Disable git-lfs. Replace disutils with setuptools. Update the citation.

CITATION.cff

@@ -8,4 +8,11 @@ authors:
     given-names: Jing
     orcid: https://orcid.org/0000-0001-9639-2907
 title: "Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy"
-date-released: 2023-05-29
+version: 0.2.0
+date-released: 2024-03-28
+identifiers:
+  - description: This is the DOI of the software paper. Please cite this DOI when you use this software.
+    type: doi
+    value: https://doi.org/10.3390/ijms25031448
+license: Apache-2.0
+repository-code: "https://github.com/JingHuangLab/openmm_deepmd_plugin"

README.md

@@ -18,7 +18,7 @@ Compile the plugin from the source with the following steps.
    ```
    conda create -n dp_openmm
    conda activate dp_openmm
-   conda install -c conda-forge openmm cudatoolkit=11.6
+   conda install -c conda-forge openmm
    ```
 
 2. Download and install the DeePMD-kit C API library by running the following command:
@@ -48,10 +48,11 @@ Compile the plugin from the source with the following steps.
    ```
    It will install the plugin to the subdirectory of `OPENMM_DIR` automatically.
 
-6. Test the plugin C++ interface and install the Python module of this plugin into conda environment by running the following commands:
+6. Test the plugin C interface and install the Python module of this plugin into conda environment by running the following commands:
    ```shell
    make test
    make PythonInstall
+   export LD_LIBRARY_PATH=${LIBDEEPMD_C_INSTALLED_DIR}/lib:$LD_LIBRARY_PATH
    python -m OpenMMDeepmdPlugin.tests.test_dp_plugin_nve
    python -m OpenMMDeepmdPlugin.tests.test_dp_plugin_nve --platform CUDA
    ```
@@ -172,7 +173,7 @@ For more practical usage of these two methods, refer to the provided simulation
 ### Alchemical Simulations with Deep Potential
 
 To perform alchemical simulations with the DP models based, combine `lambda` and `addParticlesToDPRegion`. 
-The alchemical simulations protocol with the DP models is described in `AlchemicalProtocol.pdf`.
+A detailed description about the alchemical simulations protocol with the DP models could be refered to the [paper](https://www.mdpi.com/1422-0067/25/3/1448).
 
 For an example script about alchemical simulation for water's hydration-free energy calculation, refer to [test_deepmd_alchemical.py](./python/tests/test_deepmd_alchemical.py).
 

python/setup.py

@@ -1,5 +1,5 @@
-from distutils.core import setup
-from distutils.extension import Extension
+from setuptools import setup
+from setuptools import Extension
 import os
 import platform
 
@@ -32,7 +32,7 @@
 
 
 setup(name='OpenMMDeepmdPlugin',
-      version="@GIT_HASH@",
+      version="0.2.0",
       ext_modules=[extension],
       packages=['OpenMMDeepmdPlugin', "OpenMMDeepmdPlugin.tests"],
       package_data={"OpenMMDeepmdPlugin":['data/*.pb', 'data/*.pdb']},