Bug fix in parsing internal xmls #62
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* 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 <ericwangyz@pku.edu.cn> * 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 <windwhisper.yu@gmail.com> Co-authored-by: Roy Kid <lijichen365@126.com> Co-authored-by: Jichen Li <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: crone <2223469329@qq.com> Co-authored-by: WangXinyan940 <44082181+WangXinyan940@users.noreply.github.com>
Merge devel into master
Merge devel into master
…to feat-covmap
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* feat(classical): offer tools to organize xml forcefield and match parameters. * fix(tests): change API to be consistent with dmff * feat(dmff): Add class Potential to keep OpenMM and DMFF potentials * fix(api): auto-update parameter before writing new xml file. * refactor: admp api.py using old xmlholder api * fix(fftree): make the name of API easier to be understand * update * update: admp related api * fix: fix bug in admp api * doc: programming style convention about typing and numpy style docstring * fix(tests): Add attribute to choose improper order * fix(classical): remove double check of cutoff distance in potential function. * fix(classical): avoid creating empty dict in impr parameters * fix(inter): add 1e-12 as eps value in jnp.sqrt function * fix(inter): use more tiny eps for numerical consistent * update: frontend docs * fix typo: fix typo in dev_guide * Temprary commit before test * Debugging new api for admp * peg system benchmark checked out * Update examples * Fix bug: was not reading the XZ component of multipole * remove jit for nbl.update * Modify setup.py * Require jax version smaller than 0.3.16, which is incompatible with current version of jax_md (0.1.29) * Update demo notebook in water example * Update documents and the notebook in classical FF example * Fix bug in nblist module * change allocate * fix: fix nblist jit-related bug * fix: test sequence in test_nblist.py * Fix bug in Slater ISA short range interaction * update: all tests pass * clean up code * feat: brutal Freud-based nblist * Bug fix in parsing internal xmls (#62) 1. Add NeighborFreud class to use freud package to obtain neighborlist. 2. Fix bug of parsing openmm internal force field xmls 3. Handle unmatched torsion params * settle down dependencies version * rename `nmax` to `capacity_multiplier`(consistent with jax_md); remove property:distance and dr in neighborList due to catastrophic bug * add freud-analysis require * remove overflow judgement so update in nblist can be jitted * Adapt examples to new nblist api * add md_ipi in examples to run classical MD for bulk water * modified md_ipi * modified md_ipi * new * new * new_2 * Refactor: decompose api.py and generators to separate files * feat(MBAR): Add differentiable MBAR impl * bug fix: record the name of matched template * Add unit test for MBAR estimator * feat: Estimate free energy of an extra state * set specific version no. for jax in installation guide * Update MBAR Estimator API * Update unit test for the latest MBAR API * Update github workflow to support new unit test. * Update requirement of pymbar * fix package including problem * Change cell vector to prevent numerical problem (ceil(12.0 / 1.0) would jump between 12 and 13) * Update settings.py * remove unused imports * fix "==" in requirements * update (gitignore): hmtff cache * update (api): docstring in createPotential * Update optax transforms for force field parameters * Update __init__.py * Update LJ jax force API in LennardJonesForce generator * Let energy function in TargetState use the whole trajectory instead of using single frame * Update MBAR UT to fit API change * Remove the using of numpy to make free energy & weight differentiable * Update __init__.py * Set precision again in dmff.mbar after importing pymbar * Increase MBAR numerical stability * Update an example of MBAR-based optimization * Correct the typo in document * Add openmm sample state. * Update genOptimizer to support multiple optimizers * Set default pressure to be 0 (NVT) * Add Gitee_mirror (#67) * Fix Mirror CI/CD (#68) * Add Gitee_mirror * Fix mirror CI/CD Co-authored-by: WangXinyan940 <44082181+WangXinyan940@users.noreply.github.com> * Add tutorial_utils for demo usage (#69) * Hook jax force to generator for intra potentials * Remove the requirement of mdtraj * Let NeighborList.update return (N, 3) pairs with colv_map information * Update nblist.py * bugfix: correctly recognize if the LJForce card uses type or class * SMIRKS-based typing scheme (#72) * add support for SMIRKS, bcc and virtual site * add dependencies in ut workflow * add interface to obtain topmat * code clean * fix multiple matches_dict var * add tests for building top * add tests for smirks/bcc/vsite * add dockerfile for dev env * add examples of smirks * add usage of smirks in doc * rm api doc in _date/_version * fix typo * update (doc): architecture img * update (README): citation and code structure * update (doc): bad rendered latex * update (doc): typo in usage * update (doc): smirks in XML * Hotfix in BCC parametrization (#73) * update (smirks): change bcc err to warning * hotfix: incorrect bcc matching * Save covalent map to Potential object & make energy function generator (#74) * Update python version requirement to 3.8 * Save meta data in Potential object * Add support to save meta data in Hamiltonian * Create an attribute to save meta data * Use potential.meta["cov_map"] in unittests * Build a function generator to calculate energies of a trajectory * Change API function name * fix meta data for admp generators * Make buildEnergyFunction cleaner Co-authored-by: KuangYu <windwhisper.yu@gmail.com> Co-authored-by: Yingze Wang <ericwangyz@pku.edu.cn> Co-authored-by: Roy-Kid <lijichen365@126.com> Co-authored-by: KuangYu <windwhisper.yu@gmail.com> Co-authored-by: Jichen Li <42854324+Roy-Kid@users.noreply.github.com> Co-authored-by: crone <2223469329@qq.com> Co-authored-by: Yuzhi Zhang <529133328@qq.com>
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NeighborFreudclass to usefreudpackage to obtain neighborlist.