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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 1862 by gezelter, Fri Apr 12 20:45:04 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" "${PROJECT_SOURCE_DIR}"
83 +  )
84 + ELSE()
85 +  SET(SVN_REV Release)
86 +  ADD_DEFINITIONS( -DSVN_REV=Release )
87   ENDIF()
88  
89 + check_include_file_cxx(conio.h      HAVE_CONIO_H)
90 + check_cxx_symbol_exists(strncasecmp   "string.h"   HAVE_STRNCASECMP)
91 +
92   # Optional libraries: If we can find these, we will build with them
93   # Look for OpenBabel libraries
94   find_package(OpenBabel2)
95   IF(OPENBABEL2_FOUND)
96    SET(USE_OPENBABEL)
97    include_directories(${OPENBABEL2_INCLUDE_DIR})
98 <  message(STATUS "Openbabel libs: " ${OPENBABEL2_LIBRARIES})
99 < #  TARGET_LINK_LIBRARIES(${OPENBABEL2_LIBRARIES})
98 >  # link libraries are added only for targets that need them.
99 > ELSE(OPENBABEL2_FOUND)
100 >  MESSAGE(STATUS "No OpenBabel found - will not build atom2md")
101   ENDIF(OPENBABEL2_FOUND)
102  
103 + find_package(Eigen3)
104 + if(EIGEN3_FOUND)
105 +  add_definitions(-DHAVE_EIGEN -DHAVE_EIGEN3)
106 +  include_directories(${EIGEN3_INCLUDE_DIR})
107 + else()
108 +  find_package(Eigen2) # find and setup Eigen2
109 +  if(EIGEN2_FOUND)
110 +    add_definitions (-DHAVE_EIGEN)
111 +    include_directories(${EIGEN2_INCLUDE_DIR})
112 +  endif()
113 + endif()
114 +
115   #Look for QHULL Libraries
116 < find_package(QHULL)
116 > find_package(Qhull)
117   IF(QHULL_FOUND)
118    SET(HAVE_QHULL 1)
119    include_directories(${QHULL_INCLUDE_DIR})
120    LINK_LIBRARIES(${QHULL_LIBRARIES})
121 + ELSE(QHULL_FOUND)
122 +  MESSAGE(STATUS "No Qhull found - will be missing some features")
123   ENDIF(QHULL_FOUND)
124  
56 –
125   # zlib stuff
126   find_package(ZLIB)
127   if(ZLIB_FOUND)
# Line 61 | Line 129 | if(ZLIB_FOUND)
129    add_definitions(-DHAVE_LIBZ)
130    include_directories(${ZLIB_INCLUDE_DIR})
131    LINK_LIBRARIES(${ZLIB_LIBRARIES})
132 + ELSE(ZLIB_FOUND)
133 +  MESSAGE(STATUS "No zlib found - will be missing compressed dump files")
134   endif(ZLIB_FOUND)
135  
136 < #FFTW
137 < INCLUDE(${CMAKE_MODULE_PATH}/FindFFTW.cmake)
138 < IF(FFTW_FOUND)
136 > #FFTW3
137 > IF(SINGLE_PRECISION)
138 >  find_package(FFTW3 COMPONENTS single)
139 > else()
140 >  find_package(FFTW3 COMPONENTS double)
141 > endif(SINGLE_PRECISION)
142 > if (FFTW3_FOUND)
143 >  include_directories (${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR} ${FFTW3_INCLUDE_DIR})
144    SET(HAVE_LIBFFTW 1)
145 <  SET(HAVE_FFTW3_H)
146 <  INCLUDE_DIRECTORIES(${FFTW_INCLUDE_DIR})
147 <  LINK_LIBRARIES(${FFTW_LIBRARIES})
148 < ENDIF(FFTW_FOUND)
145 >  SET(HAVE_FFTW3_H 1)
146 >  INCLUDE_DIRECTORIES(${FFTW3_INCLUDE_DIR})
147 >  LINK_LIBRARIES(${FFTW3_LIBRARIES})
148 > ELSE(FFTW3_FOUND)
149 >  MESSAGE(STATUS "No fftw3 found - will be missing some analysis modules")
150 > endif (FFTW3_FOUND)
151  
152  
153 < #include checks
154 < include(CheckIncludeFile)
155 < CHECK_INCLUDE_FILE(fftw3.h HAVE_FFTW3_H)
156 < CHECK_INCLUDE_FILE(fftw.h HAVE_FFWT_H)
157 < CHECK_INCLUDE_FILE(dfftw.h HAVE_DFFTW_H)
158 < CHECK_INCLUDE_FILE(cmath.h HAVE_CMATH_H)
159 < check_include_file(limits.h HAVE_LIMITS_H)
160 < check_include_file(stdlib.h HAVE_STDLIB_H)
161 < check_include_file(string.h HAVE_STRING_H)
162 < check_include_file("sys/ioctl.h" HAVE_SYS_IOCTL_H)
