllipsoid.cpp
583 kstocke1 1701 src/applications/nanoparticleBuilder/nanorodBuilderCmd.cpp
584     )
585    
586     set (NANOROD_PENTBUILDERSOURCE
587     src/applications/nanoparticleBuilder/nanorod_pentBuilder.cpp
588     src/applications/nanoparticleBuilder/nanorod_pentBuilderCmd.cpp
589     src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp
590     )
591    
592 gezelter 1879 set (ICOSAHEDRALBUILDERSOURCE
593     src/applications/nanoparticleBuilder/icosahedralBuilder.cpp
594     src/applications/nanoparticleBuilder/icosahedralBuilderCmd.cpp
595     )
596    
597 gezelter 1639 set (RANDOMBUILDERSOURCE
598     src/applications/randomBuilder/randomBuilder.cpp
599 gezelter 1655 src/applications/randomBuilder/randomBuilderCmd.cpp
600 gezelter 1639 )
601    
602     set(SIMPLEBUILDERSOURCE
603     src/applications/simpleBuilder/simpleBuilder.cpp
604 gezelter 1655 src/applications/simpleBuilder/simpleBuilderCmd.cpp
605 gezelter 1639 )
606    
607     set(THERMALIZERSOURCE
608     src/applications/thermalizer/thermalizer.cpp
609 gezelter 1655 src/applications/thermalizer/thermalizerCmd.cpp
610 gezelter 1639 )
611    
612 gezelter 1879 set(RECENTERSOURCE
613     src/applications/recenter/recenter.cpp
614     src/applications/recenter/recenterCmd.cpp
615     )
616    
617 gezelter 1767 add_executable(Dump2XYZ ${DUMP2XYZSOURCE} ${GETOPT_SOURCE})
618 gezelter 1639 target_link_libraries(Dump2XYZ openmd_single openmd_core openmd_single openmd_core)
619 gezelter 1767 add_executable(DynamicProps ${DYNAMICPROPSSOURCE} ${GETOPT_SOURCE})
620 gezelter 1639 target_link_libraries(DynamicProps openmd_single openmd_core openmd_single openmd_core)
621 gezelter 1767 add_executable(Hydro ${HYDROSOURCE} ${GETOPT_SOURCE})
622 gezelter 1639 target_link_libraries(Hydro openmd_single openmd_core openmd_single openmd_core)
623 gezelter 1767 add_executable(StaticProps ${STATICPROPSSOURCE} ${GETOPT_SOURCE})
624 gezelter 1639 target_link_libraries(StaticProps openmd_single openmd_core openmd_single openmd_core)
625 gezelter 1767 add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE} ${GETOPT_SOURCE})
626 gezelter 1807 target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
627 gezelter 1767 add_executable(nanorodBuilder ${NANORODBUILDERSOURCE} ${GETOPT_SOURCE})
628 gezelter 1807 target_link_libraries(nanorodBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
629 gezelter 1767 add_executable(nanorod_pentBuilder ${NANOROD_PENTBUILDERSOURCE} ${GETOPT_SOURCE})
630 gezelter 1807 target_link_libraries(nanorod_pentBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
631 gezelter 1879 add_executable(icosahedralBuilder ${ICOSAHEDRALBUILDERSOURCE} ${GETOPT_SOURCE})
632     target_link_libraries(icosahedralBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
633 gezelter 1767 add_executable(randomBuilder ${RANDOMBUILDERSOURCE} ${GETOPT_SOURCE})
634 gezelter 1807 target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
635 gezelter 1767 add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE} ${GETOPT_SOURCE})
636 gezelter 1807 target_link_libraries(simpleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
637 gezelter 1767 add_executable(thermalizer ${THERMALIZERSOURCE} ${GETOPT_SOURCE})
638 gezelter 1807 target_link_libraries(thermalizer openmd_single openmd_core openmd_single openmd_core openmd_single)
639 gezelter 1879 add_executable(recenter ${RECENTERSOURCE} ${GETOPT_SOURCE})
640     target_link_libraries(recenter openmd_single openmd_core openmd_single openmd_core openmd_single)
641 gezelter 1639
642     if (OPENBABEL2_FOUND)
643     set (ATOM2MDSOURCE
644     src/applications/atom2md/atom2md.cpp
645     src/applications/atom2md/openmdformat.cpp
646     )
647 gezelter 1767 add_executable(atom2md ${ATOM2MDSOURCE} ${GETOPT_SOURCE})
648 gezelter 1699 target_link_libraries(atom2md openmd_single openmd_core openmd_single openmd_core ${OPENBABEL2_LIBRARIES})
649 gezelter 1647 INSTALL(TARGETS atom2md RUNTIME DESTINATION bin
