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Adding scheme to README

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README.md
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<!--
Time-stamp: "Last modified 2021-02-08 13:46:00 mluebke"
Time-stamp: "Last modified 2023-01-19 12:06:10 delucia"
-->
**Po**tsdamer **R**eactive **T**ransport
@ -7,7 +7,12 @@
# Forked Project
PORT is a fork of [POET](https://doi.org/10.5281/zenodo.4757913) integrating a standalone component for transport computations and leveraging PHREEQC_RM as geochemical solver. The following README is also applicable for this project.
*PORT* is a fork of [POET](https://doi.org/10.5281/zenodo.4757913)
integrating a standalone component for transport computations and
leveraging PHREEQC_RM as geochemical solver. The following README is
also applicable for this project.
![PORT's Coupling Scheme](./docs/20221216_Scheme_PORT_en.svg)
# POET
@ -31,9 +36,11 @@ To compile POET you need several software to be installed:
- R language and environment
- CMake 3.9+
If you want to build documentation during compilation, `doxygen`and `graphviz` must be provided too.
If you want to build documentation during compilation, `doxygen`and
`graphviz` must be provided too.
The following R libraries must then be installed, which will get the needed dependencies automatically:
The following R libraries must then be installed, which will get the
needed dependencies automatically:
- [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html)
- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
@ -43,17 +50,21 @@ The following R libraries must then be installed, which will get the needed depe
### Compiling source code
The generation of makefiles is done with CMake. If you obtained POET from git, you should be able to generate Makefiles by running
The generation of makefiles is done with CMake. If you obtained POET
from git, you should be able to generate Makefiles by running
```sh
mkdir build && cd build
cmake ..
```
This will create the directory `build` and processes the CMake files and generate Makefiles from it. You're now able to run `make` to start build
process.
This will create the directory `build` and processes the CMake files
and generate Makefiles from it. You're now able to run `make` to start
build process.
If POET was obtained from the official SVN repository or the redmine at <https://redmine.cs.uni-potsdam.de/projects/poet> the branch or tag to be used have to be set via
If POET was obtained from the official SVN repository or the redmine
at <https://redmine.cs.uni-potsdam.de/projects/poet> the branch or tag
to be used have to be set via
```sh
mkdir build && cd build
@ -64,20 +75,26 @@ where currently available branches/tags are:
- dev
If everything went well you'll find the executable at `build/src/poet`, but it is recommended to install the POET project structure to a desired `CMAKE_INSTALL_PREFIX` with `make install`.
If everything went well you'll find the executable at
`build/src/poet`, but it is recommended to install the POET project
structure to a desired `CMAKE_INSTALL_PREFIX` with `make install`.
During the generation of Makefiles, various options can be specified via `cmake -D <option>=<value> [...]`. Currently there are the following available options:
During the generation of Makefiles, various options can be specified
via `cmake -D <option>=<value> [...]`. Currently there are the
following available options:
- **DHT_Debug**=_boolean_ - toggles the output of detailed statistics about DHT
usage (`cmake -D DHT_Debug=ON`). Defaults to _OFF_.
- **BUILD_DOC**=_boolean_ - toggles the generation of documantiation during
compilation process. Defaults to _ON_.
- _only from svn version:_ **POET_SET_BRANCH**=_string_ - set branch or tag whose code is used
- **DHT_Debug**=_boolean_ - toggles the output of detailed statistics
about DHT usage (`cmake -D DHT_Debug=ON`). Defaults to _OFF_.
- **BUILD_DOC**=_boolean_ - toggles the generation of documantiation
during compilation process. Defaults to _ON_.
- _only from svn version:_ **POET_SET_BRANCH**=_string_ - set branch
or tag whose code is used
### Example: Build from scratch
Assuming that only the C/C++ compiler, MPI libraries, R runtime environment and
CMake have been installed, POET can be installed as follows:
Assuming that only the C/C++ compiler, MPI libraries, R runtime
environment and CMake have been installed, POET can be installed as
follows:
```sh
# start R environment
@ -99,9 +116,10 @@ $ make -j<max_numprocs>
$ make install
```
This will install a POET project structure into `/home/<user>/poet` which is
called hereinafter `<POET_INSTALL_DIR>`. With this version of POET we **do not
recommend** to install to hierarchies like `/usr/local/` etc.
This will install a POET project structure into `/home/<user>/poet`
which is called hereinafter `<POET_INSTALL_DIR>`. With this version of
POET we **do not recommend** to install to hierarchies like
`/usr/local/` etc.
