Marco De Lucia
9d16b2e92d
removed .ai dir from this branch
2025-11-14 10:58:43 +01:00
rastogi
aa76830c5e
Stop tracking bin/dolo/ and update .gitignore
2025-11-13 16:00:47 +01:00
rastogi
51d78dbb85
updated .gitignore
2025-11-12 10:25:58 +01:00
rastogi
28bd24f9f6
Store per-cell MAPE/RRMSE and add stabilization interval
2025-11-12 10:20:28 +01:00
rastogi
6fbeaed12d
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
6c5b86cccc
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
1b2d942960
feat: bcast control_cell_ids to workers
2025-11-02 22:26:14 +01:00
rastogi
7c97f29fa6
Added ctrl_cell_ids
2025-10-30 21:36:03 +01:00
rastogi
8c388e3c6c
Restructuring prototyp 3
2025-10-30 16:15:27 +01:00
rastogi
8a247082aa
Add .gitignore
2025-10-30 16:14:22 +01:00
rastogi
104301dd5f
Merge branch 'control-loop' of git.gfz-potsdam.de:naaice/poet into control-loop
2025-10-02 13:21:57 +02:00
rastogi
7467bbe50a
feat(control): dynamic prototype, penalty_iteration, error while disabling surrogate fixed
2025-10-02 13:20:53 +02:00
Max Lübke
1af661527d
feat(grid): enable cell_ID integration in chemistry data flow
2025-09-25 15:08:13 +02:00
rastogi
c10d35fabe
rollback implemented, triggered when MAPE exceeds epsilon
2025-09-12 09:47:00 +02:00
Max Lübke
279a975359
cleanup computeStats()
2025-09-04 14:20:08 +02:00
Max Lübke
fbdec9f015
fix mssing handling of different storage locatios of work packages
2025-09-04 14:19:54 +02:00
Max Lübke
0d22cc2056
formatting MasterFunctions.cpp
2025-09-04 13:54:43 +02:00
Max Lübke
35f95430a8
stuff in computeStats
2025-09-02 13:05:47 +02:00
Max Lübke
d9026b1017
Add fgcs dolo benchmark
2025-09-02 12:04:38 +02:00
Max Lübke
d241db00b8
rename control work package and subsitute interpolated work package
2025-09-02 11:03:33 +02:00
rastogi
1e06113d64
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
0cc0c9cdf6
computeStats not working correctly, Unit Tests added
2025-09-01 12:39:01 +02:00
Max Lübke
12d39ecb9b
feat: Implement checkpointing
...
Co-authored-by: hmars-t <hmars-t@users.noreply.github.com>
2025-08-01 11:27:25 +02:00
rastogi
3002a798c7
Initial commit
2025-08-01 11:09:59 +02:00
Max Lübke
b80ee926da
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
9ab13ca547
Add CMake Build Type to Readme
2025-05-20 14:28:45 +02:00
Marco De Lucia
d169c5583b
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
fe8f2f1edf
fix: Correct boolean conversion in DHT hook call
2025-03-12 10:35:23 +01:00
Hannes Martin Signer
36776a1863
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
ae6066414b
Add option to toggle tug numerical solver approach
2025-01-29 15:53:32 +01:00
Max Lübke
caffae2d54
refactor: clean up CMakeLists.txt by removing unnecessary target_sources indentation
2025-01-09 12:18:13 +01:00
Max Lübke
e603a5a995
feat: add index tracking and flushing functionality to DHT
2025-01-09 12:18:05 +01:00
Max Lübke
375a5cb38b
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
912ab21802
[wip] add input validation for work_package in DHT_Wrapper and InterpolationModule
2024-12-20 10:12:19 +01:00
Max Lübke
db2f6cc71e
fix: update grid dimensions and refine species definitions in barite_fgcs_2.R
2024-12-20 10:08:07 +01:00
Marco De Lucia
ed27e0d4cc
Fancier benchmark for fgcs paper
2024-12-20 10:08:07 +01:00
Max Lübke
75ca4bc74e
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
aa2cb259a5
fix: remove duplicate flag for saving output as .qs file in parseInitValues
2024-12-20 10:05:49 +01:00
Marco De Lucia
894cc256b2
Fancier benchmark for fgcs paper
2024-12-20 09:24:19 +01:00
Max Lübke
efaac15a79
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
c6910eb96e
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
b9e18a1059
fix: initialize default values for RuntimeParameters in poet.hpp.in
2024-12-20 09:21:18 +01:00
