Marco De Lucia
cf2debb032
removed .ai dir from this branch
2025-11-14 10:58:43 +01:00
rastogi
ca4353723d
Stop tracking bin/dolo/ and update .gitignore
2025-11-13 16:00:47 +01:00
rastogi
475b954e91
updated .gitignore
2025-11-12 10:25:58 +01:00
rastogi
938f811bab
Store per-cell MAPE/RRMSE and add stabilization interval
2025-11-12 10:20:28 +01:00
rastogi
eea056250d
Fix cell_ID access in DHT/interpolation and restructure control cell metric computation to use row-major layout
2025-11-07 15:55:26 +01:00
rastogi
e0a0567013
Fix cell_ID access in DHT/interpolation and restructure control cell metric computation to use row-major layout
2025-11-07 15:52:39 +01:00
rastogi
9a26cf8cc9
feat: Add control logic for surrogate validation with selective PHREEQC re-execution, error metrics (MAPE/RRMSE), and automatic checkpoint/rollback
2025-11-06 20:55:02 +01:00
rastogi
ab7f06f4d1
feat: bcast control_cell_ids to workers
2025-11-02 22:26:14 +01:00
rastogi
8e377d4ca0
Added ctrl_cell_ids
2025-10-30 21:36:03 +01:00
rastogi
1901400f7b
Restructuring prototyp 3
2025-10-30 16:15:27 +01:00
rastogi
3cbb17b88f
Add .gitignore
2025-10-30 16:14:22 +01:00
rastogi
a280d3f203
Merge branch 'control-loop' of git.gfz-potsdam.de:naaice/poet into control-loop
2025-10-02 13:21:57 +02:00
rastogi
2d5def9a7f
feat(control): dynamic prototype, penalty_iteration, error while disabling surrogate fixed
2025-10-02 13:20:53 +02:00
Max Lübke
85fa04d379
feat(grid): enable cell_ID integration in chemistry data flow
2025-09-25 15:08:13 +02:00
rastogi
f33dcb99f1
feat(control): disable surrogate model after rollback until next iteration
2025-09-21 17:45:12 +02:00
rastogi
882dff4873
rollback implemented, triggered when MAPE exceeds epsilon
2025-09-12 09:47:00 +02:00
Max Lübke
733a13d9d9
cleanup computeStats()
2025-09-04 14:20:08 +02:00
Max Lübke
a4aa788de8
fix mssing handling of different storage locatios of work packages
2025-09-04 14:19:54 +02:00
Max Lübke
f2eaecd1c0
formatting MasterFunctions.cpp
2025-09-04 13:54:43 +02:00
Max Lübke
a9d0850625
stuff in computeStats
2025-09-02 13:05:47 +02:00
Max Lübke
110c755491
Add fgcs dolo benchmark
2025-09-02 12:04:38 +02:00
Max Lübke
afc010f3e4
rename control work package and subsitute interpolated work package
2025-09-02 11:03:33 +02:00
rastogi
d9d105b860
Initial control-loop setup. Unit tests for MAPE and RMSE added.
...
Note: computeStats function is not working correctly yet.
2025-09-01 12:54:24 +02:00
rastogi
c9a8fc8079
computeStats not working correctly, Unit Tests added
2025-09-01 12:39:01 +02:00
Max Lübke
2acdbb910d
feat: Implement checkpointing
...
