scholarly journals pyGIMLi: An open-source library for modelling and inversion in geophysics

2017 ◽  
Vol 109 ◽  
pp. 106-123 ◽  
Author(s):  
Carsten Rücker ◽  
Thomas Günther ◽  
Florian M. Wagner
Keyword(s):  
2015 ◽  
Vol 577 ◽  
pp. A7 ◽  
Author(s):  
H. Socas-Navarro ◽  
J. de la Cruz Rodríguez ◽  
A. Asensio Ramos ◽  
J. Trujillo Bueno ◽  
B. Ruiz Cobo

2020 ◽  
Author(s):  
Florian M. Wagner ◽  
Carsten Rücker ◽  
Thomas Günther ◽  
Friedrich Dinsel ◽  
Nico Skibbe ◽  
...  

<p>Hydrogeophysics is interdisciplinary by definition. As researchers strive to gain quantitative information on process-relevant subsurface parameters while integrating non-geophysical measurements, multi-physical geoscientific models are often developed that simulate the dynamic process and its geophysical response. Such endeavors are associated with considerable technical challenges due to coupling of different numerical models, which represents an initial hurdle for students and many practitioners. Even technically versatile users often end up with individually tailored solutions at the cost of scientific reproducibility.</p><p>We argue that the reproducibility of studies in computational hydrogeophysics, and therefore the advancement of the field itself, needs versatile open-source software. One example is pyGIMLi - a flexible and computationally efficient framework for modeling and inversion in geophysics. The library provides management for structured and unstructured 2D and 3D meshes, finite-element and finite-volume solvers, various geophysical forward operators, as well as a generalized Gauss-Newton based inversion framework.</p><p>In this contribution, we highlight some of the recent advances and use cases in research and education since its 1.0 release in 2017 (Rücker et al., 2017) including:</p><ul><li>generalized modeling and inversion frameworks for conventional, joint, time-lapse and process-based inversion</li> <li>geostatistical regularization operators for unstructured meshes (Jordi et al., 2018)</li> <li>improved constraints in the presence of petrophysical parameter transformations demonstrated by an estimation of water, ice, and air in partially frozen systems (Wagner et al., 2019)</li> <li>3D visualization leveraging upon PyVista (Sullivan and Kaszynski, 2019)</li> <li>simulation of electrical streaming potentials</li> <li>complex-valued forward modeling and inversion of induced polarization</li> <li>forward modeling with anisotropic parameters</li> <li>availability for Mac OS</li> <li>improved API and documentation</li> </ul><p>Since the library is freely available and platform-compatible, it is also well suited for teaching. We demonstrate examples from Master level university courses and public outreach, where learners can interactively change model and acquisition parameters to study their influence on a hydrogeophysical process simulation. Finally, we would like to use this opportunity to discuss future developments with the community.</p><p><strong>References</strong></p><p><span>Jordi, C., Doetsch, J., Günther, T., Schmelzbach, C., & Robertsson, J. O. (2018). Geostatistical regularization operators for geophysical inverse problems on irregular meshes. <em>Geophysical Journal International</em>, 213(2), 1374–1386. </span><span></span></p><p><span>Rücker, C., Günther, T., Wagner, F.M., 2017. pyGIMLi: An open-source library for modelling and inversion in geophysics, <em>Computers and Geosciences</em>, 109, 106-123. </span><span></span></p><p><span>Sullivan, C., & Kaszynski, A. (2019). PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK). <em>Journal of Open Source Software</em>, 4(37), 1450. </span><span></span></p><p><span>Wagner, F. M., Mollaret, C., Günther, T., Kemna, A., & Hauck, C. (2019). Quantitative imaging of water, ice and air in permafrost systems through petrophysical joint inversion of seismic refraction and electrical resistivity data. <em>Geophysical Journal International</em>, 219(3), 1866–1875. </span><span></span></p>


2019 ◽  
Vol 51 (1) ◽  
pp. 25-37 ◽  
Author(s):  
Douglas W. Oldenburg ◽  
Lindsey J. Heagy ◽  
Seogi Kang ◽  
Rowan Cockett

2019 ◽  
Author(s):  
Connor W. Coley ◽  
William H. Green ◽  
Klavs F. Jensen

There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here, we introduce an open source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying retrosynthetic transformations encoded as SMARTS strings. RDChiral is designed to enforce the introduction, destruction, retention, and inversion of tetrahedral centers as well as the cis/trans chirality of double bonds. We also introduce an open source implementation of a retrosynthetic template extraction algorithm to generate SMARTS patterns from atom-mapped reaction SMILES strings. In this manuscript, we describe the implementation of these two pieces of code and illustrate their use through many examples.<div><br></div><div>The two .json.gz files can be generated from the open source USPTO data available at https://figshare.com/articles/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873 using the code contained in the rdchiral GitHub repository. They are placed here for convenience if you would prefer to copy them into the templates/data subfolder instead of creating them from the source .rsmi file.</div>


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