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Author	SHA1	Message	Date
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