Max Lübke
cfea048fdb
fix: update dht_species values for barite and celestite in benchmark scripts
2024-12-20 09:21:18 +01:00
Max Lübke
f0eacc0f40
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
af5d2a7a70
fix: handle zero distance case in inverseDistanceWeighting to prevent division by zero
2024-12-20 09:21:18 +01:00
Max Lübke
e1d1a577bc
feat: add with_h0_o0 and with_redox parameters to ChemistryModule and related classes
2024-12-20 09:21:18 +01:00
Max Luebke
b4c437e614
feat: add support for redox in PhreeqcMatrix initialization
2024-12-20 09:21:18 +01:00
Max Lübke
0e683d98ce
feat: enhance LookupKey with const isnan method and comparison operator
2024-12-20 09:21:18 +01:00
Max Lübke
7ba9ddfa83
refactor: streamline WorkPackage constructor and improve DHT_Wrapper::fillDHT logic
2024-12-20 09:21:17 +01:00
Max Luebke
6a889b5364
feat: add dht_snaps and dht_out_dir parameters to ChemistryModule and main function
2024-12-20 09:21:17 +01:00
Max Luebke
034ec5d9f7
fix: initialize includeH0O0 to false in command line options
2024-12-20 09:21:17 +01:00
Max Luebke
50e856b28b
feat: make output of H(0) and O(0) optional
2024-12-20 09:21:17 +01:00
Max Lübke
cd53f43bd2
feat: add has_het_ids parameter to DHT initialization and related functions
2024-12-20 09:21:17 +01:00
Max Lübke
5f56ce9e3f
fix: use const reference for to_calc in InterpolationModule to improve performance
2024-12-20 09:21:17 +01:00
Max Lübke
1a680d8ca6
fix: remove double initialization of dht_enabled in ChemistryModule
2024-12-20 09:21:17 +01:00
Max Lübke
1b4691c172
feat: implement caching for interpolation calculations and add NaN handling
2024-12-20 09:21:16 +01:00
Max Luebke
07ac2bfd8d
[wip] fix: add base_totals to SurrogateSetup
2024-12-20 09:21:16 +01:00
Marco De Lucia
3a164ed716
reverting <format> since gcc < 13 does not support it
2024-12-20 09:21:16 +01:00
Marco De Lucia
c4780fe9af
Update references to .qs2 in README
2024-12-20 09:21:16 +01:00
Marco De Lucia
3d0a9041b5
Update README: qs2 as default output format, gfz.de everywhere
2024-12-20 09:21:16 +01:00
Marco De Lucia
54d6b6bbf2
Less and more informative stdout messages
2024-12-20 09:21:16 +01:00
Marco De Lucia
5493cf88a9
Added qs2 as new default format
2024-12-20 09:21:15 +01:00
Max Lübke
ff7cf31e10
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
101f00f452
Refactor CI pipeline by removing the build stage and adjusting test job dependencies
2024-12-20 09:04:30 +01:00
Max Lübke
c0d3485edb
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
426429f8a9
Update LICENSE to include updated copyright notice and additional guidelines for program distribution
2024-12-20 08:58:40 +01:00
Max Lübke
6714082646
Revert "No code changes made."
...
This reverts commit 8b35513b8824a31c21ab53c27ca2f89ce92ae36c.
2024-12-20 08:57:51 +01:00
Max Lübke
ea0c21c9da
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
8b35513b88
No code changes made.
2024-12-20 08:46:51 +01:00
Max Lübke
9d7fa5457d
Merge branch 'mdl/fgcsbench' into 'main'
...
Mdl/fgcsbench
See merge request naaice/poet!43
2024-12-13 12:19:57 +01:00
Marco De Lucia
f1b166145e
reverting <format> since gcc < 13 does not support it
2024-12-13 12:14:55 +01:00
Marco De Lucia
fbd4739360
Update references to .qs2 in README
2024-12-13 12:14:55 +01:00
Marco De Lucia
ce5db73604
Update README: qs2 as default output format, gfz.de everywhere
2024-12-13 12:14:55 +01:00
Marco De Lucia
a714211560
Less and more informative stdout messages
2024-12-13 12:14:55 +01:00
Marco De Lucia
18725bf87d
Added qs2 as new default format
2024-12-13 12:14:55 +01:00
Hannes Martin Signer
cc439e7b5e
Merge branch 'update-scheme' into 'main'
...
update poet scheme
See merge request naaice/poet!42
2024-12-10 15:03:54 +01:00
Hannes Martin Signer
4d20b7c5bd
Update 2 files
...
