Install directory now looks much more like actual OpenMM releases.

CMakeLists.txt

@@ -290,19 +290,26 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
 
-ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
+SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
+IF(OPENMM_BUILD_STATIC_LIB)
+    ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY -DOPENMMM_VALIDATE_BUILDING_STATIC_LIBRARY -DOPENMM_VALIDATE_BUILDING_STATIC_LIBRARY")
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 IF(OPENMM_BUILD_API_WRAPPERS)
     ADD_DEPENDENCIES(${SHARED_TARGET} ApiWrappers)
-    ADD_DEPENDENCIES(${STATIC_TARGET} ApiWrappers)
+    IF(OPENMM_BUILD_STATIC_LIB)
+        ADD_DEPENDENCIES(${STATIC_TARGET} ApiWrappers)
+    ENDIF(OPENMM_BUILD_STATIC_LIB)
 ENDIF(OPENMM_BUILD_API_WRAPPERS)
 
 # On Linux need to link to libdl
 FIND_LIBRARY(DL_LIBRARY dl)
 IF(DL_LIBRARY)
   TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${DL_LIBRARY})
-  TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${DL_LIBRARY})
+  IF(OPENMM_BUILD_STATIC_LIB)
+    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${DL_LIBRARY})
+  ENDIF(OPENMM_BUILD_STATIC_LIB)
 ENDIF(DL_LIBRARY)
 IF(WIN32)
     MARK_AS_ADVANCED(DL_LIBRARY)
@@ -391,7 +398,9 @@ IF(OPENMM_BUILD_FREE_ENERGY_PLUGIN)
 ENDIF(OPENMM_BUILD_FREE_ENERGY_PLUGIN)
 
 INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET})
-INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET})
+IF(OPENMM_BUILD_STATIC_LIB)
+  INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET})
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 FILE(GLOB CORE_HEADERS     include/*.h          */include/*.h)
 FILE(GLOB TOP_HEADERS      include/openmm/*.h          */include/openmm/*.h)
 FILE(GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h )
@@ -426,9 +435,54 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
 # Build and install documentation
-INCLUDE(cmake_modules/ApiDoxygen.cmake)
+
+find_package(Doxygen QUIET)
+mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
+IF(DOXYGEN_EXECUTABLE)
+    SET(DOXY_CONFIG "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
+    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in 
+          ${DOXY_CONFIG}
+          @ONLY )
+    FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
+    FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
+    ADD_CUSTOM_COMMAND(
+        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
+        DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
+        COMMENT "Generating API documentation using Doxygen")
+    ADD_CUSTOM_TARGET(DoxygenApiDocs 
+        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
+        COMMENT "Generating API documentation using Doxygen"
+        SOURCES 
+            "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in"
+            ${OPENMM_INCLUDES}
+            ${OLLA_INCLUDES}
+    ) 
+    FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/html/")
+    INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/"
+            DESTINATION "docs/api/")
+    INSTALL(FILES "docs/API Reference.html"
+            DESTINATION "docs/")
+  set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
+  if(OPENMM_GENERATE_API_DOCS)
+    ADD_CUSTOM_TARGET(GenerateDoxygenApiDocs ALL
+       DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
+       COMMENT "Generating API documentation using Doxygen"
+       SOURCES 
+            "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in"
+            ${OPENMM_INCLUDES}
+            ${OLLA_INCLUDES}
+    )
+  endif(OPENMM_GENERATE_API_DOCS)
+ENDIF(DOXYGEN_EXECUTABLE)
+
 install(FILES docs/UsersGuide/OpenMMUsersGuide.pdf
-    DESTINATION docs)
+    DESTINATION docs/)
+
+FILE(GLOB LICENSE_FILES "docs/licenses/*.txt")
+install(FILES ${LICENSE_FILES}
+    DESTINATION licenses/)
 
 ADD_SUBDIRECTORY(tests)
 ADD_SUBDIRECTORY(examples)

cmake_modules/ApiDoxygen.cmake

-INCLUDE(FindDoxygen)
+find_package(Doxygen)
 
-IF(DOXYGEN_EXECUTABLE-NOTFOUND)
-ELSE(DOXYGEN_EXECUTABLE-NOTFOUND)
+set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
+IF(DOXYGEN_FOUND)
     SET(DOXY_CONFIG "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
 
