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Adding medical workers and hospital interactions #120

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e95706d
fixed the component counting in writing plotfiles
debog Mar 27, 2025
067dfda
applied clang patch
debog Mar 27, 2025
88c07ed
added another assert to ensure sizes of varnames and output component…
debog Mar 27, 2025
629b6c8
initial implementation of assigning medical workers
debog Mar 28, 2025
071fab2
Merge branch 'fix_plotfile' into dg/medical_workers
debog Mar 28, 2025
d526b85
forgot to call the printMedicalWorkerCounts()
debog Mar 28, 2025
fcf677b
removed OpenMP pragmas for initial assignment of medical workers
debog Mar 28, 2025
2c7b147
Merge branch 'development' into dg/medical_workers
debog Mar 28, 2025
3e8f0ab
fixed the assignment of medical workers to give similar numbers on GP…
debog Apr 4, 2025
56acc64
Merge branch 'development' into dg/medical_workers
debog Apr 4, 2025
1aa0d55
using NAICS to characterize workers; -1 means non-worker, >=0 means w…
debog Apr 4, 2025
1a0a2c1
fixed a few warnings
debog Apr 4, 2025
ddbcdd7
fixed a type-mismatch warning
debog Apr 4, 2025
996ceae
Using the same NAICS codes as in urbanpop initialization; excluding m…
debog Apr 16, 2025
c9b0da5
applied clang-format patch
debog Apr 16, 2025
c6a6cab
added interactions between medical workers
debog Apr 17, 2025
9b99294
Merge branch 'development' into dg/medical_workers
debog Apr 30, 2025
dd2d8cb
Merge branch 'development' into dg/medical_workers
debog Jun 2, 2025
08302fc
implemented computing hospital capacities and treatment quality score…
debog Jun 3, 2025
e10b9b3
consolidated all hospital model MultiFab data into one MultiFab with …
debog Jun 4, 2025
33eb324
implemented "treatment quality" based on daily hospital scores that a…
debog Jun 5, 2025
c9e8d36
fixed type mismatches
debog Jun 6, 2025
553e54d
clang-format
debog Jun 6, 2025
bb59c43
fixed more variable-type mismatches
debog Jun 6, 2025
90e5b3a
bugfix: updated particle plotfile varnames for multiple diseases
debog Jun 6, 2025
900beba
writing out number of hospitals over capacity and underserved patient…
debog Jun 10, 2025
aee05b5
fixed bugs in hospital score/load computing logic; consolidated print…
debog Jun 11, 2025
2e600ff
Merge branch 'development' into dg/medical_workers
debog Sep 2, 2025
ae758c2
updated medical worker interaction function due to recent changes in …
debog Sep 3, 2025
228bb94
Merge branch 'development' into dg/medical_workers
debog Sep 3, 2025
6e17306
modified the calculation of survival/death in hospital to avoid rando…
debog Sep 4, 2025
fd69cfe
Merge branch 'development' into dg/medical_workers
debog Oct 3, 2025
7c7b1c7
added doctor <-> patient and patient <-> patient interactions in hosp…
debog Oct 17, 2025
742e975
applied clang-format patch
debog Oct 17, 2025
0d07759
added a parameter that specifies the proportion of medical workers wo…
debog Oct 31, 2025
9b9894c
using ParticleReduce for computing total medical workers
debog Nov 4, 2025
1a7a85c
added a Redistribute before plotfile writing
debog Nov 4, 2025
3dda948
creating hospital data MultiFab in AgentContainer instead of Hospital…
debog Nov 5, 2025
c4e6082
applied clang-format patch
debog Nov 5, 2025
38eabb4
added missing input to documentation
debog Nov 5, 2025
53a4ee9
fixed typo
debog Nov 5, 2025
99f5f9d
Merge branch 'development' into dg/medical_workers
debog Dec 10, 2025
5fe43e0
needed for last merge commit
debog Dec 10, 2025
4d5220e
Merge remote-tracking branch 'origin/development' into dg/medical_wor…
debog Feb 3, 2026
9dc3ab5
clang patch
debog Feb 3, 2026
9ec1661
Fix false failures in plotfile comparison: chkdiff.sh was matching `t…
debog Feb 3, 2026
235484a
Merge branch 'fix_chkdiff' into dg/medical_workers
debog Feb 3, 2026
c0ab6d0
