From efa608574799437095659d38a137849def791cc5 Mon Sep 17 00:00:00 2001 From: "R. Sommariva" Date: Wed, 12 Jul 2017 17:22:58 +0100 Subject: [PATCH] New release (#253) * add markdown to README and convert README to markdown --- README | 25 ------------------------- README.md | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 25 deletions(-) delete mode 100644 README create mode 100644 README.md diff --git a/README b/README deleted file mode 100644 index 0596ee951..000000000 --- a/README +++ /dev/null @@ -1,25 +0,0 @@ -This directory contains sources of the AtChem2 application. The tools directory contains scripts for building the AtChem2 executable for a given input, while the travis directory contains the testsuite files. The remaining subdirectories are empty, but provide a default location for input and output files. - -********************************** -* Dependencies -********************************** - -AtChem2 requires a working Fortran compiler, BLAS and LAPACK libraries, CVODE library, openlibm library, and a Python 2 installation. Running the testsuite additionally requires a numdiff installation. - -Please refer to https://github.com/AtChem/AtChem2/wiki/1.1-Dependencies for installation instructions of these dependencies. - -********************************** -* Building AtChem2 -********************************** - -Please refer to https://github.com/AtChem/AtChem2/wiki/1.-Installation for installation instructions. Very briefly: - -After having installed all dependencies, please note that at present AtChem2 requires recompilation for each new .fac file. This is all handled by the script "./tools/build.sh", which converts the .fac file into a format usable by AtChem2 (namely, it generates two Fortran files and several data files). - -Firstly, run make makefile.local and set the variable CVODELIB inside makefile.local to the location of the CVODE libraries. Type "./tools/build.sh tools/mcm_example.fac" in the top-level directory and this should create an executable name "atchem2". This is for a default configuration. Run by typing "./atchem2". - -********************************** -* Configuring and running AtChem2 -********************************** - -AtChem2 accepts several command line arguments to configure the location of output and input files, with defaults also defined if not provided. After following the build step above, run "./atchem2". diff --git a/README.md b/README.md new file mode 100644 index 000000000..7cc79533c --- /dev/null +++ b/README.md @@ -0,0 +1,34 @@ +AtChem2 +======= + +AtChem2 is an atmospheric chemistry numerical integrator, primarily designed for use with the Master Chemical Mechanism (MCM, http://mcm.leeds.ac.uk/MCM/). For more information and instructions, see the [AtChem2 wiki](https://github.com/AtChem/AtChem2/wiki). + +AtChem2 is open source, released under the [MIT license](https://opensource.org/licenses/MIT). + +Directory structure +------------------- + +The `src/` directory contains the source files of AtChem2. The `tools/` directory contains Python and shell scripts to build the AtChem2 executable for a given chemical mechanism and configuration. The `travis/` directory contains the _testsuite_ files. The remaining directories are empty, but provide a default location for the input, output and configuration files. + +Dependencies +------------ + +AtChem2 requires a Fortran compiler (GNU gfortran or Intel ifort), the BLAS and LAPACK Fortran libraries, the CVODE and openlibm libraries, and a Python 2 installation. Running the _testsuite_ additionally requires a numdiff installation. + +Detailed instructions for the installation of the dependencies can be found on the [wiki page](https://github.com/AtChem/AtChem2/wiki/1.1-Dependencies). + +Building AtChem2 +---------------- + +After installation of all the dependencies, refer to the instructions on the [wiki page](https://github.com/AtChem/AtChem2/wiki/1.-Installation) for the installation of AtChem2. + +Firstly, create a `makefile.local` file and set the variables `CVODELIB` and `OPENLIBMDIR` to the locations of the CVODE and openlibm libraries. Type `./tools/build.sh tools/mcm_example.fac` in the top-level directory and this should create an executable name `atchem2`, with a default configuration. + +Note that, at present, AtChem2 requires recompilation for each new chemical mechanism (`.fac`) file. This is handled by the script `./tools/build.sh`, which converts the `.fac` file into a format usable by AtChem2 (namely, it generates two Fortran files and several data files in the `modelConfiguration/` directory). + +Configuring and running AtChem2 +------------------------------- + +AtChem2 accepts several command line arguments to configure the location of output and input files, with defaults also defined if not provided. After completing the build step above, set the initial conditions, required outputs and other model paramters in the files inside the `modelConfiguration/` directory. + +To run the model, type `./atchem2`. More information on model configuration and execution see the [wiki page](https://github.com/AtChem/AtChem2/wiki/2.-Model-Configuration-and-Execution).