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2020-02-17T08:28:40Z
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https://dictionary.iucr.org/index.php?title=Zone_axis&diff=3291
Zone axis
2013-07-02T04:49:21Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Axe de zone</Font> (''Fr''); <Font color="red">Zonenachse</Font> (''Ge''); <Font color="green">Eje de zona</Font> (''Sp''); <Font color="brown">Ось зоны</Font> (''Ru''); <Font color="black"> Asse di zona </Font>(''It''); <Font color="purple">晶帯軸</Font> (''Ja'').<br />
<br />
<br />
== Definition ==<br />
<br />
A zone axis is a lattice row parallel to the intersection of two (or more) families of lattices planes. It is denoted by [''u'' ''v'' ''w'']. A zone axis [''u'' ''v'' ''w''] is parallel to a family of lattice planes of [[Miller indices]] (''hkl'') if:<br />
<br />
<center><br />
''uh'' + ''vk'' + ''wl'' = 0<br />
</center><br />
<br />
This is the so-called Weiss law.<br />
<br />
The indices of the zone axis defined by two lattice planes (<math> h_1, k_1, l_1 </math>), (<math> h_2, k_2, l_2</math>) are given by:<br />
<br />
<center><br />
<math><br />
{u\over {<br />
\begin{vmatrix} k_1 & l_1\\<br />
k_2 & l_2\\ \end{vmatrix}}} =<br />
{v\over {<br />
\begin{vmatrix} l_1 & h_1\\<br />
l_2 & h_2\\ \end{vmatrix}}} =<br />
{w\over {<br />
\begin{vmatrix} h_1 & k_1\\<br />
h_2 & k_2\\ \end{vmatrix}} }<br />
</math><br />
</center><br />
<br />
Conversely, any crystal face can be determined if one knows two zone axes parallel to it. It is the zone law, or ''Zonenverbandgesetz''.<br />
<br />
Three lattice planes have a common zone axis (''are in zone'') if their Miller indices (<math> h_1, k_1, l_1 </math>), (<math> h_2, k_2, l_2</math>), (<math> h_3, k_3, l_3</math>) satisfy the relation:<br />
<br />
<center><br />
<math><br />
\begin{vmatrix} h_1 & k_1 & l_1\\<br />
h_2 & k_2 & l_2\\<br />
h_3 & k_3 & l_3\\<br />
\end{vmatrix} = 0</math><br />
</center><br />
<br />
== History ==<br />
<br />
The notion of zone axis and the zone law were introduced by the German crystallographer Christian Samuel Weiss in 1804.<br />
<br />
== See also ==<br />
<br />
[[Miller indices]]<br><br />
[[reciprocal lattice]]<br />
<br />
[[Category:Fundamental crystallography]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Law_of_rational_indices&diff=3113
Law of rational indices
2011-04-19T15:45:27Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Loi des indices rationnels simples </Font>(''Fr.''). <Font color="red"> Gesetz der Rationalität </Font> (''Ge.''). <Font color="green"> Ley de la racionalidad de los indices </Font>(''Sp.'').<Font color="black"> Legge della razionalità degli indici </Font>(''It'')<br />
<br />
<br />
== Definition ==<br />
<br />
The law of rational indices states that the intercepts, ''OP'', ''OQ'', ''OR'', of the natural faces of a crystal form with the unit-cell axes '''a''', '''b''', '''c''' (see Figure 1) are inversely proportional to prime integers, ''h'', ''k'', ''l''. They are called the [[Miller indices]] of the face. They are usually small because the corresponding lattice planes are among the densest and have therefore a high interplanar spacing and low indices. <br />
<br />
[[image:MILLER-1.gif|center]]<br />
<br />
The law of rational indices was deduced by Haüy (1784, 1801) from the observation of the stacking laws required to build the natural faces of crystals by piling up elementary blocks, for instance cubes to construct the {110} faces of the rhomb-dodecahedron observed in garnets or the &#189;{210} faces of the pentagon-dodecahedron observed in pyrite, or rhombohedrons to construct the {21.1} (referred to an hegagonal lattice, {<math> 2{\bar 1}0</math>} referred to a rhombohedral lattice) scalenohedron of calcite.<br />
<br />
<center><br />
[[image: Hauy-1.gif]]<br />
[[image: Hauy-2.gif]]<br />
[[image: Hauy-3.gif]]<br />
</center><br />
<br />
(Models from Haüy's ''Traité de Minéralogie'' (1801) - the crystal forms have been redrawn in red).<br />
<br />
== History ==<br />
<br />
In 1690, C. Huyghens (1629-1695) advanced the hypothesis that the cleavage rhombohedron of calcite was the result of a stacking of flat ellipsoids and used that hypothesis to explain the cleavage properties and the double refraction of calcite. In 1773, the Swedish mineralogist T.O. Bergman (1735-1784) related the cleavage rhombohedron to the {<math> 2{\bar 1}0</math>} scalenohedron and other forms of calcite, but it is the French mineralogist R.-J.Haüy (1743-1822) who showed that the crystal forms could be reconstructed by appropriate stacking laws of minute cleavage rhombohedra for calcite and cubes for garnets (''Essai d'une théorie sur la structure des cristaux'', 1784; ''Traité de Minéralogie'', 1801).<br />
<br />
== See also ==<br />
<br />
[[Miller indices]]<br><br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Neumann%27s_principle&diff=3112
Neumann's principle
2010-11-11T07:48:13Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Principe de Neumann </Font> (''Fr''). <Font color="red"> Neumannsche Prinzip </Font> (''Ge''). <Font color="green"> Principio de Neumann </Font> (''Sp'').<Font color="black"> Principio di Neumann </Font>(''It'')<br />
<br />
<br />
== Definition ==<br />
<br />
Neumann's principle, or principle of symmetry, states that, if a crystal is invariant with respect to certain symmetry elements, any of its physical properties must also be invariant with respect to the same symmetry elements, or otherwise stated, the symmetry elements of any physical property of a crystal must include the symmetry elements of the point group of the crystal. It is generalized to physical phenomena by [[Curie laws]].<br />
<br />
== Example ==<br />
<br />
