309 Commits

This Branch

This Branch

All Branches

Author	SHA1	Message	Date
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