Co-authored-by: hmars-t <hmars-t@users.noreply.github.com>
2025-08-01 11:27:25 +02:00
rastogi
e97623c346
Initial commit
2025-08-01 11:09:59 +02:00
Max Lübke
0b952a725c
Merge branch 'ml/add-build-type-to-readme' into 'main'
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Add CMake Build Type to Readme
See merge request naaice/poet!53
2025-05-20 14:29:00 +02:00
Max Lübke
7e68789af6
Add CMake Build Type to Readme
2025-05-20 14:28:45 +02:00
Marco De Lucia
1af4cda041
Merge branch '17-new-barite-benchmarks-for-fgcs-journal' into 'main'
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Resolve "New barite benchmarks for FGCS journal"
Closes #17
See merge request naaice/poet!44
2025-05-19 12:50:30 +02:00
Max Lübke
03948bc614
fix: Correct boolean conversion in DHT hook call
2025-03-12 10:35:23 +01:00
Hannes Martin Signer
075c384c8a
Merge branch 'ml/add-tug-solver-option' into 'main'
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Add option to toggle tug numerical solver approach
See merge request naaice/poet!50
2025-01-29 16:17:52 +01:00
Max Luebke
d38c0bf4b7
Add option to toggle tug numerical solver approach
2025-01-29 15:53:32 +01:00
Max Lübke
796da7e072
refactor: clean up CMakeLists.txt by removing unnecessary target_sources indentation
2025-01-09 12:18:13 +01:00
Max Lübke
c0071bf447
feat: add index tracking and flushing functionality to DHT
2025-01-09 12:18:05 +01:00
Max Lübke
688bb5ccd1
Merge branch '17-new-barite-benchmarks-for-fgcs-journal' of git.gfz-potsdam.de:naaice/poet into 17-new-barite-benchmarks-for-fgcs-journal
2024-12-20 10:12:51 +01:00
Max Lübke
3157c13521
[wip] add input validation for work_package in DHT_Wrapper and InterpolationModule
2024-12-20 10:12:19 +01:00
Max Lübke
edd78163e4
fix: update grid dimensions and refine species definitions in barite_fgcs_2.R
2024-12-20 10:08:07 +01:00
Marco De Lucia
ec3e38e8b5
Fancier benchmark for fgcs paper
2024-12-20 10:08:07 +01:00
Max Lübke
55d2ec534e
Merge branch 'hotfix-qs-option' into 'main'
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fix: remove duplicate flag for saving output as .qs file in parseInitValues
See merge request naaice/poet!49
2024-12-20 10:07:21 +01:00
Max Lübke
a1e177fe9b
fix: remove duplicate flag for saving output as .qs file in parseInitValues
2024-12-20 10:05:49 +01:00
Marco De Lucia
e7e3e32c61
Fancier benchmark for fgcs paper
2024-12-20 09:24:19 +01:00
Max Lübke
da6f2a7e74
Merge branch 'ml/fix-interpolation' into 'main'
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Fix Interpolation and add optional features to POET benchmark description
See merge request naaice/poet!48
2024-12-20 09:23:44 +01:00
Max Lübke
7734d13516
Merge branch 'main' into 'ml/fix-interpolation'
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# Conflicts:
# src/initializer.cpp
# src/poet.cpp
# src/poet.hpp.in
2024-12-20 09:22:55 +01:00
Max Lübke
6d39e559e6
fix: initialize default values for RuntimeParameters in poet.hpp.in
2024-12-20 09:21:18 +01:00
Max Lübke
2768b25a05
fix: update dht_species values for barite and celestite in benchmark scripts
2024-12-20 09:21:18 +01:00
Max Lübke
60298c379c
Revert "feat: make output of H(0) and O(0) optional"
...
This reverts commit bdb5ce944fd001cb36c8369d8c792f2f4a54c7be.
2024-12-20 09:21:18 +01:00
Max Lübke
42be5ac36f
fix: handle zero distance case in inverseDistanceWeighting to prevent division by zero
2024-12-20 09:21:18 +01:00
Max Lübke
eb09cd2725
feat: add with_h0_o0 and with_redox parameters to ChemistryModule and related classes
2024-12-20 09:21:18 +01:00
Max Luebke
ca5b83012d
feat: add support for redox in PhreeqcMatrix initialization
2024-12-20 09:21:18 +01:00
Max Lübke
172c11dd19
feat: enhance LookupKey with const isnan method and comparison operator
2024-12-20 09:21:18 +01:00
Max Lübke
1403ad3a87
refactor: streamline WorkPackage constructor and improve DHT_Wrapper::fillDHT logic
2024-12-20 09:21:17 +01:00
Max Luebke
96778c1d95
feat: add dht_snaps and dht_out_dir parameters to ChemistryModule and main function
2024-12-20 09:21:17 +01:00
Max Luebke
dd29fce7db
fix: initialize includeH0O0 to false in command line options
2024-12-20 09:21:17 +01:00
Max Luebke
9553225d35
feat: make output of H(0) and O(0) optional
2024-12-20 09:21:17 +01:00
Max Lübke
2bbe09935b
feat: add has_het_ids parameter to DHT initialization and related functions
2024-12-20 09:21:17 +01:00
Max Lübke
201613c551
fix: use const reference for to_calc in InterpolationModule to improve performance
2024-12-20 09:21:17 +01:00
Max Lübke
00ffe84b02
fix: remove double initialization of dht_enabled in ChemistryModule
2024-12-20 09:21:17 +01:00
Max Lübke
7bb103fade
feat: implement caching for interpolation calculations and add NaN handling
2024-12-20 09:21:16 +01:00
Max Luebke
6118fbc786
[wip] fix: add base_totals to SurrogateSetup
2024-12-20 09:21:16 +01:00
Marco De Lucia
20529d6ca7
reverting <format> since gcc < 13 does not support it
2024-12-20 09:21:16 +01:00
Marco De Lucia
abcfc637b6
Update references to .qs2 in README
2024-12-20 09:21:16 +01:00
Marco De Lucia
c3bba9472e
Update README: qs2 as default output format, gfz.de everywhere
2024-12-20 09:21:16 +01:00
Marco De Lucia
cc6f83b49a
Less and more informative stdout messages
2024-12-20 09:21:16 +01:00
Marco De Lucia
ca93df57bd
Added qs2 as new default format
2024-12-20 09:21:15 +01:00
Max Lübke
43864ee2fb
Merge branch 'ml/gitlab-ci' into 'main'
...
