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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 1743 by gezelter, Tue Jun 5 18:04:02 2012 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 "${CMAKE_SOURCE_DIR}/cmake/modules")
6  
7 + if (NOT CMAKE_BUILD_TYPE)
8 +  set(CMAKE_BUILD_TYPE "Release")
9 + endif()
10  
11 + find_package(MPI)
12 + if (NOT MPI_CXX_FOUND)
13 + message(STATUS "========== OpenMD Parallel Information ==========")
14 + message(STATUS )
15 + message(STATUS "No MPI compiler found. Perhaps you want to set one explicitly?")
16 + message(STATUS "To override the default compiler, set the environment variable")
17 + message(STATUS "     export CXX=/full/path/to/mpic++")
18 + message(STATUS "in bash or ksh or sh.  In csh or tcsh, use:")
19 + message(STATUS "     setenv CXX /full/path/to/mpic++")
20 + message(STATUS "before running the cmake command.")
21 + message(STATUS )
22 + message(STATUS "=================================================")
23 + endif()
24 + IF ( MPI_CXX_FOUND )
25 +  INCLUDE_DIRECTORIES(${MPI_CXX_INCLUDE_PATH})
26 + ENDIF()
27 +
28 + include(CheckCXXCompilerFlag)
29 + include(CheckIncludeFileCXX)
30 + include(CheckCXXSymbolExists)
31 +
32   # OpenMD version number.
33   set (VERSION_MAJOR "2")
34   set (VERSION_MINOR "0")
35   set (VERSION_TINY "0")  
36 + option(SINGLE_PRECISION "Build Single precision (float) version" OFF)
37  
38 < # cmake modules that are needed to build oopse
39 < SET(CMAKE_MODULE_PATH ${OpenMD_SOURCE_DIR}/cmake/modules)
40 < SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin)
41 < SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
38 > IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
39 >  SET(CMAKE_INSTALL_PREFIX
40 >    "/usr/local/openmd" CACHE PATH "OpenMD install prefix" FORCE
41 >    )
42 > ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
43  
44 < enable_language(CXX  C)
44 > # ---------- Setup output Directories -------------------------
45 > SET (CMAKE_LIBRARY_OUTPUT_DIRECTORY
46 >  ${PROJECT_BINARY_DIR}/lib
47 >  CACHE PATH
48 >  "Single directory for all shared libraries"
49 >  )
50 > # --------- Setup the Executable output Directory -------------
51 > SET (CMAKE_RUNTIME_OUTPUT_DIRECTORY
52 >  ${PROJECT_BINARY_DIR}/bin
53 >  CACHE PATH
54 >  "Single directory for all Executables."
55 >  )
56 > # --------- Setup the static library directory -------------
57 > SET (CMAKE_ARCHIVE_OUTPUT_DIRECTORY
58 >  ${PROJECT_BINARY_DIR}/lib
59 >  CACHE PATH
60 >  "Single directory for all static libraries."
