move submodules into 3rdparty except mace-bench, rename mace-bench to...

move submodules into 3rdparty except mace-bench, rename mace-bench to batchASE, add example folder as shell example

.gitignore

@@ -261,3 +261,4 @@ config/secrets.*
 # Project specific 
 # =============================================================================
 csp_results/
+run/
\ No newline at end of file

.gitmodules

-[submodule "mace-bench"]
-	path = mace-bench
+[submodule "batchASE"]
+	path = batchASE
 	url = ssh://git@10.208.16.64:2222/wangleping/mace-bench-hygon.git
 	branch = hygon
 [submodule "mace"]

README.md

@@ -10,7 +10,7 @@ unbiased structure prediction across the full density range
 git clone https://github.com/pic-ai-robotic-chemistry/BOMLIP-CSP.git --recursive
 conda create -n BOMLIP_CSP python=3.10 -y
 conda activate BOMLIP_CSP
-cd BOMLIP-CSP/mace-bench
+cd BOMLIP-CSP/batchASE
 # using chmod -R 755 in your BOMLIP-CSP folder if you do not have exection permission
 ./reproduce/init_mace.sh
 source util/env.sh
@@ -61,10 +61,10 @@ Conformer search and structure generation could also be done in python script wi
 ### structure optimization
 Structure optimization is done by a seperate command
 ```sh
-python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" ...
+python "${TOP_DIR}/batchASE/scripts/opt_batch.py" ...
 ```
 
-Explanations for all arguments are provided in main.py and mace-bench/scripts/opt_batch.py.
+Explanations for all arguments are provided in main.py and batchASE/scripts/opt_batch.py.
 
 
 ### If you want to configure the 7net environment.
@@ -72,14 +72,14 @@ Explanations for all arguments are provided in main.py and mace-bench/scripts/op
 ```sh
 #!/bin/bash
 conda create -n 7net-cueq python=3.10 -y && conda activate 7net-cueq
-cd BOMLIP-CSP/mace-bench
+cd BOMLIP-CSP/batchASE
 ./reproduce/init_7net.sh && source util/env.sh
 ```
 
