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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a free, copyleft license for
software and other kinds of works.
The licenses for most software and other practical works are designed
to take away your freedom to share and change the works. By contrast,
the GNU General Public License is intended to guarantee your freedom to
share and change all versions of a program--to make sure it remains free
software for all its users. We, the Free Software Foundation, use the
GNU General Public License for most of our software; it applies also to
any other work released this way by its authors. You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
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0. Definitions.
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or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
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excuse you from the conditions of this License. If you cannot convey a
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License and any other pertinent obligations, then as a consequence you may
not convey it at all. For example, if you agree to terms that obligate you
to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the special requirements of the GNU Affero General Public License,
section 13, concerning interaction through a network will apply to the
combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
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be similar in spirit to the present version, but may differ in detail to
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option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
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If the Program specifies that a proxy can decide which future
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later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
{one line to give the program's name and a brief idea of what it does.}
Copyright (C) {year} {name of author}
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
{project} Copyright (C) {year} {fullname}
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
README.md
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# WRFotron
Installation instructions
WRFotron is a bunch of shell scripts to automate WRF(-Chem) simulations (on a cluster with job scheduling system), including the necessary preprocessing steps. Special focus is set to be able to chain simulations, allowing to create free-running (i.e., no nuding) simulations for chemistry-aerosol-meteorology interactions over longer time periods.
## Contributing
We are looking forward to receiving your [new issue report](https://mbees.med.uni-augsburg.de/gitlab/mbees/wrfotron/-/issues/new).
If you'd like to contribute source code directly, please [create a fork](https://mbees.med.uni-augsburg.de/gitlab/mbees/wrfotron), make your changes and then [submit a merge request](https://mbees.med.uni-augsburg.de/gitlab/mbees/wrfotron/-/merge_requests/new) to the original project.
## License and acknowledgment
WRFotron is open source and available under the Gnu Public License (GPL) in version 3. In case WRFotron was used in scientific publications, please acknowledge as follows:
*We acknowledge the use of WRFotron created by the Chair of Model-Based Environmental Exposure Science at University Augsburg, Germany, to automatise WRF(-Chem) simulations.*
## Prerequisites
* A working installation of WRF (and WRF-Chem, separately) v4.0 or greater
* A working installation of WPS v4.0 or greater
* Various preprocessing tools for WRF-Chem (e.g., mozbc, anthro_emis, megan, ...) as required
* All required input data (meteo, geog, emissions, ...)
## General naming conventions
Multiple (chained) simulations that serve a certain purpose, e.g. for a field campaign, are called an `experiment`. The
`experiment` name is the main identifier when working with WRFotron. The set of configuration options (namelist.wps, namelist.input, anthro_emis.inp, ...) for an `experiment` is called `blueprint`, and resides
in the subfolder `blueprints`/`experiment`.
## Main commands and scripts
`master.bash`: main script to start a simulation for an existing `experiment`.
`batch.bash`: main script to start a chain of simulations for an existing `experiment`. Basically calls `master.bash` multiple times.
These scripts can be called without arguments for help:
```
<me@mymachine>:. master.bash
Call with arguments <experiment> <year (YYYY)> <month (MM)> <day (DD)> <hour (hh)> <forecast time (h)> <spinup time (h)>
or <experiment> <year (YYYY)> <month (MM)> <day (DD)> <hour (hh)> <forecast time (h)> <spinup time (h)> <PID of job dependency>
* <experiment> can be a shortcut name (if experiment directory is found in subdirectory 'blueprints',
and you are calling it from the shell), or the absolute path to the experiment's settings directory.
* <spinup time> needs to be a multiple of meteoInc.
-d dry run, prepare only, do not submit or run
-b do not use batch system, execute directly in shell
```
## General workflow
When calling master.bash, a simulation directory is prepared in `$workDir`. Four jobs are submitted to the job scheduler, each depending on the previous:
- `pre.bash`: run WPS (and everything to prepare the -Chem part), create wrfinput and wrfbdy (and other) files in `$workDir`
- `main.bash`: run WRF(-Chem)
- `staging.bash`: move WRF(-Chem) output into the staging location at `$stagingDir`, where it waits to be postprocessed
- `post.bash`: at minimum, move output from `$stagingDir` to `$archiveDir`, possibly apply postprocessing actions on the output
These four general phases may consist of several subjobs, which can be seen (and adapted) in the `jobs` subdirectory.
## Installation
1. Get WRFotron
......@@ -12,19 +71,21 @@ Installation instructions
* subfolder `wrfotron` now contains your WRFotron installation
2. Set up a machine profile (if necessary)
2. Set up a machine profile
* create file with all commands to be executed prior to all runs, e.g. loading modules, setting ulimits, etc.:
`machine_profiles/your_machine.bash`
`machine_profiles/your_machine`
* link to root level as profile.bash
* link to WRFotron root level as profile.bash
`ln -s machine_profiles/your_machine.bash profile.bash`
`ln -s machine_profiles/your_machine profile.bash`
3. Experiment setup
* create a new experiment folder in blueprints, following the example
`cp -r blueprints/example blueprints/your_experiment`
* create a new experiment folder in blueprints, following the existing blueprints as examples
`cp -r blueprints/<chosen example> blueprints/<your experiment name>`
* create an experiment config for your machine
......@@ -34,9 +95,9 @@ Installation instructions
* link to experiment folder
`ln -s blueprints/your_experiment/machine_specific/alcc/batch_preambles blueprints/your_experiment/`
`ln -s blueprints/<your experiment name>/machine_specific/<machine>/batch_preambles blueprints/<your experiment name>/`
`ln -s blueprints/your_experiment/machine_specific/alcc/config.bash blueprints/your_experiment/`
`ln -s blueprints/<your experiment name>/machine_specific/<machine>/config.bash blueprints/<your experiment name>/`
4. Test
* make a run *(dates depend on the available data, obviously)*
......@@ -48,4 +109,3 @@ Installation instructions
`${workDir}/your_experiment/2001-01-01_00:00:00-2001-01-02_00:00:00`
($workDir is set in the experiment config)
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