1

Peter Moeck1, E. DeStefani1, H. Harshfield1, J. Stone-Sundberg1,2,T. Snyder3,1, W. Kaminsky4, L. Fuentes-Cobas5, J.-C. Baloche6, andD. Chateigner6

1 Nano-Crystallography Group, Department of Physics, Portland State University,Portland/Oregon2 Crystal Solutions, LLC, Portland/Oregon3 3D Systems Corporation, Wilsonville/Oregon4 Department of Chemistry, University of Washington at Seattle5 Centro de Investigación en Materiales Avanzados, S. C. Chihuahua, México6 CRISMAT-ENSICAEN and IUT-Caen, Université de Caen Normandie, France

Funding: National Science Foundation (most recent NEU: Nano-Science & Engineering: A STEMinor with General Education, EEC-1242197), NorthWest Academic Computing Consortium,Research Council of Lithuania, PANalytical, Crystal Impact, Portland State University

3D printed crystallographic models &open-access crystallography resources:

*.stl and *.wrl printing from converted CIF or STAR compliant files

2

Outline1. Crystallography Open Database (COD) in its 14th year

2. Supporting efforts at Portland State University in their13th year

3. Converting Crystallographic Information Files (CIF) to3D printing files (*.stl and *.wrl)

4. Materials Properties Open Database (MPOD) in its 6th

year

5. Creating *.stl files directly at the MPOD website

6. News from the 3D printing of crystallographic modelscommunity

7. Summary and Outlook

3

open access

over360,000entries

about one half ofall known structuredata in open openaccess !!

4http://nanocrystallography.net

5

http://www.crystallography.netmirrors worldwidehttp://cod.ibt.lthttp://cod.ensicaen.frhttp://qiserver.ugr.es/codhttp://nanocrystallography.orgweb portal: http://nanocrystallography.net

More than 360,000 entries

Advisory BoardDaniel Chateigner, Xiaolong Chen, Marco Ciriotti, Robert T.Downs, Saulius Gražulis, Werner Kaminsky, Armel Le Bail,Luca Lutterotti, Yoshitaka Matsushita, Peter Moeck, PeterMurray-Rust, Miguel Quirós Olozábal, Hareesh Rajan,Alexandre F.T. Yokochi

Crystallography Open Database

N. Jones, Atomic Secrets:100 years of Crystallography,Nature 505 (2014) 602-603;

http://www.nature.com/polopoly_fs/1.14608!/menu/main/topColumns/topLeftColumn/pdf/505602a.pdf

6

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 ofpiezoelectric gallium arsenate, Ga As O4: temperature and pressurebehavior 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 trigonalloop__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__atom_type_symbol_atom_type_oxidation_numberGa3+ 3.000As5+ 5.000O2- -2.000

loop__atom_site_label_atom_site_type_symbol_atom_site_symmetry_multiplicity_atom_site_Wyckoff_symbol_atom_site_fract_x_atom_site_fract_y_atom_site_fract_z_atom_site_occupancy_atom_site_attached_hydrogens_atom_site_calc_flagGa1 Ga3+ 3 a 0.44991(7) 0. 0.3333 1. 0 dAs1 As5+ 3 b 0.44800(8) 0. 0.8333 1. 0 dO1 O2- 6 c 0.39848(9) 0.31858(9) 0.38307(3) 1. 0 dO2 O2- 6 c 0.39674(9) 0.29595(9) 0.87152(3) 1. 0 d

loop__atom_site_aniso_label_atom_site_aniso_U_11_atom_site_aniso_U_12_atom_site_aniso_U_13_atom_site_aniso_U_22_atom_site_aniso_U_23_atom_site_aniso_U_33Ga1 0.00202(11) 0. 0. 0.00198(14) -0.00009(10) 0.00201(14)As1 0.00210(12) 0. 0. 0.00177(16) -0.00009(11) 0.00183(15)O1 0.00552(14) 0.00311(11) -0.00111(9) 0.00395(13) -0.00138(10)

0.00432(12)O2 0.00574(15) 0.00327(11) -0.00089(10) 0.00372(14) -0.00109(11)