Refactor CI pipeline by removing the build stage and adjusting test job dependencies
See merge request naaice/poet!47
2024-12-20 09:06:18 +01:00
Max Lübke
e387c415b2
Refactor CI pipeline by removing the build stage and adjusting test job dependencies
2024-12-20 09:04:30 +01:00
Max Lübke
e4d48dc92d
Merge branch 'ml/fix-license' into 'main'
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Revert "No code changes made."
See merge request naaice/poet!46
2024-12-20 09:00:27 +01:00
Max Lübke
d1a3996df4
Update LICENSE to include updated copyright notice and additional guidelines for program distribution
2024-12-20 08:58:40 +01:00
Max Lübke
4f7926f8c9
Revert "No code changes made."
...
This reverts commit f60b7cf7fcb33e9ff55e1c8050775217d9d37f1a.
2024-12-20 08:57:51 +01:00
Max Lübke
d93995866a
Merge branch 'ml/fix-license' into 'main'
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Fix license parsing error of GitLab?
See merge request naaice/poet!45
2024-12-20 08:55:43 +01:00
Max Lübke
6983ecb1aa
No code changes made.
2024-12-20 08:46:51 +01:00
Max Lübke
1a976971ca
Merge branch 'mdl/fgcsbench' into 'main'
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Mdl/fgcsbench
See merge request naaice/poet!43
2024-12-13 12:19:57 +01:00
Marco De Lucia
cb9f073c47
reverting <format> since gcc < 13 does not support it
2024-12-13 12:14:55 +01:00
Marco De Lucia
6fdf406715
Update references to .qs2 in README
2024-12-13 12:14:55 +01:00
Marco De Lucia
70bd8f7788
Update README: qs2 as default output format, gfz.de everywhere
2024-12-13 12:14:55 +01:00
Marco De Lucia
eb2c6fe728
Less and more informative stdout messages
2024-12-13 12:14:55 +01:00
Marco De Lucia
c6f4de2840
Added qs2 as new default format
2024-12-13 12:14:55 +01:00
Hannes Martin Signer
59e6f12871
Merge branch 'update-scheme' into 'main'
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update poet scheme
See merge request naaice/poet!42
2024-12-10 15:03:54 +01:00
Hannes Martin Signer
3d34b953b2
Update 2 files
...
- /docs/POET_scheme.svg
- /docs/POET.drawio
2024-12-10 15:02:45 +01:00
Max Lübke
8c0b23648f
Merge branch 'update-poet-scheme' into 'main'
...
update POET scheme
See merge request naaice/poet!41
2024-12-10 11:15:48 +01:00
Hannes Martin Signer
fcc6239bec
update POET scheme
2024-12-10 11:14:01 +01:00
Max Lübke
8035a2e9c1
Merge branch 'ml/iphreeqc-v0.3' into 'main'
...
Update IPhreeqc Submodule to v0.3
See merge request naaice/poet!40
2024-12-04 11:35:27 +01:00
Max Lübke
c6fab494ce
refactor: Replace PhreeqcEngine instances with PhreeqcRunner for improved chemistry processing
2024-12-04 10:34:13 +00:00
Max Lübke
c5c0994485
build: Enhance Dockerfile for improved environment setup and dependency management
2024-12-04 08:44:55 +00:00
Max Lübke
6443e321f8
Merge branch 'ml/misc' into 'main'
...
Various changes to build files (CMake & devcontainer)
See merge request naaice/poet!38
2024-11-07 20:57:45 +01:00
Max Lübke
851e7734f9
build: Update Dockerfile and devcontainer.json for enhanced environment setup
2024-11-07 19:56:04 +00:00
Max Lübke
e79988c7fa
build: Refactor R runtime detection in CMake to ensure required parameters are set
2024-11-07 19:56:04 +00:00
Max Lübke
509b4ed3c7
Merge branch 'ml/new-iphreeqc-api' into 'main'
...
