refactor renderXML with clean commits #25
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Ericwang6
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Jun 14, 2022
* 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 (#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 (#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 (#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. (#33) * Docs refine (#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 (#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]>
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