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opencc-by-4.0Oct 2021View details →

"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.

Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data 3D ED data sets of 5 compounds and JANA refinement files of 12 compounds Relevant tools: <ul> <li>PETS2: data reduction and analysis of electron diffraction patterns <ul> <li>Download program and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Palatinus, L. et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst. B75, 512–522 (2019). <a href="https://doi.org/10.1107/S2052520619007534">DOI: 10.1107/S2052520619007534</a></li> </ul> </li> <li>JANA2006: crystal structure model refinement program <ul> <li>Download program from <a href="http://jana.fzu.cz/">http://jana.fzu.cz/</a> and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Results here were obtained with JANA2006. We recommend using JANA2020.</li> <li>Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. Z. Kristallogr. 229, 345–352 (2014). <a href="https://doi.org/10.1515/zkri-2014-1737">DOI: 10.1515/zkri-2014-1737</a></li> </ul> </li> <li>DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives <ul> <li>Program automatically included in JANA2006/JANA2020</li> <li>Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. Acta Cryst. A71, 235–244 (2015). <a href="https://doi.org/10.1107/S2053273315001266">DOI: 10.1107/S2053273315001266</a></li> </ul> </li> </ul> 3D ED data sets: STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a>. <ul> <li>α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)</li> <li>abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)</li> <li>STW_HPM-1, continuous-rotation (1 data set, room temperature)</li> <li>STW_HPM-1, continuous-rotation (1 data set, T = 100 K, cryotransfer)</li> </ul> JANA refinement and CIF files: CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details. JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included. <ul> <li>α-quartz</li> <li>albite</li> <li>mordenite</li> <li>natrolite</li> <li>STW_HPM-1</li> <li>cobalt aluminophosphate (CAP)</li> <li>CAU-36</li> <li>α-glycine</li> <li>carbamazepine</li> <li>(+)-limaspermidine</li> <li>abiraterone acetate</li> <li>MBBF4</li> </ul> For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files. Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.

opencc-by-4.0Oct 2010View details →

Figure 1: Venn diagram of a DSm hybrid model for a 3D frame.

As another simple example of hybrid DSm model, let's consider the 3D case with the frame £ = fµ1; µ2; µ3g with the model M 6= Mf in which we force all possible conjunctions to be empty, but µ1 \ µ2. This hybrid DSm model is then represented with the Venn diagram on Fig. 1 (where boundaries of intersection of µ1 and µ2 are not precisely de¯ned if µ1 and µ2 represent only fuzzy concepts like smallness and tallness by example).

opencc-by-4.0May 2024View details →

Daily climatology of 3D ocean currents, SST and SSH based on a 22 year run of the SEA-COFS model

