Max Luebke
9978016854
Add file extension replacement and print output filename
2024-04-03 21:19:39 +00:00
Max Luebke
6d7666abbc
Refactor R functions and how they are called
2024-04-03 21:03:10 +00:00
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
