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Author SHA1 Message Date
Max Luebke
8747917832 fix: do pre-copy of fields in grid class 
The idea is to later define chains of module in the input script by
setting an input and output field and the according function to call.

Currently, the code is not ready for such a chain, but the change is
done in advance.
 2023-01-23 16:36:54 +01:00
Max Luebke
1b3420c35e refactor: remove comments from code in Grid class 2023-01-23 15:06:27 +01:00
Max Lübke
5163e5f928 Merge branch 'refactor_grid' into 'main' 
refactor: make Grid class a bit more generic

See merge request sec34/port!12
 2023-01-23 14:58:02 +01:00
Max Luebke
376e7eab80 refactor: make Grid class a bit more generic 2023-01-23 14:57:26 +01:00
Marco De Lucia
77b3f13068 doc: update README.md 2023-01-06 10:56:05 +01:00
Max Luebke
f33ffbd82b fix: bring back old time and dt output to RDS file 2023-01-06 10:56:05 +01:00
Marco De Lucia
ab786e75da refactor: apply changes from MDL 2023-01-06 10:56:05 +01:00
Max Luebke
f479f82a07 fix: setting of inner constant cells 2023-01-06 10:56:05 +01:00
Max Luebke
bae7d769e7 BREAKING CHANGE: utilize PhreeqcRM and bring back old DHT bindings 2023-01-06 10:56:01 +01:00
Max Luebke
f7dd417c14 refactor: rename ChemSim to ChemSeq 
refactor: introduce new base class BaseChemModule for both sequential
and parallel chemistry module

refactor: iterative loop of simulations in poet application via template
function

This should make the application code more readable.
 2023-01-06 10:51:03 +01:00
Max Luebke
f2c81df096 BREAKING CHANGE: substitute R bindings of Phreeqc by PhreeqcRM 2023-01-06 10:51:03 +01:00
Max Lübke
7897c27644 perf: delete DHT object after shutdown 2023-01-06 10:51:03 +01:00
Max Luebke
0a8d2613e6 chore: remove unusable input script from install macro 2023-01-06 10:51:02 +01:00
Max Luebke
788513ff83 fix: missing namespace of phreeqcrm leads to ambiguous macro names 2023-01-06 10:51:02 +01:00
Max Luebke
af9a216e83 refactor: decouple ChemSim to ChemSimSeq and ChemSimPar 
refactor: cleanup of header files
 2023-01-06 10:51:02 +01:00
Max Luebke
c8453e48ca feat: Add phreeqcrm as submodule 2023-01-06 10:51:02 +01:00
Max Luebke
100b3746f5 fix: replace deprecated calls to MD5 functions 
perf: keep EVP context in memory during lifetime of DHT_Wrapper
 2022-12-01 16:46:58 +01:00
Max Lübke
756149c061 perf: remove unused R libraries/sources 2022-11-10 16:06:12 +01:00
Max Lübke
794cefdda3 perf: remove RRuntime as there is no need anymore 2022-11-10 16:06:12 +01:00
Max Lübke
d8e3a79034 feat: update input scripts to be used with DHT 2022-11-10 16:06:12 +01:00
Max Lübke
d406409fae refactor: conversion from R into C++ buffer inside worker function 2022-11-10 16:06:11 +01:00
Max Lübke
bf9f369846 refactor: cleanup of code, renaming of chemsitry module function and some output added to the diffusion module 2022-11-10 16:06:11 +01:00
Max Lübke
5a89c78bbc feat: enable parallelization with tug 2022-11-10 16:06:11 +01:00
Max Lübke
5a0749f06e fix: differentiate between 1D and 2D boundary condition 2022-11-10 16:06:11 +01:00
Max Lübke
34a4f1eaf2 fix: multiplication with 0 when starting 1D simulation 2022-11-10 16:06:11 +01:00
Max Lübke
5b4384ba86 refactor: edit input scripts to be expected input 2022-11-10 16:06:11 +01:00
Max Lübke
776e7d14c7 feat: allow more than one iteration in sequential mode 
fix: enable timesteps to simulate
 2022-11-10 16:06:11 +01:00
Max Lübke
d40bad186d refactor: cleanup R library 2022-11-10 16:06:11 +01:00
Max Lübke
dd32c0263e fix: use resize instead of reserve 2022-11-10 16:06:11 +01:00
Max Lübke
871a2ec82a BREAKING CHANGE: integrate 'tug' as diffusion module 
It is now possible to run a simulation for one iteration in sequential
mode without the use of Rmufits.

According scripts are provided.

refactor: TransportSim renamed to DiffusionModule

refactor: parsing of R input script is now done outside of simulation
modules (except ChemSim)
 2022-11-10 16:06:08 +01:00
Max Lübke
54681134b7 build: disable documentation generation per default 2022-11-10 16:02:20 +01:00
Max Lübke
e12510c4c2 fix: restore accidentally deleted edits to locate R packages 2022-11-10 16:00:11 +01:00
Max Lübke
0ade3762f0 build: Improve R library handling in CMake 2022-11-10 15:38:38 +01:00
Max Lübke
641e85bb85 ci: Init submodules recursive 2022-10-06 12:15:53 +02:00
Max Lübke
4aac153ed8 ci: Add generic build job 2022-10-06 11:01:49 +02:00
Max Lübke
1783160ba7 build: move headers to include 
build: instead of several libraries, build one lib and link to poet
application
 2022-10-05 12:16:53 +02:00
Max Lübke
0dee58b0de Update README.md 2021-02-26 19:35:51 +01:00
Max Lübke
60a8c11cec Merge branch 'dev' 2021-02-26 19:33:04 +01:00
Max Lübke
caaf33931e deleted old makefile 2021-02-26 19:23:12 +01:00
Marco De Lucia
6c6cb19677 Update README.md, changed options syntax from e.g. "-dht" to "--dht" 2021-02-24 14:07:46 +01:00
Marco De Lucia
272933c63f Update Output.md 2021-02-24 13:33:27 +01:00
Marco De Lucia
8b7d0381f1 Update README.md 2021-02-24 12:52:28 +01:00
Max Lübke
89b958970d Prepare project to transfer to svn + set poet version with help of 
git/textfiles
 2021-02-19 17:12:53 +01:00
Max Lübke
e9fdff456c update README.md 2021-02-17 19:57:08 +01:00
Max Lübke
3bbc2f325d new file describing output of POET + added target doxygen to CMake 2021-02-17 16:26:14 +01:00
Max Lübke
6246969041 change dht_collisions to dht_evictions + use option instead of set 2021-02-17 16:24:57 +01:00
Max Lübke
a580f450c0 update gitignore 2021-02-16 11:52:55 +01:00
Max Lübke
e0c0381681 Update README.md 2021-02-09 20:05:09 +01:00
Max Lübke
19c0442e46 fixed typo 2021-02-09 20:03:50 +01:00
Max Lübke
c223d9fd9a added CMake install process + rearrange data dir 2021-02-09 20:02:03 +01:00