Committed updated Makefile and doxyfile. (These don't need to be in here.)

examples/Makefile

-# ----------------------------------------------------------------------
-# Makefile for OpenMM Preview Release 4 workshop "hello world" examples.
-# August 18, 2009
-# See https://simtk.org/home/openmm.
-# ----------------------------------------------------------------------
-# This assumes you have gcc compilers for whatever language you are
-# using: g++ for C++ and C, gfortran for Fortran 95.
-# 
-# For the C and Fortran examples, we're depending on your version of
-# OpenMM to have been built with the automatically-generated API
-# wrappers.
-#
-# This has had only minimal testing, although it has been known to
-# work. It is likely to work fine for C and C++. For Fortran, you
-# may need to add some of the C/C++ libraries: 
-#    -lc -lm -lstdc++ (or -lstdc++.6) -lgcc -lgcc_s
-# but this wasn't required for these examples on Centos 5.2 using
-# gcc 4.1.2.
-
-# Check whether this is the right capitalization for your install directory.
-OpenMM_INSTALL_DIR=/usr/local/openmm
-CFLAGS = -g 
-FFLAGS = -g -ffree-line-length-none
-
-# Extra libraries required when gfortran links with a C++ module.
-# If this doesn't work, look in /usr/lib to
-# see what versions of libstdc++.so you have and try different
-# versions.
-FCPPLIBS = -lstdc++
-
-LIB_DIR=$(OpenMM_INSTALL_DIR)/lib
-INCLUDE_DIR=$(OpenMM_INSTALL_DIR)/include
-LIBS= -lOpenMM
-
-ALL_CPP_EXAMPLES = HelloArgon HelloSodiumChloride HelloEthane HelloWaterBox
-ALL_C_EXAMPLES   = HelloArgonInC HelloSodiumChlorideInC
-ALL_F95_EXAMPLES = HelloArgonInFortran HelloSodiumChlorideInFortran
-
-ALL_PROGS = $(ALL_CPP_EXAMPLES) $(ALL_C_EXAMPLES) $(ALL_F95_EXAMPLES)
-
-default: HelloArgon
-
-all : $(ALL_PROGS)
-
-# Treat all .cpp source files the same way.
-.cpp : 
-	g++ $(CFLAGS) -I$(INCLUDE_DIR) $< -L$(LIB_DIR) $(LIBS) -o $*
-
-HelloArgonInC: HelloArgonInC.c 
-	g++ $(CFLAGS) -I$(INCLUDE_DIR) HelloArgonInC.c \
-        -L$(LIB_DIR) $(LIBS) -o HelloArgonInC
-
-HelloSodiumChlorideInC: HelloSodiumChlorideInC.c 
-	g++ $(CFLAGS) -I$(INCLUDE_DIR) HelloSodiumChlorideInC.c \
-        -L$(LIB_DIR) $(LIBS) -o HelloSodiumChlorideInC
-
-HelloArgonInFortran: HelloArgonInFortran.f90 openmm.mod 
-	gfortran $(FFLAGS) HelloArgonInFortran.f90 \
-	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloArgonInFortran
-
-HelloSodiumChlorideInFortran: HelloSodiumChlorideInFortran.f90 openmm.mod 
-	gfortran $(FFLAGS) HelloSodiumChlorideInFortran.f90 \
-	    -I$(INCLUDE_DIR) -L$(LIB_DIR) $(LIBS) $(FCPPLIBS) -o HelloSodiumChlorideInFortran
-
-
-# Build Fortran 95 Module file
-openmm.mod:
-	gfortran -c $(FFLAGS) $(INCLUDE_DIR)/OpenMMFortranModule.f90
-
-clean : 
-	rm $(ALL_PROGS) *.o *.mod *.obj *.exe
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /opt/local/bin/cmake
+
+# The command to remove a file.
+RM = /opt/local/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /opt/local/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /Users/choderaj/code/openmm/openmm.jchodera
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /Users/choderaj/code/openmm/openmm.jchodera
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+	/opt/local/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+.PHONY : edit_cache/fast
+
+# Special rule for the target install
+install: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/opt/local/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/opt/local/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/opt/local/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
+
+# Special rule for the target install/local
+install/local/fast: install/local
+.PHONY : install/local/fast
+
+# Special rule for the target list_install_components
+list_install_components:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+.PHONY : list_install_components/fast
+
+# Special rule for the target rebuild_cache
+rebuild_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
+	/opt/local/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : rebuild_cache
+
+# Special rule for the target rebuild_cache
+rebuild_cache/fast: rebuild_cache
+.PHONY : rebuild_cache/fast
+
+# Special rule for the target test
+test:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running tests..."
+	/opt/local/bin/ctest --force-new-ctest-process $(ARGS)
+.PHONY : test
+
+# Special rule for the target test
+test/fast: test
+.PHONY : test/fast
+
+# The main all target
+all: cmake_check_build_system
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(CMAKE_COMMAND) -E cmake_progress_start /Users/choderaj/code/openmm/openmm.jchodera/CMakeFiles /Users/choderaj/code/openmm/openmm.jchodera/examples/CMakeFiles/progress.marks
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/all
+	$(CMAKE_COMMAND) -E cmake_progress_start /Users/choderaj/code/openmm/openmm.jchodera/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/clean
+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
+
+# Convenience name for target.
+examples/CMakeFiles/HelloArgon.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloArgon.dir/rule