650     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
651 gezelter 1639 ENDIF (OPENBABEL2_FOUND)
652    
653    
654     set(PY_FILES
655     src/applications/hydrodynamics/diffExplainer
656     src/applications/utilities/affineScale
657     src/applications/utilities/dumpConverter
658     src/applications/utilities/md-solvator
659     src/applications/utilities/md2md
660     src/applications/utilities/mdSplit
661 gezelter 2012 src/applications/utilities/mdShrink
662 gezelter 1639 src/applications/utilities/principalAxisCalculator
663 gezelter 1795 src/applications/utilities/stat2thcond
664 gezelter 1639 src/applications/utilities/stat2visco
665 gezelter 2006 src/applications/utilities/stat2dielectric
666 gezelter 1639 src/applications/utilities/waterRotator
667 gezelter 1668 src/applications/utilities/waterReplacer
668 gezelter 1639 )
669    
670     IF(PYTHON_EXECUTABLE)
671 gezelter 1795 IF(WIN32)
672     SET(PYEXT ".py")
673     ELSE(WIN32)
674     SET(PYEXT "")
675     ENDIF(WIN32)
676    
677     foreach(PY_FILE ${PY_FILES})
678     GET_FILENAME_COMPONENT(filename "${PY_FILE}" NAME)
679     CONFIGURE_FILE(${PY_FILE}
680     "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}" @ONLY)
681     INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}"
682     DESTINATION bin
683     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
684     endforeach(PY_FILE)
685 gezelter 1639 ENDIF(PYTHON_EXECUTABLE)
686    
687     set(PERL_FILES
688     src/applications/utilities/solvator
689     src/applications/utilities/waterBoxer
690     )
691    
692     IF(PERL_FOUND)
693 gezelter 1795 IF(WIN32)
694     SET(PLEXT ".PL")
695     ELSE(WIN32)
696     SET(PLEXT "")
697     ENDIF(WIN32)
698 gezelter 1647
699 gezelter 1795 foreach(PERL_FILE ${PERL_FILES})
700     GET_FILENAME_COMPONENT(filename "${PERL_FILE}" NAME)
701     configure_file(${PERL_FILE} "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}" @ONLY)
702     INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}"
703     DESTINATION bin
704     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
705    
706     endforeach(PERL_FILE)
707 gezelter 1639 ENDIF(PERL_FOUND)
708 gezelter 1647
709 gezelter 1806
710 gezelter 1652 INSTALL(FILES AUTHORS LICENSE README INSTALL DESTINATION .
711 gezelter 1647 PERMISSIONS OWNER_READ GROUP_READ WORLD_READ)
712     INSTALL(TARGETS
713     openmd_core
714     openmd_single
715     openmd
716     Dump2XYZ
717     simpleBuilder
718     StaticProps
719     DynamicProps
720     randomBuilder
721     nanoparticleBuilder
722 gezelter 1806 nanorodBuilder
723     nanorod_pentBuilder
724 gezelter 1950 icosahedralBuilder
725 gezelter 1647 thermalizer
726 gezelter 1879 recenter
727 gezelter 1647 Hydro
728     RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
729     LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
730     ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
731     )
732    
733     install(DIRECTORY forceFields/
734     DESTINATION forceFields
735 gezelter 1650 DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
736     PATTERN ".svn" EXCLUDE
737 gezelter 1647 PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
738     install(DIRECTORY samples/
739     DESTINATION samples
740 gezelter 1650 DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
741     PATTERN ".svn" EXCLUDE
742 gezelter 1651 PATTERN "*.dump" EXCLUDE
743     PATTERN "*.stat" EXCLUDE
744 gezelter 1795 PATTERN "*.eor" EXCLUDE
745     PATTERN "*.rnemd" EXCLUDE
746 gezelter 1806 PATTERN "*.fz" EXCLUDE
747 gezelter 1647 PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
748 gezelter 1806
749     configure_file( samples/builders/runMe.in
750     "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe" @ONLY)
751     INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe"
752     DESTINATION samples/builders
753     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
754    
