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root/OpenMD/branches/development/CMakeLists.txt
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Comparing branches/development/CMakeLists.txt (file contents):
Revision 1639 by gezelter, Sat Sep 24 20:18:07 2011 UTC vs.
Revision 1830 by gezelter, Wed Jan 9 22:02:30 2013 UTC

# Line 1 | Line 1
1   # Top level cmake script for OpenMD.
2 + project(OpenMD CXX)
3 + cmake_minimum_required(VERSION 2.8.5)
4  
5 < cmake_minimum_required (VERSION 2.6)
4 < project(OpenMD)
5 > SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules")
6  
7 + if (NOT CMAKE_BUILD_TYPE)
8 +  set(CMAKE_BUILD_TYPE "Release")
9 + endif()
10  
11 + IF(WIN32)
12 +   ADD_DEFINITIONS(/D _CRT_SECURE_NO_WARNINGS)
13 + ENDIF(WIN32)
14 +
15 + find_package(MPI)
16 + if (NOT MPI_CXX_FOUND)
17 + message(STATUS "========== OpenMD Parallel Information ==========")
18 + message(STATUS )
19 + message(STATUS "No MPI compiler found. Perhaps you want to set one explicitly?")
20 + message(STATUS "To override the default compiler, set the environment variable")
21 + message(STATUS "     export CXX=/full/path/to/mpic++")
22 + message(STATUS "in bash or ksh or sh.  In csh or tcsh, use:")
23 + message(STATUS "     setenv CXX /full/path/to/mpic++")
24 + message(STATUS "before running the cmake command.")
25 + message(STATUS )
26 + message(STATUS "=================================================")
27 + endif()
28 + IF ( MPI_CXX_FOUND )
29 +  INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH})
30 + ENDIF()
31 +
32 + include(CheckCXXCompilerFlag)
33 + include(CheckIncludeFileCXX)
34 + include(CheckCXXSymbolExists)
35 +
36   # OpenMD version number.
37   set (VERSION_MAJOR "2")
38 < set (VERSION_MINOR "0")
38 > set (VERSION_MINOR "1")
39   set (VERSION_TINY "0")  
40 + option(SINGLE_PRECISION "Build Single precision (float) version" OFF)
41  
42 < # cmake modules that are needed to build oopse
43 < SET(CMAKE_MODULE_PATH ${OpenMD_SOURCE_DIR}/cmake/modules)
44 < SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
45 < SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
42 > IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
43 >  IF(WIN32)
44 >    SET(CMAKE_INSTALL_PREFIX "C:/Program Files (x86)/openmd"
45 >        CACHE PATH "OpenMD install prefix" FORCE)
46 >  ELSE(WIN32)
47 >    SET(CMAKE_INSTALL_PREFIX "/usr/local/openmd"
48 >        CACHE PATH "OpenMD install prefix" FORCE)
49 >  ENDIF(WIN32)
50 > ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
51 > ADD_DEFINITIONS( -DFRC_PATH=${CMAKE_INSTALL_PREFIX}/forceFields )
52  
53 < enable_language(CXX  C)
53 > # ---------- 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 >  ${PROJECT_BINARY_DIR}/lib
68 >  CACHE PATH
69 >  "Single directory for all static libraries."
70 >  )
71  
19 – if ( APPLE )
20 – set(MPI_COMPILER /opt/local/lib/openmpi/bin/mpic++)
21 – set(MPI_LIBRARY "MPI_LIBRARY-NOTFOUND" )
22 – endif( APPLE )
23 – FIND_PACKAGE(MPI)
24 – IF ( MPI_FOUND )
25 –  SET(CMAKE_REQUIRED_INCLUDES "${MPI_INCLUDE_PATH};${CMAKE_REQUIRED_INCLUDES}")
26 –  INCLUDE_DIRECTORIES(${MPI_INCLUDE_PATH})
27 – ENDIF()
28 –
72   FIND_PACKAGE(Subversion)
73   IF ( Subversion_FOUND AND EXISTS ${PROJECT_SOURCE_DIR}/.svn )
74    Subversion_WC_INFO(${PROJECT_SOURCE_DIR} Project)
75 <  MESSAGE("Current revision is ${Project_WC_REVISION}")
75 >  MESSAGE(STATUS "Current revision is ${Project_WC_REVISION}")
76    Subversion_WC_LOG(${PROJECT_SOURCE_DIR} Project)
77    SET(SVN_REV ${Project_WC_REVISION})
78    ADD_DEFINITIONS( -DSVN_REV=${Project_WC_REVISION} )
79 +  SET(GENERATELOGS "${PROJECT_SOURCE_DIR}/doc/svn2cl")
80 +  ADD_CUSTOM_TARGET(ChangeLog
81 +     COMMAND ${GENERATELOGS} "--group-by-day" "--include-rev"
82 +     "--linelen=78" "--output=${PROJECT_BINARY_DIR}/ChangeLog" "${PROJECT_SOURCE_DIR}"
83 +  )
84   ENDIF()
85  
86 + check_include_file_cxx(conio.h      HAVE_CONIO_H)
87 + check_cxx_symbol_exists(strncasecmp   "string.h"   HAVE_STRNCASECMP)
88 +
89   # Optional libraries: If we can find these, we will build with them
90   # Look for OpenBabel libraries
91   find_package(OpenBabel2)
92   IF(OPENBABEL2_FOUND)
93    SET(USE_OPENBABEL)
94    include_directories(${OPENBABEL2_INCLUDE_DIR})
95 <  message(STATUS "Openbabel libs: " ${OPENBABEL2_LIBRARIES})
96 < #  TARGET_LINK_LIBRARIES(${OPENBABEL2_LIBRARIES})
95 >  # link libraries are added only for targets that need them.