Update to IPhreeqc v3.8.2
See merge request naaice/poet!37
2024-11-07 14:23:58 +01:00
Max Lübke
70115c17a5
fix: Update getSolutionNames call to remove unnecessary argument
2024-11-07 14:22:58 +01:00
Max Lübke
ac116e413b
Update subproject commit in ext/iphreeqc
2024-11-07 14:22:51 +01:00
Marco De Lucia
c55d0c3943
Merge branch 'delucia-readme-patch-68839' into 'main'
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Fix: README.md
See merge request naaice/poet!36
2024-09-26 11:47:46 +02:00
Marco De Lucia
e0cea3aded
Update README.md
2024-09-26 11:45:07 +02:00
Marco De Lucia
fb2ce83ee3
Merge branch 'mdl/qs-rebased' into 'main'
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rebased mdl/enable-qs to merge with main
See merge request naaice/poet!34
2024-09-16 13:07:43 +02:00
Max Luebke
ef427513f5
fix: Corrected log10 calculation in master_iteration_end function
2024-09-16 12:05:19 +02:00
Max Luebke
aeb6587399
feat: use CLI11 as argument parser
...
feat: improve poet_initializer
2024-09-16 11:57:00 +02:00
Marco De Lucia
24c5fb66e8
fixed damn source_R
2024-09-12 16:15:21 +02:00
Marco De Lucia
0f81c54974
cosmetic fixes in DiffusionInit.cpp
2024-09-12 14:57:11 +02:00
Marco De Lucia
b52d1942f1
fix: removed Time-stamp lines from README and CMake/
2024-09-12 14:56:42 +02:00
Marco De Lucia
c1e5e97cf1
fix: removed all Time-stamp lines from src/
2024-09-12 14:56:09 +02:00
Marco De Lucia
666ba31884
fixing stuff and adding comments
2024-09-12 14:54:05 +02:00
Marco De Lucia
47371d8f47
Fixes in README and poet.cpp
2024-09-12 14:53:58 +02:00
Marco De Lucia
22ef6f22fb
Update README.md
2024-09-12 14:51:44 +02:00
Max Lübke
ec241be873
refactor: Rework deferred R function evaluation
...
applied commit
fix: Unique pointer behaviour of `global_rt_setup` was messed up
2024-09-12 14:48:05 +02:00
Marco De Lucia
42089f2282
fixed initializer. Format is given by extension in the -o argument
2024-09-12 14:42:59 +02:00
Marco De Lucia
7f761e802f
feat: fast serialization/storage using qs package via --qs flag
...
rebasing/merging
2024-09-12 14:42:24 +02:00
Marco De Lucia
214f9f87b7
cosmetic fixes in DiffusionInit.cpp
2024-09-12 12:37:49 +02:00
Marco De Lucia
6eab2a72eb
fix: removed Time-stamp lines from README and CMake/
...
Solve conflict
2024-09-12 12:37:28 +02:00
Marco De Lucia
4e73e9a3a6
fix: removed all Time-stamp lines from src/
2024-09-12 12:36:40 +02:00
Marco De Lucia
e91eefe973
fixing stuff and adding comments
2024-09-12 12:36:40 +02:00
Marco De Lucia
757dd46275
Switched default bench init storage to qs
2024-09-12 12:36:40 +02:00
Marco De Lucia
14a0ac0325
Fixing rebase conflicts
2024-09-12 12:36:11 +02:00
Marco De Lucia
9ff7a6bdaf
Update README.md
2024-09-12 11:40:03 +02:00
Max Lübke
afcb42bcaa
refactor: Rework deferred R function evaluation
...
fix: Unique pointer behaviour of `global_rt_setup` was messed up
2024-09-12 11:40:03 +02:00
Marco De Lucia
7f1330c1ca
fixed initializer. Format is given by extension in the -o argument
2024-09-12 11:40:03 +02:00
Marco De Lucia
cec00c841b
feat: fast serialization/storage using qs package via --qs flag
2024-09-12 11:39:44 +02:00
Max Lübke
942cd92afc
Merge branch 'ml/chore' into 'main'
...
chore: Update README and cleanup
See merge request naaice/poet!33
2024-08-29 14:26:13 +02:00
Max Lübke
b0e9b2f597
chore: remove preprocessed file from project structure
2024-08-29 14:25:37 +02:00
Max Lübke
1fbc7229e2
chore: Remove unnecessary code in FindRRuntime.cmake
2024-08-29 14:25:37 +02:00
Max Lübke
794bb4ce2c
doc: Update R package installation process for AI surrogate
2024-08-29 14:25:37 +02:00
Max Lübke
b037359db9
Merge branch 'ml/fix-dht' into 'main'
...