This principle may be illustrated by considering the optical indicatrix of a crystal, which is an ellipsoid. If the medium is invariant with respect to a three-fold, a four-fold or a six-fold axis (as in a trigonal, tetragonal or hexagonal crystal, for instance), its optical indicatrix must also be invariant with respect to the same axis, according to Neumann's principle. As an ellipsoid can only be ordinary or of revolution, the indicatrix of a trigonal, tetragonal or hexagonal crystal is necessarily an ellipsoid of revolution. These crystals are said to be ''uniaxial''. In a cubic crystal which has four three--fold axes, the indicatrix must have several axes of revolution, it is therefore a sphere and cubic media behave as isotropic media for properties represented by a tensor of rank 2.<br />
<br />
== History ==<br />
<br />
Franz Neumann (1795-1898)'s principle was first stated in his course at the university of Königsberg (1873/1874) and was published in the printed version of his lecture notes (Neumann F.E., 1885, ''Vorlesungen über die Theorie der Elastizität der festen Körper und des Lichtäthers'', edited by O. E. Meyer. Leipzig, B. G. Teubner-Verlag.<br />
<br />
== See also ==<br />
<br />
[[Curie laws]]<br><br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 1.1.4 of ''[http://it.iucr.org/D/ International Tables of Crystallography, Volume D]''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=International_Union_of_Crystallography&diff=3012
International Union of Crystallography
2009-04-16T05:05:53Z
<p>AndreAuthier: /* See also */</p>
<hr />
<div>=== Other languages ===<br />
<br />
Union internationale de cristallographie (''Fr.'')<br />
<br />
<br />
<br />
== Definition ==<br />
<br />
The IUCr is a scientific union adhering to the International Council for Science (ICSU). Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.<br />
<br />
The IUCr fulfils these objectives by publishing in print and electronically primary scientific journals through Crystallography Journals Online, the series of reference volumes ''International Tables for Crystallography'', distributing the quarterly IUCr Newsletter, maintaining the online World Directory/Database of Crystallographers, awarding the Ewald Prize and organising the triennial Congress and General Assembly.<br />
<br />
==== History ====<br />
<br />
Following early informal international contacts before the Second World War, coherent societies representing the young science of X-ray crystallography were formed in the USA and the UK during the early 1940s. Following a conference in London in 1946, a movement developed to create an international union. Draft Statutes and By-Laws were submitted to ICSU (at that time the International Council of Scientific Unions) and the IUCr was formally admitted to ICSU on 7 April 1947. The Union was formally inaugurated at the first of its triennial General Assemblies at Harvard University (28 July - 3 August 1948).<br />
<br />
A primary motivation of the sponsors of the IUCr was the publication of a journal managed by the crystallographic community, and in April 1948 the first issue of ''Acta Crystallographica'' appeared. Subsequently the journal was split into parts, and additional titles were added to the list of serial publications produced by the Union. Other publishing activities were undertaken, including the reference series ''International Tables for Crystallography'', abstracts of published structures in the series ''Structure Reports'' (1948-1993) that prefigured the establishment of crystallographic databases, a directory of crystallographers and informal newsletters.<br />
<br />
Scientific activities were supervised by a number of Commissions, covering in time such areas as aperiodic crystals, biological macromolecules, charge, spin and momentum densities, crystal growth, nomenclature, teaching, electron diffraction, neutron scattering, powder diffraction and small-angle scattering.<br />
<br />
<br />
==== Governance ====<br />
<br />
The Union is organized and incorporated as an Association governed by Articles 60 and following of the Swiss Civil Code and by the present Statutes of Incorporation; of unlimited duration; and domiciled in Geneva, Switzerland.<br />
<br />
The members of the Union are Adhering Bodies, one for each country (usually a National Academy, Nationale Research Council, scientific society or similar). The members jointly form the General Assembly; influence of a member depends on its category of membership, which is linked to the size of its national community and associated payment of dues.<br />
<br />
The business of the Union is conducted under the auspices of the elected Officers forming an Executive Committee, and through the work of the scientific Commissions. Administrative duties are carried out through the efforts of a salaried Executive Secretary and associated staff.<br />
<br />
http://www.iucr.org/iucr-top/logos/iucr.gif Logo © IUCr<br />
<br />
=== See also ===<br />
<br />
[http://www.iucr.org Official IUCr web site]<br><br />
[http://journals.iucr.org Crystallography Journals Online]<br><br />
[http://it.iucr.org International Tables for Crystallography]<br><br />
[http://www.icsu.org ICSU web site]<br><br />
<br />
Authier, A. (2009). ''60 years of IUCr journals.'' [http://journals.iucr.org/a/issues/2009/03/00/sh5087/index.html]<br />
<br />
Cruickshank, D. W. J. (1998). ''Aspects of the History of the International Union of Crystallography.'' [http://www.iucr.org/iucr-top/iucr/dw/sc0025.html ''Acta. Cryst.'' A'''54''', 687-696.]<br />
<br />
Kamminga, H. (1989). ''The International Union of Crystallography: its formation and early development.'' [http://www.iucr.org/iucr-top/iucr/history.html ''Acta Cryst.'' A'''45''', 581-601.]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=International_Union_of_Crystallography&diff=3011