96 > ELSE(OPENBABEL2_FOUND)
97 >  MESSAGE(STATUS "No OpenBabel found - will not build atom2md")
98   ENDIF(OPENBABEL2_FOUND)
99  
100 + find_package(Eigen3)
101 + if(EIGEN3_FOUND)
102 +  add_definitions(-DHAVE_EIGEN -DHAVE_EIGEN3)
103 +  include_directories(${EIGEN3_INCLUDE_DIR})
104 + else()
105 +  find_package(Eigen2) # find and setup Eigen2
106 +  if(EIGEN2_FOUND)
107 +    add_definitions (-DHAVE_EIGEN)
108 +    include_directories(${EIGEN2_INCLUDE_DIR})
109 +  endif()
110 + endif()
111 +
112   #Look for QHULL Libraries
113 < find_package(QHULL)
113 > set(QHULL_USE_STATIC 1)
114 > find_package(Qhull)
115   IF(QHULL_FOUND)
116    SET(HAVE_QHULL 1)
117    include_directories(${QHULL_INCLUDE_DIR})
118    LINK_LIBRARIES(${QHULL_LIBRARIES})
119 + ELSE(QHULL_FOUND)
120 +  MESSAGE(STATUS "No Qhull found - will be missing some features")
121   ENDIF(QHULL_FOUND)
122  
56 –
123   # zlib stuff
124   find_package(ZLIB)
125   if(ZLIB_FOUND)
# Line 61 | Line 127 | if(ZLIB_FOUND)
127    add_definitions(-DHAVE_LIBZ)
128    include_directories(${ZLIB_INCLUDE_DIR})
129    LINK_LIBRARIES(${ZLIB_LIBRARIES})
130 + ELSE(ZLIB_FOUND)
131 +  MESSAGE(STATUS "No zlib found - will be missing compressed dump files")
132   endif(ZLIB_FOUND)
133  
134 < #FFTW
135 < INCLUDE(${CMAKE_MODULE_PATH}/FindFFTW.cmake)
136 < IF(FFTW_FOUND)
134 > #FFTW3
135 > IF(SINGLE_PRECISION)
136 >  find_package(FFTW3 COMPONENTS single)
137 > else()
138 >  find_package(FFTW3 COMPONENTS double)
139 > endif(SINGLE_PRECISION)
140 > if (FFTW3_FOUND)
141 >  include_directories (${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR} ${FFTW3_INCLUDE_DIR})
142    SET(HAVE_LIBFFTW 1)
143 <  SET(HAVE_FFTW3_H)
144 <  INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIR})
145 <  LINK_LIBRARIES(${FFTW_LIBRARIES})
146 < ENDIF(FFTW_FOUND)
143 >  SET(HAVE_FFTW3_H 1)
144 >  INCLUDE_DIRECTORIES(${FFTW3_INCLUDE_DIR})
145 >  LINK_LIBRARIES(${FFTW3_LIBRARIES})
146 > ELSE(FFTW3_FOUND)
147 >  MESSAGE(STATUS "No fftw3 found - will be missing some analysis modules")
148 > endif (FFTW3_FOUND)
149  
150  
151 < #include checks
152 < include(CheckIncludeFile)
153 < CHECK_INCLUDE_FILE(fftw3.h HAVE_FFTW3_H)
154 < CHECK_INCLUDE_FILE(fftw.h HAVE_FFWT_H)
155 < CHECK_INCLUDE_FILE(dfftw.h HAVE_DFFTW_H)
156 < CHECK_INCLUDE_FILE(cmath.h HAVE_CMATH_H)
157 < check_include_file(limits.h HAVE_LIMITS_H)
158 < check_include_file(stdlib.h HAVE_STDLIB_H)
159 < check_include_file(string.h HAVE_STRING_H)
160 < check_include_file("sys/ioctl.h" HAVE_SYS_IOCTL_H)
86 < check_include_file(unistd.h HAVE_UNISTD_H)
151 > # add a target to generate API documentation with Doxygen
152 > find_package(Doxygen)
153 > if(DOXYGEN_FOUND)
154 >  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in" "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile" @ONLY)
155 >  add_custom_target(doc
156 >    ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile"
157 >    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doc"
158 >    COMMENT "Generating API documentation with Doxygen" VERBATIM
159 >  )
160 > endif(DOXYGEN_FOUND)
161  
88 – #symbol checks
89 – include(CheckSymbolExists)
90 –
91 – #function checks
92 – include(CheckFunctionExists)
93 – check_function_exists(atexit HAVE_ATEXIT)
94 – check_function_exists(floor HAVE_FLOOR)
95 – check_function_exists(pow HAVE_POW)
96 – check_function_exists(select HAVE_SELECT)
97 – check_function_exists(sqrt HAVE_SQRT)