fix: Error during DHT usage
See merge request naaice/poet!32
2024-08-29 08:47:45 +02:00
Max Lübke
9982fbe113
Update subproject commit reference
2024-08-29 08:35:17 +02:00
Max Lübke
73baac931e
fix: distribute species names across all processes
2024-08-29 08:35:11 +02:00
hans
1f91e4c196
Fix: merge issues
2024-06-05 16:43:33 +02:00
hans
92339342dc
Merge branch 'ai-surrogate-v03-temp' into ai_surrogate_merge
2024-06-05 16:02:30 +02:00
hans
91b99066be
Merge branch 'origin/ai-surrogate-v03-temp-mdl' into ai_surrogate_merge
2024-06-05 15:59:00 +02:00
hans
d7832d8fa6
fix: reserve vs resize in Worker
2024-06-05 15:54:19 +02:00
hans
e5d257a24d
fix: wp_start_index in Worker
2024-05-31 11:45:19 +02:00
hans
122aa963a4
fix: wp_start_index in Worker
2024-05-31 11:26:50 +02:00
Marco De Lucia
59c3eb9fbd
MDL: AI model seems correctly updated/stored
2024-05-30 13:37:28 +02:00
hans
7e79cf0c70
docs: updated graphic
2024-05-30 13:30:43 +02:00
hans
7b1c4d63f3
docs: updated graphic
2024-05-30 13:30:10 +02:00
hans
6274f98bea
docs: updated graphic
2024-05-30 13:28:48 +02:00
Hans Straile
7785e4846d
Update 0230720_Scheme_POET_en.svg
2024-05-30 13:25:15 +02:00
hans
a3a643577a
docs: updated docs for v03
2024-05-30 13:20:50 +02:00
Marco De Lucia
5b48ccb21b
MDL: added barite_50ai bench
2024-05-30 11:37:31 +02:00
Marco De Lucia
6238335b4d
MDL: some fixes and some more output to make AI run
2024-05-30 11:32:08 +02:00
hans
a526543cb7
feat: Add AI Surrogate functions to V.03
2024-05-27 15:22:29 +02:00
hans
675a95e374
feat: Add AI Surrogate functions to V.03
2024-05-27 09:09:01 +02:00
Max Lübke
6d2d053eac
Merge branch 'ml/fix-chemistry' into 'main'
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Fix chemistry
See merge request naaice/poet!30
2024-05-07 12:30:13 +02:00
Max Lübke
9099cf1d1f
chore: Update subproject commit in ext/iphreeqc
2024-05-07 09:52:31 +00:00
Max Lübke
8e542db8b9
fix: Correct logic for updating output values in WorkerRunWorkPackage
2024-05-07 08:34:18 +00:00
Max Lübke
c8e2e55c7e
Merge branch 'ml/build' into 'main'
...
Update CMakeLists.txt to conditionally add the bench subdirectory based on the...
See merge request naaice/poet!29
2024-05-06 13:27:27 +02:00
Max Lübke
717148a93c
Update CMakeLists.txt to conditionally add the bench subdirectory based on the POET_PREPROCESS_BENCHS option
2024-05-06 11:26:13 +00:00
Max Lübke
43068f5159
Merge branch 'ml/ci' into 'main'
...
Refactor CI/CD pipeline
See merge request naaice/poet!28
2024-05-06 13:17:40 +02:00
Max Lübke
1614e25ead
Refactor CI/CD pipeline
2024-05-06 13:17:39 +02:00
Max Lübke
cc45bbc191
Merge branch 'ml/surfex' into 'main'
...
Enable Surfex/Exchange reactants using IPhreeqc/POET API
See merge request naaice/poet!27
2024-05-06 12:11:50 +02:00
Max Lübke
4a544d1be0
Update Readme
2024-05-06 10:09:28 +00:00
Max Lübke
8bba4f31ea
Add EGU debug model
2024-05-06 10:09:28 +00:00
Max Lübke
21dcbd14d4
BREAKING CHANGE: Enable Surface/Exchange using new API of PhreeqcEngine
2024-05-06 10:01:57 +00:00
Max Luebke
60c3e67a5a
Fix build process to only produce benchmarks when needed
2024-04-15 09:10:11 +00:00
Max Lübke
4e74eeef8b
Fix grid size assignment in GridInit.cpp
2024-04-12 12:35:43 +00:00
Max Lübke
00392d5d62
Refactor R_lib/kin_r_library.R to use setup$maxiter instead of iter for calculating max digits
2024-04-10 10:24:00 +00:00
Max Lübke
cb7ca9f7d3
Remove doctest submodule
2024-04-10 10:24:00 +00:00
Max Lübke
b594fc93fc
Fix diffusion and chem field update order in RunMasterLoop
2024-04-10 10:24:00 +00:00
Max Lübke
e2a6cf3189
Refactor process to output as DataFrames
2024-04-10 10:24:00 +00:00
Max Lübke
09cb4997ba
Refactor R package dependencies in Dockerfile
2024-04-09 08:09:47 +00:00
Max Luebke
ca2fe83554
Add minimal flag to importList function in InitialList
2024-04-08 20:47:38 +00:00
Max Luebke
30014494d2
Refactor Field.cpp to use Rcpp DataFrame for conversion to SEXP
2024-04-08 20:31:36 +00:00
Max Luebke
001b000789
Refactor build file generation
2024-04-08 20:31:36 +00:00
Max Luebke
b3a0590bd0
Refactor benchmark files to current POET input expectations
2024-04-08 20:31:36 +00:00
Max Luebke
91e134b8f6
Refactor command line argument handling and improve script sourcing in initializer.cpp
2024-04-08 12:49:58 +00:00
Max Luebke
8bd05088bc
Refactor initializer.cpp to handle command line arguments and improve script sourcing
2024-04-08 12:02:47 +00:00
Max Luebke
af48694d22
Refactor code for grid creation and result storage
2024-04-08 11:27:06 +00:00
Max Luebke
4fa935475e
Fix inner_boundaries handling in DiffusionModule and InitialList
2024-04-08 10:32:00 +00:00
Max Luebke
93ba7837d7
Update minimum required CMake version to 3.14
2024-04-08 10:31:47 +00:00
Max Luebke
b8fd16a8d9
Refactor code according to static analyzers
2024-04-08 09:19:48 +00:00
Max Luebke
8d254f334e
Add dolo_inner benchmark
2024-04-05 08:34:41 +00:00
Max Luebke
793067f582
Move old benchmark files into old subdir
...
