Welcome to custEM!¶
Version: 0.99 ~ Date: Jan 28, 2020
** !!! Roadmap to custEM v.1.0 within the next months !!! **
- finish implementation of time domain approaches
- remove a few known bugs
- implemenet parallel interpolation
- implement plot tools for time-domain approaches
- tutorials for time-domain modeling and others
- update documentation, add important comments in the code, not only doc-strings
custEM is an open-source toolbox for customizable 3D finite-element modeling of controlled-source electromagnetic data. The toolbox is based on the finite- element library FEniCS, see https://fenicsproject.org/ . Different total and secondary electric or magnetic field as well as gauged-potential approaches are implemented. In addition, custEM contains a mesh generation submodule for the straightforward generation of tetrahedral meshes supporting a large number of marine, land-based, airborne or mixed model scenarios. Interpolation and visualization tools simplify the post-processing workflow.
Mesh generation runs on any laptop or desktop PC. Also “toy” examples can be tested on such machines. Because of using direct solvers, we recommend to get access to a cluster with >= 32 cores/threads and >=256 GB RAM for calculating sufficiently accurate models for more complex 3D setups. Anyway, already reasonable solutions for “simple” 3D modeling studies often require only first order polynomials and could be run on a desktop PC or laptop with 32-64 GB.
Please note: custEM is under continuous development. Usually, updates for debugging, adding documentation or new features are committed frequently. We plan to implement further improvements and resolve the last remaining major issues for custEM: version 1.0, in the next months.
For any kind of question about custEM, do not hesitate to contact us:
To guide you through setting up the toolbox and making third party dependencies available, please follow the installation notes. After successful installation, please try to run the three test files provided in the corresponding directory. In addition to these initial tests for the overall functionality of custEM, we refer to the provided examples. They are identical to the ones presented in the publication (Rochlitz et al., 2018). Further guides to develop solution strategies for user-specific modeling problems are available in the tutorials directory.
Please note: Even though described in other instructions separately, we want to point out that for implementation reasons, currently the mpirun syntax needs to be used for serial FEM computations as well. For instance, (instead of python run_example_1.py) use:
–> mpirun -n 1 python run_example_1.py
Anyway, mesh generation or visualization scripts always have to be called in serial with the usual command line syntax or using a python editor, for instance:
–> python mesh_example_1.py –> python plot_example_1.py
Please note: Usually, airspace conductivities are set to 1e-10 or 1e-12 Ohmm. For most CSEM setups, we found that 3-4 orders of magnitude contrast between airspace and subsurface conductivities are totally sufficient to obtain accurate solutions. Higher contrasts result in worse conditioning of the system matrix and slightly longer computation times but do not increase the solution accuracy significantly (the effect is << 1 % of relative errors).
For basic instructions, it is referred to the Installation file for more information.
It is recommended to add all the export commands to your bashrc file.
If custEM was installed via conda, it is recommended to add the ‘-u’ flag after ‘python’ or ‘python3’ in the commmand promt calls to force all prints to appear in time and not delayed, e.g.:
–> mpirun -n 12 python -u run_script.py
In order to use the provided jupyter notebook tutorials, jupyter needs to be installed after all other steps listed below:
–> pip install jupyter
Computation times might be speed up with reducing the number of mpirun processes (e.g., 8 instead of 32) and enabling OpenMP parallelization during the solution of the system of equations via MUMPS with adjusting the flag OMP_NUM_THREAD, e.g., export OMP_NUM_THERADS=4 instead of 1.
Latest implementation progress / change notes¶
19.11.2019 - custEM version 0.99
- advanced mesh tools with node and edge markers
- pyhed fixed, identical sign conversion
- pyhed incorporated as third-party conda package now, not in wrap directory
- time stepping approach optimized
- rational krylov approach added
- inverse fourier transformation based approach added
- documentation updated
- few syntax changes
12.06.2019 - custEM version 0.98
- conda installer added, installation simplified significantly
- custEM tests during conda package build enabled
- support got FEniCS version older than 2018 disabled
- documentation updated
18.04.2019 and 20.05.2019 - custEM version 0.97
- Alternate tranformation factors for PF E-field tested with help of empymod
- compatibility with FEniCS 2019.1
- potential approaches now correctly implemented with identical structure (based on E=iw*A + iw*grad*V) (based on H=iw*F + iw*grad*U)
- corresponding post_processing adapated
- F-U (Tau-Omega) approach added
- bugfixes in meshgen and bathy tools
13.03.2019 - custEM version 0.96
- lot’s of bugs fixed (overall compatibility with FEniCS 2018.1)
- multiple RHS supported for total field approaches and framwork for adding this feature for secondary field approaches already implemented
- test, example and tutorial files updated to be again compatible with a this new version of custEM
- All provided scripts were tested also with previous versions based on FEniCS 2017.2, but it is heavily recommended to use this newest version with FEnICS 2018 to benefit from the increased performance!