+.PHONY : examples/CMakeFiles/HelloArgon.dir/rule
+
+# Convenience name for target.
+HelloArgon: examples/CMakeFiles/HelloArgon.dir/rule
+.PHONY : HelloArgon
+
+# fast build rule for target.
+HelloArgon/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgon.dir/build.make examples/CMakeFiles/HelloArgon.dir/build
+.PHONY : HelloArgon/fast
+
+# Convenience name for target.
+examples/CMakeFiles/HelloArgonInC.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloArgonInC.dir/rule
+.PHONY : examples/CMakeFiles/HelloArgonInC.dir/rule
+
+# Convenience name for target.
+HelloArgonInC: examples/CMakeFiles/HelloArgonInC.dir/rule
+.PHONY : HelloArgonInC
+
+# fast build rule for target.
+HelloArgonInC/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/build
+.PHONY : HelloArgonInC/fast
+
+# Convenience name for target.
+examples/CMakeFiles/HelloEthane.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloEthane.dir/rule
+.PHONY : examples/CMakeFiles/HelloEthane.dir/rule
+
+# Convenience name for target.
+HelloEthane: examples/CMakeFiles/HelloEthane.dir/rule
+.PHONY : HelloEthane
+
+# fast build rule for target.
+HelloEthane/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloEthane.dir/build.make examples/CMakeFiles/HelloEthane.dir/build
+.PHONY : HelloEthane/fast
+
+# Convenience name for target.
+examples/CMakeFiles/HelloSodiumChloride.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloSodiumChloride.dir/rule
+.PHONY : examples/CMakeFiles/HelloSodiumChloride.dir/rule
+
+# Convenience name for target.
+HelloSodiumChloride: examples/CMakeFiles/HelloSodiumChloride.dir/rule
+.PHONY : HelloSodiumChloride
+
+# fast build rule for target.
+HelloSodiumChloride/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChloride.dir/build.make examples/CMakeFiles/HelloSodiumChloride.dir/build
+.PHONY : HelloSodiumChloride/fast
+
+# Convenience name for target.
+examples/CMakeFiles/HelloSodiumChlorideInC.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloSodiumChlorideInC.dir/rule
+.PHONY : examples/CMakeFiles/HelloSodiumChlorideInC.dir/rule
+
+# Convenience name for target.
+HelloSodiumChlorideInC: examples/CMakeFiles/HelloSodiumChlorideInC.dir/rule
+.PHONY : HelloSodiumChlorideInC
+
+# fast build rule for target.
+HelloSodiumChlorideInC/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/build
+.PHONY : HelloSodiumChlorideInC/fast
+
+# Convenience name for target.
+examples/CMakeFiles/HelloWaterBox.dir/rule:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f CMakeFiles/Makefile2 examples/CMakeFiles/HelloWaterBox.dir/rule
+.PHONY : examples/CMakeFiles/HelloWaterBox.dir/rule
+
+# Convenience name for target.
+HelloWaterBox: examples/CMakeFiles/HelloWaterBox.dir/rule
+.PHONY : HelloWaterBox
+
+# fast build rule for target.
+HelloWaterBox/fast:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloWaterBox.dir/build.make examples/CMakeFiles/HelloWaterBox.dir/build
+.PHONY : HelloWaterBox/fast
+
+Empty.o: Empty.cpp.o
+.PHONY : Empty.o
+
+# target to build an object file
+Empty.cpp.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/Empty.cpp.o
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/Empty.cpp.o
+.PHONY : Empty.cpp.o
+
+Empty.i: Empty.cpp.i
+.PHONY : Empty.i
+
+# target to preprocess a source file
+Empty.cpp.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/Empty.cpp.i
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/Empty.cpp.i
+.PHONY : Empty.cpp.i
+
+Empty.s: Empty.cpp.s
+.PHONY : Empty.s
+
+# target to generate assembly for a file
+Empty.cpp.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/Empty.cpp.s
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/Empty.cpp.s
+.PHONY : Empty.cpp.s
+
+HelloArgon.o: HelloArgon.cpp.o
+.PHONY : HelloArgon.o
+
+# target to build an object file
+HelloArgon.cpp.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgon.dir/build.make examples/CMakeFiles/HelloArgon.dir/HelloArgon.cpp.o
+.PHONY : HelloArgon.cpp.o
+
+HelloArgon.i: HelloArgon.cpp.i
+.PHONY : HelloArgon.i
+
+# target to preprocess a source file
+HelloArgon.cpp.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgon.dir/build.make examples/CMakeFiles/HelloArgon.dir/HelloArgon.cpp.i
+.PHONY : HelloArgon.cpp.i
+
+HelloArgon.s: HelloArgon.cpp.s
+.PHONY : HelloArgon.s
+
+# target to generate assembly for a file
+HelloArgon.cpp.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgon.dir/build.make examples/CMakeFiles/HelloArgon.dir/HelloArgon.cpp.s
+.PHONY : HelloArgon.cpp.s
+
+HelloArgonInC.o: HelloArgonInC.c.o
+.PHONY : HelloArgonInC.o
+
+# target to build an object file
+HelloArgonInC.c.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/HelloArgonInC.c.o
+.PHONY : HelloArgonInC.c.o
+
+HelloArgonInC.i: HelloArgonInC.c.i
+.PHONY : HelloArgonInC.i
+
+# target to preprocess a source file
+HelloArgonInC.c.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/HelloArgonInC.c.i
+.PHONY : HelloArgonInC.c.i
+
+HelloArgonInC.s: HelloArgonInC.c.s
+.PHONY : HelloArgonInC.s
+
+# target to generate assembly for a file