98 – check_function_exists(strcasecmp HAVE_STRCASECMP)
99 – check_function_exists(strchr HAVE_STRCHR)
100 – check_function_exists(strdup HAVE_STRDUP)
101 – check_function_exists(strncasecmp HAVE_STRNCASECMP)
102 – check_function_exists(strstr HAVE_STRSTR)
103 – check_function_exists(strtol HAVE_STRTOL)
104 – check_function_exists(strtoull HAVE_STRTOULL)
105 – check_function_exists(sysmp HAVE_SYSMP)
106 – check_function_exists(table HAVE_TABLE)
107 –
108 –
162   FIND_PACKAGE(Perl)
163   IF(PERL_FOUND)
164    SET(PERL ${PERL_EXECUTABLE})
165   ELSE(PERL_FOUND)
166 <  MESSAGE(STATUS "Failed to find perl")
166 >  MESSAGE(STATUS "Failed to find perl - some scripts will not be made")
167   ENDIF(PERL_FOUND)
168  
169 + SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation
170 + locations")
171 +
172   FIND_PACKAGE(PythonInterp)
173   IF(PYTHON_EXECUTABLE)
174    SET(PYTHON ${PYTHON_EXECUTABLE})
175   ELSE(PYTHON_EXECUTABLE)
176 <  MESSAGE(STATUS "Failed to find python")
176 >  MESSAGE(STATUS "Failed to find python - some scripts will not be made")
177   ENDIF(PYTHON_EXECUTABLE)
178  
123 – SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation locations")
124 –
125 –
126 – include(CMakePrintSystemInformation)
127 –
179   configure_file (
180    "${PROJECT_SOURCE_DIR}/src/config.h.cmake"
181 <  "${PROJECT_SOURCE_DIR}/src/config.h"
182 <  )
183 < include_directories (${PROJECT_SOURCE_DIR}/src)
181 >  "${PROJECT_BINARY_DIR}/config.h"
182 > )
183 > include_directories("${PROJECT_BINARY_DIR}" "${PROJECT_SOURCE_DIR}/src")
184  
134 – #CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
135 –
136 –
185   #Add executables for build
186   set (PROGRAMS
187   openmd
# Line 180 | Line 228 | src/brains/DataStorage.cpp
228   src/antlr/TreeParser.cpp
229   src/brains/BlockSnapshotManager.cpp
230   src/brains/DataStorage.cpp
231 + src/brains/ForceField.cpp
232   src/brains/MoleculeCreator.cpp
233   src/brains/PairList.cpp
234   src/brains/Register.cpp
235   src/brains/SimSnapshotManager.cpp
236   src/brains/Snapshot.cpp
237   src/brains/Stats.cpp
238 + src/constraints/Shake.cpp
239   src/constraints/Rattle.cpp
240   src/hydrodynamics/Ellipsoid.cpp
241   src/hydrodynamics/HydroProp.cpp
242   src/hydrodynamics/Sphere.cpp
243   src/integrators/DLM.cpp
244 + src/flucq/FluctuatingChargeLangevin.cpp
245 + src/flucq/FluctuatingChargeParameters.cpp
246 + src/flucq/FluctuatingChargeNVT.cpp
247 + src/flucq/FluctuatingChargePropagator.cpp
248   src/integrators/Integrator.cpp
249   src/integrators/IntegratorFactory.cpp
250   src/integrators/LangevinDynamics.cpp
# Line 213 | Line 267 | src/io/EAMAtomTypesSectionParser.cpp
267   src/io/ChargeAtomTypesSectionParser.cpp
268   src/io/DirectionalAtomTypesSectionParser.cpp
269   src/io/EAMAtomTypesSectionParser.cpp
270 + src/io/FluctuatingChargeAtomTypesSectionParser.cpp
271   src/io/ForceFieldOptions.cpp
272   src/io/GayBerneAtomTypesSectionParser.cpp
273   src/io/Globals.cpp
219 – src/io/gzstream.cpp
274   src/io/InversionTypesSectionParser.cpp
275   src/io/LennardJonesAtomTypesSectionParser.cpp
276   src/io/MultipoleAtomTypesSectionParser.cpp
277   src/io/NonBondedInteractionsSectionParser.cpp
278   src/io/OptionSectionParser.cpp
279   src/io/ParamConstraint.cpp
280 + src/io/PolarizableAtomTypesSectionParser.cpp
281   src/io/SCAtomTypesSectionParser.cpp
282   src/io/SectionParser.cpp
283   src/io/SectionParserManager.cpp
