Create README.md

Author: sstaehler

README.md

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+#AxiSEM 1.3
+ 
+##Axially symmetric Spectral Element Method
+
+Copyright 2016, Tarje Nissen-Meyer, Martin van Driel, Simon Stähler, Kasra Hosseini, Stefanie Hempel, Alexandre Fournier
+
+Webpage and distribution: http://www.axisem.info
+Contact and information:  [email protected]
+
+April, 11, 2016 
+
+## Citation
+If you are publishing results obtained with this code, please cite this paper:
+
+T. Nissen-Meyer, M. van Driel, S. C. Staehler, K. Hosseini, S. Hempel, L. Auer, A. Colombi and A. Fournier:
+**"AxiSEM: broadband 3-D seismic wavefields in axisymmetric media"**, *Solid Earth*, 5, 425-445, 2014
+doi:10.5194/se-5-425-2014 http://www.solid-earth.net/5/425/2014/
+
+## Content of the repository
+`manual_axisem_1.3.pdf` - PDF manual
+
+`MESHER` - The program to generate 2D meshes for the SEM forward solver
+
+`SOLVER` - the SEM forward solver itself
+
+`make_axisem.macros` - macro file to set compiler options
+
+`copytemplates.sh` - reset all input files to default templates 
+
+`COPYING` - The GNU General Public License
+
+`HISTORY` - changelog
+
+`README` - this file
+
+##Basic instructions for running:
+
+More details are found in the manual. For a quick start:
+
+ - The mesher has to be run first to generate a SEM mesh for the solver. 
+ - Any changes in the resolution, spherically symmetric background model, or number 
+   of processors requires a new mesh. 
+ - Changes in the source-receiver settings or 2.5D heterogeneities only need a new solver run.
+ - Changes on the moment tensor, receiver components, or filtering only need a new postprocessing run.
+ - Using Instaseis, seismograms for any depth or moment tensor can be calculated from the wavefield of one force source at the surface.
+
+General settings and explanations for parameters needed in MESHER and SOLVER 
+are found in the `inparam_*` files in the respective directories. 
+
+1) Run `copytemplates.sh` to set up a generic run with pre-set parameters
+
+2) Go into the MESHER directory, run `./submit.csh`. This compiles the code using
+gfortran and mpif90 as default compilers, and then submits a job on a single node. 
+For high resolution (seismic period below 3s), this requires significant amounts 
+of RAM, see manual.
+
+3) Check `OUTPUT`; if finished, then run `./movemesh.csh <MESH_NAME>`
+
+4) go into `SOLVER`, check the vtk files in `/MESHES/<MESH_NAME>` with Paraview, if you want
+
+5) Edit `inparam_basic` to the desired `<MESH_NAME>`
+
+6) Run `./submit.csh <RUN_NAME>` , this compiles and then submits a parallel run.
+
+7) Check `<RUN_NAME>/OUTPUT*`, which will record the progress of the run and any problems.
+
+8) All data-related output is in `<RUN_NAME>/Data/`
+
+9) Convolution with a STF and summation for a moment source is done by running
+   `postprocessing.csh` in `<RUN_NAME>`
+
+10) A more modern and efficient way of seismogram retrieval is using Instaseis,
+    a Python toolbox to retrieve seismograms for arbitrary depths and moment
+    tensors from the stored wavefield of one AxiSEM run (http://www.instaseis.net)
+
+Detailed instructions can be found in the file `manual_axisem_1.3.pdf`
+
+