International Union of Crystallography
2009-04-16T04:58:17Z
<p>AndreAuthier: </p>
<hr />
<div>=== Other languages ===<br />
<br />
Union internationale de cristallographie (''Fr.'')<br />
<br />
<br />
<br />
== Definition ==<br />
<br />
The IUCr is a scientific union adhering to the International Council for Science (ICSU). Its objectives are to promote international cooperation in crystallography and to contribute to all aspects of crystallography, to promote international publication of crystallographic research, to facilitate standardization of methods, units, nomenclatures and symbols, and to form a focus for the relations of crystallography to other sciences.<br />
<br />
The IUCr fulfils these objectives by publishing in print and electronically primary scientific journals through Crystallography Journals Online, the series of reference volumes ''International Tables for Crystallography'', distributing the quarterly IUCr Newsletter, maintaining the online World Directory/Database of Crystallographers, awarding the Ewald Prize and organising the triennial Congress and General Assembly.<br />
<br />
==== History ====<br />
<br />
Following early informal international contacts before the Second World War, coherent societies representing the young science of X-ray crystallography were formed in the USA and the UK during the early 1940s. Following a conference in London in 1946, a movement developed to create an international union. Draft Statutes and By-Laws were submitted to ICSU (at that time the International Council of Scientific Unions) and the IUCr was formally admitted to ICSU on 7 April 1947. The Union was formally inaugurated at the first of its triennial General Assemblies at Harvard University (28 July - 3 August 1948).<br />
<br />
A primary motivation of the sponsors of the IUCr was the publication of a journal managed by the crystallographic community, and in April 1948 the first issue of ''Acta Crystallographica'' appeared. Subsequently the journal was split into parts, and additional titles were added to the list of serial publications produced by the Union. Other publishing activities were undertaken, including the reference series ''International Tables for Crystallography'', abstracts of published structures in the series ''Structure Reports'' (1948-1993) that prefigured the establishment of crystallographic databases, a directory of crystallographers and informal newsletters.<br />
<br />
Scientific activities were supervised by a number of Commissions, covering in time such areas as aperiodic crystals, biological macromolecules, charge, spin and momentum densities, crystal growth, nomenclature, teaching, electron diffraction, neutron scattering, powder diffraction and small-angle scattering.<br />
<br />
<br />
==== Governance ====<br />
<br />
The Union is organized and incorporated as an Association governed by Articles 60 and following of the Swiss Civil Code and by the present Statutes of Incorporation; of unlimited duration; and domiciled in Geneva, Switzerland.<br />
<br />
The members of the Union are Adhering Bodies, one for each country (usually a National Academy, Nationale Research Council, scientific society or similar). The members jointly form the General Assembly; influence of a member depends on its category of membership, which is linked to the size of its national community and associated payment of dues.<br />
<br />
The business of the Union is conducted under the auspices of the elected Officers forming an Executive Committee, and through the work of the scientific Commissions. Administrative duties are carried out through the efforts of a salaried Executive Secretary and associated staff.<br />
<br />
http://www.iucr.org/iucr-top/logos/iucr.gif Logo © IUCr<br />
<br />
=== See also ===<br />
<br />
[http://www.iucr.org Official IUCr web site]<br><br />
[http://journals.iucr.org Crystallography Journals Online]<br><br />
[http://it.iucr.org International Tables for Crystallography]<br><br />
[http://www.icsu.org ICSU web site]<br><br />
<br />
Authier, A. (2009). ''60 years of IUCr journals.'' [http://www.iucr.org/iucr-top/iucr/dw/sh5087.html ''Acta. Cryst.'' A'''65''', 167-182.]<br />
<br />
Cruickshank, D. W. J. (1998). ''Aspects of the History of the International Union of Crystallography.'' [http://www.iucr.org/iucr-top/iucr/dw/sc0025.html ''Acta. Cryst.'' A'''54''', 687-696.]<br />
<br />
Kamminga, H. (1989). ''The International Union of Crystallography: its formation and early development.'' [http://www.iucr.org/iucr-top/iucr/history.html ''Acta Cryst.'' A'''45''', 581-601.]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Dynamical_theory&diff=2779
Dynamical theory
2008-04-11T05:22:12Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Théorie dynamique </Font>(''Fr''). <Font color="red">Dynamische Theorie </Font>(''Ge''). <Font color="green">Teoria dynámica </Font>(''Sp'').<Font color="black"> Teoria dinamica </Font>(''It'')<br />
<br />
<br />
== Overview == <br />
In the geometrical, or [[kinematical theory]], the amplitudes diffracted by a three-dimensional periodic assembly of atoms (Laue) or by a stack of planes (Darwin) is derived by adding the amplitudes of the waves diffracted by each atom or by each plane, simply taking into account the optical path differences between them, but neglecting the interaction of the propagating waves and matter. This approximation is not compatible with the law of conservation of energy and is only valid for very small or highly imperfect crystals. The purpose of the dynamical theory is to take this interaction into account. There are three forms of the dynamical theory:<br />