+HelloArgonInC.c.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloArgonInC.dir/build.make examples/CMakeFiles/HelloArgonInC.dir/HelloArgonInC.c.s
+.PHONY : HelloArgonInC.c.s
+
+HelloEthane.o: HelloEthane.cpp.o
+.PHONY : HelloEthane.o
+
+# target to build an object file
+HelloEthane.cpp.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloEthane.dir/build.make examples/CMakeFiles/HelloEthane.dir/HelloEthane.cpp.o
+.PHONY : HelloEthane.cpp.o
+
+HelloEthane.i: HelloEthane.cpp.i
+.PHONY : HelloEthane.i
+
+# target to preprocess a source file
+HelloEthane.cpp.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloEthane.dir/build.make examples/CMakeFiles/HelloEthane.dir/HelloEthane.cpp.i
+.PHONY : HelloEthane.cpp.i
+
+HelloEthane.s: HelloEthane.cpp.s
+.PHONY : HelloEthane.s
+
+# target to generate assembly for a file
+HelloEthane.cpp.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloEthane.dir/build.make examples/CMakeFiles/HelloEthane.dir/HelloEthane.cpp.s
+.PHONY : HelloEthane.cpp.s
+
+HelloSodiumChloride.o: HelloSodiumChloride.cpp.o
+.PHONY : HelloSodiumChloride.o
+
+# target to build an object file
+HelloSodiumChloride.cpp.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChloride.dir/build.make examples/CMakeFiles/HelloSodiumChloride.dir/HelloSodiumChloride.cpp.o
+.PHONY : HelloSodiumChloride.cpp.o
+
+HelloSodiumChloride.i: HelloSodiumChloride.cpp.i
+.PHONY : HelloSodiumChloride.i
+
+# target to preprocess a source file
+HelloSodiumChloride.cpp.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChloride.dir/build.make examples/CMakeFiles/HelloSodiumChloride.dir/HelloSodiumChloride.cpp.i
+.PHONY : HelloSodiumChloride.cpp.i
+
+HelloSodiumChloride.s: HelloSodiumChloride.cpp.s
+.PHONY : HelloSodiumChloride.s
+
+# target to generate assembly for a file
+HelloSodiumChloride.cpp.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChloride.dir/build.make examples/CMakeFiles/HelloSodiumChloride.dir/HelloSodiumChloride.cpp.s
+.PHONY : HelloSodiumChloride.cpp.s
+
+HelloSodiumChlorideInC.o: HelloSodiumChlorideInC.c.o
+.PHONY : HelloSodiumChlorideInC.o
+
+# target to build an object file
+HelloSodiumChlorideInC.c.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/HelloSodiumChlorideInC.c.o
+.PHONY : HelloSodiumChlorideInC.c.o
+
+HelloSodiumChlorideInC.i: HelloSodiumChlorideInC.c.i
+.PHONY : HelloSodiumChlorideInC.i
+
+# target to preprocess a source file
+HelloSodiumChlorideInC.c.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/HelloSodiumChlorideInC.c.i
+.PHONY : HelloSodiumChlorideInC.c.i
+
+HelloSodiumChlorideInC.s: HelloSodiumChlorideInC.c.s
+.PHONY : HelloSodiumChlorideInC.s
+
+# target to generate assembly for a file
+HelloSodiumChlorideInC.c.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloSodiumChlorideInC.dir/build.make examples/CMakeFiles/HelloSodiumChlorideInC.dir/HelloSodiumChlorideInC.c.s
+.PHONY : HelloSodiumChlorideInC.c.s
+
+HelloWaterBox.o: HelloWaterBox.cpp.o
+.PHONY : HelloWaterBox.o
+
+# target to build an object file
+HelloWaterBox.cpp.o:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloWaterBox.dir/build.make examples/CMakeFiles/HelloWaterBox.dir/HelloWaterBox.cpp.o
+.PHONY : HelloWaterBox.cpp.o
+
+HelloWaterBox.i: HelloWaterBox.cpp.i
+.PHONY : HelloWaterBox.i
+
+# target to preprocess a source file
+HelloWaterBox.cpp.i:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloWaterBox.dir/build.make examples/CMakeFiles/HelloWaterBox.dir/HelloWaterBox.cpp.i
+.PHONY : HelloWaterBox.cpp.i
+
+HelloWaterBox.s: HelloWaterBox.cpp.s
+.PHONY : HelloWaterBox.s
+
+# target to generate assembly for a file
+HelloWaterBox.cpp.s:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(MAKE) -f examples/CMakeFiles/HelloWaterBox.dir/build.make examples/CMakeFiles/HelloWaterBox.dir/HelloWaterBox.cpp.s
+.PHONY : HelloWaterBox.cpp.s
+
+# Help Target
+help:
+	@echo "The following are some of the valid targets for this Makefile:"
+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... HelloArgon"
+	@echo "... HelloArgonInC"
+	@echo "... HelloEthane"
+	@echo "... HelloSodiumChloride"
+	@echo "... HelloSodiumChlorideInC"
+	@echo "... HelloWaterBox"
+	@echo "... edit_cache"
+	@echo "... install"
+	@echo "... install/local"
+	@echo "... list_install_components"
+	@echo "... rebuild_cache"
+	@echo "... test"
+	@echo "... Empty.o"
+	@echo "... Empty.i"
+	@echo "... Empty.s"
+	@echo "... HelloArgon.o"
+	@echo "... HelloArgon.i"
+	@echo "... HelloArgon.s"
+	@echo "... HelloArgonInC.o"
+	@echo "... HelloArgonInC.i"
+	@echo "... HelloArgonInC.s"
+	@echo "... HelloEthane.o"
+	@echo "... HelloEthane.i"
+	@echo "... HelloEthane.s"
+	@echo "... HelloSodiumChloride.o"
+	@echo "... HelloSodiumChloride.i"
+	@echo "... HelloSodiumChloride.s"
+	@echo "... HelloSodiumChlorideInC.o"
+	@echo "... HelloSodiumChlorideInC.i"
+	@echo "... HelloSodiumChlorideInC.s"
+	@echo "... HelloWaterBox.o"
+	@echo "... HelloWaterBox.i"
+	@echo "... HelloWaterBox.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+	cd /Users/choderaj/code/openmm/openmm.jchodera && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
 

