Crystallography Open Database: educational subsets and their usage - - PowerPoint PPT Presentation

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Crystallography Open Database:

educational subsets and their usage in interdisciplinary college education at Portland State University

Peter Moeck1, Trevor J. Snyder2, Werner Kaminsky3, all members of the International Advisory Board of the Crystallography Open Database (COD), and all members of the Portland Nanoscience and Nanotechnology Academy (PNNA)

1 Depart. Physics, Portland State University, Portland / Oregon 2 XEROX Wilsonville / Oregon 3 Depart. Chemistry, University of Washington at Seattle

Funding: NorthWest Academic Computing Consortium, National Science Foundation (most recent NEU: Nano-Science & Engineering: A STE Minor with General Education, EEC-1242197), Research Council of Lithuania, PANalytical, Crystal Impact & our various home institutions 2013

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Outline

• 1. Crystallography Open Database (COD) in its 11th year
• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science and

nano-tech)

• 4. 400/500 level course assignments (without solutions)
• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science

and nano-tech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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• pen access
• ver

240,000 entries

perhaps half of all data in open access?

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http://www.crystallography.net

mirrors worldwide

http://cod.ibt.lt http://cod.ensicaen.fr http://qiserver.ugr.es/cod http://nanocrystallography.org

web portal: http://nanocrystallography.net

more than 240,000 entries

Advisory Board Daniel Chateigner, Xiaolong Chen, Marco Ciriotti, Robert T. Downs, Saulius Gražulis, Armel Le Bail, Luca Lutterotti, Yoshitaka Matsushita, Peter Moeck, Miguel Quirós Olozábal, Hareesh Rajan, Alexandre F.T. Yokochi

Crystallography Open Database

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data_1009000 _chemical_name_systematic 'Gallium arsenate (V)' _chemical_formula_structural 'Ga (As O4)' _chemical_formula_sum 'As Ga O4' _publ_section_title ; Neutron and x-ray structure refinements between 15 and 1083 K of piezoelectric gallium arsenate, Ga As O4: temperature and pressure behavior compared with other $-alpha-quartz materials ; loop_ _publ_author_name 'Philippot, E' 'Armand, P' 'Yot, P' 'Cambon, O' 'Goiffon, A' 'McIntyre, G J' 'Bordet, P' _journal_name_full 'Journal of Solid State Chemistry' _journal_coden_ASTM JSSCBI _journal_volume 146 _journal_year 1999 _journal_page_first 114 _journal_page_last 123 _cell_length_a 4.9940(1) _cell_length_b 4.9940(1) _cell_length_c 11.3871(4) _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 120 _cell_volume 245.9 _cell_formula_units_Z 3 _symmetry_space_group_name_H-M 'P 31 2 1' _symmetry_Int_Tables_number 152 _symmetry_cell_setting trigonal loop_ _symmetry_equiv_pos_as_xyz 'x,y,z' '-y,x-y,1/3+z' 'y-x,-x,2/3+z' 'y,x,-z' '-x,y-x,1/3-z' 'x-y,-y,2/3-z' loop_

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Gražulis S. et al. Nucl. Acids Res. 40 (2012) D420-D427, open access

loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_calc _refln_F_squared_meas _refln_F_squared_sigma _refln_observed_status 1 0 0 88.50 107.46 1.41 o 2 0 0 443.74 483.55 3.27 o 3 0 0 105.70 102.49 1.73 o

4 0 0 109.80 97.14 0.68 o 5 0 0 61.24 59.93 0.88 o

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34.140 75 34.160 88 34.180 90 34.200 94 34.220 129 34.240 148 34.260 201 34.280 219 34.300 313 34.320 449 34.340 580 34.360 858 34.380 1102 34.400 1600 34.420 2152 34.440 2777 34.460 2830 34.480 2766 34.500 2381 34.520 2052 34.540 1697 34.560 1354 34.580 961 34.600 696 34.620 392 34.640 265 34.660 187 34.680 146 34.700 156

and within less than a minute (even if you live some 8,000 km away) you get:

http://cod.iutcaen.unicaen.fr/

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University

(PSU, in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science and nano-tech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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much less data than COD, but emphasis on interactive visualizations

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Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

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you may have to switch this

• n yourself

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Space group P21: A screw axis along the b axis means there are 8 more screw axes parallel to [010], including one through the middle of the unit cell

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Results of the first year of counting access to nanocrystallography.research.pdx.edu, rewritten for tablet computers, end of July 2013

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Results of the first year of counting access to nanocrystallography.research.pdx.edu, rewritten for tablet computers, end of July 2013

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0% 52% 48% New Visitors Returning Visitors

Results of the first year of counting access to nanocrystallography.research.pdx.edu, rewritten for tablet computers, end of July 2013