0.00446(13_refine_ls_R_factor_all 0.025

7

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_status1 0 0 88.50 107.46 1.41 o2 0 0 443.74 483.55 3.27 o3 0 0 105.70 102.49 1.73 o4 0 0 109.80 97.14 0.68 o5 0 0 61.24 59.93 0.88 o

8

much much less data thanCOD, but emphasis oninteractive visualizations

9

10

about 950structures:inorganics,organics,and a fewproteins

11

12

Space group P21: A screw axis along the baxis means there are 8 more screw axesparallel to [010], including one through themiddle of the unit cell

13

14

15

* Portland,Oregon

16

prices for 3Dprinting willcome down !

Fig. 4 Mid 2012 “expectations versus time” graph of the Gartner group, showing 3D printing at the “peak of inflated expectations” and extrapolating to its“plateau of productivity” in 2017 (to 2022 at the latest).

17

inexpensivemonochrome printerfrom 3D SystemsCorporation ($ 999 US),based on their PlasticJet 3D printingtechnology, launchedJan. 2014, no longeravailable off factory

Projet 4500 MultijetTM printer of3D Systems Corporation, currentlythe only printer that produces colorprints in durable plastics. $69,000 US

ColorJet Printing (CJP) technologyplatform and new class of durableVisiJet® C4 Spectrum plastics.

one does not need to own a 3D printer, there are professional over-nightprint shops, e.g. http://www.3dsystems.com/quickparts

T. Snyder etal., 3D Systems’TechnologyOverview and NewApplications inManufacturing,Engineering,Science, andEducation, 3DPrinting andAdditiveManufacturing 1(2014) 169-176

$4,399 US

18

http://www.iucr.org/news/newsletter/volume-22/number-1/3d-printingmrss14-1716-fff03-09; doi:10.1557/opl.2014.872

*.cif to *.stl

W. Kaminsky et al., One-click preparation of 3Dprint files (*.stl, *.wrl) from *.cif (crystallographicinformation framework) data using Cif2VRML, PowderDiffraction 29 (2014) S42-S47

in: L. Liu, M. L. Minus,F. Rosei and V.Uskoković (eds.),Volume 1716 –“Educating andMentoring YoungMaterials Scientists forCareer Development”

19

designed with a CAD program

converted fromCIF to STL withprogramsCif2VRML andWinXMorph

P. Moeck et al.,Enlivening 300 levelgeneral educationclasses on nanoscienceand nanotechnologywith 3D printedcrystallographic models,J. Mater. Education36 (2014) 77-96

20

Caffeine printed with the so called Z-corp (MIT) technique, dried coloredgypsum water mixture dipped into superglue (now ZPrinter series of 3D SystemsCorporation, approximately $ 0.20 US per cubic centimeter, but models tend tobe a bit fragile

W. Kaminsky et al., One-clickpreparation of 3D print files (*.stl, *.wrl)from *.cif (crystallographic informationframework) data using Cif2VRML,Powder Diffraction 29 (2014) S42-S47

J. Stone-Sundberg et al., 3D printed models ofsmall and large molecules, crystal structures andmorphologies of crystals, as well as their anisotropic physicalproperties , Cryst. Res. Technol. 50 (2015) 432–441

21Herapathite, the molecule behind the early fortune of the Kodak company

a few 3D printers read *.wrl files (VRML format, say ‘vormel’ )

22

sucrose (withhydrogen bonds)

chlorophyll

small section ofdeoxyribonucleic acid (containing aplanar phenoxazine-derived bi-functionalspectroscopic probe – from original data)

all printed fromCIFs converted to*.wrl (say ‘vormel’)in durable VisiJet® C4Spectrum plastics withProJet 4500

23

http://nanocrystallography.research.pdx.edu/media/sugar_molecule_stl.stl

http://nanocrystallography.research.pdx.edu/media/sugar_morphology_stl.stl

our first two 3D print files inopen access (April 2014)

24

25Material Properties Open Database: http://mpod.cimav.edu.mx/

26In France: www.materialproperties.org, Mexican Mirror: http://mpod.cimav.edu.mx/