wrappers/python/src/swig_doxygen/doxygen/Doxyfile

@@ -517,7 +517,7 @@ QUIET                  = NO
 # generated by doxygen. Possible values are YES and NO. If left blank 
 # NO is used.
 
-WARNINGS               = YES
+WARNINGS               = NO
 
 # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
 # for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
@@ -530,7 +530,7 @@ WARN_IF_UNDOCUMENTED   = NO
 # parameters in a documented function, or documenting parameters that 
 # don't exist or using markup commands wrongly.
 
-WARN_IF_DOC_ERROR      = YES
+WARN_IF_DOC_ERROR      = NO
 
 # This WARN_NO_PARAMDOC option can be abled to get warnings for 
 # functions that are documented, but have no documentation for their parameters 
@@ -564,8 +564,14 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = "$(OPENMM_INCLUDE_PATH)/OpenMM.h" \
-                         "$(OPENMM_INCLUDE_PATH)/openmm"
+INPUT                  = "/Users/choderaj/code/openmm/openmm.jchodera/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/olla/include/openmm/Platform.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationNode.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationProxy.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/XmlSerializer.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/amoeba/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/rpmd/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/drude/openmmapi"
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
@@ -594,7 +600,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = 
+EXCLUDE                = *Impl.h
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -608,11 +614,15 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories 
 # for example use the pattern */test/*
 
-#EXCLUDE_PATTERNS       = */tests/* \
-#                         */src/* \
-#                         */.svn/*
 EXCLUDE_PATTERNS       = */tests/* \
-                         */.svn/*
+                         */openmmapi/src/* \
+                         */internal/* \
+                         */.svn/* \
+                         *amoebaKernels.h \
+                         *DrudeKernels.h \
+                         *RpmdKernels.h \
+                         *OpenMMFortranModule.f90 \
+                         *OpenMMCWrapper.h
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
 # (namespaces, classes, functions, etc.) that should be excluded from the