Merge branch 'development' into dg/medical_workers
debog Jun 2, 2026
cf7b6c3
applied clang-format patch
debog Jun 3, 2026
9acf5ed
Fix hospital capacity to use disease-treating medical workers
debog Jun 3, 2026
35cdfd3
medworkers: gate model behind model_medical_workers; redesign capacity
debog Jun 3, 2026
a98e0f2
Merge origin/development (CI C++20 bump, #156) into dg/medical_workers
debog Jun 3, 2026
abcf798
medworkers: optional real hospital placement from HIFLD/HHS data
debog Jun 4, 2026
e411dc3
medworkers: source hospital data from HHS (drop HIFLD); route staff t…
debog Jun 4, 2026
dce56cd
medworkers: use a non-surge baseline week (2020-09-27) for the exampl…
debog Jun 4, 2026
551a64a
medworkers: move hospital-data device code to its own TU (fix matrix …
debog Jun 4, 2026
ed04f8e
apply clang-format to hospital-model sources
debog Jun 4, 2026
2c73816
move bed-supply device code out of the HospitalModel template
debog Jun 4, 2026
d8074d4
Move hospital data into a HospitalData class to fix CUDA Release crash
debog Jun 5, 2026
3d07f2e
applied clang-patch
debog Jun 5, 2026
47ab9b5
add per-day medical-worker infection diagnostic
debog Jun 5, 2026
206024a
add minimum/cumulative treatment-score accumulation option (default m…
debog Jun 5, 2026
264af1f
make the treatment-quality score continuous at the capacity threshold
debog Jun 7, 2026
fa63f5f
default to tract-level hospital placement when HHS data is used
debog Jun 8, 2026
b514499
fix out-of-bounds assignment read in tract-level hospital rerouting
debog Jun 8, 2026
3fbabf4
fix death/hospitalization stats deposit under tract-level routing
debog Jun 8, 2026
3ced537
rebuild Bay Area tract hospital data on 2000-vintage tracts
debog Jun 8, 2026
212abb6
hospital model: same-county patient transfer, hospital workgroups, wo…
debog Jun 8, 2026
e800424
make transfer helpers public: CUDA bars extended __device__ lambdas i…
debog Jun 8, 2026
d4b137f
exclude medical workers from the work-neighborhood model when active
debog Jun 8, 2026
c3c36a1
Split medical workforce into hospital workgroups in the per-community…
debog Jun 9, 2026
79546ec
Add nosocomial (hospital-acquired) infection diagnostic; fix OOB deposit
debog Jun 9, 2026
a81f197
Fix multi-disease hospital ward/ICU/ventilator accounting for dual ad…
debog Jun 9, 2026
c9ed77c
Merge remote-tracking branch 'origin/development' into dg/medical_wor…
debog Jun 13, 2026
90c3d54
Re-apply shelter-in-place compliance after recovery
debog Jun 13, 2026
962fe92
Exempt medical workers from shelter-in-place
debog Jun 13, 2026
fe7ebfa
Bounded multiplicative overload mortality (mortality_multiplier_max)
debog Jun 13, 2026
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8 changes: 8 additions & 0 deletions data/.gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,14 @@ US_2010_Census_States
UrbanPop
!UrbanPop/urbanpop_nm.bin.gz
!UrbanPop/urbanpop_nm.idx
# Hospital data: ignore raw source downloads, keep processed .dat files and README
HospitalData/*.csv
HospitalData/*.zip
HospitalData/*.shp
HospitalData/*.shx
HospitalData/*.dbf
HospitalData/*.prj
HospitalData/*.cpg
# generated shapefile .shx index (GDAL rebuilds it with SHAPE_RESTORE_SHX=YES)
*_Census_Tracts/*.shx
*_Counties/*.shx
14 changes: 14 additions & 0 deletions data/HospitalData/BayArea_hospitals_2020.dat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
# ExaEpi hospital-capacity data -- utilities/build_hospital_data.py
# source: HHS COVID-19 Hospital Capacity by Facility (anag-cw7u): staffed inpatient beds (beds) + staffed adult ICU beds (icu_beds)
# state=CA year=2020 level=county week=2020-09-27
# columns: FIPS beds icu_beds n_hospitals
9
6001 2574 257 13
6013 1249 160 7
6041 279 30 4
6055 194 27 2
6075 1873 254 10
6081 680 76 6
6085 3000 424 8
6095 518 51 4
6097 509 50 7
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