G. Pepponi, S.Gražulis and D.Chateigner, MPOD: aMaterial PropertyOpen Databaselinked to structuralinformation, NuclearInstruments andMethods in PhysicsResearch B 284(2012) 10-14

27

Franz ErnstNeumann’sprinciple

“the symmetryoperations of anyphysical propertyof a crystal mustinclude thesymmetryoperations of thepoint group of thecrystal"

http://reference.iucr.org/dicti

onary/ Neumann's_principle

Loosely speaking, mostmaterials tensors describelinear (first order) responses ofa crystal to external influencesin ways that are independent ofarbitrarily chosen coordinatesystems. There are also tensordescriptions for higher orderresponses which may havedifferent symmetry properties.

L. Fuentes-Cobas et al., Implementing Graphic Outputs for the MaterialProperties Open Database (MPOD), Acta Cryst 70 (2014) C1039

28

4th rank polar tensor of elastic stiffness (anisotropicYoung’s moduli), represented by 6 x 6 matrix

6 of the 36 matrix components are independent due to pointsymmetry 32 of α-quartz (and the symmetric nature of the 2nd rankfield tensors for strain and stress) 18 non-zero components of matrixof elastic stiffness

21 independent non-zero matrix components in case of crystals withpoint symmetry 1

klijklij c Hooke’s law

nmnm c

Piezoelectric effect 3rd rank polar tensor, represented by 3 x 6 matrix,only two independent matrix components

jkijki dP nmnm dP

instead of familiarisotropic 1D form

does not exist inisotropic materials

xxkxx

F

29

30

W. Kaminsky et al., 3D printing of representation surfaces from tensor data ofKH2PO4 and low-quartz utilizing the WinTensor software, Zeits. für Kristallogr. –Crystalline Materials 230 (2015) 651–656

linear electro-optical (Pokels)effect in -quartz,

3rd rank polar tensor, existsonly in crystals that do notpossess an inversion center

red or green colors represent valueswith plus or minus signs

right handed α-quartz

point group 32,space group P322

rotational power for right α-quartz along [0001] (+z-axis)direction: ≈ 19° (counter-clockwise) per mm platethickness for 633 nm light(and SATP), correspondinggyration (pseudo-)tensor isaxial and second rank

31

ijij both effects have two independent tensorcomponents (due to point symmetry 32)

kijkij Er

klijklij c

six independenttensor components

point group 32

α-quartz

0.1 Euromagneto-electric effectin LiCoPO4 magnetic pointgroup mmm’, temperaturedepended, measured at 4.2 K

elastic stiffness in Au,three independent components

sign (color) changes for mirrors in both a-c and b-c planes, no suchchange for mirror in a-b plane, more at L. E. Fuentes-Cobas et al., in: K.H. J. Buschow, Handbook of Magnetic Materials, Vol. 24, Elsevier, 2016

elastic compliance inPbIn0.165Nb0.398Mg0.167Ti0.32O3mm2, nine independentcomponents

klijklij s

mm3

http://mpod.cimav.edu.mx/dataitem/1000095/

http://mpod.cimav.edu.mx/datafiles/1000019.mpod

a

b

32

Magnetoelectric longitudinal surface (representationsurface) of LiCoPO4Magnetic space group Pnma'Magnetic point group mmm’ = D2h:C2vSingle-crystal tensor for T = 4.2 K (ps/m)

L. E. Fuentes-Cobas et al., chapter 3 in: K. H. J.Buschow, Handbook of Magnetic Materials, Vol.24, Elsevier, 2016

convert to *.stlfile directly onthe MPODwebsite

send to 3D printer

33

Single- and poly- crystalscompared

Single-crystal longitudinalmagnetoelectricity.

red-blue 3D printing byMPOD-2 (beta)

LiCoPO4 magnetoelectricitymagnetic point group: m m m´

Magnetoelectricity exhibits a special“magnetic” symmetry:

- Vertical planes are symmetry elements,they change positive to negative.

- Horizontal planes represent anti-symmetryL. E. Fuentes et al, “Predicting the Coupling Properties of

Axially-Textured Materials”, Materials 6, 4967 (2013).