- /docs/POET_scheme.svg
- /docs/POET.drawio
2024-12-10 15:02:45 +01:00
Max Lübke
4737330786
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
e40e6cb82f
update POET scheme
2024-12-10 11:14:01 +01:00
Max Lübke
e920ab2811
Merge branch 'ml/iphreeqc-v0.3' into 'main'
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Update IPhreeqc Submodule to v0.3
See merge request naaice/poet!40
2024-12-04 11:35:27 +01:00
Max Lübke
4d63544092
refactor: Replace PhreeqcEngine instances with PhreeqcRunner for improved chemistry processing
2024-12-04 10:34:13 +00:00
Max Lübke
c1ed926198
build: Enhance Dockerfile for improved environment setup and dependency management
2024-12-04 08:44:55 +00:00
Max Lübke
e31019e957
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
0ea5d70423
build: Update Dockerfile and devcontainer.json for enhanced environment setup
2024-11-07 19:56:04 +00:00
Max Lübke
c094aeaf39
build: Refactor R runtime detection in CMake to ensure required parameters are set
2024-11-07 19:56:04 +00:00
Max Lübke
909308b000
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
1f7b9f84cf
fix: Update getSolutionNames call to remove unnecessary argument
2024-11-07 14:22:58 +01:00
Max Lübke
9650e59115
Update subproject commit in ext/iphreeqc
2024-11-07 14:22:51 +01:00
Marco De Lucia
85aeb04bc4
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
0573001758
Update README.md
2024-09-26 11:45:07 +02:00
Marco De Lucia
d603589375
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
57d05f5c76
fix: Corrected log10 calculation in master_iteration_end function
2024-09-16 12:05:19 +02:00
Max Luebke
66fb9e601c
feat: use CLI11 as argument parser
...
feat: improve poet_initializer
2024-09-16 11:57:00 +02:00
Marco De Lucia
faf0ed20c3
fixed damn source_R
2024-09-12 16:15:21 +02:00
Marco De Lucia
8e7c5b1d60
cosmetic fixes in DiffusionInit.cpp
2024-09-12 14:57:11 +02:00
Marco De Lucia
6a8edd02bf
fix: removed Time-stamp lines from README and CMake/
2024-09-12 14:56:42 +02:00
Marco De Lucia
742b0babff
fix: removed all Time-stamp lines from src/
2024-09-12 14:56:09 +02:00
Marco De Lucia
7166cef64e
fixing stuff and adding comments
2024-09-12 14:54:05 +02:00
Marco De Lucia
ee40abf68b
Fixes in README and poet.cpp
2024-09-12 14:53:58 +02:00
Marco De Lucia
2d4f4021ad
Update README.md
2024-09-12 14:51:44 +02:00
Max Lübke
76fc5bc0b4
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
e72272764d
fixed initializer. Format is given by extension in the -o argument
2024-09-12 14:42:59 +02:00
Marco De Lucia
5606a718db
feat: fast serialization/storage using qs package via --qs flag
...
rebasing/merging
2024-09-12 14:42:24 +02:00
Marco De Lucia
d0c912e078
cosmetic fixes in DiffusionInit.cpp
2024-09-12 12:37:49 +02:00
Marco De Lucia
2e1ea7f9c5
fix: removed Time-stamp lines from README and CMake/
...