61 >  )
62  
19 – if ( APPLE )
20 – set(MPI_COMPILER /opt/local/lib/openmpi/bin/mpic++)
21 – set(MPI_LIBRARY "MPI_LIBRARY-NOTFOUND" )
22 – endif( APPLE )
23 – FIND_PACKAGE(MPI)
24 – IF ( MPI_FOUND )
25 –  SET(CMAKE_REQUIRED_INCLUDES "${MPI_INCLUDE_PATH};${CMAKE_REQUIRED_INCLUDES}")
26 –  INCLUDE_DIRECTORIES(${MPI_INCLUDE_PATH})
27 – ENDIF()
28 –
63   FIND_PACKAGE(Subversion)
64   IF ( Subversion_FOUND AND EXISTS ${PROJECT_SOURCE_DIR}/.svn )
65    Subversion_WC_INFO(${PROJECT_SOURCE_DIR} Project)
66 <  MESSAGE("Current revision is ${Project_WC_REVISION}")
66 >  MESSAGE(STATUS "Current revision is ${Project_WC_REVISION}")
67    Subversion_WC_LOG(${PROJECT_SOURCE_DIR} Project)
68    SET(SVN_REV ${Project_WC_REVISION})
69    ADD_DEFINITIONS( -DSVN_REV=${Project_WC_REVISION} )
70 +  SET(GENERATELOGS "${PROJECT_SOURCE_DIR}/doc/svn2cl")
71 +  ADD_CUSTOM_TARGET(ChangeLog
72 +     COMMAND ${GENERATELOGS} "--group-by-day" "--include-rev"
73 +     "--linelen=78" "--output=${PROJECT_BINARY_DIR}/ChangeLog" "${PROJECT_SOURCE_DIR}"
74 +  )
75   ENDIF()
76  
77 + check_include_file_cxx(conio.h      HAVE_CONIO_H)
78 + check_cxx_symbol_exists(strncasecmp   "string.h"   HAVE_STRNCASECMP)
79 +
80   # Optional libraries: If we can find these, we will build with them
81   # Look for OpenBabel libraries
82   find_package(OpenBabel2)
83   IF(OPENBABEL2_FOUND)
84    SET(USE_OPENBABEL)
85    include_directories(${OPENBABEL2_INCLUDE_DIR})
86 <  message(STATUS "Openbabel libs: " ${OPENBABEL2_LIBRARIES})
87 < #  TARGET_LINK_LIBRARIES(${OPENBABEL2_LIBRARIES})
86 >  # link libraries are added only for targets that need them.
87 > ELSE(OPENBABEL2_FOUND)
88 >  MESSAGE(STATUS "No OpenBabel found - will not build atom2md")
89   ENDIF(OPENBABEL2_FOUND)
90  
91 + find_package(Eigen3)
92 + if(EIGEN3_FOUND)
93 +  add_definitions(-DHAVE_EIGEN -DHAVE_EIGEN3)
94 +  include_directories(${EIGEN3_INCLUDE_DIR})
95 + else()
96 +  find_package(Eigen2) # find and setup Eigen2
97 +  if(EIGEN2_FOUND)
98 +    add_definitions (-DHAVE_EIGEN)
99 +    include_directories(${EIGEN2_INCLUDE_DIR})
100 +  endif()
101 + endif()
102 +
103   #Look for QHULL Libraries
104 < find_package(QHULL)
104 > set(QHULL_USE_STATIC 1)
105 > find_package(Qhull)
106   IF(QHULL_FOUND)
107    SET(HAVE_QHULL 1)
108    include_directories(${QHULL_INCLUDE_DIR})
109    LINK_LIBRARIES(${QHULL_LIBRARIES})
110 + ELSE(QHULL_FOUND)
111 +  MESSAGE(STATUS "No Qhull found - will be missing some features")
112   ENDIF(QHULL_FOUND)
113  
56 –
114   # zlib stuff
115   find_package(ZLIB)
116   if(ZLIB_FOUND)
# Line 61 | Line 118 | if(ZLIB_FOUND)
118    add_definitions(-DHAVE_LIBZ)
119    include_directories(${ZLIB_INCLUDE_DIR})
120    LINK_LIBRARIES(${ZLIB_LIBRARIES})
121 + ELSE(ZLIB_FOUND)
122 +  MESSAGE(STATUS "No zlib found - will be missing compressed dump files")
123   endif(ZLIB_FOUND)
124  
125 < #FFTW
126 < INCLUDE(${CMAKE_MODULE_PATH}/FindFFTW.cmake)
127 < IF(FFTW_FOUND)
125 > #FFTW3
126 > IF(SINGLE_PRECISION)
127 >  find_package(FFTW3 COMPONENTS single)
128 > else()
129 >  find_package(FFTW3 COMPONENTS double)
130 > endif(SINGLE_PRECISION)
131 > if (FFTW3_FOUND)
132 >  include_directories (${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR} ${FFTW3_INCLUDE_DIR})
133    SET(HAVE_LIBFFTW 1)
134 <  SET(HAVE_FFTW3_H)
135 <  INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIR})
