Moved AMOEBA include files to plugins/amoeba/openmmapi/include/openmm to be...

Moved AMOEBA include files to plugins/amoeba/openmmapi/include/openmm to be consistent w/ outlay other plugins, ...

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -36,12 +36,12 @@
 #include "AmoebaReferenceMultipoleForce.h"
 #include "AmoebaReferenceVdwForce.h"
 #include "AmoebaReferenceWcaDispersionForce.h"
-#include "internal/AmoebaWcaDispersionForceImpl.h"
+#include "openmm/internal/AmoebaWcaDispersionForceImpl.h"
 #include "AmoebaReferenceUreyBradleyForce.h"
 #include "ReferencePlatform.h"
 #include "openmm/internal/ContextImpl.h"
-#include "AmoebaMultipoleForce.h"
-#include "internal/AmoebaMultipoleForceImpl.h"
+#include "openmm/AmoebaMultipoleForce.h"
+#include "openmm/internal/AmoebaMultipoleForceImpl.h"
 
 #include <cmath>
 #ifdef _MSC_VER

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -27,7 +27,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.      *
  * -------------------------------------------------------------------------- */
 
-#include "amoebaKernels.h"
+#include "openmm/amoebaKernels.h"
 #include "openmm/System.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h

@@ -27,7 +27,7 @@
 
 #include "SimTKUtilities/RealVec.h"
 #include "openmm/Vec3.h"
-#include "AmoebaMultipoleForce.h"
+#include "openmm/AmoebaMultipoleForce.h"
 #include <string>
 #include <vector>
 #include <map>

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp

@@ -38,7 +38,7 @@
 #include "openmm/Context.h"
 #include "AmoebaOpenMM.h"
 #include "openmm/System.h"
-#include "AmoebaVdwForce.h"
+#include "openmm/AmoebaVdwForce.h"
 #include "openmm/LangevinIntegrator.h"
 #include <iostream>
 #include <vector>

plugins/freeEnergy/CMakeLists.txt

@@ -16,26 +16,6 @@
 
 #INCLUDE(Dart)
 
-SET(LOG TRUE)
-# ----------------------------------------------------------------------------
-IF(LOG)
-   SET(LOG_FILE "CMakeLog.txt" )
-   FILE( WRITE ${LOG_FILE} "In OpenMM Cmake\n")
-ENDIF(LOG)
-
-IF(LOG)
-   MACRO(LOG_DIR LOG_FILE DIR_LIST )
-    
-      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
-      FOREACH(currentFile ${ARGN})
-         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
-      ENDFOREACH(currentFile)
-    
-    ENDMACRO(LOG_DIR) 
-ENDIF(LOG)
-
-# ----------------------------------------------------------------------------
-
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
 SET(OPENMM_FREE_ENERGY_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference)
@@ -104,16 +84,6 @@ ENDFOREACH(subdir)
 INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
 INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
 
-# ----------------------------------------------------------------------------
-IF(LOG)
-    FILE( APPEND ${LOG_FILE} "SOURCE_FREE_ENERGY_FILES=" ${SOURCE_FREE_ENERGY_FILES} "\n" )
-    FILE( APPEND ${LOG_FILE} "SOURCE_FREE_ENERGY_INCLUDE_FILES=" ${SOURCE_FREE_ENERGY_INCLUDE_FILES} "\n" )
-    FILE( APPEND ${LOG_FILE} "OPENMM_PATH="            ${OPENMM_PATH} "\n" )
-    FILE( APPEND ${LOG_FILE} "CUDA_PATH="              ${CUDA_PATH} "\n" )
-ENDIF(LOG)
-
-# ----------------------------------------------------------------------------
-
 # If API_FREE_ENERGY wrappers are being generated, and add them to the build.
 #SET(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS OFF CACHE BOOL "Build wrappers for C and Fortran")
 #IF(OPENMM_BUILD_API_FREE_ENERGY_WRAPPERS)

plugins/freeEnergy/platforms/cuda/CMakeLists.txt

@@ -14,29 +14,6 @@
 #   libOpenMMFreeEnergyCuda_static[_d].a
 #----------------------------------------------------
 
-# ----------------------------------------------------------------------------
-# logging
-
-SET(LOG TRUE)
-   
-IF(LOG)
-   SET(LOG_FILE "CMakeLog.txt" )
-   FILE( WRITE ${LOG_FILE} "In plugins/freeEnergy/platforms/cuda\n")
-ENDIF(LOG)
-
-IF(LOG)
-   MACRO(LOG_DIR LOG_FILE DIR_LIST )
-   
-      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
-      FOREACH(currentFile ${ARGN})
-         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
-      ENDFOREACH(currentFile)
-   
-   ENDMACRO(LOG_DIR) 
-ENDIF(LOG)
-
-# ----------------------------------------------------------------------------
-
 # Only run tests when cuda-enabled GPU is found
 SET(DO_TESTS FALSE)
 IF(NOT DEFINED CUDA_HAVE_GPU)
@@ -82,15 +59,6 @@ FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
                                      ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
 ENDFOREACH(subdir)
 
-## ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "OPENMM_SOURCE_SUBDIRS"              ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_FREE_ENERGY_SOURCE_SUBDIRS"  ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "API_FREE_ENERGY_INCLUDE_DIRS"       ${API_FREE_ENERGY_INCLUDE_DIRS} )
-   LOG_DIR( ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR"           ${CMAKE_CURRENT_SOURCE_DIR} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
 # We'll need both *relative* path names, starting with their API_FREE_ENERGY_INCLUDE_DIRS,
 # and absolute pathnames.
 SET(API_FREE_ENERGY_REL_INCLUDE_FILES)   # start these out empty
@@ -106,13 +74,6 @@ FOREACH(dir ${API_FREE_ENERGY_INCLUDE_DIRS})
     ENDFOREACH(pathname)
 ENDFOREACH(dir)
 
-## ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "API_FREE_ENERGY_REL_INCLUDE_FILES" ${API_FREE_ENERGY_REL_INCLUDE_FILES} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_DIR" ${OPENMM_DIR} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
 # collect up source files
 SET(SOURCE_FILES) # empty
 SET(SOURCE_INCLUDE_FILES)
@@ -122,20 +83,12 @@ FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
     FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h)
     SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
     SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
-    LOG_DIR( ${LOG_FILE} "Adding include dir: " ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include )
     INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/include)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src)
 INCLUDE_DIRECTORIES(${OPENMM_DIR}/platforms/cuda/src/kernels)
 
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR" ${CMAKE_CURRENT_SOURCE_DIR} )
-   FILE( APPEND ${LOG_FILE} "CMAKE_CURRENT_SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}\n" )
-   LOG_DIR( ${LOG_FILE} "SOURCE_FILES" ${SOURCE_FILES} )
-   LOG_DIR( ${LOG_FILE} "SOURCE_INCLUDE_FILES" ${SOURCE_INCLUDE_FILES} )
-ENDIF(LOG)
-
 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 # SET(FINDCUDA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cuda-cmake)

plugins/freeEnergy/platforms/cuda/sharedTarget/CMakeLists.txt

 #
 # Include CUDA related files.
 #
-# ----------------------------------------------------------------------------
-# logging
-
-SET(LOG TRUE)
-   
-IF(LOG)
-   SET(LOG_FILE "CMakeLog.txt" )
-   FILE( WRITE ${LOG_FILE} "In freeEnergy/platforms/cuda/sharedTarget Cmake\n")
-#  FILE( APPEND ${LOG_FILE} "BROOK_LIB_PATH=${BROOK_LIB_PATH}\n")
-ENDIF(LOG)
-
-IF(LOG)
-   MACRO(LOG_DIR LOG_FILE DIR_LIST )
-   
-      FILE( APPEND ${LOG_FILE} "\n${DIR_LIST}\n")
-      FOREACH(currentFile ${ARGN})
-         FILE( APPEND ${LOG_FILE} "   ${currentFile}\n" )
-      ENDFOREACH(currentFile)
-   
-   ENDMACRO(LOG_DIR) 
-ENDIF(LOG)
-
-# ----------------------------------------------------------------------------
 
 SET(OPENMM_BUILD_FREE_ENERGY_PATH ${CMAKE_SOURCE_DIR}/plugins/freeEnergy) 
 
-# ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "Pre OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "Pre OPENMM_FREE_ENERGY_SOURCE_SUBDIRS " ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "Pre SOURCE_FILES" ${SOURCE_FILES} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
 # message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
 # INCLUDE(${FINDCUDA_DIR}/FindCuda.cmake)
 # message("CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}")
@@ -46,20 +15,6 @@ FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
     CUDA_INCLUDE_DIRECTORIES(BEFORE ${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../${subdir}/include)
 ENDFOREACH(subdir)
 
-# ----------------------------------------------------------------------------
-IF(LOG)
-   LOG_DIR( ${LOG_FILE} "OPENMM_BUILD_FREE_ENERGY_PATH" ${OPENMM_BUILD_FREE_ENERGY_PATH} )
-   FILE( APPEND ${LOG_FILE} "OPENMM_BUILD_FREE_ENERGY_PATH=${OPENMM_BUILD_FREE_ENERGY_PATH}\n")
-   LOG_DIR( ${LOG_FILE} "OPENMM_SOURCE_SUBDIRS" ${OPENMM_SOURCE_SUBDIRS} )
-   LOG_DIR( ${LOG_FILE} "CMAKE_SOURCE_DIR" ${CMAKE_SOURCE_DIR} )
-   LOG_DIR( ${LOG_FILE} "CUDA_INCLUDE" ${CUDA_INCLUDE} )
-   LOG_DIR( ${LOG_FILE} "CUDA_TARGET_LINK" ${CUDA_TARGET_LINK} )
-   LOG_DIR( ${LOG_FILE} "SHARED_TARGET" ${SHARED_TARGET} )
-   LOG_DIR( ${LOG_FILE} "OPENMM_DIR" ${OPENMM_DIR} )
-   LOG_DIR( ${LOG_FILE} "SOURCE_FILES" ${SOURCE_FILES} )
-ENDIF(LOG)
-## ----------------------------------------------------------------------------
-
 # CUDA_INCLUDE_DIRECTORIES(BEFORE ${CMAKE_SOURCE_DIR}/jama/include)
 
 CUDA_INCLUDE_DIRECTORIES(${OPENMM_BUILD_FREE_ENERGY_PATH}/platforms/cuda/../src