merge devel branch into master

…n lmp (#696)

* metal testing for alloys and pair_coeff compatible with the latest lammps

* add bcc self interstitial calculations

* bcc interstitial optimization and change some default parameters in lmp

* fix lmp default parameters

* bcc interstitial optimization

* add bcc interstitial unittest

Co-authored-by: kevinwenminion <[email protected]>

The latter will not catch `KeyboardInterrupt` and `SystemExit`. See https://stackoverflow.com/a/18982726/9567349.

* fix typo in github actions release to conda

* Get from_poscar_path only when from_poscar is true (#537)

Change-Id: I17774bee345634e4e72bd783e8112eefaaf9f0d3

Co-authored-by: Zhengju Sha <[email protected]>

* Fix QE pwscf AssertionError

details in #683

Co-authored-by: Han Wang <[email protected]>
Co-authored-by: felix5572 <[email protected]>
Co-authored-by: shazj99 <[email protected]>
Co-authored-by: Zhengju Sha <[email protected]>
Co-authored-by: Han Wang <[email protected]>

* fix typo in github actions release to conda

* Get from_poscar_path only when from_poscar is true (#537)

Change-Id: I17774bee345634e4e72bd783e8112eefaaf9f0d3

Co-authored-by: Zhengju Sha <[email protected]>

* feature: merge run.py

* fix:fix syntax bug

* fix summary ratio bug

* fix: fix bug of var(calypso_run_opt_path) not defined

* reorganize code v1

* add: add unittest

* add: add some explainations of dp+calypso in README.md

* change a little bit in readme.md

* change position of function

* add deepmd-kit>=2.0.1 install_require in setup.py

* test failed cause no tensorflow module so add tensorflow in setup.py

* calc model devi in command line

* fix some small bugs of modd and PBS script of cpu

* fix unittest

* delete parse_input.dat

* fix unittest

* first reorganization

* secord reorganization

* fix bugs

* fix: fix bugs in modd_calypso.py write_modd.py and run.py

* change functions name and fix bugs

* remove modd_calypso.py

* remove: remove modd_calypso.py

* remove some useless outputs

* restore dispatcher/PBS.py

* refactor: make some changes in calypso related code

- rename model_devi_calypso.py run_calypso.py
- rename calypso.py make_calypso.py
- add new file calypso_check_outcar.py calypso_run_opt.py
- add new file calypso_run_model_devi.py
- delete write_modd.py
- modify README.md and run.py

* refactor: move calypso main code(run.py) into run_calypso.py and modify test_calypso.py

* docs: modify README.md related to CALYPSO

* delete some useless comments in run.py

* add write_model_devi_out function into make_calypso.py for passing unittest

* fix a spelling mistake in calypso_run_opt.py (famx -> fmax)

* change runopt script's name from run_opt.py to calypso_run_opt.py and fix bug in runopt script

* fix unittest

Co-authored-by: Han Wang <[email protected]>
Co-authored-by: felix5572 <[email protected]>
Co-authored-by: shazj99 <[email protected]>
Co-authored-by: Zhengju Sha <[email protected]>
Co-authored-by: Han Wang <[email protected]>

* add abacus+lcao+dpks interface for dpgen init and run.

* fix test abacus make input bug.

* Update requirements.txt

add dpdata==0.2.6 to requirements.

* Update setup.py

update dpdata to 0.2.6

* fix bugs concerning abacus in README

* update abacus example files to dpmd 2.x and dpdispatcher new version.

Co-authored-by: LiuRenxi <[email protected]>
Co-authored-by: Han Wang <[email protected]>

* doc: dpgen run machine parameters

* unpin sphinx

Fix sphinx-doc/sphinx#10291 (comment)

#718)

* Change mv to cp when downloading softlinks.

* Add explanations relevant to POTCAR's examples.

* Fix CH4's vasp-md INCAR example.

* Fix bug in make_submission of Auto-test

* Add ase, custodian, GromacsWrapper in conda packages.

* Fix bug of fp_task_min

* Add gromacswrapper to conda recipe

* Revert "Fix bug of fp_task_min"

This reverts commit 8d7f8a7.

* Add numkit recipe

* Add `convert_mdata` definition to fix simplify bug.

* Fix the usage of `pair_coeff` in `auto_test`

* Delete printed information by `dpgen -h` in manual.

* Revert "Add gromacswrapper to conda recipe"

This reverts commit 3529e91.

* Revert "Add numkit recipe"

This reverts commit d19bd77.

Merge master into devel