86 < check_include_file(unistd.h HAVE_UNISTD_H)
153 > # add a target to generate API documentation with Doxygen
154 > find_package(Doxygen)
155 > if(DOXYGEN_FOUND)
156 >  configure_file("${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in" "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile" @ONLY)
157 >  add_custom_target(doc
158 >    ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile"
159 >    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/doc"
160 >    COMMENT "Generating API documentation with Doxygen" VERBATIM
161 >  )
162 > endif(DOXYGEN_FOUND)
163  
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 –
164   FIND_PACKAGE(Perl)
165   IF(PERL_FOUND)
166    SET(PERL ${PERL_EXECUTABLE})
167   ELSE(PERL_FOUND)
168 <  MESSAGE(STATUS "Failed to find perl")
168 >  MESSAGE(STATUS "Failed to find perl - some scripts will not be made")
169   ENDIF(PERL_FOUND)
170  
171 + SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation
172 + locations")
173 +
174   FIND_PACKAGE(PythonInterp)
175   IF(PYTHON_EXECUTABLE)
176    SET(PYTHON ${PYTHON_EXECUTABLE})
177   ELSE(PYTHON_EXECUTABLE)
178 <  MESSAGE(STATUS "Failed to find python")
178 >  MESSAGE(STATUS "Failed to find python - some scripts will not be made")
179   ENDIF(PYTHON_EXECUTABLE)
180  
123 – SET(PERL_INSTALLDIRS "site" CACHE STRING "Perl installation locations")
124 –
125 –
126 – include(CMakePrintSystemInformation)
127 –
181   configure_file (
182    "${PROJECT_SOURCE_DIR}/src/config.h.cmake"
183 <  "${PROJECT_SOURCE_DIR}/src/config.h"
184 <  )
185 < include_directories (${PROJECT_SOURCE_DIR}/src)
133 <
134 < #CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/config.h.in ${CMAKE_CURRENT_BINARY_DIR}/config.h)
135 <
183 >  "${PROJECT_BINARY_DIR}/config.h"
184 > )
185 > include_directories("${PROJECT_BINARY_DIR}" "${PROJECT_SOURCE_DIR}/src")
186  
187   #Add executables for build
188   set (PROGRAMS
# Line 145 | Line 195 | thermalizer
195   randomBuilder
196   nanoparticleBuilder
197   thermalizer
198 + recenter
199   atom2md
200   Hydro)
201  
# Line 180 | Line 231 | src/brains/DataStorage.cpp
231   src/antlr/TreeParser.cpp
232   src/brains/BlockSnapshotManager.cpp
233   src/brains/DataStorage.cpp
234 + src/brains/ForceField.cpp
235   src/brains/MoleculeCreator.cpp
236   src/brains/PairList.cpp
237   src/brains/Register.cpp
238   src/brains/SimSnapshotManager.cpp
239   src/brains/Snapshot.cpp
240   src/brains/Stats.cpp
241 + src/constraints/Shake.cpp
242   src/constraints/Rattle.cpp
243   src/hydrodynamics/Ellipsoid.cpp
244   src/hydrodynamics/HydroProp.cpp
245   src/hydrodynamics/Sphere.cpp
246   src/integrators/DLM.cpp
247 + src/flucq/FluctuatingChargeLangevin.cpp
248 + src/flucq/FluctuatingChargeParameters.cpp
249 + src/flucq/FluctuatingChargeNVT.cpp
250 + src/flucq/FluctuatingChargePropagator.cpp
251   src/integrators/Integrator.cpp
252   src/integrators/IntegratorFactory.cpp
253   src/integrators/LangevinDynamics.cpp
# Line 213 | Line 270 | src/io/EAMAtomTypesSectionParser.cpp
270   src/io/ChargeAtomTypesSectionParser.cpp
271   src/io/DirectionalAtomTypesSectionParser.cpp
272   src/io/EAMAtomTypesSectionParser.cpp
273 + src/io/FluctuatingChargeAtomTypesSectionParser.cpp
274   src/io/ForceFieldOptions.cpp
275   src/io/GayBerneAtomTypesSectionParser.cpp
276   src/io/Globals.cpp