Move new benchmark files from `het` folder
2024-04-05 08:33:26 +00:00
Max Luebke
133aab2b09
Add inner_boundaries handling in DiffusionModule and InitialList
2024-04-05 08:31:32 +00:00
Max Luebke
3b3e5fcea2
Update .gitignore to ignore .codechecker directory
2024-04-05 07:05:09 +00:00
Max Luebke
03ae8e50f3
Refactor code for grid creation and result storage
2024-04-04 09:27:52 +00:00
Max Luebke
aed2ff4be1
Add functions for checking sign and negativity in dol.pqi and dolo_200.R
2024-04-04 09:27:27 +00:00
Max Luebke
ec2dff0be1
Add file extension replacement and print output filename
2024-04-03 21:19:39 +00:00
Max Luebke
320ae7a6f0
Update Dockerfile with required dependencies and install R packages
2024-04-03 21:03:16 +00:00
Max Luebke
79fd1ebe9d
Refactor R functions and how they are called
2024-04-03 21:03:10 +00:00
Max Lübke
5880f28762
Update iterations and dt values in dolo_200_rt.R
2024-04-03 16:46:50 +02:00
Max Luebke
707a78d8b6
Add parallel grid creation function and update pqc_to_grid function
2024-04-03 14:25:04 +00:00
Max Luebke
1b52e25947
Fix initialization of transport_names in ChemistryInit and GridInit
2024-04-03 14:25:04 +00:00
Max Luebke
2addcfbbf0
Update solution parameters in dol.pqi
2024-04-03 14:25:04 +00:00
Max Luebke
479bfa4c6e
Add support for missing species in init grid, which are injected (by boundary condition)
2024-04-03 14:25:04 +00:00
Max Luebke
d2b01c28fc
Update iphreeqc subproject commit
2024-04-03 10:47:33 +00:00
Max Luebke
64989a8af8
Update chem.GetField() to chem.getField() in poet.cpp
2024-04-03 10:47:32 +00:00
Max Luebke
8e20d177e1
Update runtime and test scripts
2024-04-03 10:46:54 +00:00
Max Lübke
82097e56b1
Update units in dol.pqi
2024-04-03 10:59:31 +02:00
Max Lübke
774f0b7df3
Update GIT_SUBMODULE_STRATEGY in .gitlab-ci.yml
2024-04-03 10:10:02 +02:00
Max Lübke
b665aa6307
Update Calcite and Dolomite parameters in dol.pqi
2024-04-03 10:08:37 +02:00
Max Lübke
cb6e634576
Update out_save in dolo_200_rt.R
2024-04-03 10:08:02 +02:00
Max Luebke
c95a6bea8b
Refactor to wrap everything in main function into scope, to ensure DHT is freed before MPI_FInalize
2024-04-02 20:47:32 +00:00
Max Luebke
8a78ed718e
Remove SimParams class
2024-04-02 20:38:23 +00:00
Max Luebke
6c3761bb92
Add check_sign_cal_dol_dht and fuzz_input_dht_keys functions
2024-04-02 20:35:28 +00:00
Max Luebke
853888a19b
Refactor WorkerRunWorkPackage to copy input instead of overwriting
2024-04-02 20:24:04 +00:00
Max Luebke
ca1f8a19bb
Refactor chemistry module and RHookFunction
2024-04-02 20:23:42 +00:00
Max Luebke
c7b9ab0b53
Update iteration end message in kin_r_library.R
2024-04-02 14:37:20 +00:00
Max Luebke
7d6871a180
Add profiling data for DHT and interpolation
2024-04-02 14:17:59 +00:00
Max Luebke
6d050ad34c
Add DHT functionality, still need to be validated
2024-04-02 14:14:19 +00:00
Max Luebke
40e7bbe7cc
Add chemistry initialization to InitialList class
2024-04-02 12:06:55 +00:00
Max Luebke
d196d3c25d
Add dolo_200_rt.R, dol.pqi, and dolo_200.R files for simulation setup
2024-04-02 11:41:38 +00:00
Max Luebke
1c004dfda9
Update dependencies and refactor code
2024-04-02 11:41:38 +00:00
Max Luebke
5d46360c33
Remove doctest submodule and update gitmodules
2024-04-02 10:33:56 +00:00
Max Luebke
fe4d71f680