This dataset is a daily climatology created based on a 22 year free run of the SEA-COFS model full domain (EAC 25.25 - 45.55 °S) forced with BARRA-R winds and tides, spanning from January 1994 to September 2016. The model has 30 sigma-stretch vertical levels and an across-shore resolution of 2.5 km (on shelf) – 6 km (off shelf) and 5 km along-shore. For a full description of this version of the model and its validation refer to the following papers: <ul> <li>Li, J, Roughan, M. & Kerry, C. (2021). <a href="https://doi.org/10.1029/2021GL094115%20">Dynamics of interannual eddy kinetic energy modulations in a Western Boundary Current</a>. Geophysical Research Letters,Vol 48, October 2021.DOI: <a href="https://doi.org/10.1029/2021GL094115">https://doi.org/10.1029/2021GL094115</a> <a href="http://www.oceanography.unsw.edu.au/private/publications/2021/2021GL094115.pdf">[PDF file]</a></li> <li> </li> <li>Li, J, Roughan, M. & Kerry, C. (2022). <a href="https://doi.org/10.1175/JCLI-D-21-0622.1">Variability and Drivers of Ocean Temperature Extremes in a Warming Western Boundary Current</a>. Journal Of Climate, February 2022. DOI: <a href="https://doi.org/10.1175/JCLI-D-21-0622.1">https://doi.org/10.1175/JCLI-D-21-0622.1</a> <a href="http://www.oceanography.unsw.edu.au/private/publications/2022/Li_2022.pdf">[PDF file]</a></li> </ul> This daily climatology of 365 days was created with NCO tools by taking the mean of the 22 daily average ROMS output files (one for each year) to generate each climatological day. Specific commands used are recorded in the NetCDF file history. Leap year days were excluded since its climatology was computed with only 5 instances. A sample file with the climatological data for January 1st is provided here as an example of the NetCDF format of the dataset. The entire dataset is one file of approximately 62GB and can be provided upon request.    NOTE: The ocean_time variable reflects the dates of the year 1994, but the values of the variables correspond to climatological values computed as described.  The ROMS variables below are present in this daily climatology, as well as the S-coordinate stretching curves, grid defining variables and other time independent parameters: AKs = "time-averaged salinity vertical diffusion coefficient" [meter2 seconds-1] AKt = "time-averaged temperature vertical diffusion coefficient" [meter2 seconds-1] AKv = "time-averaged vertical viscosity coefficient" [meter2 seconds-1] bustr = "time-averaged bottom u-momentum stress" [newton meter-2] bvstr = "time-averaged bottom v-momentum stress" [newton meter-2] omega = "time-averaged S-coordinate vertical momentum component" [meter3 second-1] pvorticity = "time-averaged potential vorticity" [meter-1 second-1] pvorticity = "time-averaged 2D potential vorticity" [meter-1 second-1] rho = "time-averaged density anomaly" [kilogram meter-3] rvorticity = "time-averaged relative vorticity, vertical component" [second-1] rvorticity_bar = "time-averaged 2D relative vorticity" [second-1] salt: = "time-averaged salinity" [PSU] shflux = "time-averaged surface net heat flux" [watt meter-2] ssflux = "time-averaged surface net salt flux, (E-P)*SALT" [meter second-1] sustr = "time-averaged surface u-momentum stress" [newton meter-2] svstr = "time-averaged surface v-momentum stress" [newton meter-2] temp = "time-averaged potential temperature" [Celsius] u = "time-averaged u-momentum component" [meter second-1] u_eastward = "time-averaged eastward momentum component at RHO-points" [meter second-1] ubar = "time-averaged vertically integrated u-momentum component" [meter second-1] ubar_eastward = "time-averaged eastward vertically integrated momentum component at RHO-points" [meter second-1] uu = "time-averaged u-momentum times u-momentum" [meter2 second-2] uv = "time-averaged u-momentum times v-momentum" [meter2 second-2] v = "time-averaged v-momentum component" [meter second-1] v_northward = "time-averaged northward momentum component at RHO-points" [meter second-1] vbar = "time-averaged vertically integrated v-momentum component" [meter second-1] vbar_northward = "time-averaged northward vertically integrated momentum component at RHO-points" [meter second-1] vv = "time-averaged v-momentum times v-momentum" [meter2 second-2] w = "time-averaged vertical momentum component" [meter second-1] zeta = "time-averaged free-surface" [meter]

opencc-by-4.0May 2024View details →

Data for "Antiferromagnetic phase transition in a 3D fermionic Hubbard model"

This dataset is for research article "Antiferromagnetic phase transition in a 3D fermionic Hubbard model".

opencc-by-4.0Jun 2024View details →

3D models and raw data for the "Photogrammetric 3D modelling and experimental archaeology reveals new technological insights into engraved soapstone sinker production in Western Norway (6400-3300 cal. BC)" paper, Radchenko et al. in prep.

3D models and raw data for the "Photogrammetric 3D modelling and experimental archaeology reveals new technological insights into engraved soapstone sinker production in Western Norway (6400-3300 cal. BC)" paper, Radchenko et al. in prep. 5 models of soapstone sinkers and 5 models of experimentally produced objects.

Fig. 7 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 7. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, from the Lower Cretaceous of Italy, un tangled; explanatory notes to the test structure based on different sections (not to scale). A, B. San Lorenzello section. A. Thin section DiSTSL99C.1, upper Hauterivian. B. Thin section DiSTARL36.1, lower Barremian, with three different individuals (B1, B2, B3). C. Thin section IPA.679.1 (from De Castro 1964: pl. 1: 10), paratype, Cava Grande, Punta Orlando, Hauterivian–Barremian. D. Thin section IPA.281.5 with two different individuals (D1, D2) (from De Castro 1964: pl. 1: 3, 5), paratype, Castel Morrone, Caserta, Hauterivian–Barremian. E. Thin section IPA.85.3 (from De Castro 1964: pl. 1: 14), Monte La Foresta, Salerno, Hauterivian–Barremian. F, G. San Lorenzello section. F. Thin section DiSTAR39.2 with two different individuals (F1, F2), lower Barremian; dashed line in F1 indicates the coiling axis;. G. Thin section DiSTSL90/91.1, upper Hauterivian.