136 <  LINK_LIBRARIES(${FFTW_LIBRARIES})
137 < ENDIF(FFTW_FOUND)
134 >  SET(HAVE_FFTW3_H 1)
135 >  INCLUDE_DIRECTORIES(${FFTW3_INCLUDE_DIR})
136 >  LINK_LIBRARIES(${FFTW3_LIBRARIES})
137 > ELSE(FFTW3_FOUND)
138 >  MESSAGE(STATUS "No fftw3 found - will be missing some analysis modules")
139 > endif (FFTW3_FOUND)
140  
141  
142 < #include checks
143 < include(CheckIncludeFile)
144 < CHECK_INCLUDE_FILE(fftw3.h HAVE_FFTW3_H)
145 < CHECK_INCLUDE_FILE(fftw.h HAVE_FFWT_H)
146 < CHECK_INCLUDE_FILE(dfftw.h HAVE_DFFTW_H)
147 < CHECK_INCLUDE_FILE(cmath.h HAVE_CMATH_H)
148 < check_include_file(limits.h HAVE_LIMITS_H)
149 < check_include_file(stdlib.h HAVE_STDLIB_H)
150 < check_include_file(string.h HAVE_STRING_H)
151 < check_include_file("sys/ioctl.h" HAVE_SYS_IOCTL_H)
86 < check_include_file(unistd.h HAVE_UNISTD_H)
142 > # add a target to generate API documentation with Doxygen
143 > find_package(Doxygen)
144 > if(DOXYGEN_FOUND)
145 >  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in" "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile" @ONLY)
146 >  add_custom_target(doc
147 >    ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile"
148 >    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doc"
149 >    COMMENT "Generating API documentation with Doxygen" VERBATIM
150 >  )
151 > endif(DOXYGEN_FOUND)
152  
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 –
153   FIND_PACKAGE(Perl)
154   IF(PERL_FOUND)
155    SET(PERL ${PERL_EXECUTABLE})
156   ELSE(PERL_FOUND)
157 <  MESSAGE(STATUS "Failed to find perl")
157 >  MESSAGE(STATUS "Failed to find perl - some scripts will not be made")
158   ENDIF(PERL_FOUND)
159  
160 + SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation
161 + locations")
162 +
163   FIND_PACKAGE(PythonInterp)
164   IF(PYTHON_EXECUTABLE)
165    SET(PYTHON ${PYTHON_EXECUTABLE})
166   ELSE(PYTHON_EXECUTABLE)
167 <  MESSAGE(STATUS "Failed to find python")
167 >  MESSAGE(STATUS "Failed to find python - some scripts will not be made")
168   ENDIF(PYTHON_EXECUTABLE)
169  
123 – SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation locations")
124 –
125 –
126 – include(CMakePrintSystemInformation)
127 –
170   configure_file (
171    "${PROJECT_SOURCE_DIR}/src/config.h.cmake"
172 <  "${PROJECT_SOURCE_DIR}/src/config.h"
173 <  )
174 < include_directories (${PROJECT_SOURCE_DIR}/src)
172 >  "${PROJECT_BINARY_DIR}/config.h"
173 > )
174 > include_directories("${PROJECT_BINARY_DIR}" "${PROJECT_SOURCE_DIR}/src")
175  
134 – #CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
135 –
136 –
176   #Add executables for build
177   set (PROGRAMS
178   openmd
# Line 180 | Line 219 | src/brains/DataStorage.cpp
219   src/antlr/TreeParser.cpp
220   src/brains/BlockSnapshotManager.cpp
221   src/brains/DataStorage.cpp
222 + src/brains/ForceField.cpp
223   src/brains/MoleculeCreator.cpp
224   src/brains/PairList.cpp
225   src/brains/Register.cpp
# Line 191 | Line 231 | src/integrators/DLM.cpp
231   src/hydrodynamics/HydroProp.cpp
232   src/hydrodynamics/Sphere.cpp
233   src/integrators/DLM.cpp
234 + src/flucq/FluctuatingChargeParameters.cpp
235 + src/flucq/FluctuatingChargeNVT.cpp
236 + src/flucq/FluctuatingChargePropagator.cpp
237   src/integrators/Integrator.cpp
238   src/integrators/IntegratorFactory.cpp
239   src/integrators/LangevinDynamics.cpp
