Zeolite-analyser code

This code measure some geometric features for an overall database. It enables the assessment of a multitude of geometric characteristics of the frameworks, and it reads CIF files of the periodic structures with P1 space group and SiO2 compositions. It is a new version of the https://github.com/salrodgom/GeoZeoForCIFFileDatabase code. Some new functionalities have been added.

Compilation

cd src
make

to clean:
make clean

Citation

SRG. Balestra, N. Rodríguez-Sánchez, D.Mena-Torres, AR. Ruiz-Salvador, Structural Features and Zeolite Stability: A Linearized Equation Approach, Cryst. Growth Des. , Feb., 2024,

Output files

For each processed framework the executable emits a collection of plain-text files whose names follow the pattern <structure>_<property>.dat. They provide the raw geometric descriptors that the program later summarises in console histograms and in follow-up analysis modules. The table below gives a quick reference for new users.

File pattern	What it contains	Typical use
<structure>_sio.dat	Every Si–O bond length detected in the structure (one per line).	Input for Si–O bond-length statistics and histograms.
<structure>_oo.dat	O–O distances between oxygen atoms sharing the same silicon in a tetrahedron.	Deriving averages and dispersion of O–O link lengths.
<structure>_osio.dat	Internal O–Si–O angles within each SiO₄ tetrahedron, in degrees.	Assessing tetrahedral shape and distortion.
<structure>_siosi.dat	Si–O–Si angles that describe how tetrahedra connect through bridging oxygens.	Characterising connectivity between neighbouring tetrahedra.
<structure>_ooo.dat	O–O–O angles located inside channels identified during the analysis.	Inspecting channel geometry.
<structure>_sisisi.dat	Consecutive Si–Si–Si angles along chains of tetrahedra.	Measuring opening angles along silicon chains.
<structure>_sisi.dat	Si–Si distances between silicon atoms linked through a single oxygen.	Calculating Si–Si bond statistics, NMR parameters, and staggering angles.
<structure>_Bonds.dat	Detailed log of every atom triplet considered for angle (“bend”) calculations, including indices, labels, and the resulting angle.	Full traceability of the angular data set.
<structure>_Q.dat	Tetrahedral order parameter (q) for each silicon atom, following the Chau & Hardwick metric.	Quantifying the degree of tetrahedral distortion per silicon.
<structure>_Staggering.dat	Minimum torsion angles (“first- and second-order staggering”) from O–Si–Si–O dihedrals for each connected Si pair.	Evaluating torsional staggering between neighbouring tetrahedra.
<structure>_29SiNMR.dat	Estimated ^29Si chemical shifts obtained from four literature correlations (in-house, Fyfe, Dawson, Thomas) plus the silicon index.	Predicting solid-state ^29Si NMR signatures.
<structure>_si.dat	Summary per silicon atom with its (q) value and statistical moments (mean, deviation, skewness, kurtosis) of surrounding Si–O, Si–Si, O–Si–O, Si–O–Si, and O–O data.	Compact descriptor set for each tetrahedral site.
Standard output (Histo: …)	Console report produced after reopening the .dat files to build histograms, including mean, min/max, deviation, skewness, and kurtosis.	Quick on-screen diagnostics; the same descriptors feed later thermodynamic correlations.