170 Commits

Author	SHA1	Message	Date
Max Lübke	44775ea018	fix: Correct logic for updating output values in WorkerRunWorkPackage	2024-05-07 08:34:18 +00:00
Max Lübke	480dd146f4	BREAKING CHANGE: Enable Surface/Exchange using new API of PhreeqcEngine	2024-05-06 10:01:57 +00:00
Max Lübke	e11caba0b3	Fix grid size assignment in GridInit.cpp	2024-04-12 12:35:43 +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 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	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	3ea3412516	Fix inner_boundaries handling in DiffusionModule and InitialList	2024-04-08 10:32:00 +00:00
Max Luebke	fa916cc66e	Refactor code according to static analyzers	2024-04-08 09:19:48 +00:00
Max Luebke	5cc161e25e	Add inner_boundaries handling in DiffusionModule and InitialList	2024-04-05 08:31:32 +00:00
Max Luebke	6a88de5c5d	Refactor code for grid creation and result storage	2024-04-04 09:27:52 +00:00
Max Luebke	004977b2ea	Add file extension replacement and print output filename	2024-04-03 21:19:39 +00:00
Max Luebke	5ce40617b8	Refactor R functions and how they are called	2024-04-03 21:03:10 +00:00
Max Luebke	24b2ed5b46	Fix initialization of transport_names in ChemistryInit and GridInit	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	ffd076047d	Update chem.GetField() to chem.getField() in poet.cpp	2024-04-03 10:47:32 +00:00
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	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	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	1353460c11	Update dependencies and refactor code	2024-04-02 11:41:38 +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 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 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	e6e159517d	Merge remote-tracking branch 'origin/main' into v0.x	2024-03-06 13:36:36 +00:00
Max Lübke	06c63a125b	Add R library file as string to executable	2024-03-06 12:34:02 +01:00
Max Lübke	f1f56494f9	Remove unused CMakeLists.txt file for SurrogateModels	2024-03-06 12:03:02 +01:00