34

Piezoelectricity inα-quartz

Screenshot of “MPOD-2(beta)”

(under development)

35

36

S. Gražulis et al.,CrystallographicEducation in the 21st

Century,

J. Appl. Cryst.48 (2015) 1964 –1975

37

38

Leroy Cronin:

“I don’t want chemistry reduced toplastic trinkets, I want new scienceto occur as a result of use ofubiquitous 3-D printing andmolecular design.”

in Halford B. (2014), “3D Models, Without the Kit”, Chemical andEngineering News 92, 32–33.

39

searchablecollection ofCIFs for all kindsof simulationsandvisualizations ofgrain boundaries

to be derivedfrom user inputsand freelymodifiable at theatomic level

40

p21’mn’ - polarphysical propertiescan exist

p2’mm’ - polarphysical propertiescannot exist

two color layergroup c2’mc’ - agenuine back-white group, polarphysical propertiescan exist

two color layergroup c2’mm’ – agray group, polarphysical propertiescannot exist

CeO2 Σ = 5(310)/[001] 36.9° tiltboundary, dichromaticcomplex has 3 atoms per latticepoint of dichromatic patternI4/mm’m’

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

“… disclose generic relations betweendifferent interfaces, specify crystallo-graphically equivalent variants of aninterface and classify line defects ininterfaces. The symmetry of a bicrystalimposes constraints on tensor propertiesof the bicrystal interface, providesclassification of the interfacial vibrationalmodes, discloses possible interfacialtransitions 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 originalpapers and book chaptersdiamond, Σ = 5 (310)/[001] 36.9° tiltboundary, viewed down [001], blackwhite (two color) layer group p21’am’

R. C. Pond and J. P. Hirth, in Ehrenreich, H., Solid State Physics: Advances in Researchand Applications, Volume 47, 1994, pp. 287-365

another “idea whose time has come”

41

Frieze Group 11g

SrTiO3 Σ = 13a, (510)/[001], 22.6° tiltboundary in [001] projection, sectioned at ¼[510], large disks Sr columns, medium disks pure Ocolumns, small disks mixed O and Ti columns

only pure Ocolumns arelocated atinterface1 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 patternP4/mm’m’, zero rigid body shift and expansion for simplicity

42

∑ 13aSrTiO3(510)

after free energy minimization, H. Yang et al. Phil Mag. 93 (2013) 1219-1229

Cif2VRML, http://cad4.cpac.washington.edu/Cif2VRMLHome/Cif2VRML.htm

43*.wrl file of ∑ 5 (310) [001] in SrTiO3 ready to be send to 3D color printer

Cif2VRML, http://cad4.cpac.washington.edu/Cif2VRMLHome/Cif2VRML.htm

gray: Ti, red: O, green: Sr

44

Bringing more plastics into the environment?

Some plastics are bio-degradable, …

45

PET : mostcommonthermoplasticpolymer resin ofthe polyester family

Ideonella sakeaiensisdegrades and assimilatesPET as its sole carbonsource - one man's meatis another man's poison

adheres to PET materialthen creates two uniqueenzymes that allow thematerial to bedeconstructed intomonomers that can beconsumed by thebacterium

46

some 450,000 – 500,000 CIFs in open access crystallographicdatabases (about half of all the structures known)

COD in its 14th year, more than 360,000 CIFs (EDU-COD in its 13th year, CMD inits 9th year, approx. 1,000 CIFs combined at Portland State University)

MPOD in its 6th year – update planned with even more options forcreating 3D print outs in more than one color

programs for conversion of CIF (molecule structures, crystalmorphologies, grain boundaries, representation surfaces of physicalproperties of crystals, … ) to STL and VRML by Werner Kaminskyhttp://cad4.cpac.washington.edu/, (color printing only from VRML files),free for individuals, license from UW for all commercial purposes

3D printing will come down in price significantly, good for hands-on models in class

plans for Bicrystallography Open Database

open access crystallography resource portal,nanocrystallography.net

or simply google for “open-access crystallography”

47

48

49

Several crystal properties in surfacerepresentation

050 – Elasticity 088 - Elasticity 304 - Piezoelectricity 095 - ElasticityPZN-PT Au BaTiO3 PIN-PMN-PT