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all good open access crystallography resources, e.g. CIFs, space group drawings, history, …

http://nanocrystallography.net

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education

is provided at PSU (mainly in disguise as nano- science and nano-tech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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currently, there is a total

• f 7 courses
• ffered, three
• f then at the

300 level

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PH 382, part of a new 4 course sequence on

the basis of recent NSF funding

Three lecture course sequence, one laboratory course under development, supporting information on poster by Morris, Weasel and Moeck Introduction to Nanoscience and Nanotechnology for STEM and non STEM students as part of Portland State’s general education program, called University Studies – Science Cluster My approach:

that is nonsense why? Because this guy worked it

• ut more

than 100 years ago!

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“… there is no such thing as nanotechnology. Nanotechnology is now the buzzword and an umbrella term to designate nothing less than the state-of-the-art in science and technology in what is the normal progression and evolution of the relationship of humankind with its habitat and environment.”

• D. Jost, “Nanotechnology for Policymakers, An Introduction from the Physical Science Perspective”, nccr

trade regulations, Swiss national center of competence in research, working paper no. 2009/21, May 2009; http://phase1.nccr-trade.org/images/stories/publications/IP9/ed.Nanotechnology Introduction v9 march2009.pdf

whole course has the message “do consider taking more science and engineering classes, it’s both interesting and useful at the same time”

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“I am not inventing antigravity, which is possible someday only if the laws are not what we think. I am telling you what could be possible if the laws are what we think; we are not doing it simply because we haven’t gotten around to it.”

There’s plenty …

Eng. Sci. 23(5) 22-36, 1960

”... “it is an unwritten rule on Nature Nanotechnology that Richard Feynman’s famous 1959 lecture ‘There’s Plenty of room at the Bottom’ should not be referred to at the start of articles unless absolutely necessary,” wrote editor in chief Peter Rodgers in the December 2009 isue … Not that Rodgers has anything against the talk, he went on to say—he’d simply like to see a little variety in his opening lines. (He forbids references to Moore’s law for the same reason.) …”

DS (might be Sara DiPalma, copy editor of Engineering and Science Volume LXXIII, Number 1, WINTER 2010) http://calteches.library.caltech.edu/705/1/ES73.1.2010.pdf

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from 1905/1906 onwards Nanoscience becomes quantitative, published February 8, 1906

ibid vol. 34, pp. 591- 592, 1911

• A. Einstein, “Eine neue

Bestimmung der Moleküldimensionen”, Annalen der Physik, vol. 19, pp. 289-306, 1906

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Michael Faraday, Experimental relations of gold (and other metals) to light; the Bakerian lecture,

• Phil. Trans. Royal Soc.

London, vol. 147, pp. 145-181, 1857

So qualitative nanoscience is some 150 years old !

Leading eventually to improved silver based photography, colloids, sols and gels, polymers (collectively soft materials), catalysts, … are all nanoengineered products

Faraday’s conjecture on size dependency of a physical property “… a mere variation in the size

• f the particles gave rise to a

variety of resultant colours …”

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Light green: $0.02 - 0.22 Dark green: $2.62 Nanotechnology Undergraduate Education (NUE) in Engineering, Active Awards

NSF must have liked some of our ideas, now we are on the map, …

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PH 481/581, Introduction to Nano-materials

science and engineering, running since 2006

Arthur von Hippel’s 1956 vision for the then emerging field of materials science and engineering

”… instead of taking prefabricated materials and trying to devise engineering applications consistent with their macroscopic properties, one builds materials from their atoms and molecules for the purpose at hand.”

• A. R. von Hippel, “Molecular Engineering”, Science, vol. 123 (issue 3191), pp. 315-317, 1956; MIT Techn. Rep.

101, October 1955; Molecular Science and Molecular Engineering, Technology Press of MIT Press and Wiley & Sons, New York, 1959.

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sizes, shapes, dimensionality in nanometer region

modified Materials Science and -Engineering Tetrahedron, linking interconnected key concepts as well as interactions between Materials Scientists and -Engineers

“... system materials engineering emphasizes the study of the interactions between individual composites of a system, and how these interactions give rise to the function and performance of the final system."

http://www.nature.com/nmat/journal/v11/n 7/fig_tab/nmat3367_F2.html, P. Yang, J-M.

