ignore eclipse project file

Former-commit-id: 9950804b43b7bace07b7f70920dc4999813240da

.gitignore

@@ -1 +1,2 @@
 /build-linux64-server/
+/.project

Chombo/lib/mk/Make.lib

@@ -0,0 +1,17 @@
+# -*- Mode: Makefile;  -*-
+
+makefiles+=lib_src_$(lbase)
+
+usage:
+	@echo "This makefile supports targets:"
+	@echo "     all lib $(lbase) clean realclean usage"
+
+include $(CHOMBO_HOME)/mk/Make.defs
+
+# The `all-lib', `lib-only', `$(lbase)', `clean' and `realclean' targets are defined in `Make.rules'
+.PHONY: all lib usage
+
+all: all-lib
+lib: lib-only
+
+include $(CHOMBO_HOME)/mk/Make.rules

NFsim_v1.11/NFcode/bin/makefile

@@ -0,0 +1,81 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+-include ../makefile.init
+
+RM := rm -rf
+
+# All of the sources participating in the build are defined here
+-include sources.mk
+-include src/nauty24/subdir.mk
+-include src/NFutil/MTrand/subdir.mk
+-include src/NFutil/subdir.mk
+-include src/NFtest/transcription/subdir.mk
+-include src/NFtest/tlbr/subdir.mk
+-include src/NFtest/simple_system/subdir.mk
+-include src/NFtest/agentcell/cell/subdir.mk
+-include src/NFtest/agentcell/subdir.mk
+-include src/NFscheduler/subdir.mk
+-include src/NFreactions/transformations/subdir.mk
+-include src/NFreactions/reactions/subdir.mk
+-include src/NFreactions/reactantLists/subdir.mk
+-include src/NFreactions/mappings/subdir.mk
+-include src/NFreactions/subdir.mk
+-include src/NFoutput/subdir.mk
+-include src/NFinput/TinyXML/subdir.mk
+-include src/NFinput/subdir.mk
+-include src/NFfunction/muParser/subdir.mk
+-include src/NFfunction/subdir.mk
+-include src/NFcore/reactionSelector/subdir.mk
+-include src/NFcore/moleculeLists/subdir.mk
+-include src/NFcore/subdir.mk
+-include src/subdir.mk
+-include subdir.mk
+-include objects.mk
+
+ifneq ($(MAKECMDGOALS),clean)
+ifneq ($(strip $(C++_DEPS)),)
+-include $(C++_DEPS)
+endif
+ifneq ($(strip $(C_DEPS)),)
+-include $(C_DEPS)
+endif
+ifneq ($(strip $(CC_DEPS)),)
+-include $(CC_DEPS)
+endif
+ifneq ($(strip $(CPP_DEPS)),)
+-include $(CPP_DEPS)
+endif
+ifneq ($(strip $(CXX_DEPS)),)
+-include $(CXX_DEPS)
+endif
+ifneq ($(strip $(C_UPPER_DEPS)),)
+-include $(C_UPPER_DEPS)
+endif
+endif
+
+-include ../makefile.defs
+
+# Add inputs and outputs from these tool invocations to the build variables 
+
+# All Target
+all: NFsim
+
+# Tool invocations
+NFsim: $(OBJS) $(USER_OBJS)
+	@echo 'Building target: $@'
+	@echo 'Invoking: GCC C++ Linker'
+	g++  -o "NFsim" $(OBJS) $(USER_OBJS) $(LIBS)
+	@echo 'Finished building target: $@'
+	@echo ' '
+
+# Other Targets
+clean:
+	-$(RM) $(OBJS)$(C++_DEPS)$(C_DEPS)$(CC_DEPS)$(CPP_DEPS)$(EXECUTABLES)$(CXX_DEPS)$(C_UPPER_DEPS) NFsim
+	-@echo ' '
+
+.PHONY: all clean dependents
+.SECONDARY:
+
+-include ../makefile.targets

