rebuild the project folders; replace mace-bench with the latest project

.gitmodules

@@ -2,3 +2,7 @@
 	path = mace-bench
 	url = ssh://git@10.208.16.64:2222/huafeng/mace-bench-hygon.git
 	branch = hygon
+[submodule "mace"]
+	path = mace
+	url = ssh://git@10.208.16.64:2222/huafeng/MACE.git
+	branch = fasteq-mace-bench

mace @ eb85199d

+Subproject commit eb85199d3b279bd5b4bb64bf9db06a8a9ff4edd9

pyproject.toml

@@ -3,11 +3,34 @@ name = "bomlip-csp"
 version = "0.1.0"
 description = "Add your description here"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.10, <3.11"
 dependencies = [
+    "ase==3.23.0",
     "networkx==3.2.1",
     "numpy==1.26.4",
+    "pyyaml>=6.0.3",
     "rdkit-pypi>=2022.9.5",
     "scipy==1.14.1",
+    "setuptools>=82.0.1",
+    "torch",
+    "torch-geometric>=2.7.0",
+    "torch-scatter==2.1.2",
     "tqdm==4.67.1",
+    "mace-torch",
+    "joblib>=1.5.3",
 ]
+
+[tool.uv.sources]
+torch = { path = "../whl/torch-2.5.1+das.opt1.dtk25042-cp310-cp310-manylinux_2_28_x86_64.whl" }
+mace-torch = { path = "./mace", editable = true } 
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["basic_function", "mace-bench/src/batchopt"]
+
+[tool.uv.extra-build-dependencies]
+torch-scatter = ["torch"]
+

main.py → scripts/search_gen.py

+from pathlib import Path; import sys; sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
 from basic_function import format_parser
 from basic_function import packaged_function
 from basic_function import conformer_search

search_gen_proc.sh → scripts/sh_search_gen.sh

@@ -8,6 +8,7 @@
 
 # --- Determine config file path (default: config.sh in the same directory) ---
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+PROJECT_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
 CONFIG_FILE="${1:-${SCRIPT_DIR}/config.sh}"
 
 if [ ! -f "${CONFIG_FILE}" ]; then
@@ -28,8 +29,7 @@ if [ -z "${SMILES}" ]; then
 fi
 
 # --- Set up directory ---
-TOP_DIR="${SCRIPT_DIR}"
-TAR_DIR="${TOP_DIR}/${OUTPUT_DIR}"
+TAR_DIR="${PROJECT_DIR}/${OUTPUT_DIR}"
 
 mkdir -p "${TAR_DIR}"
 cd "${TAR_DIR}" || { echo "Error: Cannot access directory ${TAR_DIR}"; exit 1; }
@@ -50,7 +50,7 @@ echo " Max workers:          ${MAX_WORKERS}"
 echo "=========================================="
 
 # --- Run the pipeline ---
-python "${TOP_DIR}/main.py" \
+python "${SCRIPT_DIR}/search_gen.py" \
     --path "${TAR_DIR}" \
     --smiles "${SMILES}" \
     --molecule_num_in_cell ${MOLECULE_NUM_IN_CELL} \