Tarascon, Nature Materials 11 (2012) 560-563

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The confluence of energy scales is illustrated in this graph, which shows how thermal, chemical, mechanical, and electrostatic energies associated with an object scale with size. As the characteristic object size approaches that at which molecular machines

• perate (shaded), all the energies converge. The horizontal line shows the thermal energy scale kT which, of course, does not

depend on an object's size. We estimate binding energy (purple) by considering an electron in a box; for comparison, the graph shows measured binding energies for hydrogen bonds (square), phosphate groups in ATP (triangle), and covalent bonds (circle), along with characteristic energies for nuclear and subatomic particles. In estimating the bending energy (blue), we took an elastic rod with an aspect ratio of 20:1 bent into a semicircular arc, and to compute the fracture energy (green) we estimated the energy in chemical bonds in a longitudinal cross section of the rod. The electrostatic energy (orange) was obtained for a spherical protein with singly charged amino acids of specified size distributed on the surface.

• R. Phillips, S. R. Quake, “The

Biological Frontier of Physics”, Physics Today, May 2006, pp. 38-43.

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science and nano-tech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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http://web.pdx.edu/~pmoeck/nanoMSE.htm

Coursework read the “Crystal Structure Visualizations in three dimensions with support from the open access nanocrystallography database” J. Mater.

• Educ. 28(1), 87-95 (2006) by P. Moeck et al. and answer the following questions
• n its basis, your actual working with open access databases, and from what you

have learned in class.

• 1. What does the acronym CIF for?
• 2. How many entries are currently in the COD? (Check out their website for an actual number.)
• 3. What are the lattice parameters of NaCl?
• 4. How many formulae units are in the conventional unit cell ?
• 5. How many atoms are in the conventional unit cell?
• 6. Provide a screenshot of the conventional NaCl unit cell along the [100] direction.
• 7. Provide a screeshot of NaCl unit cell along the [110] direction.
• 8. Provide a screenshot of the conventional NaCl cell along the [111] direction.
• 9. What are the positions of the Na and Cl atom in the so called asymmetric unit?
• 10. Provide a screenshot of the conventional cell of FeO along the [111] direction, what are the

similarities and differences to the conventional cell of NaCl?

Joint assignment over a couple of weeks for both graduates and undergrads

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“Since much of nano-materials science and engineering necessarily involves communications within teams of nano-scientist and nano-engineers, one major

• bjective of this course is to prepare you for working in interdisciplinary teams.

So you will have to read a couple of papers and write an informative opinion piece about it, that piece is supposed to communicate something, so you have to absorb the information first, then to think about the needs of the people you are going to address, what they need to know, (skip what they already know), why they need to know what you are going to communicate to them, .. This should be well thought through and typically no longer than a page.”

For example first homework assignment:

http://web.pdx.edu/~pmoeck/pdf/biotech%20future.pdf Freeman Dyson, Our Biotech Future, The New York Review of Books, http://www.nybooks.com/articles/archives/2007/jul/19/our-biotech-future/ for both graduates and undergraduates, in addition for graduates: http://web.pdx.edu/~pmoeck/pdf/biology%20next%20revolution.pdf Nigel Goldenfeld and Carl Woese, Biology’s next revolution, http://arxiv.org/abs/q- bio/0702015

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also used in this class,

• Prof. Werner Kaminsky’s

WinXMorph: http://cad4.cpac.washingt

• n.edu/WinXMorphHome

/WinXMorph.htm

allows for interactive discussions of: crystal forms, tracht and habit, exomorphosis, relation between habit and structure, free surface energy, Gibbs-Curie law, equilibrium polyhedron, Wulff law, …

students can check out how changing the “distance” in the program (which is proportional to a face’s growth velocity), changes the relative size of a face and how that leads to variations in the habit,…

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science and nano-tech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information

Files (CIF)

• 6. Summary and Outlook

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Virtual reality is great …

• Prof. Werner Kaminsky’s CIF2VRML:

http://128.95.152.162/Cif2VRMLHome/Cif2VRML.htm

scientist also like to build 3D models because …

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Left: Reconstruction of the double helix model of deoxyribose nucleic acid containing some of the original metal plates; Right: used by Francis Crick and James Dewey Watson in 1953, (Source: Science Museum, http://www.sciencemuseum.org.uk/images/i045/10313925.aspx)

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Left: Hard sphere model of the diamond structure (space filling ≈ 34 %) by W.

• H. Bragg, Museum of the Royal Institution, London, photo by André Authier.

(Source: http://blog.oup.com/2013/08/100th-anniversary-first-crystal-structure- determinations-bragg/#sthash.50BE8wiT.6mYKaBKB.dpuf.) Right: Ball and stick model of the diamond structure. (Source: FIG. 7 in W. H. Bragg and W. L. Bragg, The structure of diamond, Proc. R. Soc. Lond. A 89, 277; published September 22, 1913.)

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Wooden crystal morphology models of past centuries. (Source: Google Image search).