Solve conflict
2024-09-12 12:37:28 +02:00
Marco De Lucia
4be947e5f2
fix: removed all Time-stamp lines from src/
2024-09-12 12:36:40 +02:00
Marco De Lucia
c39d40dc45
fixing stuff and adding comments
2024-09-12 12:36:40 +02:00
Marco De Lucia
f15eb084d0
Switched default bench init storage to qs
2024-09-12 12:36:40 +02:00
Marco De Lucia
2e115c865b
Fixing rebase conflicts
2024-09-12 12:36:11 +02:00
Marco De Lucia
e7c0f6cc49
Update README.md
2024-09-12 11:40:03 +02:00
Max Lübke
eee1f0d689
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
d35a9a6d95
fixed initializer. Format is given by extension in the -o argument
2024-09-12 11:40:03 +02:00
Marco De Lucia
4090c0a78f
feat: fast serialization/storage using qs package via --qs flag
2024-09-12 11:39:44 +02:00
Max Lübke
1210bdf487
Merge branch 'ml/chore' into 'main'
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chore: Update README and cleanup
See merge request naaice/poet!33
2024-08-29 14:26:13 +02:00
Max Lübke
9119504dcb
chore: remove preprocessed file from project structure
2024-08-29 14:25:37 +02:00
Max Lübke
23b4182a97
chore: Remove unnecessary code in FindRRuntime.cmake
2024-08-29 14:25:37 +02:00
Max Lübke
ee92c75330
doc: Update R package installation process for AI surrogate
2024-08-29 14:25:37 +02:00
Max Lübke
3d9e6ae13d
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
1f9ffe999f
Update subproject commit reference
2024-08-29 08:35:17 +02:00
Max Lübke
e25ebfffdb
fix: distribute species names across all processes
2024-08-29 08:35:11 +02:00
hans
b125016dab
Fix: merge issues
2024-06-05 16:43:33 +02:00
hans
c2ee1a7f04
Merge branch 'ai-surrogate-v03-temp' into ai_surrogate_merge
2024-06-05 16:02:30 +02:00
hans
df6127fbda
Merge branch 'origin/ai-surrogate-v03-temp-mdl' into ai_surrogate_merge
2024-06-05 15:59:00 +02:00
hans
efea0d5c19
fix: reserve vs resize in Worker
2024-06-05 15:54:19 +02:00
hans
692c47781e
fix: wp_start_index in Worker
2024-05-31 11:45:19 +02:00
hans
dad82f22ba
fix: wp_start_index in Worker
2024-05-31 11:26:50 +02:00
Marco De Lucia
7f522157d1
MDL: AI model seems correctly updated/stored
2024-05-30 13:37:28 +02:00
hans
330fcc897c
docs: updated graphic
2024-05-30 13:30:43 +02:00
hans
e8dabdcfe2
docs: updated graphic
2024-05-30 13:30:10 +02:00
hans
f452ee3d81
docs: updated graphic
2024-05-30 13:28:48 +02:00
Hans Straile
9bf3c058df
Update 0230720_Scheme_POET_en.svg
2024-05-30 13:25:15 +02:00
hans
4b07880a06
docs: updated docs for v03
2024-05-30 13:20:50 +02:00
Marco De Lucia
b974b96d27
MDL: added barite_50ai bench
2024-05-30 11:37:31 +02:00
Marco De Lucia
d00369def7
MDL: some fixes and some more output to make AI run
2024-05-30 11:32:08 +02:00
hans
99d0b8c70d
feat: Add AI Surrogate functions to V.03
2024-05-27 15:22:29 +02:00
hans
a55a7ae095
feat: Add AI Surrogate functions to V.03
2024-05-27 09:09:01 +02:00
Max Lübke
e3633b4485
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
365017d811
chore: Update subproject commit in ext/iphreeqc
2024-05-07 09:52:31 +00:00
Max Lübke
282282e8b6
fix: Correct logic for updating output values in WorkerRunWorkPackage
2024-05-07 08:34:18 +00:00
Max Lübke
c660d5f117
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
9ac57682f1
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
9addc002a2
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
41fbd44c52
Refactor CI/CD pipeline
2024-05-06 13:17:39 +02:00
Max Lübke
8cab722ae3
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
0992143be5
Update Readme
2024-05-06 10:09:28 +00:00
Max Lübke
a12ac2c3d5
Add EGU debug model
2024-05-06 10:09:28 +00:00
Max Lübke
2b69da0c5d
