doc: add Interfaces out of DeePMD-kit

README.md

@@ -122,6 +122,7 @@ A full [document](doc/train/train-input-auto.rst) on options in the training inp
     - [LAMMPS commands](doc/third-party/lammps-command.md)
     - [Run path-integral MD with i-PI](doc/third-party/ipi.md)
     - [Run MD with GROMACS](doc/third-party/gromacs.md)
+    - [Interfaces out of DeePMD-kit](doc/third-party/out-of-deepmd-kit.md)
 
 # Code structure
 

doc/third-party/index.md

@@ -6,4 +6,5 @@ Note that the model for inference is required to be compatible with the DeePMD-k
 - [Run MD with LAMMPS](lammps.md)
 - [LAMMPS commands](lammps-command.md)
 - [Run path-integral MD with i-PI](ipi.md)
-- [Run MD with GROMACS](gromacs.md)
+- [Run MD with GROMACS](gromacs.md)
+- [Interfaces out of DeePMD-kit](out-of-deepmd-kit.md)

doc/third-party/index.rst

@@ -11,3 +11,4 @@ Note that the model for inference is required to be compatible with the DeePMD-k
    lammps-command
    ipi
    gromacs
+   out-of-deepmd-kit

doc/third-party/out-of-deepmd-kit.md

@@ -0,0 +1,31 @@
+# Interfaces out of DeePMD-kit
+
+The codes of the following interfaces are not a part of the DeePMD-kit package and maintained by other repositories. We list these interfaces here for user convenience.
+
+## dpdata
+
+[dpdata](https://github.com/deepmodeling/dpdata) provides the `predict` method for `System` class:
+
+```py
+import dpdata
+dsys = dpdata.LabeledSystem('OUTCAR')
+dp_sys = dsys.predict("frozen_model_compressed.pb")
+```
+
+By inferring with the DP model `frozen_model_compressed.pb`, dpdata will generate a new labeled system `dp_sys` with inferred energies, forces, and virials.
+
+## OpenMM plugin for DeePMD-kit
+
+An [OpenMM](https://github.com/openmm/openmm) plugin is provided from [JingHuangLab/openmm_deepmd_plugin](https://github.com/JingHuangLab/openmm_deepmd_plugin), written by the [Huang Lab](http://www.compbiophysics.org/) at the Westlake University.
+
+## AMBER interface to DeePMD-kit
+
+An [AMBER](https://ambermd.org/) interface to DeePMD-kit is written by the [York Lab](https://theory.rutgers.edu/) from the Rutgers University. Details can be found in [this paper](https://doi.org/10.1021/acs.jctc.1c00201). The code is available upon request from the authors.
+
+## DP-GEN
+
+[DP-GEN](https://github.com/deepmodeling/dpgen) provides a workflow to generate accurate DP models by calling DeePMD-kit's command line interface (CLI) in the local or the remote server. Details can be found in [this paper](https://doi.org/10.1016/j.cpc.2020.107206).
+
+## MLatom
+
+[Mlatom](http://mlatom.com/) provides an interface to the DeePMD-kit within MLatom's workflow by calling DeePMD-kit's CLI. Details can be found in [this paper](https://doi.org/10.1007/s41061-021-00339-5).