Makefile

# Makefile for ComChemKit
# Enhanced Safety Edition v0.000.1

# Directory structure
SRC_DIR = src
BUILD_DIR = build
TEST_DIR = tests

# Compiler settings
# Allow CXX override from environment, otherwise auto-detect
ifndef CXX
# Auto-detect compiler. Prefers Intel compilers (icpx, icpc, icc) over GCC (g++).
COMPILER_LIST := icpx icpc icc g++
CXX := $(firstword $(foreach c,$(COMPILER_LIST),$(if $(shell command -v $(c)),$(c))))
endif

# Fallback to a default if no compiler is found in PATH and print a warning.
ifeq ($(CXX),)
    $(warning "No supported compiler (icpx, icpc, icc, g++) found in PATH. Defaulting to g++.")
    CXX = g++
endif
$(info Using compiler: $(CXX))
CXXFLAGS = -std=c++17 -Wall -Wextra -O3 -pthread -I$(SRC_DIR)

# Add Intel-specific flags if using Intel compiler
ifneq ($(filter icpx icpc icc,$(CXX)),)
    CXXFLAGS += -fp-model=precise
endif
DEBUGFLAGS = -g -DDEBUG_BUILD -fsanitize=address -fno-omit-frame-pointer
LDFLAGS = -pthread

# Add Intel-specific linking flags after LDFLAGS definition
ifneq ($(filter icpx icpc icc,$(CXX)),)
    # Intel compilers often require explicit TBB linking for parallel algorithms
    # Add TBB library if available, with error handling
    LDFLAGS += -ltbb
	# Use -static-libstdc++ to avoid loading library
    #LDFLAGS += -ltbb -static-libstdc++ 

    # Note: If TBB is not available, the compilation will fail with a clear error
    # In such cases, users should install Intel TBB or use GCC instead
    $(info Intel compiler detected. Adding TBB library linking.)
    $(info If compilation fails with TBB errors, please install Intel TBB or use GCC.)
endif

# Platform detection
ifeq ($(OS),Windows_NT)
    UNAME_S := Windows
else
    UNAME_S := $(shell uname -s)
endif
ifeq ($(UNAME_S),Linux)
    LDFLAGS += -lrt -lstdc++fs
endif
ifeq ($(UNAME_S),Darwin)
    # macOS specific flags if needed
endif

# Source files
SOURCES = $(SRC_DIR)/main.cpp \
          $(SRC_DIR)/commands/signal_handler.cpp \
          $(SRC_DIR)/extraction/qc_extractor.cpp \
          $(SRC_DIR)/job_management/job_scheduler.cpp \
          $(SRC_DIR)/commands/command_system.cpp \
          $(SRC_DIR)/job_management/job_checker.cpp \
          $(SRC_DIR)/utilities/config_manager.cpp \
          $(SRC_DIR)/utilities/metadata.cpp \
          $(SRC_DIR)/high_level/high_level_energy.cpp \
          $(SRC_DIR)/extraction/coord_extractor.cpp \
          $(SRC_DIR)/input_gen/parameter_parser.cpp \
          $(SRC_DIR)/utilities/utils.cpp \
          $(SRC_DIR)/ui/interactive_mode.cpp \
          $(SRC_DIR)/input_gen/create_input.cpp \
          $(SRC_DIR)/ui/help_utils.cpp \
          $(SRC_DIR)/thermo/thermo.cpp \
          $(SRC_DIR)/thermo/calc.cpp \
          $(SRC_DIR)/thermo/loadfile.cpp \
          $(SRC_DIR)/thermo/util.cpp \
          $(SRC_DIR)/thermo/atommass.cpp \
          $(SRC_DIR)/thermo/symmetry.cpp \
          $(SRC_DIR)/thermo/help_utils.cpp \
          $(SRC_DIR)/commands/command_registry.cpp \
          $(SRC_DIR)/commands/extract_command.cpp \
          $(SRC_DIR)/commands/checker_command.cpp \
          $(SRC_DIR)/commands/high_level_command.cpp \
          $(SRC_DIR)/commands/extract_coords_command.cpp \
          $(SRC_DIR)/commands/create_input_command.cpp \
          $(SRC_DIR)/commands/thermo_command.cpp \
          $(SRC_DIR)/commands/ivcoord_command.cpp \
          $(SRC_DIR)/ivcoord/gaussian_ivcoord_parser.cpp \
          $(SRC_DIR)/ivcoord/ivcoord_runner.cpp