 The optimization command for 7net is given in csp.sh
 ```sh
 # Use a fixed batch size for structural optimization
-python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
+python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
     --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \
     --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
     --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \

scripts/csp.sh → example/csp.sh

@@ -21,7 +21,7 @@ python "${TOP_DIR}/main.py" --path ${TAR_DIR} --smiles "C1CC2=COC=C12" \
 # opt structures using mace step, --batch_size 0 means auto batch size only for mace
 mkdir -p "${TAR_DIR}/mace_opt"
 cd "${TAR_DIR}/mace_opt"
-python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
+python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
     --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 80 --batch_size 0 \
     --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
     --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 1 --cueq true \
@@ -30,7 +30,7 @@ python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/
 # opt structures using 7net
 # mkdir -p "${TAR_DIR}/7net_opt"
 # cd "${TAR_DIR}/7net_opt"
-# python "${TOP_DIR}/mace-bench/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
+# python "${TOP_DIR}/batchASE/scripts/opt_batch.py" --target_folder "${TAR_DIR}/structures" \
 #     --molecule_single 13 --gpu_offset 0 --n_gpus 8 --num_workers 48 --batch_size 2 \
 #     --max_steps 3000 --filter1 UnitCellFilter --filter2 UnitCellFilter \
 #     --optimizer1 BFGSFusedLS --optimizer2 BFGS --num_threads 2 --cueq true \

scripts/generation.sh → example/generation.sh

@@ -50,7 +50,7 @@ echo " Max workers:          ${MAX_WORKERS}"
 echo "=========================================="
 
 # --- Run the pipeline ---
-python "${SCRIPT_DIR}/generation.py" \
+python "../scripts/generation.py" \
     --path "${TAR_DIR}" \
     --smiles "${SMILES}" \
     --molecule_num_in_cell ${MOLECULE_NUM_IN_CELL} \

scripts/relaxation.sh → example/relaxation.sh

@@ -91,7 +91,7 @@ ORDERED_FILES_ARG=""
 CUEQ_ARG=""
 [ "${CUEQ}" = true ] && CUEQ_ARG="--cueq true"
 
-python "${PROJECT_DIR}/mace-bench/scripts/mace_opt_batch.py" \
+python "${PROJECT_DIR}/batchASE/scripts/mace_opt_batch.py" \
     --target_folder "${TARGET_FOLDER}" \
     --molecule_single ${MOLECULE_SINGLE} \
     --gpu_offset ${GPU_OFFSET} \

scripts/relaxation_config.sh → example/relaxation_config.sh

@@ -53,7 +53,7 @@ N_GPUS=8
 GPU_OFFSET=0
 NUM_WORKERS=8
 BATCH_SIZE=25
-NUM_THREADS=4
+NUM_THREADS=1
 BIND_CORES=""
 MAX_STEPS=50
 FMAX=0.01

pyproject.toml

@@ -24,9 +24,9 @@ dependencies = [
 
 [tool.uv.sources]
 torch = { path = "/data/wangleping/torch-2.5.1+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" }
-mace-torch = { path = "./mace", editable = true } 
-cuequivariance-torch = { path = "./cuequivariance_torch/cuequivariance_torch", editable = true }
-fasteq = { path = "./FastEq", editable = true } 
+mace-torch = { path = "./3rdparty/mace", editable = true } 
+cuequivariance-torch = { path = "./3rdparty/cuequivariance_torch/cuequivariance_torch", editable = true }
+fasteq = { path = "./3rdparty/FastEq", editable = true } 
 triton = { path = "../../../../data/wangleping/triton-3.0.0+das.opt1.dtk25041-cp310-cp310-manylinux_2_28_x86_64.whl" }
 
 [tool.uv]
@@ -39,7 +39,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["basic_function", "mace-bench/src/batchopt"]
+packages = ["basic_function", "batchASE/src/batchopt"]
 
 [tool.uv.extra-build-dependencies]
 cuequivariance-torch = ["hatchling"] 

uv.lock

@@ -116,10 +116,10 @@ dependencies = [
 [package.metadata]
 requires-dist = [
     { name = "ase", specifier = "==3.23.0" },
-    { name = "cuequivariance-torch", editable = "cuequivariance_torch/cuequivariance_torch" },
-    { name = "fasteq", editable = "FastEq" },
+    { name = "cuequivariance-torch", editable = "3rdparty/cuequivariance_torch/cuequivariance_torch" },
+    { name = "fasteq", editable = "3rdparty/FastEq" },
     { name = "joblib", specifier = ">=1.5.3" },
-    { name = "mace-torch", editable = "mace" },
+    { name = "mace-torch", editable = "3rdparty/mace" },
     { name = "networkx", specifier = "==3.2.1" },
     { name = "numpy", specifier = "==1.26.4" },
     { name = "pyyaml", specifier = ">=6.0.3" },
@@ -226,7 +226,7 @@ wheels = [
 
 [[package]]
 name = "cuequivariance-torch"
-source = { editable = "cuequivariance_torch/cuequivariance_torch" }
+source = { editable = "3rdparty/cuequivariance_torch/cuequivariance_torch" }
 dependencies = [
     { name = "cuequivariance" },
 ]
@@ -261,7 +261,7 @@ wheels = [
 [[package]]
 name = "fasteq"
 version = "0.1.0"
-source = { editable = "FastEq" }
+source = { editable = "3rdparty/FastEq" }
 
 [[package]]
 name = "filelock"
@@ -452,7 +452,7 @@ wheels = [
 [[package]]
 name = "mace-torch"
 version = "0.3.15"
-source = { editable = "mace" }
+source = { editable = "3rdparty/mace" }
 dependencies = [
     { name = "ase" },
     { name = "configargparse" },