<br />
== Darwin's theory == <br />
<br />
[[Image:Darwin.gif|right]]<br />
Charles Darwin (the grandson of the author of the theory of evolution) takes into account the interaction between the waves partially transmitted (<math> S_n, \ S_{n+1} </math>) and partially reflected (<math> T_n, \ T_{n+1} </math>) at the successive atomic planes, ''n'', ''n''+1 etc. by recurrence equations.<br />
<br />
== Ewald's theory == <br />
<br />
Paul Ewald solves the propagation equation deduced from Maxwell's equations in a medium constituted by a three-dimensional periodic array of discrete scattering dipoles.<br />
<br />
== Laue's theory == <br />
<br />
Max von Laue considers that the negative and positive electric charges are distributed in a continuous way throughout the volume of the crystal. Since the crystal must be neutral, they cancel out and the local electric charge and density of current are equal to zero. The interaction of electromagnetic waves with the positive charges is neglected as a first approximation in the usual dynamical theory, although resonant nuclear scattering of X-rays exists and has been observed for &#947;- and X-rays. The medium is polarized under the influence of the electric field and '''E''' = '''D'''/&#949;, where '''D''' is the electric displacement and <math>\epsilon = \epsilon_0(1 + \chi) </math> varies with the space coordinates. The continuous dielectric susceptibility, or polarizability, &#967;, takes into account the interaction of the electromagnetic radiation with the distribution of electric charges. By eliminating '''D''', the magnetic field, '''H''', and the magnetic induction, '''B''', in Maxwell's equations, one obtains a wave equation for '''E''':<br />
<br />
<center><br />
<br />
curl curl <math>{\bold E} - 4 \pi ^2 k^2 (1 + \chi({\bold r})) {\bold E} = 0 </math><br />
</center><br />
<br />
where ''k'' = 1/&#955; is the wave number in vacuum.<br />
<br />
While div '''E''' is equal to zero, this is not true for div '''D''', and the electric displacement is in general a more suitable quantity than the electric field because it simplifies the description of the polarization states of the field inside the crystal. It is used in Laue's formulation of the dynamical theory. With a small approximation the propagation equation becomes:<br />
<br />
<center><br />
<br />
<math>\Delta {\bold D}</math> + curl curl <math>\chi ({\bold r}){\bold E} + 4 \pi ^2 k^2 {\bold D} = 0 </math><br />
</center><br />
<br />
For material waves such as electrons or neutrons, the propagation equation is derived from Schrödinger's equation:<br />
<br />
<center><br />
<br />
<math> \Delta \Psi + 4\ \pi^ 2k^2\left[1 + \chi ({\bold r})\right]\Psi = 0 </math><br />
</center><br />
<br />
where <br />
<br />
*<math>\chi({\bold r}) = \varphi ({\bold r})/ W </math> in the case of electron diffraction (<math> \varphi ({\bold r})</math>, potential in the crystal and ''W'' accelerating voltage) <br><br />
*<math>\chi({\bold r}) = - 2mV({\bold r})/h^2k^2 </math> in the case of neutron diffraction (<math> V({\bold r}</math>), Fermi pseudo-potential).<br />
<br />
The purpose of the dynamical theory is to solve the propagation equation taking into account the boundary conditions. It offers many similarities with the band theory of solids. The difference is that, in the band theory, one studies the possible energies of electrons as a function of their wavenumber while, in diffraction theory, the energy is constant and one looks for the possible positions of the wavectors in reciprocal space. <br />
<br />
== History == <br />
<br />
* Laue's geometrical theory: Friedrich W., Knipping P. & Laue M. von (1912), ''Sitzungsberichte der Kgl. Bayer. Akad. der Wiss.'', 303-322, reprinted in ''Ann. Phys.'' (1913), '''41''', 971. Interferenz-Erscheinungen bei Röntgenstrahlen.<br><br />
* Darwin's geometrical theory: Darwin C.G., (1914), ''Phil. Mag.'', '''27''', 315-333. ''The Theory of X-ray Reflection''.<br><br />
* Darwin's geometrical theory: Darwin C.G., (1914), ''Phil. Mag.'', '''27''', 675-690. ''The Theory of X-ray Reflection. Part II''.<br><br />
* Ewald's dynamical theory: Ewald P.P. (1917), Ann. Physik, '''54''', 519-597, ''Zur Begründung der Kristalloptik. III. Die Kristalloptik der Röntgenstrahlen.''<br><br />
* Laue's dynamical theory: Laue M. von, (1931), ''Ergeb. Exakt. Naturwiss.'', '''10''', 133-158, ''Die dynamische Theorie der Röntgenstrahlinterferenzen in neuer Form.'' & (1931), ''Röntgenstrahl-Interferenzen.'', Akademische Verlagsgesellschaft, Frankfurt am Main.<br><br />
<br />
For a detailed eaccount of the historical developments, see P. P. Ewald, 1962, IUCr, [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction], Section 15.<br />
<br />
== See also ==<br />
<br />
Section 5.1 of ''International Tables of Crystallography, Volume B'' for X-rays<br />
<br />
Section 5.2 of ''International Tables of Crystallography, Volume B'' for electrons<br />
<br />
Section 5.3 of ''International Tables of Crystallography, Volume B'' for neutrons<br />
<br />
Authier A. (2005) ''Dynamical Theory of X-ray Diffraction'', Oxford: IUCr/Oxford University Press<br />
[[Category:X-rays]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Twinning_by_metric_merohedry&diff=2766
Twinning by metric merohedry
2008-04-10T12:28:03Z
<p>AndreAuthier: </p>
<hr />
<div><p><font color="blue"> Maclage par mériédrie métrique</font>(<i>Fr</i>). <font color="black"> Meroedria metrica</font>(<i>It</i>)<br />
</p><br />
<br />
Twinning by metric merohedry is a special case of [[twinning by merohedry]] which occurs when:<br />
* the lattice of the individual has accidentally a specialized metric which corresponds to a higher holohedry<br />
