Merge branch 'devel'

Merge pull request deepmodeling#45 from deepmodeling/devel

Merge devel into master

Release DMFF v0.1.0 (deepmodeling#38)

* add nblist wrapper and its docs

* fix(generator): existing jax bond/angle generators

* fix: LJ bug; all classical code can be jitted; bug at test_gaff2_force

* fix test_gaff2_force bug

* fix: non-differentiable error, move args check in the api.py

* fix: remove redundancy `box=jnp.array(box)`; confirm isinstance_jnp is jit-compatiable

* refine(pme): code prettify

* refine(utils): code prettify

* add(nblist): add jit and auto update nblist

* refine(classical): rm unused import

* refactor(classical): add dispCorr

* add(classical): add free energy support

* refactor renderXML with clean commits (deepmodeling#25)

* feat:rewrite renderXML with very clean commit history

* fix bug in Torsion renderXML

* add test_utils as a placehold

* fix: fix typo in api.py

* docs: add renderXML related api usages

* refine(fep): rm debugging codes

* add(cicd): CI/CD workflows

* add(ut): ut for regularize_pairs and buffer_scales

* fix(CI/CD): activate conda env

* fix(CI/CD): wrong number in test_nblist

* add(requirement): add dependencies list

* add(CI/CD): unittest workflows

* add(requirements): dependencies list

* add test_utils.py

* fix: modified unit test results

* add `r` to avoid latex being recognized as an escape character

* fix(ut): wrong number in test_nblist

* Fix unit test related problems (deepmodeling#27)

* add test_utils.py

* fix: modified unit test results

* add `r` to avoid latex being recognized as an escape character

* fix(ut): wrong number in test_nblist

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

* refine(ut): code prettify in test_nblist

* Add CI/CD Workflows (deepmodeling#26)

* add(CI/CD): unittest workflows

* add(requirements): dependencies list

* refine(ut): code prettify in test_nblist

* update(api): switch default dispcorr to False

* Chore: clean admp module up

* chore: clean up classical and api.py

* fix(ut): withdraw last commit about fix wrong number in test_nblist

* update(api): fix dispcorr countmat bugs

* update(pme): code prettify & gmx ewald coeff determine

* add(constants): module to control constants

* add(unittest): fep ut

* update(test_nblist): unused imports

* update(gitignore): acpype cache

* refactor(test_classical): split to several files

* refactor(test_classical): rename test_classical

* fix(inter): PME in classical forcefield

* update(fep): use dmff.common.constants

* update(pme): default args in setup_ewald_parameters

* Fix the nb list description in doc

* update mkdocs.yml and a simple test of api generator

* fix: add step_pol arg in ADMPPmeForce __init__ to fix it can not be jitted bug

* add step_pol arg in ADMPPmeForce __init__ to fix it can not be jitted bug

* Improve docstrings in sgnn

* add read_input_info in dmff.admp.parse.py to deal with info in pdb and xml (input:pdb,xml output: multipoles/polarizabilities/tholes...)
use forcefield.xml instead of other xmls, add read_admp_xml in parser in order to read the new form of xml file
change line 795 in pme.py and add distribute_matrix in pairwise.py in order to wrap a jit outside my admp_calculator

* Update some examples and ref_outs

* feat: auto gen docs refs

* fix: typo in requirements.txt

* add change leading terms in api.py

* add fluctuated leading term computation in dmff.api

* add fluctuated leading term compute in dmff.api

* use dmff.api to deal with input ; wrap admp_calculator to change fixed params into fluctuated one amf jit

* wrap compute leading term in run.py

* add a markdown and a generate_calculator outside admp_calculator function

* feat(classical): Hamiltonian can create total energy function now. (deepmodeling#33)

* Docs refine (deepmodeling#34)

* add(CI/CD): unittest workflows

* add(requirements): dependencies list

* update(doc): fix bad render of \hat

* update(doc): add examples and doc struct refine

* Improve the fluctuating charge jupyter notebook demo

* Delete parser_bk.py

* Fix the fluctuating atom charge demo

* feat: update docs configs

* fix: fix test_nblist bug

* update: license in docs

* fix: import missing in api.py (may caused by formatter)

* FIX: wrong links in docs and add requirements (deepmodeling#37)

* update(doc): fix bad render of \hat

* update(doc): add examples and doc struct refine

* hotfix(docs): license bugs

Co-authored-by: Kuang Yu <[email protected]>
Co-authored-by: Roy Kid <[email protected]>
Co-authored-by: Jichen Li <[email protected]>
Co-authored-by: crone <[email protected]>
Co-authored-by: WangXinyan940 <[email protected]>