# Line 249 | Line 304 | src/mdParser/MDTreeParser.cpp
304   src/mdParser/MDLexer.cpp
305   src/mdParser/MDParser.cpp
306   src/mdParser/MDTreeParser.cpp
307 < src/minimizers/MinimizerFactory.cpp
308 < src/minimizers/MinimizerParameterSet.cpp
307 > src/optimization/OptimizationFactory.cpp
308 > src/optimization/Armijo.cpp
309 > src/optimization/BFGS.cpp
310 > src/optimization/ConjugateGradient.cpp
311 > src/optimization/Constraint.cpp
312 > src/optimization/EndCriteria.cpp
313 > src/optimization/LineSearch.cpp
314 > src/optimization/LineSearchBasedMethod.cpp
315 > src/optimization/SteepestDescent.cpp
316 > src/optimization/PotentialEnergyObjectiveFunction.cpp
317 > src/optimization/MinimizerParameters.cpp
318   src/nonbonded/EAM.cpp
319   src/nonbonded/Electrostatic.cpp
320   src/nonbonded/GB.cpp
# Line 273 | Line 337 | src/primitives/UreyBradleyBend.cpp
337   src/primitives/StuntDouble.cpp
338   src/primitives/Torsion.cpp
339   src/primitives/UreyBradleyBend.cpp
340 + src/perturbations/ElectricField.cpp
341   src/restraints/MolecularRestraint.cpp
342   src/restraints/ObjectRestraint.cpp
278 – src/selection/DistanceFinder.cpp
343   src/selection/HullFinder.cpp
344   src/selection/IndexFinder.cpp
345   src/selection/NameFinder.cpp
# Line 291 | Line 355 | src/types/CutoffGroupStamp.cpp
355   src/types/CharmmTorsionType.cpp
356   src/types/Component.cpp
357   src/types/CutoffGroupStamp.cpp
358 < src/types/DirectionalAtomType.cpp
358 > src/types/DirectionalAdapter.cpp
359 > src/types/EAMAdapter.cpp
360 > src/types/FixedChargeAdapter.cpp
361 > src/types/FluctuatingChargeAdapter.cpp
362   src/types/FragmentStamp.cpp
363 + src/types/GayBerneAdapter.cpp
364   src/types/ImproperCosineInversionType.cpp
365   src/types/InversionStamp.cpp
366 + src/types/LennardJonesAdapter.cpp
367   src/types/MoleculeStamp.cpp
368 + src/types/MultipoleAdapter.cpp
369   src/types/NonBondedInteractionType.cpp
370 + src/types/PolarizableAdapter.cpp
371   src/types/RestraintStamp.cpp
372   src/types/RigidBodyStamp.cpp
373   src/types/ShapeAtomType.cpp
374 + src/types/StickyAdapter.cpp
375 + src/types/SuttonChenAdapter.cpp
376   src/types/TorsionStamp.cpp
377   src/types/ZconsStamp.cpp
305 – src/UseTheForce/Amber_FF.cpp
306 – src/UseTheForce/CLAYFF.cpp
307 – src/UseTheForce/DUFF.cpp
308 – src/UseTheForce/EADM_FF.cpp
309 – src/UseTheForce/EAM_FF.cpp
310 – src/UseTheForce/ForceField.cpp
311 – src/UseTheForce/ForceFieldFactory.cpp
312 – src/UseTheForce/MnM_FF.cpp
313 – src/UseTheForce/SC_FF.cpp
314 – src/UseTheForce/SHAPES_FF.cpp
378   src/utils/ElementsTable.cpp
379   src/utils/MoLocator.cpp
317 – src/utils/OpenMDBitSet.cpp
380   src/utils/PropertyMap.cpp
381   src/utils/StringTokenizer.cpp
382   src/utils/StringUtils.cpp
# Line 329 | Line 391 | src/visitors/ZconsVisitor.cpp
391   src/visitors/ReplacementVisitor.cpp
392   src/visitors/RigidBodyVisitor.cpp
393   src/visitors/ZconsVisitor.cpp
394 + src/rnemd/RNEMDParameters.cpp
395   )
396  
397   set( PARALLEL_SOURCE
# Line 337 | Line 400 | src/constraints/ZconstraintForceManager.cpp
400   src/brains/SimInfo.cpp
401   src/brains/Thermo.cpp
402   src/constraints/ZconstraintForceManager.cpp
403 < src/integrators/RNEMD.cpp
403 > src/flucq/FluctuatingChargeConstraints.cpp
404 > src/flucq/FluctuatingChargeObjectiveFunction.cpp
405 > src/integrators/LangevinHullForceManager.cpp
406 > src/rnemd/RNEMD.cpp
407   src/integrators/Velocitizer.cpp