HEADERS = $(SRC_DIR)/commands/signal_handler.h \
          $(SRC_DIR)/extraction/qc_extractor.h \
          $(SRC_DIR)/job_management/job_scheduler.h \
          $(SRC_DIR)/commands/command_system.h \
          $(SRC_DIR)/job_management/job_checker.h \
          $(SRC_DIR)/utilities/config_manager.h \
          $(SRC_DIR)/utilities/metadata.h \
          $(SRC_DIR)/high_level/high_level_energy.h \
          $(SRC_DIR)/extraction/coord_extractor.h \
          $(SRC_DIR)/input_gen/parameter_parser.h \
          $(SRC_DIR)/utilities/utils.h \
          $(SRC_DIR)/utilities/version.h \
          $(SRC_DIR)/ui/interactive_mode.h \
          $(SRC_DIR)/input_gen/create_input.h \
          $(SRC_DIR)/ui/help_utils.h \
          $(SRC_DIR)/thermo/thermo.h \
          $(SRC_DIR)/thermo/calc.h \
          $(SRC_DIR)/thermo/loadfile.h \
          $(SRC_DIR)/thermo/util.h \
          $(SRC_DIR)/thermo/atommass.h \
          $(SRC_DIR)/thermo/symmetry.h \
          $(SRC_DIR)/thermo/chemsys.h \
          $(SRC_DIR)/thermo/help_utils.h \
          $(SRC_DIR)/commands/icommand.h \
          $(SRC_DIR)/commands/command_registry.h \
          $(SRC_DIR)/commands/extract_command.h \
          $(SRC_DIR)/commands/checker_command.h \
          $(SRC_DIR)/commands/high_level_command.h \
          $(SRC_DIR)/commands/extract_coords_command.h \
          $(SRC_DIR)/commands/create_input_command.h \
          $(SRC_DIR)/commands/thermo_command.h \
          $(SRC_DIR)/commands/ivcoord_command.h \
          $(SRC_DIR)/ivcoord/ivcoord_data.h \
          $(SRC_DIR)/ivcoord/ivcoord_parser_base.h \
          $(SRC_DIR)/ivcoord/gaussian_ivcoord_parser.h \
          $(SRC_DIR)/ivcoord/ivcoord_runner.h

OBJECTS = $(SOURCES:%.cpp=$(BUILD_DIR)/%.o)
TARGET = $(BUILD_DIR)/bin/cck

# Ensure build directory structure exists (cross-platform fallback using CMake)
MKDIR_P = cmake -E make_directory $1

$(shell $(call MKDIR_P,$(BUILD_DIR)/bin))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/extraction))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/high_level))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/input_gen))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/job_management))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/ui))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/utilities))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/thermo))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/commands))
$(shell $(call MKDIR_P,$(BUILD_DIR)/$(SRC_DIR)/ivcoord))

# Default target
all: $(TARGET)

# Build the main executable
$(TARGET): $(OBJECTS)
	$(CXX) $(OBJECTS) -o $@ $(LDFLAGS)

# Compile source files to object files
$(BUILD_DIR)/%.o: %.cpp $(HEADERS)
	@$(call MKDIR_P,$(dir $@))
	$(CXX) $(CXXFLAGS) -c $< -o $@

# Debug build with additional safety checks
debug: CXXFLAGS += $(DEBUGFLAGS)
debug: LDFLAGS += -fsanitize=address
debug: clean $(TARGET)

# Release build with optimizations
release: CXXFLAGS += -O3 -DNDEBUG -march=native
release: clean $(TARGET)

# Cluster-safe build (conservative optimizations)
cluster: CXXFLAGS += -O2 -DCLUSTER_BUILD
cluster: clean $(TARGET)

# Clean build artifacts
clean:
	cmake -E rm -rf $(BUILD_DIR) $(TARGET)

# Install to system (requires sudo)
install: $(TARGET)
	mkdir -p /usr/local/bin
	cp $(TARGET) /usr/local/bin/
	chmod +x /usr/local/bin/$(TARGET)

