Aleaverfay/kinforest from stencil #299
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…to build programmatically
Automated construction of both "id" and "parent" tensors now working properly.
The tricky part here is that we had to first construct the child_list and child_list_span tensors that describe the descendants of each atom so that we could then traverse up and down the parent tree and thus correct the frame_x, _y, and _z tensors. TO DO: replace bubble sort with mgpu's segmented sort to better handle cases where we might have a large number of descendants of a single node (e.g. the root!) but to still produce a deterministic kintree in spite of the non-determinism that the atomic-increment based ordering that I have currently.
… from restype stencils
Works for a single Pose in the PoseStack
…the fold tree spanning multiple blocks or perhaps multiple edges as "scan paths."
This corectly resets the "scans" offsets to 0 for the beginning of each generation. I believe this version should actually work for the forward pass. Here goes nothing!
…m/uw-ipd/tmol into aleaverfay/kinforest_from_stencil
…dule tests working
…jump_ff_edge_rooted_at_scan_path_seg
…/tmol into aleaverfay/kinforest_from_stencil
…mization + smoke test
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This is just the beginning of a sketch of the algorithm to construct kintrees on the GPU using pre-computed per-residue kintrees and then integrating them all together.