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Fix get_neighbor* and Reactions related to OffLatticeSpace #445

Merged
merged 21 commits into from
Jan 30, 2020
Merged

Fix get_neighbor* and Reactions related to OffLatticeSpace #445

merged 21 commits into from
Jan 30, 2020

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0ncorhynchus
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@0ncorhynchus 0ncorhynchus commented Jan 23, 2020 •
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  • Refactor and fix get_neighbor* functions.
  • Fix manipulation of a vacant.
  • Change the type of SpatiocyteWorld::coordinate_type.

related to #430

@0ncorhynchus
♻️ Add Voxel::get_neighbor_randomly()
177e20e
@0ncorhynchus
♻️ Add another Voxel::get_neighbor_randomly()
7577208 
For StepEvent2D
@0ncorhynchus
♻️ StepEvent2D uses Voxel::get_neighbor_randomly()
2dc40f8
@0ncorhynchus
♻️ Remove rng from args of get_neighbor_randomly()
2eb1725
@0ncorhynchus
♻️ Move functions for neighbor to SpatiocyteWorld
41807bb
@0ncorhynchus
♻️ Change the types of intefaces_ and neighbors_
9f24487
@0ncorhynchus
♻️ Refactor add_structure() and remove is_inside()
b4693e5
@0ncorhynchus
♻️ Change the arguments of gen_particle_from()
02cdd43
@0ncorhynchus
♻️ Add find_space_and_voxel_pool()
cb60782
@0ncorhynchus
♻️ Add find_space_and_molecule_pool()
2e8516a
@0ncorhynchus
🔥 Remove coordinate2voxel()
f629617
@0ncorhynchus
🐛 Fix bug around locating molecules
b889161
@0ncorhynchus
🔥 Remove SpatiocyteWorld::coordinate_type
4759c2d
@0ncorhynchus
🐛 Fix num_voxels* and num_molecules*
d99f989
@0ncorhynchus
🐛 Fix the bug of SpatiocyteWorld::add_molecules()
de79eb5
@0ncorhynchus
♻️ Refactor get_molecule_info()
12ac0c8
@0ncorhynchus
🐛 Get information from a model before add a space
aef1f5f
@0ncorhynchus
✅ Add test for get_molecule_info()
e356131
@0ncorhynchus
🐛 Fix get_location() with a vacant voxel
186b1ec
@0ncorhynchus
🐛 Fix SpatiocyteWorld::check_neighbor()
b0fe1aa
@0ncorhynchus
🐛 Fix reactions with OffLatticeSpace
0f3e1c4
@0ncorhynchus 0ncorhynchus mentioned this pull request Jan 23, 2020
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@0ncorhynchus 0ncorhynchus merged commit 67ed134 into ecell:offlattice Jan 30, 2020
@0ncorhynchus 0ncorhynchus deleted the fix_offlattice branch January 30, 2020 01:20
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@0ncorhynchus