* the twin operation belongs to this higher holohedry only<br />
<br />
If H is the individual point group, D(H) the corresponding holohedry and D(L) the point group of the lattice, twinning by metric merohedry corresponds to D(L) &sup; D(H) &supe; H<br />
<br />
Twinning by metric merohedry can be seen as the degeneration of [[twinning by reticular merohedry]] to [[twin index]] 1, or of [[twinning by pseudomerohedry]] to [[twin obliquity]] zero.<br />
<br />
==Example==<br />
A monoclinic crystal of point group H = 2 with angle &beta; = 90º has a orthorhombic lattice. It may undergo two types of twinning by merohedry:<br />
* if the twin operation belongs to the monoclinic holohedry D(H) = 2/''m'', twinning is the classical twinning by merohedry, also termed ''twinning by syngonic merohedry'';<br />
* if the twin operation belongs to the orthorhombic holohedry D(L) = ''mmm'', twinning is by metric merohedry.<br />
<br />
==Historical note==<br />
Friedel (1904, p. 143; 1926, p. 56-57) called metric merohedry '''mériédrie d’ordre supérieur''' (higher order merohedry) but stated that it was either unlikely or equivalent to a pseudo-merohedry of low obliquity. Nowadays several examples of true metric merohedry (within experimental uncertainty) are known.<br />
<br />
[[Category:Twinning]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Molecular_replacement&diff=2748
Molecular replacement
2008-04-08T13:57:06Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Méthode du remplacement moléculaire </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
An approach to solving the [[phase problem]] by concentrating on phase relationships that arise through X-ray diffraction from similar molecular components. The components can be molecular fragments related through noncrystallographic symmetry (''e.g.'' icosahedral subunits of a virus) or a similar molecule such as a homologous protein with high sequence identity.<br />
<br />
== Discussion ==<br />
<br />
The technique is most commonly used in biological crystallography. Typically, an attempt is made to fit the structure under investigation (the 'target' structure) to a previously solved ('probe') structure. The probe may be a different crystal form of the same protein; or it may be a different protein with a high level of sequence identity, which correlates well with structural resemblance. As a rule of thumb, molecular replacement is often straightforward if the probe is well characterised and shares at least 40% sequence identity with the target.<br />
<br />
[[Image:RTfunctioninMR.gif|frame|Figure 1. Illustration of the rotation and translation functions applied to superimpose a probe and target structure in molecular replacement.|right]]<br />
<br />
Figure 1 illustrates schematically the process of repositioning the probe structure (the solid motif) in the new unit cell to coincide with the target structure (red outline motif). Rotation and transformation matrices must be applied. [[Patterson methods]] are suitable for determining the rotation function '''R''', since intramolecular vectors are all shifted to the origin of a Patterson map. The orientational fit (''i.e.'' the quality of the calculated rotation function) has usually been assessed by monitoring [[R factor|''R'' factors]] or [[real-space correlation coefficient]]s. Increasingly, modern programs use maximum likelihood based algorthms. <br />
<br />
The translation function '''T''' is then determined to shift the now correctly orientated probe model to the correct coordinates within the asymmetric unit. Space-group symmetries can be used to help reduce the computationally intense calculations required.<br />
<br />
== History ==<br />
<br />
Early applications of the technique concentrated on large virus structures with icosahedral symmetry. [Rossmann, M. G. &amp; Blow, D. M. (1962). [http://dx.doi.org/10.1107/S0365110X62000067 Acta Cryst. 15, 24–31]. ''The detection of sub-units within the crystallographic asymmetric unit.''] In the 1960s the early development of the molecular replacement technique was aimed primarily at ''ab initio'' phase determination. It was only in the 1970s, when more structures became available, that it was possible to use the technique to solve homologous structures with suitable search models.<br />
<br />
== See also ==<br />
<br />
Noncrystallographic symmetry.<br />
D. M. Blow. ''International Tables for Crystallography'' (2006). Vol. F, ch. 13.1, pp. 263-268 [http://dx.doi.org/10.1107/97809553602060000681 doi:10.1107/97809553602060000681] <br />
<br />
<br />
[[Category:Biological crystallography]]<br />
[[Category:Structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Dynamical_theory&diff=2730
Dynamical theory
2008-04-05T04:48:08Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Théorie dynamique </Font>(''Fr''). <Font color="red">Dynamische Theorie </Font>(''Ge''). <Font color="green">Teoria dynámica </Font>(''Sp'').<Font color="black"> Teoria dinamica </Font>(''It'')<br />
<br />
<br />
== Overview == <br />
In the geometrical, or [[kinematical theory]], the amplitudes diffracted by a three-dimensional periodic assembly of atoms (Laue) or by a stack of planes (Darwin) is derived by adding the amplitudes of the waves diffracted by each atom or by each plane, simply taking into account the optical path differences between them, but neglecting the interaction of the propagating waves and matter. This approximation is not compatible with the law of conservation of energy and is only valid for very small or highly imperect crystals. The purpose of the dynamical theory is to take these interaction into account. There are three forms of the dynamical theory: <br />
<br />
== Darwin's theory == <br />
<br />