# Line 213 | Line 256 | src/io/EAMAtomTypesSectionParser.cpp
256   src/io/ChargeAtomTypesSectionParser.cpp
257   src/io/DirectionalAtomTypesSectionParser.cpp
258   src/io/EAMAtomTypesSectionParser.cpp
259 + src/io/FluctuatingChargeAtomTypesSectionParser.cpp
260   src/io/ForceFieldOptions.cpp
261   src/io/GayBerneAtomTypesSectionParser.cpp
262   src/io/Globals.cpp
# Line 223 | Line 267 | src/io/ParamConstraint.cpp
267   src/io/NonBondedInteractionsSectionParser.cpp
268   src/io/OptionSectionParser.cpp
269   src/io/ParamConstraint.cpp
270 + src/io/PolarizableAtomTypesSectionParser.cpp
271   src/io/SCAtomTypesSectionParser.cpp
272   src/io/SectionParser.cpp
273   src/io/SectionParserManager.cpp
# Line 249 | Line 294 | src/mdParser/MDTreeParser.cpp
294   src/mdParser/MDLexer.cpp
295   src/mdParser/MDParser.cpp
296   src/mdParser/MDTreeParser.cpp
297 < src/minimizers/MinimizerFactory.cpp
298 < src/minimizers/MinimizerParameterSet.cpp
297 > src/optimization/OptimizationFactory.cpp
298 > src/optimization/Armijo.cpp
299 > src/optimization/BFGS.cpp
300 > src/optimization/ConjugateGradient.cpp
301 > src/optimization/Constraint.cpp
302 > src/optimization/EndCriteria.cpp
303 > src/optimization/LineSearch.cpp
304 > src/optimization/LineSearchBasedMethod.cpp
305 > src/optimization/SteepestDescent.cpp
306 > src/optimization/PotentialEnergyObjectiveFunction.cpp
307   src/nonbonded/EAM.cpp
308   src/nonbonded/Electrostatic.cpp
309   src/nonbonded/GB.cpp
# Line 291 | Line 344 | src/types/CutoffGroupStamp.cpp
344   src/types/CharmmTorsionType.cpp
345   src/types/Component.cpp
346   src/types/CutoffGroupStamp.cpp
347 < src/types/DirectionalAtomType.cpp
347 > src/types/DirectionalAdapter.cpp
348 > src/types/EAMAdapter.cpp
349 > src/types/FixedChargeAdapter.cpp
350 > src/types/FluctuatingChargeAdapter.cpp
351   src/types/FragmentStamp.cpp
352 + src/types/GayBerneAdapter.cpp
353   src/types/ImproperCosineInversionType.cpp
354   src/types/InversionStamp.cpp
355 + src/types/LennardJonesAdapter.cpp
356   src/types/MoleculeStamp.cpp
357 + src/types/MultipoleAdapter.cpp
358   src/types/NonBondedInteractionType.cpp
359 + src/types/PolarizableAdapter.cpp
360   src/types/RestraintStamp.cpp
361   src/types/RigidBodyStamp.cpp
362   src/types/ShapeAtomType.cpp
363 + src/types/StickyAdapter.cpp
364 + src/types/SuttonChenAdapter.cpp
365   src/types/TorsionStamp.cpp
366   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
367   src/utils/ElementsTable.cpp
368   src/utils/MoLocator.cpp
369   src/utils/OpenMDBitSet.cpp
# Line 329 | Line 381 | src/visitors/ZconsVisitor.cpp
381   src/visitors/ReplacementVisitor.cpp
382   src/visitors/RigidBodyVisitor.cpp
383   src/visitors/ZconsVisitor.cpp
384 + src/rnemd/RNEMDParameters.cpp
385   )
386  
387   set( PARALLEL_SOURCE
# Line 337 | Line 390 | src/constraints/ZconstraintForceManager.cpp
390   src/brains/SimInfo.cpp
391   src/brains/Thermo.cpp
392   src/constraints/ZconstraintForceManager.cpp
393 < src/integrators/RNEMD.cpp
393 > src/flucq/FluctuatingChargeConstraints.cpp
394 > src/flucq/FluctuatingChargeObjectiveFunction.cpp
395 > src/integrators/LangevinHullForceManager.cpp
396 > src/rnemd/RNEMD.cpp
397   src/integrators/Velocitizer.cpp
398   src/io/DumpReader.cpp
399   src/io/DumpWriter.cpp
# Line 347 | Line 403 | src/math/ParallelRandNumGen.cpp
403   src/io/ZConsWriter.cpp
404   src/io/ifstrstream.cpp
405   src/math/ParallelRandNumGen.cpp