Fig. 10 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 10. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, from Castel Morrone, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous. A. DiSTARL36.1, oblique section showing (A1), compared with the 3D sectioned model (cut in frontal view, A2), also represented sideways (A3). B. DiSTARL36.1, longitudinal section (B1), compared with the 3D sectioned model (cut in frontal view, B2), also represented sideways (B3). C. DiSTARL36.1, oblique section (C1), compared with the 3D sectioned model (cut in frontal view, C2), also represented sideways (C3). Scale bars 100 μm.

Fig. 4 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 4. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, San Lorenzello section, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous (A–L) and Križ section, Mljet Island, Croatia Hauterivian–lowermost Barremian, Lower Cretaceous (M–O); various transverse (A–J3, J5, M) and oblique (J4, K, L, N and O) sections. A. Thin section DiSTARL28. B. Thin section DiSTARL331. C. Thin section DiSTARL34. D. Thin section DiSTARL37 with two individuals (D1, D2). E. Thin section DiSTARL8. F. Thin section DiSTARL362. G. Thin section DiSTARL36. H. Thin section DiSTARL212. I. Thin section DiSTARL392 with two individuals (I1, I2). J. Thin section DiSTARL361 with five individuals (J1–J5). K. Thin section DiSTARL29 with two individuals (K1, K2). L. Thin section DiSTARL92. M–O. Thin sections IGZ-MK, after Husinec and Sokač (2006: unfigured specimens from Mljet Island, Croatia). Rather largesized specimens (F and K1) might belong to microspheric generation.

Fig. 6 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 6. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, Castel Morrone, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous. Sub)axial sections (A–E), oblique sections (F, G, I, J), transverse section (H). A. Thin section DiSTARBA.4418.2 with two individuals (A1, A2); the dashed line in A2 points out alternated chambers resulting from the trochospiral arrangement. B. Thin section DiSTARBA.4418.3 with two individuals (B1, B2). C. Thin section DiSTARBA.4418.12. D. Thin section DiSTARBA.4418.15. E. Thin section DiSTARBA.4418.1 with two individuals (E1, E2). F. Thin section DiSTARBA.4418.13. G. Thin section DiSTARBA.4418.11. H. Thin section DiSTARBA.4418.3. I. Thin section DiSTARBA.4418.4. J. Thin section DiSTARBA.4418.2. Abbreviation: co, columella.

Fig. 3 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 3. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, San Lorenzello section, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous (A–J, L) and Križ section, Mljet Island, Croatia, Lower Cretaceous (K); various (sub)axial sections. A. Thin section DiSTARL29 with two individuals (A1, A2). B. Thin section DiSTARL8. C. Thin section DiSTARL392 with three individuals (C1–C3). D. Thin section DiSTARL361 with two individuals (D1, D2). E. Thin section DiSTARL391. F. Thin section DiST/SL9091.1. G. Thin section DiSTARL35. H. Thin section DiSTARL36. I. Thin section DiSTARL41. J. Thin section DiST/SL99C.2. K. Thin section IGZMK with two individuals (K1, K2), after Husinec and Sokač (2006: fig. 7J and I). L. Thin section DiSTARL37. Rather largesized specimens (A, K2) might belong to microspheric generation. Abbreviation: ch, chamber.

Fig. 12 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 12. Palaeobiogeographic distribution of species of Campanellula De Castro, 1964. Occurrence of species has been plotted on an Early Cretaceous ca.120 Ma) paleogeographic map, after http://portal.gplates.org/.

Fig. 11 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 11. Scheme of the species of Campanellula De Castro, 1964. A. Campanellula capuensis De Castro, 1964, IPA.281.1, holotype (drawing from De Castro 1964: pl. 1: 1), Castel Morrone, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous. B. Campanellula herishtensis Schlagintweit, Rashidi, and Hanifzadeh, 2019, T 726 (number Gmm 13950F110), holotype (drawing from Schlagintweit et al. 2019: fig. 5L), Ardakan, Province of Yazd, Central Iran, lower Gargasian, Aptian, Lower Cretaceous.