408   src/io/DumpReader.cpp
409   src/io/DumpWriter.cpp
# Line 347 | Line 413 | src/math/ParallelRandNumGen.cpp
413   src/io/ZConsWriter.cpp
414   src/io/ifstrstream.cpp
415   src/math/ParallelRandNumGen.cpp
350 – src/minimizers/CGFamilyMinimizer.cpp
351 – src/minimizers/Minimizer.cpp
352 – src/minimizers/PRCG.cpp
353 – src/minimizers/SDMinimizer.cpp
416   src/parallel/ForceDecomposition.cpp
417   src/parallel/ForceMatrixDecomposition.cpp
418   src/restraints/RestraintForceManager.cpp
419   src/restraints/ThermoIntegrationForceManager.cpp
420 + src/selection/DistanceFinder.cpp
421   src/utils/ProgressBar.cpp
422 < src/utils/simError.c
422 > src/utils/simError.cpp
423 > src/utils/OpenMDBitSet.cpp
424 > src/optimization/Problem.cpp
425   )
426  
427 + IF(ZLIB_FOUND)
428 + set(ZLIB_SOURCE
429 + src/io/gzstream.cpp
430 + )
431 + ENDIF(ZLIB_FOUND)
432 +
433   IF(QHULL_FOUND)
434   set(QHULL_SOURCE
435   src/integrators/LangevinHullDynamics.cpp
# Line 371 | Line 442 | ENDIF(QHULL_FOUND)
442   )
443   ENDIF(QHULL_FOUND)
444  
445 < add_library(openmd_core STATIC ${SOURCE} ${QHULL_SOURCE} )
445 > IF(WIN32)
446 > set(GETOPT_SOURCE
447 > src/utils/wingetopt.cpp
448 > )
449 > ENDIF(WIN32)
450 >
451 > add_library(openmd_core STATIC ${SOURCE} ${QHULL_SOURCE} ${ZLIB_SOURCE} )
452   add_library(openmd_single STATIC ${PARALLEL_SOURCE} ${QHULL_PARALLEL_SOURCE} )
453  
454   IF(MPI_FOUND)
# Line 390 | Line 467 | target_link_libraries(openmd_MPI openmd_parallel openm
467   COMPILE_DEFINITIONS IS_MPI
468   )
469   target_link_libraries(openmd_MPI openmd_parallel openmd_core openmd_parallel openmd_core)
470 +  INSTALL(TARGETS
471 +        openmd_parallel openmd_MPI
472 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
473 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
474 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
475 + )
476   ENDIF (MPI_FOUND)
477  
478   set (DUMP2XYZSOURCE
479   src/applications/dump2Xyz/Dump2XYZ.cpp
480 < src/applications/dump2Xyz/Dump2XYZCmd.c
480 > src/applications/dump2Xyz/Dump2XYZCmd.cpp
481   )
482  
483   set (DYNAMICPROPSSOURCE
# Line 410 | Line 493 | src/applications/dynamicProps/RCorrFunc.cpp
493   src/applications/dynamicProps/ParticleTimeCorrFunc.cpp
494   src/applications/dynamicProps/RadialRCorrFunc.cpp
495   src/applications/dynamicProps/RCorrFunc.cpp
496 + src/applications/dynamicProps/SelectionCorrFunc.cpp
497   src/applications/dynamicProps/StressCorrFunc.cpp
498   src/applications/dynamicProps/SystemDipoleCorrFunc.cpp
499   src/applications/dynamicProps/ThetaCorrFunc.cpp
500   src/applications/dynamicProps/TimeCorrFunc.cpp
501   src/applications/dynamicProps/VCorrFunc.cpp
502 < src/applications/dynamicProps/DynamicPropsCmd.c
502 > src/applications/dynamicProps/DynamicPropsCmd.cpp
503   )
504  
505   set (HYDROSOURCE
# Line 428 | Line 512 | src/applications/hydrodynamics/ShapeBuilder.cpp
512   src/applications/hydrodynamics/HydrodynamicsModelFactory.cpp
513   src/applications/hydrodynamics/RoughShell.cpp
514   src/applications/hydrodynamics/ShapeBuilder.cpp
515 < src/applications/hydrodynamics/HydroCmd.c
515 > src/applications/hydrodynamics/HydroCmd.cpp
516   )
517  
518   set (STATICPROPSSOURCE
# Line 456 | Line 540 | src/applications/staticProps/TetrahedralityParam.cpp
540   src/applications/staticProps/SCDOrderParameter.cpp
541   src/applications/staticProps/StaticProps.cpp
542   src/applications/staticProps/TetrahedralityParam.cpp