755    
756 gezelter 1651 INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/doc/OpenMDmanual.pdf"
757     DESTINATION doc
758     PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
759 gezelter 1694
760     message( STATUS)
761     message( STATUS "========== OpenMD Build Information ==========")
762     message( STATUS "Current revision ........... = ${SVN_REV}")
763     message( STATUS "CMAKE_SYSTEM ............... = ${CMAKE_SYSTEM}")
764     message( STATUS "==============================================")
765     message( STATUS "CMAKE_BUILD_TYPE ........... = ${CMAKE_BUILD_TYPE}")
766     message( STATUS "CMAKE_INSTALL_PREFIX ....... = ${CMAKE_INSTALL_PREFIX}")
767 gezelter 1695 message( STATUS "Build as SINGLE_PRECISION .. = ${SINGLE_PRECISION}")
768 gezelter 1694 message( STATUS "CMAKE_CXX_COMPILER ......... = ${CMAKE_CXX_COMPILER}")
769     message( STATUS "MPI_CXX_COMPILER ........... = ${MPI_CXX_COMPILER}")
770     message( STATUS "MPI_CXX_INCLUDE_PATH ....... = ${MPI_CXX_INCLUDE_PATH}")
771     message( STATUS "MPI_CXX_LIBRARIES .......... = ${MPI_CXX_LIBRARIES}")
772 gezelter 1699 message( STATUS "OPENBABEL2_ROOT ............ = ${OPENBABEL2_ROOT}")
773 gezelter 1694 message( STATUS "OPENBABEL2_INCLUDE_DIR ..... = ${OPENBABEL2_INCLUDE_DIR}")
774     message( STATUS "OPENBABEL2_LIBRARIES ....... = ${OPENBABEL2_LIBRARIES}")
775 gezelter 1695 message( STATUS "QHULL_ROOT ................. = ${QHULL_ROOT}")
776 gezelter 1694 message( STATUS "QHULL_INCLUDE_DIR .......... = ${QHULL_INCLUDE_DIR}")
777     message( STATUS "QHULL_LIBRARIES ............ = ${QHULL_LIBRARIES}")
778 gezelter 1695 message( STATUS "ZLIB_ROOT .................. = ${ZLIB_ROOT}")
779 gezelter 1694 message( STATUS "ZLIB_INCLUDE_DIR ........... = ${ZLIB_INCLUDE_DIR}")
780     message( STATUS "ZLIB_LIBRARIES ............. = ${ZLIB_LIBRARIES}")
781 gezelter 1699 message( STATUS "FFTW3_ROOT ................. = ${FFTW3_ROOT}")
782 gezelter 1694 message( STATUS "FFTW3_INCLUDE_DIR .......... = ${FFTW3_INCLUDE_DIR}")
783     message( STATUS "FFTW3_LIBRARIES ............ = ${FFTW3_LIBRARIES}")
784 gezelter 1695 message( STATUS "PERL_EXECUTABLE ............ = ${PERL_EXECUTABLE}")
785     message( STATUS "PYTHON_EXECUTABLE .......... = ${PYTHON_EXECUTABLE}")
786 gezelter 1694 message( STATUS "DOXYGEN_EXECUTABLE ......... = ${DOXYGEN_EXECUTABLE}")
787 gezelter 1695 message( STATUS )
788 gezelter 1696 message( STATUS "To override these options, add -D{OPTION_NAME}=... to the cmake command" )
789     message( STATUS "Particularly useful defines are for:")
790     message( STATUS )
791 gezelter 1699 message( STATUS " -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} (where OpenMD will be installed)")
792     message( STATUS " -DOPENBABEL2_ROOT=/path/to/openbabel")
793     message( STATUS " -DQHULL_ROOT=/path/to/qhull")
794     message( STATUS " -DFFTW3_ROOT=/path/to/fftw3")
795 gezelter 1696 message( STATUS )
796 gezelter 1790 IF(WIN32)
797     message( STATUS "To build and install OpenMD, enter: ")
798     message( STATUS " msbuild /m ALL_BUILD.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
799     message( STATUS "followed by:")
800     message( STATUS " msbuild /m INSTALL.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
801     ELSE(WIN32)
802     message( STATUS "To build and install OpenMD, enter \"make\" and \"make install\"")
803     ENDIF(WIN32)
804 gezelter 1696 message( STATUS )
805 gezelter 1795
806     # build a CPack driven installer package
807     IF(NOT DEFINED CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS)
808     SET(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
809     ENDIF()
810     include (InstallRequiredSystemLibraries)
811     set (CPACK_RESOURCE_FILE_LICENSE
812     "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
813     set (CPACK_PACKAGE_VERSION_MAJOR "${VERSION_MAJOR}")
814     set (CPACK_PACKAGE_VERSION_MINOR "${VERSION_MINOR}")
815     include (CPack)