350 – src/minimizers/CGFamilyMinimizer.cpp
351 – src/minimizers/Minimizer.cpp
352 – src/minimizers/PRCG.cpp
353 – src/minimizers/SDMinimizer.cpp
406   src/parallel/ForceDecomposition.cpp
407   src/parallel/ForceMatrixDecomposition.cpp
408   src/restraints/RestraintForceManager.cpp
409   src/restraints/ThermoIntegrationForceManager.cpp
410   src/utils/ProgressBar.cpp
411 < src/utils/simError.c
411 > src/utils/simError.cpp
412 > src/optimization/Problem.cpp
413   )
414  
415   IF(QHULL_FOUND)
# Line 390 | Line 443 | target_link_libraries(openmd_MPI openmd_parallel openm
443   COMPILE_DEFINITIONS IS_MPI
444   )
445   target_link_libraries(openmd_MPI openmd_parallel openmd_core openmd_parallel openmd_core)
446 +  INSTALL(TARGETS
447 +        openmd_parallel openmd_MPI
448 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
449 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
450 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
451 + )
452   ENDIF (MPI_FOUND)
453  
454   set (DUMP2XYZSOURCE
455   src/applications/dump2Xyz/Dump2XYZ.cpp
456 < src/applications/dump2Xyz/Dump2XYZCmd.c
456 > src/applications/dump2Xyz/Dump2XYZCmd.cpp
457   )
458  
459   set (DYNAMICPROPSSOURCE
# Line 415 | Line 474 | src/applications/dynamicProps/VCorrFunc.cpp
474   src/applications/dynamicProps/ThetaCorrFunc.cpp
475   src/applications/dynamicProps/TimeCorrFunc.cpp
476   src/applications/dynamicProps/VCorrFunc.cpp
477 < src/applications/dynamicProps/DynamicPropsCmd.c
477 > src/applications/dynamicProps/DynamicPropsCmd.cpp
478   )
479  
480   set (HYDROSOURCE
# Line 428 | Line 487 | src/applications/hydrodynamics/ShapeBuilder.cpp
487   src/applications/hydrodynamics/HydrodynamicsModelFactory.cpp
488   src/applications/hydrodynamics/RoughShell.cpp
489   src/applications/hydrodynamics/ShapeBuilder.cpp
490 < src/applications/hydrodynamics/HydroCmd.c
490 > src/applications/hydrodynamics/HydroCmd.cpp
491   )
492  
493   set (STATICPROPSSOURCE
# Line 457 | Line 516 | src/applications/staticProps/TwoDGofR.cpp
516   src/applications/staticProps/StaticProps.cpp
517   src/applications/staticProps/TetrahedralityParam.cpp
518   src/applications/staticProps/TwoDGofR.cpp
519 < src/applications/staticProps/StaticPropsCmd.c
519 > src/applications/staticProps/StaticPropsCmd.cpp
520   )
521  
522   set (NANOPARTICLEBUILDERSOURCE
523   src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp
524   src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp
525 < src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c
525 > src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp
526   )
527  
528 + set (NANORODBUILDERSOURCE
529 + src/applications/nanoparticleBuilder/nanorodBuilder.cpp
530 + src/applications/nanoparticleBuilder/shapedLatticeRod.cpp
531 + src/applications/nanoparticleBuilder/nanorodBuilderCmd.cpp
532 + )
533 +
534 + set (NANOROD_PENTBUILDERSOURCE
535 + src/applications/nanoparticleBuilder/nanorod_pentBuilder.cpp
536 + src/applications/nanoparticleBuilder/nanorod_pentBuilderCmd.cpp
537 + src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp
538 + )
539 +
540   set (RANDOMBUILDERSOURCE
541   src/applications/randomBuilder/randomBuilder.cpp
542 < src/applications/randomBuilder/randomBuilderCmd.c
542 > src/applications/randomBuilder/randomBuilderCmd.cpp
543   )
544  
545   set(SIMPLEBUILDERSOURCE
546   src/applications/simpleBuilder/simpleBuilder.cpp