[[Image:Darwin.gif|right]]<br />
Charles Darwin (the grandson of the author of the theory of evolution) takes into account the interaction between the waves partially transmitted (<math> S_n, \ S_{n+1} </math>) and partially reflected (<math> T_n, \ T_{n+1} </math>) at the successive atomic planes, ''n'', ''n''+1 etc. by recurrence equations.<br />
<br />
== Ewald's theory == <br />
<br />
Paul Ewald solves the propagation equation deduced from Maxwell's equations in a medium constituted by a three-dimensional periodic array of discrete scattering dipoles.<br />
<br />
== Laue's theory == <br />
<br />
Max von Laue considers that the negative and positive electric charges are distributed in a continuous way throughout the volume of the crystal. Since the crystal must be neutral, they cancel out and the local electric charge and density of current are equal to zero. The interaction of electromagnetic waves with the positive charges is neglected as a first approximation in the usual dynamical theory, although resonant nuclear scattering of X-rays exists and has been observed for &#947;- and X-rays. The medium is polarized under the influence of the electric field and '''E''' = '''D'''/&#949;, where '''D''' is the electric displacement and <math>\epsilon = \epsilon_0(1 + \chi) </math> varies with the space coordinates. The continuous dielectric susceptibility, or polarizability, &#967;, takes into account the interaction of the electromagnetic radiation with the distribution of electric charges. By eliminating '''D''', the magnetic field, '''H''', and the magnetic induction, '''B''', in Maxwell's equations, one obtains a wave equation for '''E''':<br />
<br />
<center><br />
<br />
curl curl <math>{\bold E} - 4 \pi ^2 k^2 (1 + \chi({\bold r})) {\bold E} = 0 </math><br />
</center><br />
<br />
where ''k'' = 1/&#955; is the wave number in vacuum.<br />
<br />
While div '''E''' is equal to zero, this is not true for div '''D''', and the electric displacement is in general a more suitable quantity than the electric field because it simplifies the description of the polarization states of the field inside the crystal. It is used in Laue's formulation of the dynamical theory. With a small approximation the propagation equation becomes:<br />
<br />
<center><br />
<br />
<math>\Delta {\bold D}</math> + curl curl <math>\chi ({\bold r}){\bold E} + 4 \pi ^2 k^2 {\bold D} = 0 </math><br />
</center><br />
<br />
For material waves such as electrons or neutrons, the propagation equation is derived from Schrödinger's equation:<br />
<br />
<center><br />
<br />
<math> \Delta \Psi + 4\ \pi^ 2k^2\left[1 + \chi ({\bold r})\right]\Psi = 0 </math><br />
</center><br />
<br />
where <br />
<br />
*<math>\chi({\bold r}) = \varphi ({\bold r})/ W </math> in the case of electron diffraction (<math> \varphi ({\bold r})</math>, potential in the crystal and ''W'' accelerating voltage) <br><br />
*<math>\chi({\bold r}) = - 2mV({\bold r})/h^2k^2 </math> in the case of neutron diffraction (<math> V({\bold r}</math>), Fermi pseudo-potential).<br />
<br />
The purpose of the dynamical theory is to solve the propagation equation taking into account the boundary conditions. It offers many similarities with the band theory of solids. The difference is that, in the band theory, one studies the possible energies of electrons as a function of their wavenumber while, in diffraction theory, the energy is constant and one looks for the possible positions of the wavectors in reciprocal space. <br />
<br />
== History == <br />
<br />
* Laue's geometrical theory: Friedrich W., Knipping P. & Laue M. von (1912), ''Sitzungsberichte der Kgl. Bayer. Akad. der Wiss.'', 303-322, reprinted in ''Ann. Phys.'' (1913), '''41''', 971. Interferenz-Erscheinungen bei Röntgenstrahlen.<br><br />
* Darwin's geometrical theory: Darwin C.G., (1914), ''Phil. Mag.'', '''27''', 315-333. ''The Theory of X-ray Reflection''.<br><br />
* Darwin's geometrical theory: Darwin C.G., (1914), ''Phil. Mag.'', '''27''', 675-690. ''The Theory of X-ray Reflection. Part II''.<br><br />
* Ewald's dynamical theory: Ewald P.P. (1917), Ann. Physik, '''54''', 519-597, ''Zur Begründung der Kristalloptik. III. Die Kristalloptik der Röntgenstrahlen.''<br><br />
* Laue's dynamical theory: Laue M. von, (1931), ''Ergeb. Exakt. Naturwiss.'', '''10''', 133-158, ''Die dynamische Theorie der Röntgenstrahlinterferenzen in neuer Form.'' & (1931), ''Röntgenstrahl-Interferenzen.'', Akademische Verlagsgesellschaft, Frankfurt am Main.<br><br />
<br />
For a detailed eaccount of the historical developments, see P. P. Ewald, 1962, IUCr, [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction], Section 15.<br />
<br />
== See also ==<br />
<br />
Section 5.1 of ''International Tables of Crystallography, Volume B'' for X-rays<br />
<br />
Section 5.2 of ''International Tables of Crystallography, Volume B'' for electrons<br />
<br />
Section 5.3 of ''International Tables of Crystallography, Volume B'' for neutrons<br />
<br />
Authier A. (2005) ''Dynamical Theory of X-ray Diffraction'', Oxford: IUCr/Oxford University Press<br />
[[Category:X-rays]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Rietveld_method&diff=2729
Rietveld method
2008-04-05T04:35:52Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Méthode de Rietveld </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
Method of analysing powder diffraction data in which the crystal structure is refined by fitting the entire profile of the diffraction pattern to a calculated profile using a least-squares approach. There is no intermediate step of extracting structure factors, and so patterns containing many overlapping Bragg peaks can be analysed.<br />
<br />
<br />
<br />
== History ==<br />
<br />
