295 Commits

This Branch

This Branch

All Branches

Author	SHA1	Message	Date
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
Max Luebke	76b83db4bc	Remove doctest submodule and update gitmodules	2024-04-02 10:33:56 +00:00
Max Luebke	af840e756e	Update CMakeLists.txt and include headers in test files	2024-04-02 09:25:18 +00:00
Max Luebke	a2dc30962f	Remove unnecessary includes and update function signature	2024-04-02 09:16:58 +00:00
Max Lübke	2c51cd90ef	Update dependencies and refactor code	2024-03-28 14:23:20 +00:00
Max Lübke	0bfc95bb52	Add Basic heterogeneous diffusion functionality	2024-03-27 20:34:48 +00:00
Max Luebke	a04344e435	Add total_grid_cells to ChemistryInit struct	2024-03-21 22:33:40 +00:00
Max Lübke	4fc0d5547b	Add support for importing and exporting initial grid in InitialList class	2024-03-21 21:36:09 +00:00
Max Lübke	7d4c14c356	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	2797351057	Update include statement and add CMakeLists.txt for DataStructures	2024-03-20 22:33:23 +00:00
Max Luebke	8cd69bcde4	Update grid and diffusion setup in test.R	2024-03-19 22:03:22 +00:00
Max Lübke	793c2bb4ff	Add resolvePqcBound function and refactor parseBoundaries2D function	2024-03-19 15:37:29 +00:00
Max Lübke	ebfa10c236	Update alpha matrix parsing	2024-03-19 14:07:25 +00:00
Max Lübke	badb01b4fe	Refactor initialization code for diffusion and grid	2024-03-19 13:39:59 +00:00
Max Lübke	d77aad7d2e	Add file reading functionality and update script and database handling	2024-03-19 13:11:42 +00:00
Max Lübke	8328fd1390	Refactor grid initialization and update member access in InitialList	2024-03-19 12:32:16 +00:00
Max Lübke	8d6aafbec4	Update getModuleSizes function to use new API	2024-03-19 09:48:31 +00:00
Max Lübke	c9cf6c92e7	Refactor pqc_to_grid function to use matrix instead of data.table	2024-03-19 09:47:40 +00:00
Max Luebke	60c3d7b022	Save latest changes, boundaries still missing or incomplete	2024-03-19 08:12:20 +00:00
Max Luebke	9990c12de4	Add modify_module_sizes function and modify module_sizes in InitialList class	2024-03-13 23:50:13 +01:00
Max Luebke	e102550835	Update function name to replaceRawKeywordIDs in GridInit.cpp	2024-03-13 22:06:07 +01:00
Max Luebke	eaf4b2b712	Update RAW Keywords to always refer to ID 1	2024-03-13 22:05:06 +01:00
Max Luebke	31d09ecc27	Update CMakeLists.txt and add new files for barite_het simulation	2024-03-13 17:11:53 +01:00
Max Luebke	5357bdf975	Remove installation of poet binary	2024-03-13 16:58:37 +01:00
Max Luebke	bcabe5bcc4	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	24b0607e94	Add apps directory and initializer application	2024-03-07 13:54:53 +00:00
Max Lübke	a6063776ea	Fix path in GitLab CI script	2024-03-07 13:41:50 +00:00
Max Lübke	29018afa13	Update dependencies in ci.Dockerfile	2024-03-07 13:41:34 +00:00
Max Lübke	5c44146633	Fix build of pages	2024-03-07 13:39:27 +00:00
Max Lübke	912c083353	Add Dockerfile for CI environment	2024-03-07 13:39:14 +00:00
Max Lübke	e6e159517d	Merge remote-tracking branch 'origin/main' into v0.x	2024-03-06 13:36:36 +00:00
Max Lübke	1b0d2c92fe	Update doxygen configuration	2024-03-06 12:25:30 +00:00