219 – src/io/gzstream.cpp
277   src/io/InversionTypesSectionParser.cpp
278   src/io/LennardJonesAtomTypesSectionParser.cpp
279   src/io/MultipoleAtomTypesSectionParser.cpp
280   src/io/NonBondedInteractionsSectionParser.cpp
281   src/io/OptionSectionParser.cpp
282   src/io/ParamConstraint.cpp
283 + src/io/PolarizableAtomTypesSectionParser.cpp
284   src/io/SCAtomTypesSectionParser.cpp
285   src/io/SectionParser.cpp
286   src/io/SectionParserManager.cpp
# Line 249 | Line 307 | src/mdParser/MDTreeParser.cpp
307   src/mdParser/MDLexer.cpp
308   src/mdParser/MDParser.cpp
309   src/mdParser/MDTreeParser.cpp
310 < src/minimizers/MinimizerFactory.cpp
311 < src/minimizers/MinimizerParameterSet.cpp
310 > src/optimization/OptimizationFactory.cpp
311 > src/optimization/Armijo.cpp
312 > src/optimization/BFGS.cpp
313 > src/optimization/ConjugateGradient.cpp
314 > src/optimization/Constraint.cpp
315 > src/optimization/EndCriteria.cpp
316 > src/optimization/LineSearch.cpp
317 > src/optimization/LineSearchBasedMethod.cpp
318 > src/optimization/SteepestDescent.cpp
319 > src/optimization/PotentialEnergyObjectiveFunction.cpp
320 > src/optimization/MinimizerParameters.cpp
321   src/nonbonded/EAM.cpp
322   src/nonbonded/Electrostatic.cpp
323   src/nonbonded/GB.cpp
# Line 273 | Line 340 | src/primitives/UreyBradleyBend.cpp
340   src/primitives/StuntDouble.cpp
341   src/primitives/Torsion.cpp
342   src/primitives/UreyBradleyBend.cpp
343 + src/perturbations/ElectricField.cpp
344   src/restraints/MolecularRestraint.cpp
345   src/restraints/ObjectRestraint.cpp
278 – src/selection/DistanceFinder.cpp
346   src/selection/HullFinder.cpp
347   src/selection/IndexFinder.cpp
348   src/selection/NameFinder.cpp
# Line 291 | Line 358 | src/types/CutoffGroupStamp.cpp
358   src/types/CharmmTorsionType.cpp
359   src/types/Component.cpp
360   src/types/CutoffGroupStamp.cpp
361 < src/types/DirectionalAtomType.cpp
361 > src/types/DirectionalAdapter.cpp
362 > src/types/EAMAdapter.cpp
363 > src/types/FixedChargeAdapter.cpp
364 > src/types/FluctuatingChargeAdapter.cpp
365   src/types/FragmentStamp.cpp
366 + src/types/GayBerneAdapter.cpp
367   src/types/ImproperCosineInversionType.cpp
368   src/types/InversionStamp.cpp
369 + src/types/LennardJonesAdapter.cpp
370   src/types/MoleculeStamp.cpp
371 + src/types/MultipoleAdapter.cpp
372   src/types/NonBondedInteractionType.cpp
373 + src/types/PolarizableAdapter.cpp
374   src/types/RestraintStamp.cpp
375   src/types/RigidBodyStamp.cpp
376   src/types/ShapeAtomType.cpp
377 + src/types/StickyAdapter.cpp
378 + src/types/SuttonChenAdapter.cpp
379   src/types/TorsionStamp.cpp
380   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
381   src/utils/ElementsTable.cpp
382   src/utils/MoLocator.cpp
317 – src/utils/OpenMDBitSet.cpp
383   src/utils/PropertyMap.cpp
384   src/utils/StringTokenizer.cpp
385   src/utils/StringUtils.cpp
# Line 329 | Line 394 | src/visitors/ZconsVisitor.cpp
394   src/visitors/ReplacementVisitor.cpp
395   src/visitors/RigidBodyVisitor.cpp
396   src/visitors/ZconsVisitor.cpp
397 + src/rnemd/RNEMDParameters.cpp
398 + src/clusters/Icosahedron.cpp
399 + src/clusters/Decahedron.cpp
400   )
401  
402   set( PARALLEL_SOURCE
# Line 337 | Line 405 | src/constraints/ZconstraintForceManager.cpp
405   src/brains/SimInfo.cpp
406   src/brains/Thermo.cpp
407   src/constraints/ZconstraintForceManager.cpp
