233 Commits

Author	SHA1	Message	Date
Max Lübke	9122e51980	refactor: Rework deferred R function evaluation ... fix: Unique pointer behaviour of `global_rt_setup` was messed up	2024-09-12 11:40:03 +02:00
Marco De Lucia	fec92ad3d3	fixed initializer. Format is given by extension in the -o argument	2024-09-12 11:40:03 +02:00
Marco De Lucia	8d0be5ae0d	feat: fast serialization/storage using qs package via --qs flag	2024-09-12 11:39:44 +02:00
Max Lübke	cc943371a1	fix: distribute species names across all processes	2024-08-29 08:35:11 +02:00
hans	a65f4992ae	Fix: merge issues	2024-06-05 16:43:33 +02:00
hans	742ac96406	Merge branch 'origin/ai-surrogate-v03-temp-mdl' into ai_surrogate_merge	2024-06-05 15:59:00 +02:00
hans	dcfe2c58db	fix: reserve vs resize in Worker	2024-06-05 15:54:19 +02:00
hans	bea250cc88	fix: wp_start_index in Worker	2024-05-31 11:26:50 +02:00
Marco De Lucia	b75b37e0f8	MDL: AI model seems correctly updated/stored	2024-05-30 13:37:28 +02:00
hans	f8864d991a	docs: updated docs for v03	2024-05-30 13:20:50 +02:00
Marco De Lucia	69ebc516ba	MDL: some fixes and some more output to make AI run	2024-05-30 11:32:08 +02:00
hans	53b9479cad	feat: Add AI Surrogate functions to V.03	2024-05-27 15:22:29 +02:00
hans	95cb95998e	feat: Add AI Surrogate functions to V.03	2024-05-27 09:09:01 +02:00
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