[Code scan] Document or build graph.pb generation in infer_water

[njzjz]

This issue comes from a Codex global scan of deepmodeling/deepmd-kit at commit 73de44b1f94471b2e3bdb6b11f57b34d7bc791bb.

Problem

The examples/infer_water README tells users to run CMake and make:

deepmd-kit/examples/infer_water/README.md

Lines 5 to 10 in 73de44b

	Build the project using
	```sh
	cmake -DCMAKE_PREFIX_PATH=$deepmd_root .
	make
	```

The CMake project builds the four inference binaries:

deepmd-kit/examples/infer_water/CMakeLists.txt

Lines 7 to 25 in 73de44b

	# C++ example
	add_executable(infer_water_cc infer_water.cpp)
	# link DeePMD-kit C++ API
	target_link_libraries(infer_water_cc PRIVATE DeePMD::deepmd_cc)
	# C example
	add_executable(infer_water_c infer_water.c)
	# link DeePMD-kit C API
	target_link_libraries(infer_water_c PRIVATE DeePMD::deepmd_c)
	# header-only example
	add_executable(infer_water_hpp infer_water_hpp.cpp)
	# link DeePMD-kit C API
	target_link_libraries(infer_water_hpp PRIVATE DeePMD::deepmd_c)
	# nlist
	add_executable(infer_water_nlist infer_water_nlist.cpp)
	# link DeePMD-kit C API
	target_link_libraries(infer_water_nlist PRIVATE DeePMD::deepmd_c)

Those binaries all open graph.pb from the current working directory:

deepmd-kit/examples/infer_water/infer_water.c

Lines 7 to 20 in 73de44b

	int main() {
	const char* model = "graph.pb";
	double coord[] = {1., 0., 0., 0., 0., 1.5, 1., 0., 3.};
	double cell[] = {10., 0., 0., 0., 10., 0., 0., 0., 10.};
	int atype[] = {1, 0, 1};
	// init C pointers with given memory
	double* e = malloc(sizeof(*e));
	double* f = malloc(sizeof(*f) * 9); // natoms * 3
	double* v = malloc(sizeof(*v) * 9);
	double* ae = malloc(sizeof(*ae) * 9); // natoms
	double* av = malloc(sizeof(*av) * 27); // natoms * 9
	// DP model
	DP_DeepPot* dp = DP_NewDeepPot(model);
	DP_DeepPotCompute(dp, 3, coord, atype, cell, e, f, v, ae, av);

deepmd-kit/examples/infer_water/infer_water.cpp

Lines 4 to 11 in 73de44b

	int main() {
	deepmd::DeepPot dp("graph.pb");
	std::vector<double> coord = {1., 0., 0., 0., 0., 1.5, 1., 0., 3.};
	std::vector<double> cell = {10., 0., 0., 0., 10., 0., 0., 0., 10.};
	std::vector<int> atype = {1, 0, 1};
	double e;
	std::vector<double> f, v;
	dp.compute(e, f, v, coord, atype, cell);

deepmd-kit/examples/infer_water/infer_water_hpp.cpp

Lines 6 to 13 in 73de44b

	int main() {
	deepmd::hpp::DeepPot dp("graph.pb");
	std::vector<double> coord = {1., 0., 0., 0., 0., 1.5, 1., 0., 3.};
	std::vector<double> cell = {10., 0., 0., 0., 10., 0., 0., 0., 10.};
	std::vector<int> atype = {1, 0, 1};
	double e;
	std::vector<double> f, v;
	dp.compute(e, f, v, coord, atype, cell);

deepmd-kit/examples/infer_water/infer_water_nlist.cpp

Lines 18 to 31 in 73de44b

	int main() {
	DeepPot dp("graph.pb");
	std::vector<double> coord = {1., 0., 0., 0., 0., 1.5, 1., 0., 3.};
	std::vector<double> cell = {10., 0., 0., 0., 10., 0., 0., 0., 10.};
	std::vector<int> atype = {1, 0, 1};
	// neighbor list
	std::vector<std::vector<int>> nlist_vec = {{1, 2}, {0, 2}, {0, 1}};
	double e;
	std::vector<double> f, v;
	std::vector<int> ilist(3), numneigh(3);
	std::vector<int*> firstneigh(3);
	InputNlist nlist(3, &ilist[0], &numneigh[0], &firstneigh[0]);
	convert_nlist(nlist, nlist_vec);
	dp.compute(e, f, v, coord, atype, cell, 0, nlist, 0);

graph.pb is ignored rather than checked in:

deepmd-kit/examples/infer_water/.gitignore

Line 10 in 73de44b

graph.pb

There is a convert_model.c helper that can create it, but the helper is not built by CMakeLists.txt and the README does not tell users to run it:

deepmd-kit/examples/infer_water/convert_model.c

Lines 4 to 6 in 73de44b

	int main() {
	DP_ConvertPbtxtToPb("../../source/tests/infer/deeppot.pbtxt", "graph.pb");
	return 0;

Impact

Following the documented build commands produces binaries that fail at runtime unless the user already knows how to create graph.pb. The hidden conversion helper also depends on a test fixture path, which makes the example less self-contained.

Suggested fix

Either document the required model-generation step explicitly, or wire convert_model.c into the CMake project as a helper target and have the README run it before the inference examples.