408 < src/integrators/RNEMD.cpp
408 > src/flucq/FluctuatingChargeConstraints.cpp
409 > src/flucq/FluctuatingChargeObjectiveFunction.cpp
410 > src/integrators/LangevinHullForceManager.cpp
411 > src/rnemd/RNEMD.cpp
412   src/integrators/Velocitizer.cpp
413   src/io/DumpReader.cpp
414   src/io/DumpWriter.cpp
# Line 347 | Line 418 | src/math/ParallelRandNumGen.cpp
418   src/io/ZConsWriter.cpp
419   src/io/ifstrstream.cpp
420   src/math/ParallelRandNumGen.cpp
350 – src/minimizers/CGFamilyMinimizer.cpp
351 – src/minimizers/Minimizer.cpp
352 – src/minimizers/PRCG.cpp
353 – src/minimizers/SDMinimizer.cpp
421   src/parallel/ForceDecomposition.cpp
422   src/parallel/ForceMatrixDecomposition.cpp
423   src/restraints/RestraintForceManager.cpp
424   src/restraints/ThermoIntegrationForceManager.cpp
425 + src/selection/DistanceFinder.cpp
426   src/utils/ProgressBar.cpp
427 < src/utils/simError.c
427 > src/utils/simError.cpp
428 > src/utils/OpenMDBitSet.cpp
429 > src/optimization/Problem.cpp
430   )
431  
432 + IF(ZLIB_FOUND)
433 + set(ZLIB_SOURCE
434 + src/io/gzstream.cpp
435 + )
436 + ENDIF(ZLIB_FOUND)
437 +
438   IF(QHULL_FOUND)
439   set(QHULL_SOURCE
440   src/integrators/LangevinHullDynamics.cpp
# Line 371 | Line 447 | ENDIF(QHULL_FOUND)
447   )
448   ENDIF(QHULL_FOUND)
449  
450 < add_library(openmd_core STATIC ${SOURCE} ${QHULL_SOURCE} )
450 > IF(WIN32)
451 > set(GETOPT_SOURCE
452 > src/utils/wingetopt.cpp
453 > )
454 > ENDIF(WIN32)
455 >
456 > add_library(openmd_core STATIC ${SOURCE} ${QHULL_SOURCE} ${ZLIB_SOURCE} )
457   add_library(openmd_single STATIC ${PARALLEL_SOURCE} ${QHULL_PARALLEL_SOURCE} )
458  
459   IF(MPI_FOUND)
# Line 390 | Line 472 | target_link_libraries(openmd_MPI openmd_parallel openm
472   COMPILE_DEFINITIONS IS_MPI
473   )
474   target_link_libraries(openmd_MPI openmd_parallel openmd_core openmd_parallel openmd_core)
475 +  INSTALL(TARGETS
476 +        openmd_parallel openmd_MPI
477 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
478 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
479 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
480 + )
481   ENDIF (MPI_FOUND)
482  
483   set (DUMP2XYZSOURCE
484   src/applications/dump2Xyz/Dump2XYZ.cpp
485 < src/applications/dump2Xyz/Dump2XYZCmd.c
485 > src/applications/dump2Xyz/Dump2XYZCmd.cpp
486   )
487  
488   set (DYNAMICPROPSSOURCE
# Line 410 | Line 498 | src/applications/dynamicProps/RCorrFunc.cpp
498   src/applications/dynamicProps/ParticleTimeCorrFunc.cpp
499   src/applications/dynamicProps/RadialRCorrFunc.cpp
500   src/applications/dynamicProps/RCorrFunc.cpp
501 + src/applications/dynamicProps/SelectionCorrFunc.cpp
502   src/applications/dynamicProps/StressCorrFunc.cpp
503   src/applications/dynamicProps/SystemDipoleCorrFunc.cpp
504   src/applications/dynamicProps/ThetaCorrFunc.cpp
505   src/applications/dynamicProps/TimeCorrFunc.cpp
506   src/applications/dynamicProps/VCorrFunc.cpp
507 < src/applications/dynamicProps/DynamicPropsCmd.c
507 > src/applications/dynamicProps/DynamicPropsCmd.cpp
508   )
509  
510   set (HYDROSOURCE
# Line 428 | Line 517 | src/applications/hydrodynamics/ShapeBuilder.cpp
517   src/applications/hydrodynamics/HydrodynamicsModelFactory.cpp
518   src/applications/hydrodynamics/RoughShell.cpp
519   src/applications/hydrodynamics/ShapeBuilder.cpp
520 < src/applications/hydrodynamics/HydroCmd.c