547 < src/applications/simpleBuilder/simpleBuilderCmd.c
547 > src/applications/simpleBuilder/simpleBuilderCmd.cpp
548   )
549  
550   set(THERMALIZERSOURCE
551   src/applications/thermalizer/thermalizer.cpp
552 < src/applications/thermalizer/thermalizerCmd.c
552 > src/applications/thermalizer/thermalizerCmd.cpp
553   )
554  
555   add_executable(Dump2XYZ ${DUMP2XYZSOURCE})
# Line 491 | Line 562 | target_link_libraries(nanoparticleBuilder openmd_singl
562   target_link_libraries(StaticProps openmd_single openmd_core openmd_single openmd_core)
563   add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE})
564   target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core)
565 + add_executable(nanorodBuilder ${NANORODBUILDERSOURCE})
566 + target_link_libraries(nanorodBuilder openmd_single openmd_core openmd_single openmd_core)
567 + add_executable(nanorod_pentBuilder ${NANOROD_PENTBUILDERSOURCE})
568 + target_link_libraries(nanorod_pentBuilder openmd_single openmd_core openmd_single openmd_core)
569   add_executable(randomBuilder ${RANDOMBUILDERSOURCE})
570   target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core)
571   add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE})
# Line 505 | Line 580 | src/applications/atom2md/openmdformat.cpp
580   )
581    add_executable(atom2md ${ATOM2MDSOURCE})
582    target_link_libraries(atom2md openmd_single openmd_core openmd_single openmd_core ${OPENBABEL2_LIBRARIES})
583 +  INSTALL(TARGETS atom2md RUNTIME DESTINATION bin
584 +          PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
585   ENDIF (OPENBABEL2_FOUND)
586  
587  
# Line 518 | Line 595 | src/applications/utilities/waterRotator
595   src/applications/utilities/principalAxisCalculator
596   src/applications/utilities/stat2visco
597   src/applications/utilities/waterRotator
598 + src/applications/utilities/waterReplacer
599   )
600  
601   IF(PYTHON_EXECUTABLE)
602     foreach(PY_FILE ${PY_FILES})
603 <      configure_file(${PY_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PY_FILE} @ONLY)
603 >      GET_FILENAME_COMPONENT(filename "${PY_FILE}" NAME)
604 >      CONFIGURE_FILE(${PY_FILE}
605 >                     "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}" @ONLY)
606 >      INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}"
607 >              DESTINATION bin
608 >              PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
609     endforeach(PY_FILE)
527 – #INSTALL(FILES ${PY_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
610   ENDIF(PYTHON_EXECUTABLE)
611  
612   set(PERL_FILES
# Line 534 | Line 616 | IF(PERL_FOUND)
616  
617   IF(PERL_FOUND)
618     foreach(PERL_FILE ${PERL_FILES})
619 <      configure_file(${PERL_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PERL_FILE} @ONLY)
619 >      GET_FILENAME_COMPONENT(filename "${PERL_FILE}" NAME)
620 >      configure_file(${PERL_FILE} "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}" @ONLY)
621 >      INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}"
622 >              DESTINATION bin
623 >              PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
624 >
625     endforeach(PERL_FILE)
539 – #INSTALL(FILES ${PERL_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
626   ENDIF(PERL_FOUND)
627 +
628 + INSTALL(FILES AUTHORS LICENSE README INSTALL DESTINATION .