543 + src/applications/staticProps/TetrahedralityParamZ.cpp
544   src/applications/staticProps/TwoDGofR.cpp
545 < src/applications/staticProps/StaticPropsCmd.c
545 > src/applications/staticProps/StaticPropsCmd.cpp
546   )
547  
548   set (NANOPARTICLEBUILDERSOURCE
549   src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp
550   src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp
551 < src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c
551 > src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp
552   )
553  
554 + set (NANORODBUILDERSOURCE
555 + src/applications/nanoparticleBuilder/nanorodBuilder.cpp
556 + src/applications/nanoparticleBuilder/shapedLatticeRod.cpp
557 + src/applications/nanoparticleBuilder/nanorodBuilderCmd.cpp
558 + )
559 +
560 + set (NANOROD_PENTBUILDERSOURCE
561 + src/applications/nanoparticleBuilder/nanorod_pentBuilder.cpp
562 + src/applications/nanoparticleBuilder/nanorod_pentBuilderCmd.cpp
563 + src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp
564 + )
565 +
566   set (RANDOMBUILDERSOURCE
567   src/applications/randomBuilder/randomBuilder.cpp
568 < src/applications/randomBuilder/randomBuilderCmd.c
568 > src/applications/randomBuilder/randomBuilderCmd.cpp
569   )
570  
571   set(SIMPLEBUILDERSOURCE
572   src/applications/simpleBuilder/simpleBuilder.cpp
573 < src/applications/simpleBuilder/simpleBuilderCmd.c
573 > src/applications/simpleBuilder/simpleBuilderCmd.cpp
574   )
575  
576   set(THERMALIZERSOURCE
577   src/applications/thermalizer/thermalizer.cpp
578 < src/applications/thermalizer/thermalizerCmd.c
578 > src/applications/thermalizer/thermalizerCmd.cpp
579   )
580  
581 < add_executable(Dump2XYZ ${DUMP2XYZSOURCE})
581 > add_executable(Dump2XYZ ${DUMP2XYZSOURCE} ${GETOPT_SOURCE})
582   target_link_libraries(Dump2XYZ openmd_single openmd_core openmd_single openmd_core)
583 < add_executable(DynamicProps ${DYNAMICPROPSSOURCE})
583 > add_executable(DynamicProps ${DYNAMICPROPSSOURCE} ${GETOPT_SOURCE})
584   target_link_libraries(DynamicProps openmd_single openmd_core openmd_single openmd_core)
585 < add_executable(Hydro ${HYDROSOURCE})
585 > add_executable(Hydro ${HYDROSOURCE} ${GETOPT_SOURCE})
586   target_link_libraries(Hydro openmd_single openmd_core openmd_single openmd_core)
587 < add_executable(StaticProps ${STATICPROPSSOURCE})
587 > add_executable(StaticProps ${STATICPROPSSOURCE} ${GETOPT_SOURCE})
588   target_link_libraries(StaticProps openmd_single openmd_core openmd_single openmd_core)
589 < add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE})
590 < target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core)
591 < add_executable(randomBuilder ${RANDOMBUILDERSOURCE})
592 < target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core)
593 < add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE})
594 < target_link_libraries(simpleBuilder openmd_single openmd_core openmd_single openmd_core)
595 < add_executable(thermalizer ${THERMALIZERSOURCE})
596 < target_link_libraries(thermalizer openmd_single openmd_core openmd_single openmd_core)
589 > add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE} ${GETOPT_SOURCE})
590 > target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
591 > add_executable(nanorodBuilder ${NANORODBUILDERSOURCE} ${GETOPT_SOURCE})
592 > target_link_libraries(nanorodBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