BREAKING CHANGE: Enable Surface/Exchange using new API of PhreeqcEngine
2024-05-06 10:01:57 +00:00
Max Luebke
e7d9afd971
Fix build process to only produce benchmarks when needed
2024-04-15 09:10:11 +00:00
Max Lübke
c101564ee8
Fix grid size assignment in GridInit.cpp
2024-04-12 12:35:43 +00:00
Max Lübke
546f6fadbe
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
47a6a14100
Remove doctest submodule
2024-04-10 10:24:00 +00:00
Max Lübke
b3fd383674
Fix diffusion and chem field update order in RunMasterLoop
2024-04-10 10:24:00 +00:00
Max Lübke
32f7f5af70
Refactor process to output as DataFrames
2024-04-10 10:24:00 +00:00
Max Lübke
721388ae12
Refactor R package dependencies in Dockerfile
2024-04-09 08:09:47 +00:00
Max Luebke
41d00fd079
Add minimal flag to importList function in InitialList
2024-04-08 20:47:38 +00:00
Max Luebke
830e139122
Refactor Field.cpp to use Rcpp DataFrame for conversion to SEXP
2024-04-08 20:31:36 +00:00
Max Luebke
5182b6aa20
Refactor build file generation
2024-04-08 20:31:36 +00:00
Max Luebke
d53db0d5a5
Refactor benchmark files to current POET input expectations
2024-04-08 20:31:36 +00:00
Max Luebke
d5e4b03339
Refactor command line argument handling and improve script sourcing in initializer.cpp
2024-04-08 12:49:58 +00:00
Max Luebke
89cc239583
Refactor initializer.cpp to handle command line arguments and improve script sourcing
2024-04-08 12:02:47 +00:00
Max Luebke
fb62fd5a7f
Refactor code for grid creation and result storage
2024-04-08 11:27:06 +00:00
Max Luebke
05d6170943
Fix inner_boundaries handling in DiffusionModule and InitialList
2024-04-08 10:32:00 +00:00
Max Luebke
18fd280f99
Update minimum required CMake version to 3.14
2024-04-08 10:31:47 +00:00
Max Luebke
2c7fc089cc
Refactor code according to static analyzers
2024-04-08 09:19:48 +00:00
Max Luebke
9a7b6f0f24
Add dolo_inner benchmark
2024-04-05 08:34:41 +00:00
Max Luebke
e57f7923dd
Move old benchmark files into old subdir
...
Move new benchmark files from `het` folder
2024-04-05 08:33:26 +00:00
Max Luebke
07cf952cee
Add inner_boundaries handling in DiffusionModule and InitialList
2024-04-05 08:31:32 +00:00
Max Luebke
2ebbb48e4b
Update .gitignore to ignore .codechecker directory
2024-04-05 07:05:09 +00:00
Max Luebke
e891774d6c
Refactor code for grid creation and result storage
2024-04-04 09:27:52 +00:00
Max Luebke
3add44ce25
Add functions for checking sign and negativity in dol.pqi and dolo_200.R
2024-04-04 09:27:27 +00:00
Max Luebke
9978016854
Add file extension replacement and print output filename
2024-04-03 21:19:39 +00:00
Max Luebke
8097723d8e
Update Dockerfile with required dependencies and install R packages
2024-04-03 21:03:16 +00:00
Max Luebke
6d7666abbc
Refactor R functions and how they are called
2024-04-03 21:03:10 +00:00
Max Lübke
9eeb1502e1
Update iterations and dt values in dolo_200_rt.R
2024-04-03 16:46:50 +02:00
Max Luebke
0cf6d65128
Add parallel grid creation function and update pqc_to_grid function
2024-04-03 14:25:04 +00:00
Max Luebke
dd5c14aa88
Fix initialization of transport_names in ChemistryInit and GridInit
2024-04-03 14:25:04 +00:00
Max Luebke
7655376f89
Update solution parameters in dol.pqi
2024-04-03 14:25:04 +00:00
Max Luebke
dc3502685c
Add support for missing species in init grid, which are injected (by boundary condition)
2024-04-03 14:25:04 +00:00
Max Luebke
7be00983e5
Update iphreeqc subproject commit
2024-04-03 10:47:33 +00:00
Max Luebke
d389347ad3
Update chem.GetField() to chem.getField() in poet.cpp
2024-04-03 10:47:32 +00:00
Max Luebke
465a6595b0
Update runtime and test scripts
2024-04-03 10:46:54 +00:00