The method was applied originally by H. Rietveld [(1967). [http://dx.doi.org/10.1107/S0365110X67000234 ''Acta Cryst.'' '''22''', 151–152]. ''Line profiles of neutron powder diffraction peaks for structure refinement''; (1969). [http://dx.doi.org/10.1107/S0021889869006558 ''J. Appl. Cryst.'' '''2''', 65–71]. ''A profile refinement method for nuclear and magnetic structures''] to the refinement of neutron intensities recorded at a fixed wavelength. Subsequently, it has been used successfully for analysing powder data with neutrons or X-rays as the primary radiation and with scattered intensities measured at a fixed wavelength (and variable scattering angle) or at a fixed scattering angle (and variable wavelength).<br />
<br />
== See also ==<br />
The Rietveld method.<br />
A. Albinati and B. T. M. Willis. ''International Tables for Crystallography'' (2006). Vol. C, ch. 8.6, pp. 710-712 [http://dx.doi.org/10.1107/97809553602060000614 doi:10.1107/97809553602060000614]<br />
<br />
The Rietveld Method, edited by R.A. Young. (1993), Oxford: IUCr/Oxford University Press.<br />
[[Category:Structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Heavy-atom_method&diff=2722
Heavy-atom method
2008-04-04T05:24:42Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Méthode de l'atome lourd </Font> (''Fr'').<br />
<br />
An application of [[Patterson methods]] in crystal [[structure determination]]. For a compound containing a heavy atom (''i.e.'' one with a significantly higher [[atomic scattering factor]] than the others present) the diffraction phases calculated from the position of the heavy atom are used to compute a first approximate [[electron density map]]. Further portions of the structure are recognisable as additional peaks in the map. Successive approximate electron density maps may then be calculated to solve the entire structure.<br />
<br />
== Discussion ==<br />
<br />
[[Image:sfac4.gif|right]]<br />
<br />
The figure shows how the [[structure factor]] is derived by vector addition of the scattered waves from the different contributing atoms in the unit cell. Consider the case of an atom with a very much higher scattering factor than any of the others <math>(\,\,f_0 >> \sum_i f_i \,\,)</math>; it is clear that the total phase angle <math>\phi</math> will be small, and that the net phase of the structure factor differs very little from that of the heavy-atom component alone.<br />
<br />
If the positions of known heavy atoms can be determined in this way, then the Patterson map, which describes interatomic vectors, allows nearby peaks to be assigned to other atoms in accordance with expected molecular geometry. These are then used in calculating phase angles for the next approximate electron density map.<br />
<br />
A practical limitation is that a heavy atom that dominates the vector distribution is also likely to dominate the X-ray scattering as a whole, and overwhelm diffraction peaks from less strongly scattering species.<br />
<br />
[[Category:Structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Phase_problem&diff=2713
Phase problem
2008-04-03T08:35:20Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Problème des phases </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
Waves diffracted from a primitive lattice of simple scatterers obey [[Bragg's law]], which allows ready determination of interplanar distances and thus the easy recovery of a description of the crystal lattice. Where the scattering objects are complex (''e.g.'' in molecular crystals) the diffracted radiation suffers a phase shift arising from the spatial distribution of individual scatterers. The amplitudes of the resulting [[structure factor]]s are directly derivable from the experimental measured intensities of the diffracted beams, but the phases are not. Without a knowledge of the phases, it is not possible to reconstruct the individual atomic positions. Estimating the phases is an essential step in successful [[structure determination]].<br />
<br />
== Methods of solution ==<br />
<br />
A number of techniques exist to determine the phases associated with the structure factors. In general, they provide estimates of a set of phases, which are used to calculate a set of structure factors that may be compared with experimental observations. Among the techniques currently employed are:<br />
<br />
* Guessing the structure<br />
* [[Patterson methods]]<br />
* [[molecular replacement]]<br />
* [[direct methods]]<br />
* [[multiple isomorphous replacement]]<br />
* [[anomalous dispersion]]<br />
<br />
<br />
[[Category:structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Patterson_methods&diff=2712
Patterson methods
2008-04-03T08:33:05Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Méthodes de Patterson </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The family of methods employed in [[structure determination]] to derive relationships between the scattering centres in a crystal lattice when the diffraction phases are unknown. They depend upon interpretation of the Patterson function<br />
<br />
<math>P(uvw) = (1/V)\sum_{h} \sum_{k} \sum_{l} {\{|F(hkl)|^2 \cos[2\pi(hu + kv + lw)]\}}</math><br />
<br />
to reveal interatomic vectors within the unit cell.<br />
<br />
== Discussion ==<br />
<br />
An electron density map can be constructed from an inverse Fourier transform of the [[structure factor]]s of a wave diffracted from a crystal. Diffracted intensities can be measured directly, and are related to the square of the amplitudes of the structure factors; but the diffraction phases cannot be determined by direct observation. The Patterson function represents a convolution of electron density with itself. It loses all phase information, but reduces to a function of <math>|F(hkl)|^2</math> alone, and is thus derivable from the measured intensities.<br />