Update CMakeLists.txt and include headers in test files
2024-04-02 09:25:18 +00:00
Max Luebke
08a2baba11
Remove unnecessary includes and update function signature
2024-04-02 09:16:58 +00:00
Max Lübke
80ce92699f
Update dependencies and refactor code
2024-03-28 14:23:20 +00:00
Max Lübke
7a31858aaf
Add Basic heterogeneous diffusion functionality
2024-03-27 20:34:48 +00:00
Max Luebke
cb56f4aa10
Add total_grid_cells to ChemistryInit struct
2024-03-21 22:33:40 +00:00
Max Lübke
d8dddf14f2
Add support for importing and exporting initial grid in InitialList class
2024-03-21 21:36:09 +00:00
Max Lübke
5d4a05fe9b
Add Init/CMakeLists.txt and ChemistryInit.cpp files, and update initializer.cpp and InitialList.hpp
2024-03-20 23:46:57 +00:00
Max Lübke
265638ab17
Update include statement and add CMakeLists.txt for DataStructures
2024-03-20 22:33:23 +00:00
Max Luebke
8969fea7e2
Update grid and diffusion setup in test.R
2024-03-19 22:03:22 +00:00
Max Lübke
bc923b75e6
Add resolvePqcBound function and refactor parseBoundaries2D function
2024-03-19 15:37:29 +00:00
Max Lübke
6ec98077d7
Update alpha matrix parsing
2024-03-19 14:07:25 +00:00
Max Lübke
e3f002de49
Refactor initialization code for diffusion and grid
2024-03-19 13:39:59 +00:00
Max Lübke
b0c65ddbda
Add file reading functionality and update script and database handling
2024-03-19 13:11:42 +00:00
Max Lübke
feb8efa73d
Refactor grid initialization and update member access in InitialList
2024-03-19 12:32:16 +00:00
Max Lübke
ab7efbc3a8
Update getModuleSizes function to use new API
2024-03-19 09:48:31 +00:00
Max Lübke
9fdda31151
Refactor pqc_to_grid function to use matrix instead of data.table
2024-03-19 09:47:40 +00:00
Max Luebke
2b74fca740
Save latest changes, boundaries still missing or incomplete
2024-03-19 08:12:20 +00:00
Max Luebke
371eb1367a
Add modify_module_sizes function and modify module_sizes in InitialList class
2024-03-13 23:50:13 +01:00
Max Luebke
8f698149da
Update function name to replaceRawKeywordIDs in GridInit.cpp
2024-03-13 22:06:07 +01:00
Max Luebke
d012936c6d
Update RAW Keywords to always refer to ID 1
2024-03-13 22:05:06 +01:00
Max Luebke
9b144f8ec5
Update CMakeLists.txt and add new files for barite_het simulation
2024-03-13 17:11:53 +01:00
Max Luebke
3d203f307f
Remove installation of poet binary
2024-03-13 16:58:37 +01:00
Max Luebke
a1e771f7ed
Add iphreeqc and init_r_lib submodules, and make necessary changes to CMakeLists.txt and src/initializer.cpp
2024-03-13 16:57:44 +01:00
Max Lübke
c050613614
Add apps directory and initializer application
2024-03-07 13:54:53 +00:00
Max Lübke
acfdc75bcc
Merge branch 'v0.x' into 'main'
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Fix path in GitLab CI
See merge request naaice/poet!25
2024-03-07 14:43:03 +01:00
Max Lübke
2f72ebc73d
Fix path in GitLab CI script
2024-03-07 13:41:50 +00:00
Max Lübke
d86e7fa8f7
Update dependencies in ci.Dockerfile
2024-03-07 13:41:34 +00:00
Max Lübke
c2530df8e3
Merge branch 'v0.x' into 'main'
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CI fixes
See merge request naaice/poet!24
2024-03-07 14:40:15 +01:00
Max Lübke
6e055a52e1
Fix build of pages
2024-03-07 13:39:27 +00:00
Max Lübke
49917d2d23
Add Dockerfile for CI environment
2024-03-07 13:39:14 +00:00
Max Lübke
157a8303e5
Merge branch 'v0.x' into 'main'
...
