Add plugin for gromacs

[Ericwang6]

Add plugin for gromacs and relevant docs / examples

[Ericwang6]

4. Examples can be smaller.

Well, do you mean reducing the number of atoms in our examples? I believe that methane in water is the smallest example to illustrate a DP/MM simulation.

[Ericwang6]

2. The current CMake system is not used. For example, make gromacs to generate the plugin like make lammps.

Here, the plugin is designed to provide scripts for users to manually modify the source code of gromacs. And I don't think it's necessary to use the cmake system.

[njzjz]

5. For json.hpp: I think there is already one in third_party directory.

The version here is 3.9.1, which is higher than that in third_party directory. And that old version is incompatible.

Upgrading old version to new one?

[njzjz]

3. I don't think it's necessary to separate different versions. Preprocessor macros should be enough.

@AnguseZhang and I both prefer to keep version-based patches as plumed does. Because there may be too may differences between versions in GROMACS... In this way can we ensure that users of different versions of GROMACS can use our plugin.

I think deepmd_plugin.cpp and deepmd_plugin.h is not a version-based file, and all patch files can be merged into one file.

[Ericwang6]

1. For json.hpp: I think there is already one in third_party directory.

The version here is 3.9.1, which is higher than that in third_party directory. And that old version is incompatible.

Upgrading old version to new one?

Sure. I'm not sure whether it will cause incompatibility for deepmd-kit. But I can test on it first.

[Ericwang6]

1. I don't think it's necessary to separate different versions. Preprocessor macros should be enough.

@AnguseZhang and I both prefer to keep version-based patches as plumed does. Because there may be too may differences between versions in GROMACS... In this way can we ensure that users of different versions of GROMACS can use our plugin.

I think deepmd_plugin.cpp and deepmd_plugin.h is not a version-based file, and all patch files can be merged into one file.

OK. Would you plz provide a reference on how to merge the patches into one file? I don't know how to do it actually...

[njzjz]

git-format-patch

[Ericwang6]

@njzjz Uploading json.hpp to 3.9.1 will cause compilation errors in deepmd-kit

[amcadmus]

5. For json.hpp: I think there is already one in third_party directory.

The version here is 3.9.1, which is higher than that in third_party directory. And that old version is incompatible.

which part is incompatible? plz provide more on how you tested and the error log.

currently json.hpp is used by dp_ipi. We may want to upgrade dp_ipi accordingly.

[Ericwang6]

Follow @njzjz 's advice, I've refactored the code in order to compile the gmx plugin along with deepmd-kit. Therefore, the number of changes and commits become too many to track for reviewers. So I'll close this pr first and open another pr for review.