Max Lübke
9fb97aeda9
Update units in dol.pqi
2024-04-03 10:59:31 +02:00
Max Lübke
72079543db
Update GIT_SUBMODULE_STRATEGY in .gitlab-ci.yml
2024-04-03 10:10:02 +02:00
Max Lübke
efc1bda554
Update Calcite and Dolomite parameters in dol.pqi
2024-04-03 10:08:37 +02:00
Max Lübke
5f0dc14802
Update out_save in dolo_200_rt.R
2024-04-03 10:08:02 +02:00
Max Luebke
4784fc3e12
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
b5dedb3422
Remove SimParams class
2024-04-02 20:38:23 +00:00
Max Luebke
9b38cd2dc1
Add check_sign_cal_dol_dht and fuzz_input_dht_keys functions
2024-04-02 20:35:28 +00:00
Max Luebke
e380e8fd19
Refactor WorkerRunWorkPackage to copy input instead of overwriting
2024-04-02 20:24:04 +00:00
Max Luebke
90287ab445
Refactor chemistry module and RHookFunction
2024-04-02 20:23:42 +00:00
Max Luebke
f2e8f6023d
Update iteration end message in kin_r_library.R
2024-04-02 14:37:20 +00:00
Max Luebke
bda9993bcb
Add profiling data for DHT and interpolation
2024-04-02 14:17:59 +00:00
Max Luebke
47aa43d1e1
Add DHT functionality, still need to be validated
2024-04-02 14:14:19 +00:00
Max Luebke
082a758f18
Add chemistry initialization to InitialList class
2024-04-02 12:06:55 +00:00
Max Luebke
bd4d7a38ca
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
fb725f0b50
Update dependencies and refactor code
2024-04-02 11:41:38 +00:00
Max Luebke
f184fb7962
Remove doctest submodule and update gitmodules
2024-04-02 10:33:56 +00:00
Max Luebke
20d0eb52ae
Update CMakeLists.txt and include headers in test files
2024-04-02 09:25:18 +00:00
Max Luebke
53f68a2e56
Remove unnecessary includes and update function signature
2024-04-02 09:16:58 +00:00
Max Lübke
a345191d5a
Update dependencies and refactor code
2024-03-28 14:23:20 +00:00
Max Lübke
38a631f0ab
Add Basic heterogeneous diffusion functionality
2024-03-27 20:34:48 +00:00
Max Luebke
d3632156a5
Add total_grid_cells to ChemistryInit struct
2024-03-21 22:33:40 +00:00
Max Lübke
756988da31
Add support for importing and exporting initial grid in InitialList class
2024-03-21 21:36:09 +00:00
Max Lübke
94a4f71038
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
4e86e7f86d
Update include statement and add CMakeLists.txt for DataStructures
2024-03-20 22:33:23 +00:00
Max Luebke
ce2f9e237f
Update grid and diffusion setup in test.R
2024-03-19 22:03:22 +00:00
Max Lübke
bbeff06083
Add resolvePqcBound function and refactor parseBoundaries2D function
2024-03-19 15:37:29 +00:00
Max Lübke
64ec44034c
Update alpha matrix parsing
2024-03-19 14:07:25 +00:00
Max Lübke
1d24e670e5
Refactor initialization code for diffusion and grid
2024-03-19 13:39:59 +00:00
Max Lübke
b6a5a7a6a2
Add file reading functionality and update script and database handling
2024-03-19 13:11:42 +00:00
Max Lübke
14411ac319
Refactor grid initialization and update member access in InitialList
2024-03-19 12:32:16 +00:00
Max Lübke
15d9b06516
Update getModuleSizes function to use new API
2024-03-19 09:48:31 +00:00
Max Lübke
822e069492
Refactor pqc_to_grid function to use matrix instead of data.table
2024-03-19 09:47:40 +00:00
Max Luebke
f832a9e0db
Save latest changes, boundaries still missing or incomplete
2024-03-19 08:12:20 +00:00
Max Luebke
87de816f93
Add modify_module_sizes function and modify module_sizes in InitialList class
2024-03-13 23:50:13 +01:00
Max Luebke
62ad47952b
Update function name to replaceRawKeywordIDs in GridInit.cpp
2024-03-13 22:06:07 +01:00
Max Luebke
2a0dc93778
Update RAW Keywords to always refer to ID 1
2024-03-13 22:05:06 +01:00
Max Luebke
f7a4bcd0aa
Update CMakeLists.txt and add new files for barite_het simulation