Fig. 9 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 9. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, from Castel Morrone, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous. A. DiSTARL36.1, transversal section showing six chambers per whorl (A1), compared with the 3D model transversally cut (upper view displaying eight chamber per whorl (A2), also represented in lateral view (A3). B. DiSTARL36.1 tangential section (B1), compared with the 3D model tangentially cut (frontal view of the section, B2), also represented in lateral view (B3). C. DiSTARL35.1, tangentialoblique section (C1), compared with the 3D sectioned model cut in frontal view, C2), also represented in lateral view (C3). D. DiSTARL34.1, oblique section through last tours (D1), compared with the 3D sectioned model (cut in frontal view, D2), also represented in lateral view (D3). Scale bars 100 μm.

Fig. 5 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 5. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, San Lorenzello section, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous; various tangential sections. A. Thin section DiSTARL331. B. Thin section DiSTARL34. C. Thin section DiSTARL35 with two individuals (C1, C2). D. Thin section DiSTARL382. E. Thin section DiSTARL212. F. Thin section DiSTARL13. G. Thin section DiSTARL59. H. Thin section DiSTARL37 with two individuals (explain H1, H2). I. Thin section DiSTARL361 with three individuals (I1–I3). J. Thin section DiSTARL391 with two individuals (J1, J2). K. Thin section DiSTARL392. L. Thin section DiSTARL59. M. Thin section DiSTARL333. Rather largesized specimen (E) might belong to microspheric generation.

Fig. 8 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 8. Lituolinid foraminifer Campanellula capuensis De Castro, 1964, from Castel Morrone, Italy, upper Hauterivian–lower Barremian, Lower Cretaceous. IPA.281.1, 3D test reconstruction of the holotype (De Castro 1964: pl. 1: 1:). Left (A1) and frontal right (A2) views of the test.

Fig. 1 in The reinstated identity of agglutinated foraminifer Campanellula capuensis from the Lower Cretaceous of southern Italy by means of a 3D model investigation

Fig. 1. Position of the studied localities. A. A contour map of the Italian Peninsula showing location of the Campania Region. B. Enlargement of the Campania Region with the two studied localities: San Lorenzello section (Benevento Province; red star) and the type locality of Campanellula capuensis De Castro, 1964) near Castel Morrone village (Caserta Province; yellow star). C. Panoramic view of the San Lorenzello section (from Google Earth). D. Panoramic view of the Campanellula capuensis type locality along the SP174 road (from Google Earth).

Fig. 10 in Virtual 3D modeling of the ammonoid conch to study its hydrostatic properties

Fig. 10. Model showing the shell orientation (φ) attained during neutral buoyancy for Maorites seymourianus models. White circle, center of buoyancy; asterisk, center of mass.

Fig. 9. A in Virtual 3D modeling of the ammonoid conch to study its hydrostatic properties

Fig. 9. A. Comparison of the model geometry for Maorites seymourianus defined by the Equation 3, and the closest logarithmic spiral (dotted line) found for these data (radius r = 88.97e-0.12Θ, determination coefficient R2 = 0.988). B. Close up of the initial whorls showing the slow increase in growth rate at the beginning of the ontogeny. The arrows indicate the differences in growth between the polynomial curve (solid arrows) and the logarithmic curve (dashed arrows).

Fig. 7 in Virtual 3D modeling of the ammonoid conch to study its hydrostatic properties

Fig. 7. The final simplified model of the conch of Maorites seymourianus. A. External elements of the conch in lateral view, the smooth areas emulate rectiradiate constrictions; the phragmocone in dark gray, the body chamber in grey. B. Internal elements within the phragmocone; the siphuncle in black, the septa in grey.

Fig. 3 in Virtual 3D modeling of the ammonoid conch to study its hydrostatic properties

Fig. 3. Example of the alignment process using only two specimens. Here it is graphed the radius against the angle showing the curves that describe the geometry of two specimens of Maorites seymourianus. A. The geometry of CPBA 16847 (reference) is defined by a function r = h(Θ) and its domain is [0 rad; 19.90 rad] in black (solid line), the geometry of CPBA 16838 is defined by a function r = i(Θ) and its domain is [0 rad; 20.42 rad] in grey. The normalization process consists of finding the results for an appropriate radius, in this case r = 20 mm (dotted line). Following, the difference in angle must be calculated (ΔΘ = 1.38 rad) and then the domain of the functions is adjusted accordingly. B. Curves after normalization, the difference in angle was applied to the domain of CPBA 16838, the new domain of the function is [1.38 rad; 21.80 rad]. Abbreviations: Θ, angle; r, radius.