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298 Commits 14 Branches 10 Tags
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154 Commits

Author SHA1 Message Date
Max Luebke
dd5c14aa88 Fix initialization of transport_names in ChemistryInit and GridInit 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
d389347ad3 Update chem.GetField() to chem.getField() in poet.cpp 2024-04-03 10:47:32 +00:00
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
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
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
fb725f0b50 Update dependencies and refactor code 2024-04-02 11:41:38 +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 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 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
Max Luebke
62ad47952b Update function name to replaceRawKeywordIDs in GridInit.cpp 2024-03-13 22:06:07 +01:00
Max Luebke
2a0dc93778 Update RAW Keywords to always refer to ID 1 2024-03-13 22:05:06 +01:00
Max Luebke
f7a4bcd0aa Update CMakeLists.txt and add new files for barite_het simulation 2024-03-13 17:11:53 +01:00
Max Luebke
ec555c879c Remove installation of poet binary 2024-03-13 16:58:37 +01:00
Max Luebke
3380eb4a8f 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
1c170d687b Merge remote-tracking branch 'origin/main' into v0.x 2024-03-06 13:36:36 +00:00
Max Lübke
ab83d8c350 Add R library file as string to executable 2024-03-06 12:34:02 +01:00
Max Lübke
0fa0aa699b Remove unused CMakeLists.txt file for SurrogateModels 2024-03-06 12:03:02 +01:00
Max Lübke
ffb4fe6bc6 Add OMPI_SKIP_MPICXX to target_compile_definitions in CMakeLists.txt 2024-03-06 12:01:19 +01:00
Max Lübke
7abf987123 Add Macros.hpp and RInsidePOET.hpp*** 
***Add RInsidePOET class and RHookFunction template***
***Update include paths in SimParams.hpp***
***Update CMakeLists.txt to link poetlib***
***Update DHT_Wrapper.hpp include path***
***Update DiffusionModule.cpp include path***
***Update poet.cpp include paths***
***Add poet.hpp.in
 2024-03-06 11:59:12 +01:00
Max Lübke
62412e8d87 Refactor build process 
Now include/app paths are combined in the src dir.
 2024-03-06 11:26:52 +01:00
Max Lübke
bb12c1bb81 feat: instead of always storing exact input and output make it dependent 
on the usage of interpolation
 2023-11-01 10:55:46 +01:00
Max Lübke
384f5bd336 feat: make storage of input values in DHT optional 2023-09-08 22:43:52 +02:00
Max Lübke
5cd517510f fix: output DHT size in megabyte 2023-09-07 09:12:44 +02:00
Marco De Lucia
e9ce4eeb1d fix: stdout time for diffusion step. Fixes in READMEs 2023-08-26 17:34:21 +02:00
Marco De Lucia
b961c26a85 testing staged changes 2023-08-17 14:29:09 +02:00
Max Luebke
a5c8982b98 feat: implement SEXP export of Field structure 
feat: implement NamedVector based on Rcpp::NumericVector

feat: remove hard coded checks and substitute by R hook functions,
defined in the input script

refactor: modify API of DHT_Wrapper/InterpolationModule to expect a work
package structure, where input/output values are stored as 2D vectors

test: add tests for NamedVector

test: extend tests for Field
 2023-08-17 10:51:54 +02:00
Max Luebke
74ebe3e1f1 fix: only write PHT dump file if advised to do so 2023-08-15 17:33:10 +02:00
Marco De Lucia
344f73af23 fix: unnest pht- and dht-related outputs and stats collection in WorkerPostIter and WorkerPostSim 2023-08-11 14:44:26 +02:00
Marco De Lucia
fef482f5e0 fix: rounded_key instead of roundedKey 2023-08-11 11:04:11 +02:00
Max Luebke
f81fdfa3b4 fix: remove reworked part in output 2023-08-10 14:17:17 +02:00
Max Luebke
ff8da12193 feat: enable interpolation without DHT lookup 2023-08-10 14:15:26 +02:00
Marco De Lucia
5ce26df771 MDL: replaced all cout/cerr with macros MSG, ERRMSG... 2023-08-09 12:22:03 +02:00
Marco De Lucia
bb6ebf6ada MDL: add stdout message from initialisation in SimParams 2023-08-09 09:50:09 +02:00