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Author	SHA1	Message	Date
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