520 > src/applications/hydrodynamics/HydroCmd.cpp
521   )
522  
523   set (STATICPROPSSOURCE
# Line 456 | Line 545 | src/applications/staticProps/TetrahedralityParam.cpp
545   src/applications/staticProps/SCDOrderParameter.cpp
546   src/applications/staticProps/StaticProps.cpp
547   src/applications/staticProps/TetrahedralityParam.cpp
548 + src/applications/staticProps/TetrahedralityParamZ.cpp
549   src/applications/staticProps/TwoDGofR.cpp
550 < src/applications/staticProps/StaticPropsCmd.c
550 > src/applications/staticProps/StaticPropsCmd.cpp
551   )
552  
553   set (NANOPARTICLEBUILDERSOURCE
554   src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp
555   src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp
556 < src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.c
556 > src/applications/nanoparticleBuilder/nanoparticleBuilderCmd.cpp
557   )
558  
559 + set (NANORODBUILDERSOURCE
560 + src/applications/nanoparticleBuilder/nanorodBuilder.cpp
561 + src/applications/nanoparticleBuilder/shapedLatticeRod.cpp
562 + src/applications/nanoparticleBuilder/nanorodBuilderCmd.cpp
563 + )
564 +
565 + set (NANOROD_PENTBUILDERSOURCE
566 + src/applications/nanoparticleBuilder/nanorod_pentBuilder.cpp
567 + src/applications/nanoparticleBuilder/nanorod_pentBuilderCmd.cpp
568 + src/applications/nanoparticleBuilder/shapedLatticePentRod.cpp
569 + )
570 +
571 + set (ICOSAHEDRALBUILDERSOURCE
572 + src/applications/nanoparticleBuilder/icosahedralBuilder.cpp
573 + src/applications/nanoparticleBuilder/icosahedralBuilderCmd.cpp
574 + )
575 +
576   set (RANDOMBUILDERSOURCE
577   src/applications/randomBuilder/randomBuilder.cpp
578 < src/applications/randomBuilder/randomBuilderCmd.c
578 > src/applications/randomBuilder/randomBuilderCmd.cpp
579   )
580  
581   set(SIMPLEBUILDERSOURCE
582   src/applications/simpleBuilder/simpleBuilder.cpp
583 < src/applications/simpleBuilder/simpleBuilderCmd.c
583 > src/applications/simpleBuilder/simpleBuilderCmd.cpp
584   )
585  
586   set(THERMALIZERSOURCE
587   src/applications/thermalizer/thermalizer.cpp
588 < src/applications/thermalizer/thermalizerCmd.c
588 > src/applications/thermalizer/thermalizerCmd.cpp
589   )
590  
591 < add_executable(Dump2XYZ ${DUMP2XYZSOURCE})
591 > set(RECENTERSOURCE
592 > src/applications/recenter/recenter.cpp
593 > src/applications/recenter/recenterCmd.cpp
594 > )
595 >
596 > add_executable(Dump2XYZ ${DUMP2XYZSOURCE} ${GETOPT_SOURCE})
597   target_link_libraries(Dump2XYZ openmd_single openmd_core openmd_single openmd_core)
598 < add_executable(DynamicProps ${DYNAMICPROPSSOURCE})
598 > add_executable(DynamicProps ${DYNAMICPROPSSOURCE} ${GETOPT_SOURCE})
599   target_link_libraries(DynamicProps openmd_single openmd_core openmd_single openmd_core)
600 < add_executable(Hydro ${HYDROSOURCE})
600 > add_executable(Hydro ${HYDROSOURCE} ${GETOPT_SOURCE})
601   target_link_libraries(Hydro openmd_single openmd_core openmd_single openmd_core)
602 < add_executable(StaticProps ${STATICPROPSSOURCE})
602 > add_executable(StaticProps ${STATICPROPSSOURCE} ${GETOPT_SOURCE})
603   target_link_libraries(StaticProps openmd_single openmd_core openmd_single openmd_core)
604 < add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE})
605 < target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core)
606 < add_executable(randomBuilder ${RANDOMBUILDERSOURCE})