-    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in 
+    CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in 
           ${DOXY_CONFIG}
           @ONLY )
 
-    ADD_CUSTOM_TARGET(DoxygenApiDocs ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}) 
-
+    ADD_CUSTOM_COMMAND(
+        OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/html/index.html"
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
+        COMMENT "Generating API documentation using Doxygen"
+        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
+    ADD_CUSTOM_TARGET(DoxygenApiDocs 
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
+        COMMENT "Generating API documentation using Doxygen"
+        SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in") 
     FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/html/")
-    INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/"
-            DESTINATION "doc/api/"
-            )
-ENDIF(DOXYGEN_EXECUTABLE-NOTFOUND)
+
+    IF(OPENMM_GENERATE_API_DOCS)
+        INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/html/"
+                DESTINATION "docs/api/")
+    ENDIF(OPENMM_GENERATE_API_DOCS)
+ELSE(DOXYGEN_FOUND)
+ENDIF(DOXYGEN_FOUND)
 

docs/API Reference.html

+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html>
+<head>
+<meta http-equiv="REFRESH" content="0;url=api/index.html"></HEAD>
+<BODY>
+</BODY>
+</HTML>
\ No newline at end of file

docs/licenses/LGPL.txt

+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

docs/licenses/Licenses.txt

+OpenMM was developed by Simbios, the NIH National Center for Physics-Based
+Simulation of Biological Structures at Stanford, funded under the NIH Roadmap
+for Medical Research, grant U54 GM072970. See https://simtk.org.
+
+Portions copyright © 2008-2009 Stanford University and the Authors.
+
+There are several licenses which cover different parts of OpenMM as described
+below.
+
+
+1. API and Reference Platform
+
+The OpenMM API and the Reference Platform may be used under the terms of the
+MIT License:
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject
+to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
+2. CUDA and OpenCL Platforms
+
+The CUDA Platform and OpenCL Platform may be used under the terms of the GNU
+Lesser General Public License.  A copy of this license may be found in the
+accompanying file "LGPL.txt".  It in turn incorporates the terms of the GNU
+General Public License, which may be found in the accompanying file "GPL.txt".
+
+
+3. SIMD-oriented Fast Mersenne Twister (SFMT)
+
+OpenMM uses the SFMT library which is copyright 2006-2007 Mutsuo Saito, Makoto
+Matsumoto and Hiroshima University.  It may be used under the following terms:
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+    * Neither the name of the Hiroshima University nor the names of
+      its contributors may be used to endorse or promote products
+      derived from this software without specific prior written
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+4. Hilbert Curve
+
+OpenMM uses an implementation of Hilbert curves which is copyright 1998-2000
+Rice University.  It may be used under the following terms:
+
+This software is copyrighted by Rice University.  It may be freely copied,
+modified, and redistributed, provided that the copyright notice is
+preserved on all copies.
+
+There is no warranty or other guarantee of fitness for this software,
+it is provided solely "as is".  Bug reports or fixes may be sent
+to the author, who may or may not act on them as he desires.
+
+You may include this software in a program or other software product,
+but must display the notice:
+
+Hilbert Curve implementation copyright 1998, Rice University
+
+in any place where the end-user would see your own copyright.
+
+If you modify this software, you should include a notice giving the
+name of the person performing the modification, the date of modification,
+and the reason for such modification.
+
+
+5. GPU-BBSort
+
+The CUDA platform uses the GPU-BBSort library written by Chen Shifu.  It
+includes the following license statement:
+
+The code is distributed under BSD license, you are allowed to use, modify
+or sell this code, but a statement is required if you used this code any where.
\ No newline at end of file

examples/CMakeLists.txt

@@ -22,8 +22,10 @@ SET(C_EXAMPLES HelloArgonInC HelloSodiumChlorideInC)
 SET(F_EXAMPLES HelloArgonInFortran HelloSodiumChlorideInFortran)
 