# Install to user's local bin
install-user: $(TARGET)
	mkdir -p ~/bin
	cp $(TARGET) ~/bin/
	chmod +x ~/bin/$(TARGET)

# Create a test build with maximum warnings
test-build: CXXFLAGS += -Wpedantic -Wcast-align -Wcast-qual -Wctor-dtor-privacy \
                        -Wdisabled-optimization -Wformat=2 -Winit-self -Wlogical-op \
                        -Wmissing-declarations -Wmissing-include-dirs -Wnoexcept \
                        -Wold-style-cast -Woverloaded-virtual -Wredundant-decls \
                        -Wshadow -Wsign-conversion -Wsign-promo -Wstrict-null-sentinel \
                        -Wstrict-overflow=5 -Wswitch-default -Wundef
test-build: clean $(TARGET)

# Quick test with sample files
test: $(TARGET)
	@echo "Testing ComChemKit..."
	@if [ -f $(TEST_DIR)/data/test-1.log ] && [ -f $(TEST_DIR)/data/test-2.log ]; then \
		./$(TARGET) --resource-info; \
		./$(TARGET) -q -f csv; \
		echo "Test completed. Check output files."; \
	else \
		echo "Test files not found. Please ensure test files exist in $(TEST_DIR)/data/"; \
	fi

# Check for memory leaks (requires valgrind)
memcheck: debug
	@if command -v valgrind >/dev/null 2>&1; then \
		valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes \
		./$(TARGET) -q; \
	else \
		echo "Valgrind not found. Install valgrind for memory checking."; \
	fi

# Create distribution package
dist: clean
	@mkdir -p gaussian-extractor-$(shell date +%Y%m%d)
	@cp -r $(SRC_DIR) $(TEST_DIR) docs scripts CMakeLists.txt README.MD .clang-format gaussian-extractor-$(shell date +%Y%m%d)/
	@tar czf gaussian-extractor-$(shell date +%Y%m%d).tar.gz gaussian-extractor-$(shell date +%Y%m%d)/
	@rm -rf gaussian-extractor-$(shell date +%Y%m%d)/
	@echo "Distribution package created: gaussian-extractor-$(shell date +%Y%m%d).tar.gz"

# Help target
help:
	@echo "ComChemKit Makefile - Available targets:"
	@echo ""
	@echo "  all          - Build the program (default)"
	@echo "  debug        - Build with debug symbols and AddressSanitizer"
	@echo "  release      - Build optimized release version"
	@echo "  cluster      - Build cluster-safe version"
	@echo "  test-build   - Build with maximum compiler warnings"
	@echo "  clean        - Remove build artifacts"
	@echo "  install      - Install to /usr/local/bin (requires sudo)"
	@echo "  install-user - Install to ~/bin"
	@echo "  test         - Run basic functionality test"
	@echo "  memcheck     - Run with valgrind memory checker"
	@echo "  dist         - Create distribution package"
	@echo "  help         - Show this help message"
	@echo ""
	@echo "Compiler Support:"
	@echo "  Auto-detects: icpx, icpc, icc, g++ (in order of preference)"
	@echo "  Force GCC:    make CXX=g++"
	@echo "  Intel issues: Requires TBB library. If compilation fails with"
	@echo "                'execution' or TBB errors, use: make CXX=g++"
	@echo ""
	@echo "Version Management:"
	@echo "  scripts/update_version.sh <version>  - Update version across all files"
	@echo "  ./cck --version     - Check current version"
	@echo ""
	@echo "Usage examples:"
	@echo "  make                    # Build with default settings"
	@echo "  make CXX=g++            # Force GCC compilation"
	@echo "  make debug              # Build debug version"
	@echo "  make cluster            # Build for cluster deployment"
	@echo "  make clean install-user # Clean build and install to user bin"

# Declare phony targets
.PHONY: all debug release cluster clean install install-user test-build test memcheck dist help