09.01.2019 - custEM version 0.95
- version 0.94 included
- custEM now compatible with FEniCS 2018.1
- Significant performance boost due to parallel HDF5 support for FEniCS conda package and new MUMPS version, no matrix size restrictions anymore!
- Performance boost due to debugged symmetric MUMPS solver (previous custEM versions were bugged and called the general LU solver)
- Full Maxwell equations with displacement currents for E-field approach available, in progress for H-field approach
- H-field approach debugged
- Time-domain time-stepping approach added (not fully supported yet)
- Bathymetry/Topography meshing tools improved
- Irregular topography data supported
28.08.2018 - custEM version 0.93
- bug for primary E-fields of line sources fixed!
- alternative and superior way of incorporating transmitters in meshes added
- examples 2 reworked
- first steps for meshing costal areas with topography, bathymetry initialized
28.08.2018 - custEM version 0.92
- ReadtheDocs bug fixed: API for modules added!
- restructured repository (custEM modules now subdirectory of repository)
- examples added to table of contents
23.08.2018 - custEM version 0.91
- fixed sorting-bug workaround for primary-field calculations!
- removed minor bugs in meshgen submodule
- added topography meshing tutorial to the tutorials directory
- enabled edge preservation by using not only .poly but also .edge files for TetGen which is especially an advantage for implementing all kind of CSEM transmitters. As a consequence, TetGen does not need to be called with the ‘-M’ flag anymore for edge preservation, which saves up to 30% of dofs!
Previous implementation achievements are listed in the Implementation history section for documentation purposes.
Upcoming features / improvements / bug removals¶
The points listed here are minor improvements which are definitely planned to be implemented in the near future. If major achievements, for instance, support for time-domain modeling, are ready to be implemented, there will be a clearly visible announcement.
- implement support for non-vacuum magnetic permeabilities and if required, anisotropic permeabilities can be considered if required by users
- mixed bathymetry/topography support for coastal environments
- flexible interpolation grids and not only straight or crooked (topography) lines and faces with a regular node spacing
- embedded interpolation-mesh generation during mpirun computations
- continue visualization tutorial and add more examples
Please note: The python API documentation in the section modules is not available on ReadtheDocs due to issues with automated API-documentations. Anyway, the complete API documentation is available as “hmtl_doc” zip-file in the docs directory of the custEM repository and can be accessed via opening the “index.html” file in the zip directory with your favorite browser.
The following content was generated automatically. The documentation of modules and classes already provides a good overview about the specific usage of the corresponding functionalities in custEM. However, an overhaul of a few parts is necessary, for instance:
- write proper headers of all python files
- add a few doc-strings that do not exactly match the rst syntax
- add link between submodules and classes
- correct specifications, e.g., module, class, instance, function or method
This is going to be conducted step by step when resolving final implementation issues which we plan to resolve for the custEM: version 1.0.
Tutorials are available in the tutorials directory in the custEM repository as jupyter notebook, python script, and in html format. The html documentation of the Tutorials can be also accessed in the corresponding section. Please note that the tutorials are still under development and in particular, the usage of jupyter notebooks is not straightforward in combination with multiprocessing. We are about to fix related issues, but for now, secondary field computations and interpolation are not possible if the run_tutorial is started from the jupyter notebook. For running this tutorial, please use the provided run_tutorial.py python script and call it from the command line with the mpirun syntax, e.g.:
–> mpirun -n x python run_tutorial.py
with x, the number of cores.
Copyright 2016-2018 by R. Rochlitz
The custEM toolbox is licensed under the GNU LESSER GENERAL PUBLIC LICENSE (LGPL), just as FEniCS. The terms of the LGPL are listed in the License file.
Rochlitz, R., Skibbe, N. and Günther, T., (2018), custEM: customizable finite element simulation of complex controlled-source electromagnetic data, GEOPHYSICS Software and Algorithms.
Next to us, don’t forget to give credits to the authors of FEniCS, pyGIMLi or TetGen if submodules based on these developments are used for your purposes.