 Adam Husar
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fcf1427724
Changed license from GPL to MIT, removed some empty/unused files
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3 年之前 |
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Adam Husar
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85d001e55c
Replaced region and geometry pobject id in MolOrRxnCountTerm with region
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3 年之前 |
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Adam Husar
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abd68b8124
Split type LEAF of RegionExprNode into LEAF_SURFACE_REGION and
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3 年之前 |
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Adam Husar
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344e1b3896
Added warning about unused region in CountTerm and error when a
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3 年之前 |
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Adam Husar
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4f40600ef9
Cleaned up TODOs and refactored code
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3 年之前 |
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Adam Husar
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6ff7a88f82
Moved BNG-conversion related methods to new class BNGConverter,
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3 年之前 |
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Adam Husar
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6bfa479d0c
Parsing BNGL name directly in Complex ctor independently on subsystem
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3 年之前 |
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Adam Husar
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06b0b151b1
Fixed handling of skip_events_up_to_time for a checkpointed iteration
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3 年之前 |
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Adam Husar
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65670c843a
Fixed addition of checkpointed molecules into partition
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3 年之前 |
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Adam Husar
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0b004dc169
Putting checkpointed molcules both vol and surf into the same array to
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3 年之前 |
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Adam Husar
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0697597565
Using initial rng state when restoring a checkpoint
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3 年之前 |
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Adam Husar
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238c1f5480
Using initial_iteration and initial_time from checkpoint
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3 年之前 |
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Adam Husar
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6edaf15b7d
Using small_vector for arrays in counts
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3 年之前 |
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Adam Husar
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87daf7e51d
Revert "Tentative merging of count items into a single event"
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3 年之前 |
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Adam Husar
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d84e7ba049
Tentative merging of count items into a single event
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3 年之前 |
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Adam Husar
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e262948d5e
Preparation for intermembrane surf-surf reactions
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3 年之前 |
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Adam Husar
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e126dd0187
Unified BNG naming with API by renaming MolType to ElemMolType,
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4 年之前 |
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Adam Husar
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22172f9565
Renamed API ComponentInstance to Component, ElementaryMoleculeInstance
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4 年之前 |
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Adam Husar
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e2f2b918fc
Added support for immediate releases through Model.release_molecules
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4 年之前 |
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Adam Husar
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3c25338c59
Fixed case when a clamped molecule has orientation defined
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4 年之前 |
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Adam Husar
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4a122cdc8b
Conversion of clamp concentration from mcell4 API
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4 年之前 |
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Adam Husar
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f0ca701939
Initial support for @IN and @OUT compartment classes, not validated,
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4 年之前 |
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Adam Husar
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1d1d9ecd25
Check that SurfaceRegion cannot have the same name as a compartment
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4 年之前 |
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Adam Husar
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02a314c39b
Added support for compartments in surf rxns
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4 年之前 |
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Adam Husar
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18e490125c
Removed API class VolumeCompartment, moved related information to
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4 年之前 |
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Adam Husar
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c6182fdf8d
Added check that diffusion constant must be set
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4 年之前 |
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Adam Husar
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306a69419a
Rename API::ComplexInstance to API::Complex
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4 年之前 |
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Adam Husar
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5189e7522d
Finished support for BNGL observables that use compartments
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4 年之前 |
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Adam Husar
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5a2c87b3c1
Introduced default orientation for complexes, compartment improvements
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4 年之前 |
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Adam Husar
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d0acfe1648
Added conversion of VolumeCompartment to BNG::Compartment
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4 年之前 |