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• Prof. Werner Kaminsky’s WinXMorph:

http://cad4.cpac.washington.edu/WinXMorphHome/WinXMorph.htm 3D printed model of α-quartz as printed

• ut by Dr. Trevor Snyder (at XEROX

Wilsonville, ($5 but prices will come down further) also supporting poster Moeck, Snyder, and Kaminsky

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$300,000 - $”500 k” $500 - $1,000

https://www.youtube.com/w atch?v=ddtJVww8Zvw https://www.youtube.com/ watch?v=n9SGAS52ZCA https://www.youtube. com/watch?v=yTh0rz CXefQ

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prices for 3D printing will come down !

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• approx. $50
• approx. $20 as both build and support

material is needed (two nozzle machine)

• approx. $0.2

when printed

• n a $500 to

$1,000 hobby machine (prints only build material)

prices will come down further

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x 6

demonstrating to the students that this is actually the hexagonal unit cell

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x 3

demonstrating to the students that the hexagonal prism is not the unit cell and that there is no such Bravais lattice

also useful for explaining the 4 index lattice direction and Miller plane indices for hexagonal crystals taking out a few sphere caps allows for better assessment of the intersites

1

a r

2

a r

3

a r

1

a r

2

a r

] 00 1 [ ] 0010 [ ] 000 1 [ ] 0100 [ ] 1100 [ ] 1000 [ ≡ ≡ ≡ ≡ ≡ hexagonal lattice but not for structure with basis

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set of “reduced sphere size” models for better assessment

• f the intersites

first three also unit cells for the three cubic Bravais lattices

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• 1. Crystallography Open Database (COD) in its 11th

year

• 2. Supporting efforts at Portland State University (PSU,

in their 10th year)

• 3. Courses where basic crystallographic education is

provided at PSU (mainly in disguise as nano-science and nanotech)

• 4. 400/500 level course assignments (without

solutions)

• 5. 3D printing from Crystallographic Information Files

(CIF)

• 6. Summary and Outlook

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• pen access crystallographic databases, combined some 350,000 –

400,000 entries in CIF format

• pen access crystallography resource portal, nanocrystallography.net

COD in it’s 11th year, more than 240,000 CIFs EDU-COD and CMD in their 10th year, approx. 1,000 CIFs used in teaching nano-materials science and -engineering at the 400/500 level for 8 years will be used in new 300 level course as well, starting in the spring of 2014 free programs for conversion of CIF (molecule structure, crystal morphology) to STL by Prof. Werner Kaminsky http://cad4.cpac.washington.edu/ 3D printing will further come down in prizes, good for hand on models in class plans for Bicrystallography Open Database

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Bicrystallography Open Database

searchable collection

• f CIFs for all kinds
• f simulations and

visualizations of grain boundaries to be derived from user inputs and freely modifiable at the atomic level

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p21’mn’ - polar physical properties can exist p2’mm’ - polar physical properties cannot exist

two color layer group c2’mc’ - a genuine back- white group, polar physical properties can exist two color layer group c2’mm’ – a gray group, polar physical properties cannot exist

CeO2 Σ = 5 (310)/[001] 36.9° tilt boundary, dichromatic

complex has 3 atoms per lattice point of dichromatic pattern I4/mm’m’

CeO2 Σ = 5 (120)/[001] 53.1° tilt boundary viewed down [001]

“… disclose generic relations between different interfaces, specify crystallo- graphically equivalent variants of an interface and classify line defects in

• interfaces. The symmetry of a bicrystal

imposes constraints on tensor properties

• f the bicrystal interface, provides

classification of the interfacial vibrational modes, discloses possible interfacial transitions etc.”

• V. Janovec, Th. Hahn and H. Klapper, Twinning and domain structures,

International Tables for Crystallography (2006), Vol. D, ch. 3.2, pp. 377-392.

Bicrystallography Open Database

No textbook, only a few original papers and book chapters

diamond, Σ = 5 (310)/[001] 36.9° tilt boundary, viewed down [001], black white (two color) layer group p21’am’

• R. C. Pond and J. P. Hirth, in Ehrenreich, H., Solid State Physics: Advances in Research

and Applications, Volume 47, 1994, pp. 287-365

another “idea whose time has come”

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Frieze Group 11g

SrTiO3 Σ = 13a, (510)/[001], 22.6° tilt boundary in [001] projection, sectioned at ¼

[510], large disks Sr columns, medium disks pure O columns, small disks mixed O and Ti columns

• nly pure O

columns are located at interface

1 nm

Aberration-corrected translation-symmetry averaged STEM Z- contrast, H. Yang et al., Phil. Mag. 2012, 1-11, iFirst Article.

primitive cubic lattice, 5 atoms per lattice point of dichromatic pattern P4/mm’m’, zero rigid body shift and expansion for simplicity

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