 SET(BUILD_TESTING_SHARED 1)
-SET(BUILD_TESTING_STATIC 1)
-
+SET(BUILD_TESTING_STATIC OFF)
+IF(OPENMM_BUILD_STATIC_LIB)
+    SET(BUILD_TESTING_STATIC ON)
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 		
 FOREACH(EX_ROOT ${CPP_EXAMPLES})
     IF (BUILD_TESTING_SHARED)

plugins/freeEnergy/CMakeLists.txt

@@ -127,8 +127,10 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 ADD_LIBRARY(${SHARED_FREE_ENERGY_TARGET} SHARED ${SOURCE_FREE_ENERGY_FILES} ${SOURCE_FREE_ENERGY_INCLUDE_FILES} ${API_FREE_ENERGY_ABS_INCLUDE_FILES})
 SET_TARGET_PROPERTIES(${SHARED_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
 
-ADD_LIBRARY(${STATIC_FREE_ENERGY_TARGET} STATIC ${SOURCE_FREE_ENERGY_FILES} ${SOURCE_FREE_ENERGY_INCLUDE_FILES} ${API_FREE_ENERGY_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${STATIC_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+IF(OPENMM_BUILD_STATIC_LIB)
+  ADD_LIBRARY(${STATIC_FREE_ENERGY_TARGET} STATIC ${SOURCE_FREE_ENERGY_FILES} ${SOURCE_FREE_ENERGY_INCLUDE_FILES} ${API_FREE_ENERGY_ABS_INCLUDE_FILES})
+  SET_TARGET_PROPERTIES(${STATIC_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 #IF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)
 #    ADD_DEPENDENCIES(${SHARED_FREE_ENERGY_TARGET} ApiWrappers)
@@ -139,7 +141,9 @@ SET_TARGET_PROPERTIES(${STATIC_FREE_ENERGY_TARGET} PROPERTIES COMPILE_FLAGS "-DO
 FIND_LIBRARY(DL_LIBRARY dl)
 IF(DL_LIBRARY)
   TARGET_LINK_LIBRARIES(${SHARED_FREE_ENERGY_TARGET} ${DL_LIBRARY})
-  TARGET_LINK_LIBRARIES(${STATIC_FREE_ENERGY_TARGET} ${DL_LIBRARY})
+  IF(OPENMM_BUILD_STATIC_LIB)
+    TARGET_LINK_LIBRARIES(${STATIC_FREE_ENERGY_TARGET} ${DL_LIBRARY})
+  ENDIF(OPENMM_BUILD_STATIC_LIB)
 ENDIF(DL_LIBRARY)
 
 SET( OpenMMLib OpenMM )
@@ -148,7 +152,9 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
     SET(OpenMMLib ${OpenMMLib}_d)
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 TARGET_LINK_LIBRARIES( ${SHARED_FREE_ENERGY_TARGET} ${SHARED_TARGET} )
-TARGET_LINK_LIBRARIES( ${STATIC_FREE_ENERGY_TARGET} ${STATIC_TARGET} )
+IF(OPENMM_BUILD_STATIC_LIB)
+  TARGET_LINK_LIBRARIES( ${STATIC_FREE_ENERGY_TARGET} ${STATIC_TARGET} )
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 ADD_SUBDIRECTORY(platforms/reference/tests)
 
@@ -178,8 +184,10 @@ ENDIF(OPENMM_BUILD_FREE_ENERGY_CUDA_LIB)
 #    ADD_SUBDIRECTORY(platforms/opencl)
 #ENDIF(OPENMM_BUILD_OPENCL_LIB)
 
-INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_FREE_ENERGY_TARGET})
-INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_FREE_ENERGY_TARGET})
+INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib/plugins ${SHARED_FREE_ENERGY_TARGET})
+IF(OPENMM_BUILD_STATIC_LIB)
+  INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib/plugins ${STATIC_FREE_ENERGY_TARGET})
+ENDIF(OPENMM_BUILD_STATIC_LIB)
 FILE(GLOB CORE_HEADERS     include/*.h          */include/*.h)
 FILE(GLOB TOP_HEADERS      include/openmm/*.h          */include/openmm/*.h)
 FILE(GLOB INTERNAL_HEADERS include/openmm/internal/*.h */include/openmm/internal/*.h )

plugins/freeEnergy/platforms/cuda/CMakeLists.txt

@@ -140,4 +140,6 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # SET(FINDCUDA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cuda-cmake)
 
-SUBDIRS (sharedTarget staticTarget)
+# SUBDIRS (sharedTarget staticTarget)
+SUBDIRS (sharedTarget)
+