593 > add_executable(nanorod_pentBuilder ${NANOROD_PENTBUILDERSOURCE} ${GETOPT_SOURCE})
594 > target_link_libraries(nanorod_pentBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
595 > add_executable(randomBuilder ${RANDOMBUILDERSOURCE} ${GETOPT_SOURCE})
596 > target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
597 > add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE} ${GETOPT_SOURCE})
598 > target_link_libraries(simpleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
599 > add_executable(thermalizer ${THERMALIZERSOURCE} ${GETOPT_SOURCE})
600 > target_link_libraries(thermalizer openmd_single openmd_core openmd_single openmd_core openmd_single)
601  
602   if (OPENBABEL2_FOUND)
603   set (ATOM2MDSOURCE
604   src/applications/atom2md/atom2md.cpp
605   src/applications/atom2md/openmdformat.cpp
606   )
607 <  add_executable(atom2md ${ATOM2MDSOURCE})
607 >  add_executable(atom2md ${ATOM2MDSOURCE} ${GETOPT_SOURCE})
608    target_link_libraries(atom2md openmd_single openmd_core openmd_single openmd_core ${OPENBABEL2_LIBRARIES})
609 +  INSTALL(TARGETS atom2md RUNTIME DESTINATION bin
610 +          PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
611   ENDIF (OPENBABEL2_FOUND)
612  
613  
# Line 516 | Line 619 | src/applications/utilities/principalAxisCalculator
619   src/applications/utilities/md2md
620   src/applications/utilities/mdSplit
621   src/applications/utilities/principalAxisCalculator
622 + src/applications/utilities/stat2thcond
623   src/applications/utilities/stat2visco
624   src/applications/utilities/waterRotator
625 + src/applications/utilities/waterReplacer
626   )
627  
628   IF(PYTHON_EXECUTABLE)
629 <   foreach(PY_FILE ${PY_FILES})
630 <      configure_file(${PY_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PY_FILE} @ONLY)
631 <   endforeach(PY_FILE)
632 < #INSTALL(FILES ${PY_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
629 >  IF(WIN32)
630 >    SET(PYEXT ".py")
631 >  ELSE(WIN32)
632 >    SET(PYEXT "")
633 >  ENDIF(WIN32)
634 >
635 >  foreach(PY_FILE ${PY_FILES})
636 >    GET_FILENAME_COMPONENT(filename "${PY_FILE}" NAME)
637 >    CONFIGURE_FILE(${PY_FILE}
638 >                  "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}" @ONLY)
639 >    INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}"
640 >            DESTINATION bin
641 >            PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
642 >  endforeach(PY_FILE)
643   ENDIF(PYTHON_EXECUTABLE)
644  
645   set(PERL_FILES
# Line 533 | Line 648 | IF(PERL_FOUND)
648   )
649  
650   IF(PERL_FOUND)
651 <   foreach(PERL_FILE ${PERL_FILES})
652 <      configure_file(${PERL_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PERL_FILE} @ONLY)
653 <   endforeach(PERL_FILE)
654 < #INSTALL(FILES ${PERL_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
651 >  IF(WIN32)
652 >    SET(PLEXT ".PL")
653 >  ELSE(WIN32)
654 >    SET(PLEXT "")
655 >  ENDIF(WIN32)
656 >
657 >  foreach(PERL_FILE ${PERL_FILES})
658 >     GET_FILENAME_COMPONENT(filename "${PERL_FILE}" NAME)
659 >     configure_file(${PERL_FILE} "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}" @ONLY)
660 >     INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}"
661 >             DESTINATION bin
662 >             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
663 >
664 >  endforeach(PERL_FILE)
665   ENDIF(PERL_FOUND)
666 +
667 +
668 + INSTALL(FILES AUTHORS LICENSE README INSTALL DESTINATION .
