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112 Commits

Author SHA1 Message Date
Marco De Lucia
93088f9bf5 testing staged changes 2023-08-17 14:29:09 +02:00
Max Luebke
c5a991c4c9 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
c4de48b17e fix: only write PHT dump file if advised to do so 2023-08-15 17:33:10 +02:00
Marco De Lucia
6f20cb897b 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
7a10217751 fix: rounded_key instead of roundedKey 2023-08-11 11:04:11 +02:00
Max Luebke
e82544a25d fix: remove reworked part in output 2023-08-10 14:17:17 +02:00
Max Luebke
164406ff25 feat: enable interpolation without DHT lookup 2023-08-10 14:15:26 +02:00
Marco De Lucia
8707da42c3 MDL: replaced all cout/cerr with macros MSG, ERRMSG... 2023-08-09 12:22:03 +02:00
Marco De Lucia
4181e189a1 MDL: add stdout message from initialisation in SimParams 2023-08-09 09:50:09 +02:00
Max Luebke
88662d6b2e fix: pass copy of map to DHT parsing 2023-08-04 13:40:20 +02:00
Max Luebke
52d8b164e6 fix: use output index also for weighting 2023-08-03 21:23:50 +02:00
Max Luebke
f7d8f8751a fix: apply weights to output values (rates) instead of input values 2023-08-03 17:22:59 +02:00
Max Luebke
d5d098d6cd Merge branch 'ml-doc' into v0.x 2023-08-02 14:00:44 +02:00
Max Luebke
37ee74faaf perf: remove unused parameters from paramlist and parameter structure 
doc: update doc to latest changes

data: update benchmarks to latest changes
 2023-08-02 14:00:14 +02:00
Max Luebke
4f9e66253f fix: remove mass balance check 2023-08-01 23:19:16 +02:00
Max Luebke
0c2597d97f feat: introduce LookupKey and rounding schemes 
feat: implement data clustering using PHT

feat: implement interpolation

refactor: use named vector for DHT species definition and significant digits

data: remove unusable input scripts

data: move Phreeqc database to benchmark dir

refactor: rename dolomite benchmark directory

refactor: remove DHT prop type from input script
 2023-08-01 18:34:50 +02:00
Max Luebke
bae5e96b7a refactor: remove support for PhreeqcRM support 2023-07-21 12:43:57 +02:00
Max Luebke
2914f59c13 build: build one poet library 2023-07-21 12:35:55 +02:00
Max Luebke
55dffe9308 feat: toggle progressbar by commandline option 2023-07-12 12:56:36 +02:00
Max Lübke
f9da7830f2 fix: re-enable DHT correctly 
feat: store excess H and O instead of total values
 2023-04-24 16:58:48 +02:00
Max Luebke
89fc291e79 BREAKING CHANGE: use Field data structure instead of plain 1D vector to 
store concentrations
 2023-04-24 14:25:55 +02:00
Max Luebke
5492560f6c feat: add surface module 2023-04-17 15:52:27 +02:00
Max Luebke
1716382b84 refactor: remove bits/stdint-uintn.h as header 2023-04-17 12:37:43 +02:00
Max Luebke
3fdf586e0d BREAKING CHANGE: use dump mechanism of PhreeqcRM-GFZ to get and set 
internal variables

feat: enables exchange

data: added exchange only benchmark

data: applied required changes to benchmarks
 2023-04-17 12:37:43 +02:00
Max Luebke
607b939208 fix: remove unnecessary RoundToZero function from DiffusionModule 2023-04-13 17:26:18 +02:00
Max Luebke
956951fc80 fix: wrong key size in DHT 2023-04-05 11:46:10 +02:00
Max Luebke
9f290d584a fix: remove openssl includes 2023-03-31 15:18:56 +02:00
Max Luebke
18eff17773 build: remove crypto library as dependency 2023-03-31 15:18:56 +02:00
Max Luebke
f1a10a9b22 fix: use Murmur hashing for DHT lookup 2023-03-28 14:27:00 +02:00
Max Luebke
32d35190cb fix: write fields using R after chem simulation 2023-03-07 13:44:41 +01:00
Max Luebke
e6819b59bc BREAKING CHANGE: Introduce ChemistryModule as extension of PhreeqcRM 2023-03-07 13:44:41 +01:00
Max Luebke
a493054f9d refactor: In SimParams, relocate trivial getter/setters to header file 
refactor: change vector data types of dht_signif_vector and
dht_prop_type_vector to both uint32
 2023-03-06 18:07:41 +01:00
Max Luebke
fc79d1d0a8 refactor: DHT_Wrapper class 
feat: add setters to DHT_Wrapper to set prop type vector and signif
vector

refactor: remove dependency from SimParams structure

feat: introduce new header defining DHT types
 2023-03-06 18:07:41 +01:00
Max Luebke
86db80ffc3 feat: add Field data structure as substitution of field declaration 
using std::vector
 2023-03-03 15:41:11 +01:00
Max Luebke
7639bcb045 fix: remove rounding to significant digit +1 2023-02-06 14:04:50 +01:00
Max Luebke
8142a10d00 refactor: combine DHT results to one struct 
This struct stores both used keys and resulting data with work package
size and Phreeqc mapping during call of `checkDHT`.

This makes a second fuzzing of keys during `fillDHT` obsolete.
 2023-01-24 16:11:03 +01:00
Max Luebke
f7404110ab fix: calculation of wp_sizes_vector 2023-01-24 16:11:01 +01:00
Max Lübke
9ffe3da7e1 fix: set porosity to 1 (hardcoded for now) 2023-01-24 16:10:08 +01:00
Marco De Lucia
080b2f99f2 MDL: suppressed warnings (hard coded for now); added 1k*2k simulation bench/dolo_diffu_inner_large 2023-01-24 16:10:08 +01:00
Max Lübke
9e4aea38e3 fix: set all values less than 10E-14 to zero 2023-01-24 16:10:08 +01:00
Max Lübke
526d61eaa7 use "native" input as rounding without pH/pe calculation 2023-01-24 16:10:08 +01:00
Max Lübke
cd5bbfa9a3 adding different cases of prop types and zero value 2023-01-24 16:10:08 +01:00
Max Lübke
5ef228c27f refactor: pass work packages as constant reference to DHT functions 2023-01-24 16:10:08 +01:00
Max Lübke
575d881158 build: add option to enable DHT debug infos 2023-01-24 16:10:08 +01:00
Max Lübke
4118fe4ed0 fix: handle negative values in keyelement with significant as signed integer 2023-01-24 16:10:08 +01:00
Max Lübke
14cb03e746 feat: use new rounding function and datatype for keys 2023-01-24 16:10:08 +01:00
Max Lübke
38d6b299a9 refactor: move key and data size calculation to DHT_Wrapper 2023-01-24 16:10:08 +01:00
Max Lübke
f32a3f3342 perf: return SimParams as const 2023-01-24 16:10:08 +01:00
Max Luebke
16eb78ae31 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
f53a69f014 refactor: remove comments from code in Grid class 2023-01-23 15:06:27 +01:00