Using <i>Mathematica</i> as a platform for crystallographic computing

Ramsnes, Stian; Larsen, Helge B.; Thorkildsen, Gunnar

doi:10.1107/s1600576718018071

Cited by 5 publications

(6 citation statements)

References 8 publications

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“…Once the package had been thoroughly generalised and tested, the first article [75] was written, giving the package an official and-more importantly-a peer-reviewed launch. While acknowledging that MaXrd is by no measure revolutionary, it is a simple, practical and helpful tool, which has received warm responses by the people whose interest happens to intersect both crystallography and Mathematica.…”

Section: A Quick Tour Of the Packagementioning

confidence: 99%

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Direct- and reciprocal space structure modelling: Contributions to the advanced understanding of inclusion compounds

Ramsnes¹

2022

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The main content of this thesis falls naturally into one of two parts. The chapters come in an order which follows the research development, but encapsulates single topics enough to allow the reader some flexibility. In short, this work concerns the study of one particular inclusion compound, and all the programming utilities that have been developed in an attempt to tackle this structure as well as others like it. We have sought to gather more details about what happens to the structure in the midst of a chaotic phase transition. This has been done by a non-standard approach of diligent entity construction, seeking to bring a model to perfection by invoking direct space modelling with reciprocal space validation. The idea is simple, but has proven more difficult to conduct to an end. Part I comprises the structural information and data analysis of the central analysis subject: the thiourea-ferrocene inclusion compound (TFIC). It is divided into chapters with a logical progression: starting with a background on host–guest inclusion complexes and details on the TFIC from the literature in Chapter 1. Then, our experimental details and qualitative investigation is compiled in Chapter 2. The next step is data reduction and structure solutions, covered in Chapter 3. Some background theory and information on twinning is covered in Appendix A. Part II starts off with a presentation of the developed Mathematica package in Chapter 4. The reader will learn what it is and how it may serve as a utility in the field of crystallo- graphy. Its origin, functionality and purpose will be examined in a summary of its two articles. The subject of model construction will be emphasised, and the thesis will cul- minate with demonstrations of its capability in Chapter 5 where models are tailored to the specific TFIC system. The associated simulations of the diffraction patterns are com- pared with experimental counterparts in order to ascertain what characteristics may be ascribed to the structure during the prominent phase transition; discussions that bring the separate topics together are made in the concluding Chapter 6, which summarises the most important findings on the TFIC. The following work (published, or to be published) comprises this thesis, listed chronologically: Stian Ramsnes, Helge Bøvik Larsen and Gunnar Thorkildsen. ‘Using Mathematica as a platform for crystallographic computing’. In: Journal of Applied Crystallography 1 (Feb. 2019), pp. 214–218. doi: 10.1107/S1600576718018071 (see page 156) Stian Penev Ramsnes, Helge Bøvik Larsen and Gunnar Thorkildsen. ‘MaXrd up- dated with emphasis on model construction and reciprocal-space simulations’. In: Journal of Applied Crystallography 53.6 (Dec. 2020), pp. 1620–1624. doi: 10 . 1107/ S160057672001328X (see page 161) Stian Penev Ramsnes et al. ‘Complementary Synchrotron Diffraction and Simula- tion Studies on a Ferrocene:Thiourea Inclusion Compound’. To be 2022 The first paper concerns the release of the Mathematica X-ray diffraction package (MaXrd). In essence, it contains point- and space group information from the International Tables for Crystallography and tabulated data on scattering factors and cross sections, required for calculations related to X-ray physics. Included are also functions to utilise this data, with a documentation demonstrating their usage. Highlighted functionality includes ex- traction of symmetry data, data import from cif files, calculations of structure factors, linear absorption coefficients and unit cell transformations. The second article was submitted once a practical structure modelling extension had been sufficiently generalised. The imported cif data could now be employed to create and visualise crystal structures. Many additions depended on the original symmetry-related foundation, but a few brought novel concepts into the package, such as the function for making domains. The focus on model construction was motivated by the study of a host– guest complex, hence the ability to embed one crystal entity into another. With the possibility to simulate the diffraction patterns (reciprocal space maps), a way of comparing a customised structure with experimental data was realised. The third article conveys our findings on the thiourea–ferrocene inclusion compound. Complementary studies have been conducted in three areas: qualitative exploration of reciprocal space, quantitative structure solutions of synchrotron data and various model investigations with the MaXrd utility package in Mathematica. We discuss both support- ing evidence and shortcomings of the prevalent high- and low-temperature phases of the TFIC structure. It is said that if you’re unable to provide a clean and short explanation on a subject, you don’t understand it well enough. In any case, capturing the thesis in a single sentence is a good exercise. Since the first part is about method development, a conclusive remark does not fit as much as for the second part, for which a fitting and simplistic one-liner conclusion for the layman may be: The cold makes the guest molecules inside the honeycomb network halt their motion and shatters the neat pattern, but heating it makes everything fine again, even if the crystal was a twin to begin with.

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Section: A Quick Tour Of the Packagementioning

confidence: 99%

“…For more details on the essentials of MaXrd, consult the Mathematica documentation or see Ramsnes et al [75] .…”

Section: A Quick Tour Of the Packagementioning

confidence: 99%

Direct- and reciprocal space structure modelling: Contributions to the advanced understanding of inclusion compounds

Ramsnes¹

2022

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“…With the availability of consistent representation of arbitrary crystals in the form of crystallographic information files (CIFs; Hall et al, 1991), extensive databases that contain collections of CIFs such as the Materials Project (Jain et al, 2013) and the Open Quantum Materials Database (Saal et al, 2013), and advanced 3D computational geometry libraries in software/languages such as Mathematica (Wolfram, 2021), MATLAB (The MathWorks, 2021) and Python (Vollprecht, 2021), automated computation of planar densities of arbitrary crystals for arbitrary lattice planes is possible. In this work, we present such a workflow using Mathematica's built-in computational geometry functions in conjunction with MaXrd (Ramsnes et al, 2019), which facilitates both importing CIF files and dealing with crystal symmetry domain knowledge. This package is implemented on the full collection of Materials Project compounds as obtained via the Materials Application Programming Interface (API) (Ong et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

High-throughput calculation of atomic planar density for compounds

Baird¹,

Sparks²

2022

J Appl Cryst

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A large collection of element-wise planar densities for compounds obtained from the Materials Project is calculated using brute force computational geometry methods, where the planar density is given by the total fractional area of atoms intersecting a supercell's crystallographic plane divided by the area of the supercell's crystallographic plane. It is demonstrated that the element-wise maximum lattice plane densities can be useful as machine learning features. The methods described here are implemented in an open-source Mathematica package hosted at https://github.com/sgbaird/LatticePlane.

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“…The initial version of MaXrd (Ramsnes et al, 2019) contained the essential symmetry information from International Tables for Crystallography, Vol. A (Hahn, 2002).…”

Section: Introductionmentioning

confidence: 99%