Update README.md

README.md

@@ -5,11 +5,11 @@
 # POET
 
 POET is a coupled reactive transport simulator implementing a parallel
-architecture and a fast distributed hash table.
+architecture and a fast, original MPI-based Distributed Hash Table.
 
 ## External Libraries
 
-We use external libraries:
+The following external header library is shipped with POET:
 
 - **argh** - https://github.com/adishavit/argh (BSD license)
 
@@ -24,20 +24,19 @@ To compile POET you need several software to be installed:
 - R language and environment
 - CMake 3.9+
 
-If documantiation should be build 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:
+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)
 - [RInside](https://cran.r-project.org/web/packages/RInside/index.html)
-- [RedModRphree](https://gitext.gfz-potsdam.de/delucia/RedModRphree)
-- [Rmufits](https://gitext.gfz-potsdam.de/delucia/Rmufits)
+- [RedModRphree](https://git.gfz-potsdam.de/delucia/RedModRphree)
+- [Rmufits](https://git.gfz-potsdam.de/delucia/Rmufits)
 
 ### Compiling source code
 
-The generation of makefiles is done with CMake. If you obtain POET from a git repository 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
@@ -79,8 +78,8 @@ $ R
 
 # install R dependencies
 > install.packages(c("devtools", "Rcpp", "RInside"))
-> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/RedModRphree.git")
-> devtools::install_git("https://gitext.gfz-potsdam.de/delucia/Rmufits.git")
+> devtools::install_gitlab("delucia/RedModRphree", host="https://git.gfz-potsdam.de")
+> devtools::install_gitlab("delucia/Rmufits", host="https://git.gfz-potsdam.de")
 > q(save="no")
 
 # cd into POET project root
@@ -94,8 +93,8 @@ $ 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 I would not
-recommend to install to hierarchies like `/usr/local/` etc.
+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:
 
@@ -115,12 +114,12 @@ The correspondending directory tree would look like this:
         └── parallel_r_library.R
 ```
 
-The R libraries will be read in during runtime and the paths are hardcoded
+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.
 
-To display the generetated html documentation just open `docs/html/index.html`
+To display the generated html documentation just open `docs/html/index.html`
 with the browser of your choice.
 
 ## Running
@@ -155,7 +154,7 @@ The following parameters can be set:
 
 #### Additions to `dht-signif`
 
-Only used if no vector is given in setup file. For individual valuies per column
+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`
@@ -171,9 +170,10 @@ 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. To start the simulation
-with 4 processes `cd` into your previously installed POET-dir
-`<POET_INSTALL_DIR>/bin` and run:
+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
@@ -182,7 +182,7 @@ mpirun -n 4 ./poet ../data/SimDol2D.R 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 points and
+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:
 
@@ -190,15 +190,6 @@ activate the usage of the DHT. The resulting call would look like this:
 mpirun -n 4 ./poet -dht SimDol2D.R output
 ```
 
-## Examples included (more to come)
-
-- **SimDol2D.R** - simple chemistry (Calcite/Dolomite) on a 50x50 2D grid, 20
-  time steps 2)
-- ~~**SimDolKtz.R** - simple chemistry (Calcite/Dolomite) on Ketzin grid (~650k
-  elements), 20 time steps The flow snapshots are **NOT INCLUDED** in project
-  directory but must be provided separately.~~ At this moment **SimDolKtz.R** is
-  not supported.
-
 ## About the usage of MPI_Wtime()
 
 Implemented time measurement functions uses `MPI_Wtime()`. Some important