NFsim_v1.11/NFcode/bin/objects.mk

@@ -0,0 +1,8 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+USER_OBJS :=
+
+LIBS :=
+

NFsim_v1.11/NFcode/bin/sources.mk

@@ -0,0 +1,49 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+O_SRCS := 
+CPP_SRCS := 
+C_UPPER_SRCS := 
+C_SRCS := 
+S_UPPER_SRCS := 
+OBJ_SRCS := 
+ASM_SRCS := 
+CXX_SRCS := 
+C++_SRCS := 
+CC_SRCS := 
+OBJS := 
+C++_DEPS := 
+C_DEPS := 
+CC_DEPS := 
+CPP_DEPS := 
+EXECUTABLES := 
+CXX_DEPS := 
+C_UPPER_DEPS := 
+
+# Every subdirectory with source files must be described here
+SUBDIRS := \
+src/nauty24 \
+src/NFutil \
+src/NFutil/MTrand \
+src/NFtest/transcription \
+src/NFtest/tlbr \
+src/NFtest/simple_system \
+src/NFtest/agentcell/cell \
+src/NFtest/agentcell \
+src \
+src/NFscheduler \
+src/NFreactions/transformations \
+src/NFreactions/reactions \
+src/NFreactions/reactantLists \
+src/NFreactions/mappings \
+src/NFreactions \
+src/NFoutput \
+src/NFinput \
+src/NFinput/TinyXML \
+src/NFfunction/muParser \
+src/NFfunction \
+src/NFcore \
+src/NFcore/reactionSelector \
+src/NFcore/moleculeLists \
+

NFsim_v1.11/NFcode/bin/src/NFcore/moleculeLists/subdir.mk

@@ -0,0 +1,24 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFcore/moleculeLists/moleculeList.cpp 
+
+OBJS += \
+./src/NFcore/moleculeLists/moleculeList.o 
+
+CPP_DEPS += \
+./src/NFcore/moleculeLists/moleculeList.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFcore/moleculeLists/%.o: ../src/NFcore/moleculeLists/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+

NFsim_v1.11/NFcode/bin/src/NFcore/reactionSelector/subdir.mk

@@ -0,0 +1,27 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFcore/reactionSelector/directSelector.cpp \
+../src/NFcore/reactionSelector/logClassSelector.cpp 
+
+OBJS += \
+./src/NFcore/reactionSelector/directSelector.o \
+./src/NFcore/reactionSelector/logClassSelector.o 
+
+CPP_DEPS += \
+./src/NFcore/reactionSelector/directSelector.d \
+./src/NFcore/reactionSelector/logClassSelector.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFcore/reactionSelector/%.o: ../src/NFcore/reactionSelector/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+

NFsim_v1.11/NFcode/bin/src/NFcore/subdir.mk

@@ -0,0 +1,45 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFcore/complex.cpp \
+../src/NFcore/complexList.cpp \
+../src/NFcore/molecule.cpp \
+../src/NFcore/moleculeType.cpp \
+../src/NFcore/observable.cpp \
+../src/NFcore/reactionClass.cpp \
+../src/NFcore/system.cpp \
+../src/NFcore/templateMolecule.cpp 
+
+OBJS += \
+./src/NFcore/complex.o \
+./src/NFcore/complexList.o \
+./src/NFcore/molecule.o \
+./src/NFcore/moleculeType.o \
+./src/NFcore/observable.o \
+./src/NFcore/reactionClass.o \
+./src/NFcore/system.o \
+./src/NFcore/templateMolecule.o 
+
+CPP_DEPS += \
+./src/NFcore/complex.d \
+./src/NFcore/complexList.d \
+./src/NFcore/molecule.d \
+./src/NFcore/moleculeType.d \
+./src/NFcore/observable.d \
+./src/NFcore/reactionClass.d \
+./src/NFcore/system.d \
+./src/NFcore/templateMolecule.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFcore/%.o: ../src/NFcore/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+