2024-03-13 17:11:53 +01:00
Max Luebke
ec555c879c
Remove installation of poet binary
2024-03-13 16:58:37 +01:00
Max Luebke
3380eb4a8f
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
27e99052b2
Add apps directory and initializer application
2024-03-07 13:54:53 +00:00
Max Lübke
805f674043
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
2612bf04ed
Fix path in GitLab CI script
2024-03-07 13:41:50 +00:00
Max Lübke
ff6cf66be1
Update dependencies in ci.Dockerfile
2024-03-07 13:41:34 +00:00
Max Lübke
9d2c839a3d
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
2c5c6dd166
Fix build of pages
2024-03-07 13:39:27 +00:00
Max Lübke
99a62420e7
Add Dockerfile for CI environment
2024-03-07 13:39:14 +00:00
Max Lübke
f2ae204ddc
Merge branch 'v0.x' into 'main'
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Preparation for EuroPar24 contribution
See merge request naaice/poet!23
2024-03-06 14:37:39 +01:00
Max Lübke
1c170d687b
Merge remote-tracking branch 'origin/main' into v0.x
2024-03-06 13:36:36 +00:00
Max Lübke
7181465835
Update doxygen configuration
2024-03-06 12:25:30 +00:00
Max Lübke
a3683f0459
Add Dockerfile and devcontainer.json for VS Code development environment
2024-03-06 12:25:17 +00:00
Max Lübke
263f23534d
Remove R_lib subdirectory from CMakeLists.txt
2024-03-06 12:24:07 +00:00
Max Lübke
66d64a5772
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
ab83d8c350
Add R library file as string to executable
2024-03-06 12:34:02 +01:00
Max Lübke
f542c5638b
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
0fa0aa699b
Remove unused CMakeLists.txt file for SurrogateModels
2024-03-06 12:03:02 +01:00
Max Lübke
ffb4fe6bc6
Add OMPI_SKIP_MPICXX to target_compile_definitions in CMakeLists.txt
2024-03-06 12:01:19 +01:00
Max Lübke
a2ebc3f1d7
Update CMakeLists.txt and include headers in test files
2024-03-06 11:59:18 +01:00
Max Lübke
7abf987123
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
fbff818e48
Remove unused 'app' directory
2024-03-06 11:32:45 +01:00
Max Lübke
62412e8d87
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
e5ed6f9f87
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
ee0bd9167c
Update initial and boundary conditions for dolo large model
2024-02-26 12:34:42 +01:00
Max Lübke
caa54ebf5d
Add .vscode to .gitignore
2024-02-22 09:47:05 +01:00
Marco De Lucia
0b14de480b
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
433f095f58
Update file dolo_interp_long.R
2023-11-21 16:25:50 +01:00
Max Lübke
75702bb351
docs: improve main SVG
2023-11-01 11:01:38 +01:00
Max Lübke
bb12c1bb81
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
384f5bd336
feat: make storage of input values in DHT optional
2023-09-08 22:43:52 +02:00
Max Lübke
5cd517510f
fix: output DHT size in megabyte
2023-09-07 09:12:44 +02:00
Marco De Lucia
2b896fa070
docs: README for surfex bench
2023-08-26 18:39:50 +02:00
Marco De Lucia
e9ce4eeb1d
fix: stdout time for diffusion step. Fixes in READMEs
2023-08-26 17:34:21 +02:00
Marco De Lucia
bd5be576a7
docs: readmes for dolo & barite
2023-08-26 17:22:22 +02:00
Marco De Lucia
f0c9c3ea71
ICs, BCs, fixes
2023-08-26 14:24:26 +02:00
Marco De Lucia
b86931bffe
refs, eqs and text
2023-08-26 13:55:06 +02:00
Marco De Lucia
dbb25dc0af
more eqs and text
2023-08-26 13:41:00 +02:00
Marco De Lucia
a8d23a9563
eqs and text
2023-08-26 13:10:17 +02:00
Marco De Lucia
44c6e45fef
some fixes
2023-08-26 12:50:12 +02:00
Marco De Lucia
3c530a68d0
Revert "Update file README.org"
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This reverts commit 79ef735be72bfa3461efbef9c1b2b80af0d177f6
2023-08-26 12:49:31 +02:00
