Release DMFF v0.2.0 #71
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1. Load, modify, and write force field XML files correctly. 2. Use both OpenMM system and DMFF potential together. 3. Create Potential class to manage the OpenMM system and DMFF potential. 4. Implement ForceFieldTree and TypeMatcher to help write a new Generator.
…nto roy/xmlholder
fix(fftree): make the name of API easier to be understand
…nto roy/xmlholder
update front api and docstring convention
fix(unittest): fix classical UTs and remove double check of cutoff distance in potential calculation.
fix(inter): fix numerical problem in sqrt function of LJ potential
fix(inter): use more tiny eps for numerical consistent
update: frontend docs
Feat: Add NBFix, MBAR estimator, and optimizer
* Add Gitee_mirror * Fix mirror CI/CD Co-authored-by: WangXinyan940 <44082181+WangXinyan940@users.noreply.github.com>
Fix bug of patching "class" field in Lennard-Jones potential
WangXinyan940
requested review from
Ericwang6,
KuangYu and
Roy-Kid
and removed request for
Ericwang6 and
KuangYu
KuangYu
approved these changes
Nov 24, 2022
* 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
* update (smirks): change bcc err to warning
#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>
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