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Created with Raphaël 2.2.012Mar4Feb20Jan16318Dec161312512Nov22Oct842119Sep18131027Aug26242322212017161413876542130Jul2526Mar1Dec22Nov161429Oct2627Jul20191011May13Feb1Nov31Oct18Feb729Nov29Oct2827252128Sep13Jul20May5Mar210Feb7Dec320Aug28Jul10Jun522Apr18Mar95328Feb2524211918128724Jan227212Dec618Nov31Oct927Sep26255427Aug201310Jul10May30Apr8525Mar21158Feb129Jan19321Dec189215Nov417Oct129Sep282725232221201918171514131110765429Aug2824212017131023Jul2018171613106328Jun1514139Apr754130Mar27232221202128Feb2621Dec2017Oct18Sep31Aug30112124Jul2018131211107629Jun2827261514138131May2910Apr754329Mar2726128Feb262423222120191716153add cadnanomastermasterchange pandas behaviornicknickImprove how mrdna generates bead models; use `model.generate_bead_model(..., version=1.0)` for legacy behaviorMerge remote-tracking branch 'refs/remotes/origin/master'Fix specialization of bead types to ensure unique typesAdd support for vector angle potentials; fix nonbonded interaction bugadd nicksadd nick data, modify patterns for pandasadd nick related datapinyili2pinyili2correct the behavior for writing the particlesmodify reading pandas wayUpdate arbdmodel/submodule to arbmodel commit a4196d3Repair atomic_simulate() after breaking in commit afe2d1fCopy arbmodel commit 7ceb134 to arbdmodel/submoduleMake existing code compatible with new arbdmodelAdd arbdmodel module files to facilitate importingAdd arbdmodel copy with commit ID 4075481Move local arbmodel copy to arbdmodel/submodule/arbdmodelAvoid bonded potential duplication after multiple simulate commandsAdd ability to apply grid potentials to orientation beadsadd segPrevent PointParticle (or other Child objects) from looking up explicitly excluded methods such as __hash__ and __copy__ from ParticleType; Add ParticleType __copy__ and __deepcopy__ methods that return to ensure types do not change upon copying a group or modelFix typomake assign bead type competitable with arbdmodelsegment model fixesmake mrdna competitable with current arbdmodelMerge branch 'pinyili2' of gitlab.engr.illinois.edu:tbgl/tools/mrdna into pinyili2add arbd model to branchaddaddaadd arbd model to branchgeneralized fwd helix directionsset angle to 180Remove some unused codeFix matrix transpose in new quaterion_from_matrix routineAdd explicitly_unstacked argument to oxDNA reader to ensure we get terminal_crossover connectionsMerge branch 'pinyili2' of gitlab.engr.illinois.edu:tbgl/tools/mrdna into pinyili2add arbdmodeladd