607 < target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core)
608 < add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE})
609 < target_link_libraries(simpleBuilder openmd_single openmd_core openmd_single openmd_core)
610 < add_executable(thermalizer ${THERMALIZERSOURCE})
611 < target_link_libraries(thermalizer openmd_single openmd_core openmd_single openmd_core)
604 > add_executable(nanoparticleBuilder ${NANOPARTICLEBUILDERSOURCE} ${GETOPT_SOURCE})
605 > target_link_libraries(nanoparticleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
606 > add_executable(nanorodBuilder ${NANORODBUILDERSOURCE} ${GETOPT_SOURCE})
607 > target_link_libraries(nanorodBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
608 > add_executable(nanorod_pentBuilder ${NANOROD_PENTBUILDERSOURCE} ${GETOPT_SOURCE})
609 > target_link_libraries(nanorod_pentBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
610 > add_executable(icosahedralBuilder ${ICOSAHEDRALBUILDERSOURCE} ${GETOPT_SOURCE})
611 > target_link_libraries(icosahedralBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
612 > add_executable(randomBuilder ${RANDOMBUILDERSOURCE} ${GETOPT_SOURCE})
613 > target_link_libraries(randomBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
614 > add_executable(simpleBuilder ${SIMPLEBUILDERSOURCE} ${GETOPT_SOURCE})
615 > target_link_libraries(simpleBuilder openmd_single openmd_core openmd_single openmd_core openmd_single)
616 > add_executable(thermalizer ${THERMALIZERSOURCE} ${GETOPT_SOURCE})
617 > target_link_libraries(thermalizer openmd_single openmd_core openmd_single openmd_core openmd_single)
618 > add_executable(recenter ${RECENTERSOURCE} ${GETOPT_SOURCE})
619 > target_link_libraries(recenter openmd_single openmd_core openmd_single openmd_core openmd_single)
620  
621   if (OPENBABEL2_FOUND)
622   set (ATOM2MDSOURCE
623   src/applications/atom2md/atom2md.cpp
624   src/applications/atom2md/openmdformat.cpp
625   )
626 <  add_executable(atom2md ${ATOM2MDSOURCE})
626 >  add_executable(atom2md ${ATOM2MDSOURCE} ${GETOPT_SOURCE})
627    target_link_libraries(atom2md openmd_single openmd_core openmd_single openmd_core ${OPENBABEL2_LIBRARIES})
628 +  INSTALL(TARGETS atom2md RUNTIME DESTINATION bin
629 +          PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
630   ENDIF (OPENBABEL2_FOUND)
631  
632  
# Line 516 | Line 638 | src/applications/utilities/principalAxisCalculator
638   src/applications/utilities/md2md
639   src/applications/utilities/mdSplit
640   src/applications/utilities/principalAxisCalculator
641 + src/applications/utilities/stat2thcond
642   src/applications/utilities/stat2visco
643   src/applications/utilities/waterRotator
644 + src/applications/utilities/waterReplacer
645   )
646  
647   IF(PYTHON_EXECUTABLE)
648 <   foreach(PY_FILE ${PY_FILES})
649 <      configure_file(${PY_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PY_FILE} @ONLY)
650 <   endforeach(PY_FILE)
651 < #INSTALL(FILES ${PY_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
648 >  IF(WIN32)
649 >    SET(PYEXT ".py")
650 >  ELSE(WIN32)
651 >    SET(PYEXT "")
652 >  ENDIF(WIN32)
653 >
654 >  foreach(PY_FILE ${PY_FILES})
655 >    GET_FILENAME_COMPONENT(filename "${PY_FILE}" NAME)
656 >    CONFIGURE_FILE(${PY_FILE}
657 >                  "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}" @ONLY)