669 +        PERMISSIONS OWNER_READ GROUP_READ WORLD_READ)
670 + INSTALL(TARGETS
671 +        openmd_core
672 +        openmd_single
673 +        openmd
674 +        Dump2XYZ
675 +        simpleBuilder
676 +        StaticProps
677 +        DynamicProps
678 +        randomBuilder
679 +        nanoparticleBuilder
680 +        nanorodBuilder
681 +        nanorod_pentBuilder
682 +        thermalizer
683 +        Hydro
684 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
685 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
686 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
687 + )
688 +
689 + install(DIRECTORY forceFields/  
690 +        DESTINATION forceFields
691 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
692 +        PATTERN ".svn" EXCLUDE
693 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
694 + install(DIRECTORY samples/      
695 +        DESTINATION samples
696 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
697 +        PATTERN ".svn" EXCLUDE
698 +        PATTERN "*.dump" EXCLUDE
699 +        PATTERN "*.stat" EXCLUDE
700 +        PATTERN "*.eor" EXCLUDE
701 +        PATTERN "*.rnemd" EXCLUDE
702 +        PATTERN "*.fz" EXCLUDE
703 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
704 +
705 + configure_file( samples/builders/runMe.in
706 +                "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe" @ONLY)
707 + INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe"
708 +             DESTINATION samples/builders
709 +             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)                
710 +
711 +
712 + INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/doc/OpenMDmanual.pdf"
713 +        DESTINATION doc
714 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
715 +
716 + message( STATUS)
717 + message( STATUS "========== OpenMD Build Information ==========")
718 + message( STATUS "Current revision ........... = ${SVN_REV}")
719 + message( STATUS "CMAKE_SYSTEM ............... = ${CMAKE_SYSTEM}")
720 + message( STATUS "==============================================")
721 + message( STATUS "CMAKE_BUILD_TYPE ........... = ${CMAKE_BUILD_TYPE}")
722 + message( STATUS "CMAKE_INSTALL_PREFIX ....... = ${CMAKE_INSTALL_PREFIX}")
723 + message( STATUS "Build as SINGLE_PRECISION .. = ${SINGLE_PRECISION}")
724 + message( STATUS "CMAKE_CXX_COMPILER ......... = ${CMAKE_CXX_COMPILER}")
725 + message( STATUS "MPI_CXX_COMPILER ........... = ${MPI_CXX_COMPILER}")
726 + message( STATUS "MPI_CXX_INCLUDE_PATH ....... = ${MPI_CXX_INCLUDE_PATH}")
727 + message( STATUS "MPI_CXX_LIBRARIES .......... = ${MPI_CXX_LIBRARIES}")
728 + message( STATUS "OPENBABEL2_ROOT ............ = ${OPENBABEL2_ROOT}")
729 + message( STATUS "OPENBABEL2_INCLUDE_DIR ..... = ${OPENBABEL2_INCLUDE_DIR}")
730 + message( STATUS "OPENBABEL2_LIBRARIES ....... = ${OPENBABEL2_LIBRARIES}")
731 + message( STATUS "QHULL_ROOT ................. = ${QHULL_ROOT}")
732 + message( STATUS "QHULL_INCLUDE_DIR .......... = ${QHULL_INCLUDE_DIR}")
733 + message( STATUS "QHULL_LIBRARIES ............ = ${QHULL_LIBRARIES}")
734 + message( STATUS "ZLIB_ROOT .................. = ${ZLIB_ROOT}")
735 + message( STATUS "ZLIB_INCLUDE_DIR ........... = ${ZLIB_INCLUDE_DIR}")
736 + message( STATUS "ZLIB_LIBRARIES ............. = ${ZLIB_LIBRARIES}")
737 + message( STATUS "FFTW3_ROOT ................. = ${FFTW3_ROOT}")
738 + message( STATUS "FFTW3_INCLUDE_DIR .......... = ${FFTW3_INCLUDE_DIR}")
739 + message( STATUS "FFTW3_LIBRARIES ............ = ${FFTW3_LIBRARIES}")
740 + message( STATUS "PERL_EXECUTABLE ............ = ${PERL_EXECUTABLE}")
741 + message( STATUS "PYTHON_EXECUTABLE .......... = ${PYTHON_EXECUTABLE}")
742 + message( STATUS "DOXYGEN_EXECUTABLE ......... = ${DOXYGEN_EXECUTABLE}")
743 + message( STATUS )
744 + message( STATUS "To override these options, add -D{OPTION_NAME}=... to the cmake command" )
745 + message( STATUS "Particularly useful defines are for:")
746 + message( STATUS )
747 + message( STATUS "  -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} (where OpenMD will be installed)")
748 + message( STATUS "       -DOPENBABEL2_ROOT=/path/to/openbabel")
749 + message( STATUS "            -DQHULL_ROOT=/path/to/qhull")
750 + message( STATUS "            -DFFTW3_ROOT=/path/to/fftw3")
751 + message( STATUS )
752 + IF(WIN32)
753 +  message( STATUS "To build and install OpenMD, enter: ")
754 +  message( STATUS "  msbuild /m ALL_BUILD.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
755 +  message( STATUS "followed by:")
756 +  message( STATUS "  msbuild /m INSTALL.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
757 + ELSE(WIN32)
758 +  message( STATUS "To build and install OpenMD, enter \"make\" and \"make install\"")
759 + ENDIF(WIN32)
760 + message( STATUS )
761 +
762 + # build a CPack driven installer package
763 + IF(NOT DEFINED CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS)
764 +   SET(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
765 + ENDIF()
766 + include (InstallRequiredSystemLibraries)
767 + set (CPACK_RESOURCE_FILE_LICENSE  
768 +     "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
769 + set (CPACK_PACKAGE_VERSION_MAJOR "${VERSION_MAJOR}")
770 + set (CPACK_PACKAGE_VERSION_MINOR "${VERSION_MINOR}")
771 + include (CPack)

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