Merge pull request deepmodeling#1217 from amcadmus/master

Merge recent updates on devel to master.

Merge pull request deepmodeling#1177 from deepmodeling/devel

Merge recent development on devel into master

Merge pull request deepmodeling#1126 from deepmodeling/devel

Merge devel into master

Merge pull request deepmodeling#1047 from amcadmus/master

Merge devel into master

Fix the expanding logic of `SLURM_JOB_NODELIST` and add unit tests fo…

…r parallel training. (deepmodeling#913)

* Add unit tests of `cluster` and `env`.

* Fix the expanding logic of `SLURM_JOB_NODELIST`.

`NOT_LOADABLE` should be `tuple` (deepmodeling#825)

remove unused tqdm (deepmodeling#746)

tqdm is not used at present. It may be
imported in deepmodeling#350 for tests, but since it
is not really used for production, it is safe
to remove this requirement.

Doc api cc (deepmodeling#663)

* Doxyfile cannot be installed from pip, therefore I precompiled with doxyfile to generated xml/ from C++. And then api_cc.rst can be generated by breathe from xml/.

* Edit conf.py to include doxygen

* Edit conf.py to enable doxygen on readthedocs

* Add specification in conf.py to refine the html layout of api_cc.rst

* Included exhale to make prettier C++ API.

* Update conf.py

* add a function description to see if it works

* it should be put into the header file?

* add documents for DeepPot and DeepTensor

* add documents for some common functions

Co-authored-by: tuoping <[email protected]>
Co-authored-by: Jinzhe Zeng <[email protected]>

append to out_file when LAMMPS restarts (deepmodeling#640)

This ensures the out file will not be override when LAMMPS restarts.
This commit may be conflicted with deepmodeling#392. Commit
@5597ea2b49f96e99a52a9779b04b6c12e5a79a04 should be dropped.

Merge pull request deepmodeling#547 from amcadmus/devel

fix bug of using old name se_a, changed to se_e2_a