658 >    INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PYEXT}"
659 >            DESTINATION bin
660 >            PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
661 >  endforeach(PY_FILE)
662   ENDIF(PYTHON_EXECUTABLE)
663  
664   set(PERL_FILES
# Line 533 | Line 667 | IF(PERL_FOUND)
667   )
668  
669   IF(PERL_FOUND)
670 <   foreach(PERL_FILE ${PERL_FILES})
671 <      configure_file(${PERL_FILE} "${EXECUTABLE_OUTPUT_PATH}"/${PERL_FILE} @ONLY)
672 <   endforeach(PERL_FILE)
673 < #INSTALL(FILES ${PERL_FILES} DESTINATION ${EXECUTABLE_OUTPUT_PATH})
670 >  IF(WIN32)
671 >    SET(PLEXT ".PL")
672 >  ELSE(WIN32)
673 >    SET(PLEXT "")
674 >  ENDIF(WIN32)
675 >
676 >  foreach(PERL_FILE ${PERL_FILES})
677 >     GET_FILENAME_COMPONENT(filename "${PERL_FILE}" NAME)
678 >     configure_file(${PERL_FILE} "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}" @ONLY)
679 >     INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${filename}${PLEXT}"
680 >             DESTINATION bin
681 >             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
682 >
683 >  endforeach(PERL_FILE)
684   ENDIF(PERL_FOUND)
685 +
686 +
687 + INSTALL(FILES AUTHORS LICENSE README INSTALL DESTINATION .
688 +        PERMISSIONS OWNER_READ GROUP_READ WORLD_READ)
689 + INSTALL(TARGETS
690 +        openmd_core
691 +        openmd_single
692 +        openmd
693 +        Dump2XYZ
694 +        simpleBuilder
695 +        StaticProps
696 +        DynamicProps
697 +        randomBuilder
698 +        nanoparticleBuilder
699 +        nanorodBuilder
700 +        nanorod_pentBuilder
701 +        thermalizer
702 +        recenter
703 +        Hydro
704 +  RUNTIME DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
705 +  LIBRARY DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
706 +  ARCHIVE DESTINATION lib PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ
707 + )
708 +
709 + install(DIRECTORY forceFields/  
710 +        DESTINATION forceFields
711 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
712 +        PATTERN ".svn" EXCLUDE
713 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
714 + install(DIRECTORY samples/      
715 +        DESTINATION samples
716 +        DIRECTORY_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
717 +        PATTERN ".svn" EXCLUDE
718 +        PATTERN "*.dump" EXCLUDE
719 +        PATTERN "*.stat" EXCLUDE
720 +        PATTERN "*.eor" EXCLUDE
721 +        PATTERN "*.rnemd" EXCLUDE
722 +        PATTERN "*.fz" EXCLUDE
723 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
724 +
725 + configure_file( samples/builders/runMe.in
726 +                "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe" @ONLY)
727 + INSTALL(FILES "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/runMe"
728 +             DESTINATION samples/builders
729 +             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)                
730 +
731 +
732 + INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/doc/OpenMDmanual.pdf"
733 +        DESTINATION doc
734 +        PERMISSIONS OWNER_READ OWNER_WRITE GROUP_READ WORLD_READ)
735 +
736 + message( STATUS)
737 + message( STATUS "========== OpenMD Build Information ==========")
738 + message( STATUS "Current revision ........... = ${SVN_REV}")
739 + message( STATUS "CMAKE_SYSTEM ............... = ${CMAKE_SYSTEM}")