Preparation for EuroPar24 contribution
See merge request naaice/poet!23
2024-03-06 14:37:39 +01:00
Max Lübke
09adce1f8b
Merge remote-tracking branch 'origin/main' into v0.x
2024-03-06 13:36:36 +00:00
Max Lübke
251f760564
Update doxygen configuration
2024-03-06 12:25:30 +00:00
Max Lübke
4887699b35
Add Dockerfile and devcontainer.json for VS Code development environment
2024-03-06 12:25:17 +00:00
Max Lübke
4b7700cb2a
Remove R_lib subdirectory from CMakeLists.txt
2024-03-06 12:24:07 +00:00
Max Lübke
62c0a74048
Merge branch 'include_scripts' into 'v0.x'
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Add R library file as string to executable
See merge request naaice/poet!21
2024-03-06 12:34:49 +01:00
Max Lübke
10c31e3a9a
Add R library file as string to executable
2024-03-06 12:34:02 +01:00
Max Lübke
13e79382fe
Merge branch 'restructure' into 'v0.x'
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Refactor build process
See merge request naaice/poet!20
2024-03-06 12:03:49 +01:00
Max Lübke
2bfee6c99f
Remove unused CMakeLists.txt file for SurrogateModels
2024-03-06 12:03:02 +01:00
Max Lübke
f7323c05c3
Add OMPI_SKIP_MPICXX to target_compile_definitions in CMakeLists.txt
2024-03-06 12:01:19 +01:00
Max Lübke
3613d52d1e
Update CMakeLists.txt and include headers in test files
2024-03-06 11:59:18 +01:00
Max Lübke
1250dc59d9
Add Macros.hpp and RInsidePOET.hpp***
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***Add RInsidePOET class and RHookFunction template***
***Update include paths in SimParams.hpp***
***Update CMakeLists.txt to link poetlib***
***Update DHT_Wrapper.hpp include path***
***Update DiffusionModule.cpp include path***
***Update poet.cpp include paths***
***Add poet.hpp.in
2024-03-06 11:59:12 +01:00
Max Lübke
52fdbb8d2f
Remove unused 'app' directory
2024-03-06 11:32:45 +01:00
Max Lübke
fb8a8d24b6
Refactor build process
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Now include/app paths are combined in the src dir.
2024-03-06 11:26:52 +01:00
Max Lübke
3d9f8d84cd
Fix broken Dolo large benchmark
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Update surfex to a larger grid size
2024-03-01 12:57:42 +01:00
Max Lübke
6c4df5f375
Update initial and boundary conditions for dolo large model
2024-02-26 12:34:42 +01:00
Max Lübke
b5eb0e6592
Add .vscode to .gitignore
2024-02-22 09:47:05 +01:00
Marco De Lucia
bb7e684d8f
fix: updated bench/barite/{barite.R, barite_interp_eval.R}, added bench/barite/barite_200.R
2024-01-12 12:50:54 +01:00
Max Lübke
de3b2db455
Update file dolo_interp_long.R
2023-11-21 16:25:50 +01:00
Max Lübke
87c32156b9
docs: improve main SVG
2023-11-01 11:01:38 +01:00
Max Lübke
ffce08f406
feat: instead of always storing exact input and output make it dependent
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on the usage of interpolation
2023-11-01 10:55:46 +01:00
Max Lübke
a9a14cf333
feat: make storage of input values in DHT optional
2023-09-08 22:43:52 +02:00
Max Lübke
c4995f86c0
fix: output DHT size in megabyte
2023-09-07 09:12:44 +02:00
Marco De Lucia
4ddf243520
docs: README for surfex bench
2023-08-26 18:39:50 +02:00
Marco De Lucia
5a38e5df0f
fix: stdout time for diffusion step. Fixes in READMEs
2023-08-26 17:34:21 +02:00
Marco De Lucia
efd01ea390
docs: readmes for dolo & barite
2023-08-26 17:22:22 +02:00
Marco De Lucia
d2039354eb
ICs, BCs, fixes
2023-08-26 14:24:26 +02:00
Marco De Lucia
8b8444edd4
refs, eqs and text
2023-08-26 13:55:06 +02:00
Marco De Lucia
5b9bc2c70c
more eqs and text
2023-08-26 13:41:00 +02:00
Marco De Lucia
ac9dc30eca
eqs and text
2023-08-26 13:10:17 +02:00
Marco De Lucia
451c37aac3
some fixes
2023-08-26 12:50:12 +02:00
Marco De Lucia
b8096411f6
Revert "Update file README.org"
...
This reverts commit 462cf2f08e7426661b419a2f52bb48287f847d94
2023-08-26 12:49:31 +02:00