629 +        PERMISSIONS OWNER_READ GROUP_READ WORLD_READ)
630 + INSTALL(TARGETS
631 +        openmd_core
632 +        openmd_single
633 +        openmd
634 +        Dump2XYZ
635 +        simpleBuilder
636 +        StaticProps
637 +        DynamicProps
638 +        randomBuilder
639 +        nanoparticleBuilder
640 +        thermalizer
641 +        Hydro
642 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
643 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
644 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
645 + )
646 +
647 + install(DIRECTORY forceFields/  
648 +        DESTINATION forceFields
649 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
650 +        PATTERN ".svn" EXCLUDE
651 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
652 + install(DIRECTORY samples/      
653 +        DESTINATION samples
654 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
655 +        PATTERN ".svn" EXCLUDE
656 +        PATTERN "*.dump" EXCLUDE
657 +        PATTERN "*.stat" EXCLUDE
658 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
659 + INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/doc/OpenMDmanual.pdf"
660 +        DESTINATION doc
661 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
662 +
663 + message( STATUS)
664 + message( STATUS "========== OpenMD Build Information ==========")
665 + message( STATUS "Current revision ........... = ${SVN_REV}")
666 + message( STATUS "CMAKE_SYSTEM ............... = ${CMAKE_SYSTEM}")
667 + message( STATUS "==============================================")
668 + message( STATUS "CMAKE_BUILD_TYPE ........... = ${CMAKE_BUILD_TYPE}")
669 + message( STATUS "CMAKE_INSTALL_PREFIX ....... = ${CMAKE_INSTALL_PREFIX}")
670 + message( STATUS "Build as SINGLE_PRECISION .. = ${SINGLE_PRECISION}")
671 + message( STATUS "CMAKE_CXX_COMPILER ......... = ${CMAKE_CXX_COMPILER}")
672 + message( STATUS "MPI_CXX_COMPILER ........... = ${MPI_CXX_COMPILER}")
673 + message( STATUS "MPI_CXX_INCLUDE_PATH ....... = ${MPI_CXX_INCLUDE_PATH}")
674 + message( STATUS "MPI_CXX_LIBRARIES .......... = ${MPI_CXX_LIBRARIES}")
675 + message( STATUS "OPENBABEL2_ROOT ............ = ${OPENBABEL2_ROOT}")
676 + message( STATUS "OPENBABEL2_INCLUDE_DIR ..... = ${OPENBABEL2_INCLUDE_DIR}")
677 + message( STATUS "OPENBABEL2_LIBRARIES ....... = ${OPENBABEL2_LIBRARIES}")
678 + message( STATUS "QHULL_ROOT ................. = ${QHULL_ROOT}")
679 + message( STATUS "QHULL_INCLUDE_DIR .......... = ${QHULL_INCLUDE_DIR}")
680 + message( STATUS "QHULL_LIBRARIES ............ = ${QHULL_LIBRARIES}")
681 + message( STATUS "ZLIB_ROOT .................. = ${ZLIB_ROOT}")
682 + message( STATUS "ZLIB_INCLUDE_DIR ........... = ${ZLIB_INCLUDE_DIR}")
683 + message( STATUS "ZLIB_LIBRARIES ............. = ${ZLIB_LIBRARIES}")
684 + message( STATUS "FFTW3_ROOT ................. = ${FFTW3_ROOT}")
685 + message( STATUS "FFTW3_INCLUDE_DIR .......... = ${FFTW3_INCLUDE_DIR}")
686 + message( STATUS "FFTW3_LIBRARIES ............ = ${FFTW3_LIBRARIES}")
687 + message( STATUS "PERL_EXECUTABLE ............ = ${PERL_EXECUTABLE}")
688 + message( STATUS "PYTHON_EXECUTABLE .......... = ${PYTHON_EXECUTABLE}")
689 + message( STATUS "DOXYGEN_EXECUTABLE ......... = ${DOXYGEN_EXECUTABLE}")
690 + message( STATUS )
691 + message( STATUS "To override these options, add -D{OPTION_NAME}=... to the cmake command" )
692 + message( STATUS "Particularly useful defines are for:")
693 + message( STATUS )
694 + message( STATUS "  -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} (where OpenMD will be installed)")
695 + message( STATUS "       -DOPENBABEL2_ROOT=/path/to/openbabel")
696 + message( STATUS "            -DQHULL_ROOT=/path/to/qhull")
697 + message( STATUS "            -DFFTW3_ROOT=/path/to/fftw3")
698 + message( STATUS )
699 + message( STATUS "To build and install OpenMD, enter \"make\" and \"make install\"")
700 + message( STATUS )

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