740 + message( STATUS "==============================================")
741 + message( STATUS "CMAKE_BUILD_TYPE ........... = ${CMAKE_BUILD_TYPE}")
742 + message( STATUS "CMAKE_INSTALL_PREFIX ....... = ${CMAKE_INSTALL_PREFIX}")
743 + message( STATUS "Build as SINGLE_PRECISION .. = ${SINGLE_PRECISION}")
744 + message( STATUS "CMAKE_CXX_COMPILER ......... = ${CMAKE_CXX_COMPILER}")
745 + message( STATUS "MPI_CXX_COMPILER ........... = ${MPI_CXX_COMPILER}")
746 + message( STATUS "MPI_CXX_INCLUDE_PATH ....... = ${MPI_CXX_INCLUDE_PATH}")
747 + message( STATUS "MPI_CXX_LIBRARIES .......... = ${MPI_CXX_LIBRARIES}")
748 + message( STATUS "OPENBABEL2_ROOT ............ = ${OPENBABEL2_ROOT}")
749 + message( STATUS "OPENBABEL2_INCLUDE_DIR ..... = ${OPENBABEL2_INCLUDE_DIR}")
750 + message( STATUS "OPENBABEL2_LIBRARIES ....... = ${OPENBABEL2_LIBRARIES}")
751 + message( STATUS "QHULL_ROOT ................. = ${QHULL_ROOT}")
752 + message( STATUS "QHULL_INCLUDE_DIR .......... = ${QHULL_INCLUDE_DIR}")
753 + message( STATUS "QHULL_LIBRARIES ............ = ${QHULL_LIBRARIES}")
754 + message( STATUS "ZLIB_ROOT .................. = ${ZLIB_ROOT}")
755 + message( STATUS "ZLIB_INCLUDE_DIR ........... = ${ZLIB_INCLUDE_DIR}")
756 + message( STATUS "ZLIB_LIBRARIES ............. = ${ZLIB_LIBRARIES}")
757 + message( STATUS "FFTW3_ROOT ................. = ${FFTW3_ROOT}")
758 + message( STATUS "FFTW3_INCLUDE_DIR .......... = ${FFTW3_INCLUDE_DIR}")
759 + message( STATUS "FFTW3_LIBRARIES ............ = ${FFTW3_LIBRARIES}")
760 + message( STATUS "PERL_EXECUTABLE ............ = ${PERL_EXECUTABLE}")
761 + message( STATUS "PYTHON_EXECUTABLE .......... = ${PYTHON_EXECUTABLE}")
762 + message( STATUS "DOXYGEN_EXECUTABLE ......... = ${DOXYGEN_EXECUTABLE}")
763 + message( STATUS )
764 + message( STATUS "To override these options, add -D{OPTION_NAME}=... to the cmake command" )
765 + message( STATUS "Particularly useful defines are for:")
766 + message( STATUS )
767 + message( STATUS "  -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} (where OpenMD will be installed)")
768 + message( STATUS "       -DOPENBABEL2_ROOT=/path/to/openbabel")
769 + message( STATUS "            -DQHULL_ROOT=/path/to/qhull")
770 + message( STATUS "            -DFFTW3_ROOT=/path/to/fftw3")
771 + message( STATUS )
772 + IF(WIN32)
773 +  message( STATUS "To build and install OpenMD, enter: ")
774 +  message( STATUS "  msbuild /m ALL_BUILD.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
775 +  message( STATUS "followed by:")
776 +  message( STATUS "  msbuild /m INSTALL.vcxproj /p:Configuration=${CMAKE_BUILD_TYPE}")
777 + ELSE(WIN32)
778 +  message( STATUS "To build and install OpenMD, enter \"make\" and \"make install\"")
779 + ENDIF(WIN32)
780 + message( STATUS )
781 +
782 + # build a CPack driven installer package
783 + IF(NOT DEFINED CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS)
784 +   SET(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
785 + ENDIF()
786 + include (InstallRequiredSystemLibraries)
787 + set (CPACK_RESOURCE_FILE_LICENSE  
788 +     "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
789 + set (CPACK_PACKAGE_VERSION_MAJOR "${VERSION_MAJOR}")
790 + set (CPACK_PACKAGE_VERSION_MINOR "${VERSION_MINOR}")
791 + include (CPack)

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