The correspondending directory tree would look like this:
@ -122,21 +140,23 @@ The correspondending directory tree would look like this:
```
The R libraries will be loaded at runtime and the paths are hardcoded
absolute paths inside `poet.cpp`. So, if you consider to move `bin/poet` either
change paths of the R source files and recompile POET or also move `R_lib/*`
according to the binary.
absolute paths inside `poet.cpp`. So, if you consider to move
`bin/poet` either change paths of the R source files and recompile
POET or also move `R_lib/*` according to the binary.
To display the generated html documentation just open `docs/html/index.html`
with the browser of your choice.
To display the generated html documentation just open
`docs/html/index.html` with the browser of your choice.
## Running
Before POET is ready to run, a working directory must be created. In this
directory you should find the executable file, the R scripts
`<POET_ROOT>/R_lib/kin_r_library.R` and `<POET_ROOT>/R_lib/parallel_r_library.R`
and the simulation description e.g. `<POET_ROOT>/data/chem_problems/SimDol2D.R`.
Before POET is ready to run, a working directory must be created. In
this directory you should find the executable file, the R scripts
`<POET_ROOT>/R_lib/kin_r_library.R` and
`<POET_ROOT>/R_lib/parallel_r_library.R` and the simulation
description e.g. `<POET_ROOT>/data/chem_problems/SimDol2D.R`.
Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>` where:
Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>`
where:
- **OPTIONS** - runtime parameters (explained below)
- **SIMFILE** - simulation described as R script (currently supported:
@ -161,8 +181,8 @@ The following parameters can be set:
#### Additions to `dht-signif`
Only used if no vector is given in setup file. For individual values per column
use R vector `signif_vector` in `SIMFILE`.
Only used if no vector is given in setup file. For individual values
per column use R vector `signif_vector` in `SIMFILE`.
#### Additions to `dht-snaps`
@ -176,22 +196,24 @@ Following values can be set:
### Example: Running from scratch
We will continue the above example and start a simulation with `SimDol2D.R`,
which is the only simulation supported at this moment. The required flow velocities
snapshots are included in the R package Rmufits. It's a 2D, 50x50 grid, with 20 time
steps. To start the simulation with 4 processes `cd` into your previously installed
We will continue the above example and start a simulation with
`SimDol2D.R`, which is the only simulation supported at this moment.
The required flow velocities snapshots are included in the R package
Rmufits. It's a 2D, 50x50 grid, with 20 time steps. To start the
simulation with 4 processes `cd` into your previously installed
POET-dir `<POET_INSTALL_DIR>/bin` and run:
```sh
mpirun -n 4 ./poet ../data/SimDol2D.R output
```
After a finished simulation all data generated by POET will be found in the
directory `output`.
After a finished simulation all data generated by POET will be found
in the directory `output`.
You might want to use the DHT to cache previously simulated data and
reuse them in further time-steps. Just append `--dht` to the options of POET to
activate the usage of the DHT. The resulting call would look like this:
reuse them in further time-steps. Just append `--dht` to the options
of POET to activate the usage of the DHT. The resulting call would
look like this:
```sh
mpirun -n 4 ./poet --dht SimDol2D.R output
@ -199,9 +221,9 @@ mpirun -n 4 ./poet --dht SimDol2D.R output
## About the usage of MPI_Wtime()
Implemented time measurement functions uses `MPI_Wtime()`. Some important
information from the OpenMPI Man Page:
Implemented time measurement functions uses `MPI_Wtime()`. Some
important information from the OpenMPI Man Page:
For example, on platforms that support it, the clock_gettime() function will be
used to obtain a monotonic clock value with whatever precision is supported on
that platform (e.g., nanoseconds).
For example, on platforms that support it, the clock_gettime()
function will be used to obtain a monotonic clock value with whatever
precision is supported on that platform (e.g., nanoseconds).

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util/data_evaluation/RFun_Eval.R
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## Simple library of functions to assess and visualize the results of the coupled simulations
## Time-stamp: "Last modified 2023-01-17 19:12:13 delucia"
## Time-stamp: "Last modified 2023-01-18 16:02:58 delucia"
require(RedModRphree)
require(Rmufits) ## essentially for PlotCartCellData
require(Rcpp)
sourceCpp(file = "./interpret_keys.cpp")
curdir <- dirname(sys.frame(1)$ofile) ##path.expand(".")
print(paste("RFun_Eval.R is in ", curdir))
sourceCpp(file = paste0(curdir, "/interpret_keys.cpp"))
# Wrapper around previous sourced Rcpp function
ConvertDHTKey <- function(value) {