AxiSEMLib

AxiSEMLib is a python library that provides several extensions for the AxiSEM:

• Synthesize accurate seismograms/strain/stress at any point of the earth.
• Teleseismic injection interfaces between AxiSEM, SPECFEM3D and SPECFEM3D-injection
• Reciprocity validation and Instaseis-like Database.

And there are several modifications in AxiSEM

• Fix source location problem
• Dump elastic parameters in discontinuous form.

Part of the code are adapted from Instaseis, so LGPL license is applied.

Download required packages

1. Compilers: C++/Fortran compilers which support c++14 (tested on GCC >=7.5, ICC >=18.4.0), cmake >= 3.12, and MPI libraries.

2. create a new environment with conda:

conda create -n axisem_lib python=3.8 
conda activate axisem_lib
conda install numpy scipy numba pyproj tqdm
pip install pybind11-global

3. Install several packages:

• parallel-hdf5 using your installed MPI libraries.
• netcdf-fortran, only serial version.
• mpi4py: You can build it by using existing mpi libraries:

MPICC=mpicc pip install mpi4py --no-binary mpi4py

• h5py-mpi using existing parallel-hdf5 libraries:

CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/path/to/parallel-hdf5 pip install --no-binary=h5py h5py

4. build AxiSEMLib by using:

mkdir -p build; cd build;
cmake .. -DCXX=g++ -DFC=gfortran  -DPYTHON_EXECUTABLE=`which python`
make -j4; make install 

Prepare AxiSEM Mesh

• Go to directory axisem and change compiler options in make_axisem.macros. Remember to set USE_NETCDF = true, set NETCDF_PATH.

• Go to MESHER/, set parameters including DOMINANT_PERIOD and number of slices in inparam_mesh. Please make sure this dominant period is slightly shorter than the minimum period used in SEM(you can find it in SPECFEM's output_generate_databases.txt) If you want to use a smoothed version of ak135/prem model, you can run scripts under smooth_model/main.py, and set the parameters like:

BACKGROUND_MODEL external
EXT_MODEL ak135.smooth.bm

• Run mesh generation ./submit.csh and ./movemesh.csh mesh_name. Then the mesh files will be moved to SOLVER/MESHES as the mesh_name you set.

Prepare AxiSEM Solver files

There are two files you should edit: inparam_basic and inparam_advanced.

In param_basic you should set SEISMOGRAM_LENGTH as you required, and you should set ATTENUATION to false because the current version only support isotropic elastic model. And you can set some other parameters like SIMULATION_TYPE. If SIMULATION_TYPE is not moment, you should also edit inparam_source.

In inparam_advanced, you should set the part of several parameters as below:

# GLL points to save, starting and ending GLL point index 
# (overwritten with 0 and npol for dumptype displ_only)
KERNEL_IBEG         0
KERNEL_IEND         4
KERNEL_JBEG         0
KERNEL_JEND         4

KERNEL_WAVEFIELDS   true
KERNEL_DUMPTYPE     displ_only
KERNEL_SPP          8/16/32 (depend on your dominant frequency)

# you should add this one 
# KERNEL  dump  after DUMP_T0
DUMP_T0       200. 

# epicenter distance
KERNEL_COLAT_MIN   25.
KERNEL_COLAT_MAX   100.

# minimal and maximal radius in km for kernel wavefields
# (only for dumptype displ_only)
KERNEL_RMIN        5000.
KERNEL_RMAX        6372.

Then you can prepare your CMTSOLUTION and STATIONS. You can follow examples in run_all_events.sh, which will submit all events in CMT_DIR

Run AxiSEM simulation

Run it on your cluster.

Transpose the output field for better performance.

Set the variables in submit_transpose.sh, then:

bash submit_transpose.sh 

Try examples in EXAMPLES/ !