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[WIP] Merge NPMC changes back into main branch #3

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wants to merge 49 commits into from
Closed

[WIP] Merge NPMC changes back into main branch #3

wants to merge 49 commits into from

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sivonxay
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@sivonxay sivonxay commented Nov 4, 2022 •
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In order to unify NPMC back into RNMC, a couple changes need(ed) to be made:

  1. Solvers will be unique to each application.
  2. (unsure yet) Simulation may need to be tweaked.
    • After an event, NPMC requires passing the Reaction that fired back to the model to resolve what changes in state are required.

Changes:

  • Added Checkpoint and Restarting

sivonxay and others added 30 commits April 29, 2022 13:51
@sivonxay
pass around reactions rather than propensities
c3cfa73
@sivonxay
Fix # of states in counter
efd6f35
@sivonxay
No need to count species, it is in the metadata table
8ab8f02
@sivonxay
missed semicolon
5ebcb10
@sivonxay
resize distance matrix axis 1
e549127
Fixed bugs in restructuring
15abab2
@sivonxay
Remove print statements
30cc01d
@sivonxay
Keep copy of current_reactions in the solver only
4ccd353
@sivonxay
Add check to ensure site i is not the same as site j
0dd2332
@sivonxay
Add debugging prints
aa0c763
@sivonxay
Add interaction_radius_bound
ceb73bb
@sivonxay
Debugging
fbad137
@sivonxay
Add alot of debugging
481de7c
@sivonxay
Change reactions_to_remove to a set
d9356ed
@sivonxay
Convert site_reaction_dependency to vector of sets
25d3c5f
@sivonxay
Fixed issue missing 1 reaction in the first step
2e791af
@sivonxay
Remove extraneous print
193da41
@sivonxay
Lessthan or equal to radius bound
c0a3a6d
@sivonxay
Remove a 2 site reaction from the both dependencies before deletion
dd41630
@sivonxay
Delete reactions individually rather than as a whole unit
2a15ad6
@sivonxay
Some debugging prints and fix issues
938e151
@sivonxay
Make states a constant argument
1140aa5
@sivonxay
Fix issue with tracking site-reaction dependency for one-site interac…
1d1ce89 
…tions
@sivonxay
Remove all debugging print statements
6dd1c61
@sivonxay
use endl instead of \n
f8bded7
@sivonxay
Clean up code
2d44b81
@sivonxay
Use references and pointers to avoid copying vectors of reactions
d61f70a
@sivonxay
Rearrange variables to be initialized
05238b7
@sivonxay
Rearrange if statement to make it more logical.
c0b5a9e
@sivonxay
Cast int to unsigned int before comparison with an unsigned int
7d44aaa
sivonxay added 19 commits May 4, 2022 17:18
@sivonxay
Breakout computing new reactions to a function
04dc6ed
@sivonxay
Rearrange inputs into update_reactions
1958bfe
@sivonxay
Remove Tree and Sparse solver, since they don't work with NPMC
16b9581
@sivonxay
Removed instances of deletion while iterating
fc67662
@sivonxay
Handle termination from SIGTERM and SIGINT
60096ab
@sivonxay
Add interrupt from SIGTERM and save final state and steps to db
6f931ff
@sivonxay
Explicitly close database and print errors whenever one arrises when …
214ccb3 
…executing SQL commands
@sivonxay
Remove unused Parameters struct
eaff183
@sivonxay
Make a separate delete statement
f951495
@sivonxay
Remove unused Parameters struct (and references to it)
0148348
@sivonxay
Refactor TrajectoriesSql to WriteTrajectoriesSql
f950cd9
@sivonxay
Add ReadTrajectoriesSql
2e1b00e
@sivonxay
Added checkpoint and resume
c72dbcf
@sivonxay
Added checkpoint and resume
140152e
@sivonxay
Merge remote-tracking branch 'sivonxay/pass_reactions' into pass_reac…
9eda90a 
…tions
@sivonxay
Resolve conflicts
ef5e110
@sivonxay
get things to compile with gcc
5fc4463
@sivonxay
Only activate checkpointing on SIGTERM(15) and SIGINIT(2)
7c84f12
@sivonxay
Merge branch 'BlauGroup:main' into pass_reactions
b0948c5
@espottesmith espottesmith mentioned this pull request Oct 7, 2024
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@sivonxay @espottesmith