Split some large files (fs_nonlocal_tools.cpp, onsite_proj.cpp, to_wannier90_lcao.cpp, etc.) into smaller ones

AGENTS.md

@@ -34,6 +34,10 @@ rules. Read the complete governance document before making or reviewing changes:
   is required.
 - Report the exact verification performed. Do not claim completion without
   fresh test or check output.
+- For multi-step refactors (e.g., splitting a large `.cpp` into several
+  files), build and commit after each step rather than batching all changes
+  before verification. This keeps the blast radius small when a step
+  surfaces a missing include or instantiation error.
 - Prefer `std::vector` over raw `new`/`delete` for dynamic arrays; before
   converting class members, confirm no external code consumes them as raw
   pointers (e.g., `std::vector<bool>` has no `.data()`), and use
@@ -106,6 +110,8 @@ rules. Read the complete governance document before making or reviewing changes:
 python3 tools/03_code_analysis/agent_governance_check.py --staged
 python3 tools/03_code_analysis/agent_governance_check.py --base upstream/develop --head HEAD --format text
 pre-commit run abacus-agent-governance --all-files
+# Score changed C++ files for quality debt (pass line is 60):
+python3 tools/03_code_analysis/code_quality_score.py $(git diff --name-only upstream/develop...HEAD | grep -E '\.(cpp|h)$')
 ```
 
 The repository text files have been normalized to LF once. Day-to-day line

generate_build_info.sh

@@ -257,7 +257,8 @@ if [ "${USE_CUDA}" == "ON" ]; then
 fi
 # --- Final File Generation ---
 
-INPUT_FILE="source_io/build_info.h.in"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+INPUT_FILE="${SCRIPT_DIR}/source/source_io/build_info.h.in"
 
 # Use sed to replace all placeholders with detected values
 # Note the use of different delimiters (#) for paths to avoid conflicts with /

source/Makefile

@@ -6,6 +6,10 @@ OBJ_DIR = $(BUILD_DIR)/obj
 BIN_DIR = $(BUILD_DIR)/bin
 BUILD_INFO_DIR = $(BUILD_DIR)/source_io
 
+# The first rule in this file only generates build_info.h, so make would
+# stop after generating that header unless the default goal is set here.
+.DEFAULT_GOAL := abacus
+
 include $(ABACUS_ROOT)Makefile.vars
 
 #==========================
@@ -252,18 +256,25 @@ ${OBJ_DIR}/parse_args.o: $(ABACUS_ROOT)source_io/parse_args.cpp $(BUILD_INFO_DIR
 	@mkdir -p $(dir $@)
 	${CXX} ${OPTS} ${OPTS_MPI} -c ${HONG} $< -o $@
 
+# Explicit rule: source_cell/module_symmetry and source_estate/module_charge
+# both contain a symm_rho.cpp. VPATH resolves symm_rho.o to the source_cell
+# one (listed first), so the Symmetry_rho implementation needs an explicit
+# object name to be compiled from the correct source.
+${OBJ_DIR}/symm_rho_charge.o: $(ABACUS_ROOT)source_estate/module_charge/symm_rho.cpp
+	@mkdir -p $(dir $@)
+	${CXX} ${OPTS} ${OPTS_MPI} -c ${HONG} $< -o $@
+
 ###### END of ABACUS INFO PART ######
 
 #==========================
 # MAKING OPTIONS
 #==========================
 abacus:
-	@ if [ ! -d $(OBJ_DIR) ]; then mkdir $(OBJ_DIR); fi
-	@ if [ ! -d $(BIN_DIR) ]; then mkdir $(BIN_DIR); fi
-	@ $(MAKE) $(BIN_DIR)/${VERSION}.$(suffix)
+	@ mkdir -p $(OBJ_DIR) $(BIN_DIR)
+	@ $(MAKE) -f $(firstword $(MAKEFILE_LIST)) $(BIN_DIR)/${VERSION}.$(suffix)
 
 test:
-	@ $(MAKE) abacus
+	@ $(MAKE) -f $(firstword $(MAKEFILE_LIST)) abacus
 	@ cd $(ABACUS_ROOT)../tests/integrate/;sh Autotest.sh -a $(realpath $(BIN_DIR))/ABACUS.mpi -n $(TESTNP)
 
 pw $(BIN_DIR)/${VERSION}-PW.x:
@@ -280,7 +291,8 @@ $(BIN_DIR)/${VERSION}.$(suffix) : ${FP_OBJS} ${PDIAG_OBJS} ${HEADERS}
 #==========================
 # Note: The specific rule for parse_args.o above is more precise.
 # This generic rule will apply to all other .cpp files.
-${OBJ_DIR}/%.o:$(realpath $(BIN_DIR))%.cpp
+${OBJ_DIR}/%.o:%.cpp
+	@ mkdir -p $(dir $@)
 	${CXX} ${OPTS} ${OPTS_MPI} -c ${HONG} $< -o $@
 
 .PHONY:clean test