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Author	SHA1	Message	Date
Max Lübke	480dd146f4	BREAKING CHANGE: Enable Surface/Exchange using new API of PhreeqcEngine	2024-05-06 10:01:57 +00:00
Max Luebke	d7c23c6b3c	Fix build process to only produce benchmarks when needed	2024-04-15 09:10:11 +00:00
Max Lübke	e11caba0b3	Fix grid size assignment in GridInit.cpp	2024-04-12 12:35:43 +00:00
Max Lübke	6d36dd7a2e	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	7ee438b667	Remove doctest submodule	2024-04-10 10:24:00 +00:00
Max Lübke	f4661a591c	Fix diffusion and chem field update order in RunMasterLoop	2024-04-10 10:24:00 +00:00
Max Lübke	103b26a097	Refactor process to output as DataFrames	2024-04-10 10:24:00 +00:00
Max Lübke	f2c5caf307	Refactor R package dependencies in Dockerfile	2024-04-09 08:09:47 +00:00
Max Luebke	e27ce205fb	Add minimal flag to importList function in InitialList	2024-04-08 20:47:38 +00:00
Max Luebke	8856825c23	Refactor Field.cpp to use Rcpp DataFrame for conversion to SEXP	2024-04-08 20:31:36 +00:00
Max Luebke	c42b335aae	Refactor build file generation	2024-04-08 20:31:36 +00:00
Max Luebke	a2f04836a4	Refactor benchmark files to current POET input expectations	2024-04-08 20:31:36 +00:00
Max Luebke	7febb31bf9	Refactor command line argument handling and improve script sourcing in initializer.cpp	2024-04-08 12:49:58 +00:00
Max Luebke	c9ff062514	Refactor initializer.cpp to handle command line arguments and improve script sourcing	2024-04-08 12:02:47 +00:00
Max Luebke	62e734e0d5	Refactor code for grid creation and result storage	2024-04-08 11:27:06 +00:00
Max Luebke	3ea3412516	Fix inner_boundaries handling in DiffusionModule and InitialList	2024-04-08 10:32:00 +00:00
Max Luebke	8d64c83123	Update minimum required CMake version to 3.14	2024-04-08 10:31:47 +00:00
Max Luebke	fa916cc66e	Refactor code according to static analyzers	2024-04-08 09:19:48 +00:00
Max Luebke	e6092c9166	Add dolo_inner benchmark	2024-04-05 08:34:41 +00:00
Max Luebke	a24b4f5f51	Move old benchmark files into old subdir ... Move new benchmark files from `het` folder	2024-04-05 08:33:26 +00:00
Max Luebke	5cc161e25e	Add inner_boundaries handling in DiffusionModule and InitialList	2024-04-05 08:31:32 +00:00
Max Luebke	35049e1a77	Update .gitignore to ignore .codechecker directory	2024-04-05 07:05:09 +00:00
Max Luebke	6a88de5c5d	Refactor code for grid creation and result storage	2024-04-04 09:27:52 +00:00
Max Luebke	d07cfd3465	Add functions for checking sign and negativity in dol.pqi and dolo_200.R	2024-04-04 09:27:27 +00:00
Max Luebke	004977b2ea	Add file extension replacement and print output filename	2024-04-03 21:19:39 +00:00
Max Luebke	0a00ea86e6	Update Dockerfile with required dependencies and install R packages	2024-04-03 21:03:16 +00:00
Max Luebke	5ce40617b8	Refactor R functions and how they are called	2024-04-03 21:03:10 +00:00
Max Lübke	2b6f17f18c	Update iterations and dt values in dolo_200_rt.R	2024-04-03 16:46:50 +02:00
Max Luebke	33f3368d6e	Add parallel grid creation function and update pqc_to_grid function	2024-04-03 14:25:04 +00:00
Max Luebke	24b2ed5b46	Fix initialization of transport_names in ChemistryInit and GridInit	2024-04-03 14:25:04 +00:00
Max Luebke	9976538c11	Update solution parameters in dol.pqi	2024-04-03 14:25:04 +00:00
Max Luebke	38053fd4d0	Add support for missing species in init grid, which are injected (by boundary condition)	2024-04-03 14:25:04 +00:00
Max Luebke	57aaff4d69	Update iphreeqc subproject commit	2024-04-03 10:47:33 +00:00
Max Luebke	ffd076047d	Update chem.GetField() to chem.getField() in poet.cpp	2024-04-03 10:47:32 +00:00
Max Luebke	41b811f048	Update runtime and test scripts	2024-04-03 10:46:54 +00:00
Max Lübke	7aea66387a	Update units in dol.pqi	2024-04-03 10:59:31 +02:00
Max Lübke	f2e0942737	Update GIT_SUBMODULE_STRATEGY in .gitlab-ci.yml	2024-04-03 10:10:02 +02:00
Max Lübke	13b6cf6549	Update Calcite and Dolomite parameters in dol.pqi	2024-04-03 10:08:37 +02:00
Max Lübke	4468945dec	Update out_save in dolo_200_rt.R	2024-04-03 10:08:02 +02:00
Max Luebke	8da05bcf4a	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	ebfa47a494	Remove SimParams class	2024-04-02 20:38:23 +00:00
Max Luebke	246fbf4434	Add check_sign_cal_dol_dht and fuzz_input_dht_keys functions	2024-04-02 20:35:28 +00:00
Max Luebke	04ce6d35d6	Refactor WorkerRunWorkPackage to copy input instead of overwriting	2024-04-02 20:24:04 +00:00
Max Luebke	5972afe12f	Refactor chemistry module and RHookFunction	2024-04-02 20:23:42 +00:00
Max Luebke	658fe00bc9	Update iteration end message in kin_r_library.R	2024-04-02 14:37:20 +00:00
Max Luebke	a9a798dd4a	Add profiling data for DHT and interpolation	2024-04-02 14:17:59 +00:00
Max Luebke	c667bee7d8	Add DHT functionality, still need to be validated	2024-04-02 14:14:19 +00:00
Max Luebke	b229377adb	Add chemistry initialization to InitialList class	2024-04-02 12:06:55 +00:00
Max Luebke	14b111662d	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	1353460c11	Update dependencies and refactor code	2024-04-02 11:41:38 +00:00