NFsim_v1.11/NFcode/bin/src/NFfunction/muParser/subdir.mk

@@ -0,0 +1,45 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFfunction/muParser/muParser.cpp \
+../src/NFfunction/muParser/muParserBase.cpp \
+../src/NFfunction/muParser/muParserBytecode.cpp \
+../src/NFfunction/muParser/muParserCallback.cpp \
+../src/NFfunction/muParser/muParserComplex.cpp \
+../src/NFfunction/muParser/muParserError.cpp \
+../src/NFfunction/muParser/muParserInt.cpp \
+../src/NFfunction/muParser/muParserTokenReader.cpp 
+
+OBJS += \
+./src/NFfunction/muParser/muParser.o \
+./src/NFfunction/muParser/muParserBase.o \
+./src/NFfunction/muParser/muParserBytecode.o \
+./src/NFfunction/muParser/muParserCallback.o \
+./src/NFfunction/muParser/muParserComplex.o \
+./src/NFfunction/muParser/muParserError.o \
+./src/NFfunction/muParser/muParserInt.o \
+./src/NFfunction/muParser/muParserTokenReader.o 
+
+CPP_DEPS += \
+./src/NFfunction/muParser/muParser.d \
+./src/NFfunction/muParser/muParserBase.d \
+./src/NFfunction/muParser/muParserBytecode.d \
+./src/NFfunction/muParser/muParserCallback.d \
+./src/NFfunction/muParser/muParserComplex.d \
+./src/NFfunction/muParser/muParserError.d \
+./src/NFfunction/muParser/muParserInt.d \
+./src/NFfunction/muParser/muParserTokenReader.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFfunction/muParser/%.o: ../src/NFfunction/muParser/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+

NFsim_v1.11/NFcode/bin/src/NFfunction/subdir.mk

@@ -0,0 +1,33 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFfunction/compositeFunction.cpp \
+../src/NFfunction/funcParser.cpp \
+../src/NFfunction/function.cpp \
+../src/NFfunction/localFunction.cpp 
+
+OBJS += \
+./src/NFfunction/compositeFunction.o \
+./src/NFfunction/funcParser.o \
+./src/NFfunction/function.o \
+./src/NFfunction/localFunction.o 
+
+CPP_DEPS += \
+./src/NFfunction/compositeFunction.d \
+./src/NFfunction/funcParser.d \
+./src/NFfunction/function.d \
+./src/NFfunction/localFunction.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFfunction/%.o: ../src/NFfunction/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+

NFsim_v1.11/NFcode/bin/src/NFinput/TinyXML/subdir.mk

@@ -0,0 +1,33 @@
+################################################################################
+# Automatically-generated file. Do not edit!
+################################################################################
+
+# Add inputs and outputs from these tool invocations to the build variables 
+CPP_SRCS += \
+../src/NFinput/TinyXML/tinystr.cpp \
+../src/NFinput/TinyXML/tinyxml.cpp \
+../src/NFinput/TinyXML/tinyxmlerror.cpp \
+../src/NFinput/TinyXML/tinyxmlparser.cpp 
+
+OBJS += \
+./src/NFinput/TinyXML/tinystr.o \
+./src/NFinput/TinyXML/tinyxml.o \
+./src/NFinput/TinyXML/tinyxmlerror.o \
+./src/NFinput/TinyXML/tinyxmlparser.o 
+
+CPP_DEPS += \
+./src/NFinput/TinyXML/tinystr.d \
+./src/NFinput/TinyXML/tinyxml.d \
+./src/NFinput/TinyXML/tinyxmlerror.d \
+./src/NFinput/TinyXML/tinyxmlparser.d 
+
+
+# Each subdirectory must supply rules for building sources it contributes
+src/NFinput/TinyXML/%.o: ../src/NFinput/TinyXML/%.cpp
+	@echo 'Building file: $<'
+	@echo 'Invoking: GCC C++ Compiler'
+	g++ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o "$@" "$<"
+	@echo 'Finished building: $<'
+	@echo ' '
+
+