<br />
Without phase information, the Patterson map (''i.e.'' the Patterson function evaluated at points <math>u, v, w</math> throughout the unit cell) may be interpreted as a map of vectors between the scattering atoms. Vectors in a Patterson correspond to vectors in the real crystal cell, translated to the Patterson origin. Their weights are proportional to the product of electron densities at the tips of the vectors in the real cell.<br />
<br />
The Patterson unit cell has the same size as the real crystal cell. The symmetry of the Patterson comprises the Laue point group of the crystal cell plus any additional lattice symmetry due to Bravais centring. The reduction of the real space group to the Laue symmetry is produced by the translation of all vectors to the Patterson origin and the introduction of a centre of symmetry.<br />
<br />
For small structures, it may be possible to work out the original positions of the atoms that would give rise to the observed Patterson maxima (called ''deconvoluting'' the Patterson), but the procedure does not scale well for larger molecules. For <math>n</math> atoms in a unit cell, there will be <math>n^2</math> vectors (of which <math>n</math> self-vectors from an atom to itself accumulate to form a large origin peak).<br />
<br />
Nevertheless, if other techniques are used to establish the position of one atom, the Patterson function becomes useful in determining the locations of other atoms.<br />
<br />
== History ==<br />
<br />
Patterson introduced the method of determining interatomic distances from a Fourier transform of intensities in 1934 [Patterson, A. L. (1934). [http://dx.doi.org/10.1103/PhysRev.46.372 ''Phys. Rev.'' '''46''', 372-376.] ''A Fourier series method for the determination of the components of interatomic distances in crystals'']. The following year he introduced modifications to improve the practical application of the Patterson function: removal of the Patterson origin peak, [[sharpened Patterson function|sharpening]] of the overall function, and removing peaks due to atoms in special positions [Patterson, A. L. (1935). ''Z. Kristallogr.'' '''90''', 517–542. ''A direct method for the determination of the components of interatomic distances in crystals''].<br />
<br />
== See also ==<br />
<br />
Patterson and molecular-replacement techniques.<br />
M. G. Rossmann and E. Arnold. ''International Tables for Crystallography'' (2006). Vol. B, ch. 2.3, pp. 235-263 [http://dx.doi.org/10.1107/97809553602060000556 doi:10.1107/97809553602060000556]<br />
<br />
[[Category:Structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Structure_factor&diff=2682
Structure factor
2008-03-31T15:52:55Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Facteur de structure atomique </Font>(''Fr'').<br />
<br />
== Definition ==<br />
<br />
The '''structure factor''' <math>\mathbf{F}_{hkl}</math> is a mathematical function describing the amplitude and phase of a wave diffracted from crystal lattice planes characterised by [[Miller indices]] <math>h, k, l</math>.<br />
<br />
The structure factor may be expressed as<br />
<br />
<math>\mathbf{F}_{hkl} = F_{hkl}\exp(i\alpha_{hkl})<br />
= \sum_j f_j\exp[2\pi i (hx_j + ky_j +<br />
lz_j)] </math><br />
<br />
<math>\qquad = \sum_j f_j\cos[2\pi (hx_j + ky_j + lz_j)]<br />
+ i\sum_{j} f_j\sin[2\pi (hx_j + ky_j + lz_j)]</math><br />
<br />
<math>\qquad = A_{hkl} + iB_{hkl}</math><br />
<br />
where the sum is over all atoms in the unit cell, <math>x_j, y_j, z_j</math> are the positional coordinates of the <math>j</math>th atom, <math>f_j</math> is the scattering factor of the <math>j</math>th atom, and <math>\alpha_{hkl}</math> is the phase of the diffracted beam.<br />
<br />
The intensity of a diffracted beam is directly related to the amplitude of the structure factor, but the phase must normally be deduced by indirect means. In [[structure determination]], phases are estimated and an initial description of the positions and anisotropic displacements of the scattering atoms is deduced. From this initial model, structure factors are calculated and compared with those experimentally observed. Iterative [[refinement]] procedures attempt to minimise the difference between calculation and experiment, until a satisfactory fit has been obtained.<br />
<br />
== Units ==<br />
<br />
The units of the structure-factor amplitude depend on the incident radiation. For X-ray crystallography they are multiples of the unit of scattering by a single electron (<math>2.82 \times 10^{-15}</math> m); for neutron scattering by atomic nuclei the unit of scattering length of <math>10^{-14}</math> m is commonly used.<br />
<br />
== See also ==<br />
[http://www.iucr.org/iucr-top/cteach/pamphlets/3/index.html Introduction to the Calculation of Structure Factors], teaching pamphlet No. 3 of the [[International Union of Crystallography]]<br />
<br />
The structure factor.<br />
P. Coppens. ''International Tables for Crystallography'' (2006). Vol. B, ch. 1.2, pp. 10-24 [http://dx.doi.org/10.1107/97809553602060000550 doi:10.1107/97809553602060000550] <br />
<br />
[[Category:Structure determination]][[Category:X-rays]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Atomic_scattering_factor&diff=2681
Atomic scattering factor
2008-03-31T15:52:14Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Facteur de structure atomique </Font>(''Fr'').<br />
<br />
== Definition ==<br />
<br />
A measure of the scattering power of an isolated atom. Also known as the '''atomic form factor'''. The scattering factor depends on the scattering amplitude of an individual atom and also the [[Bragg angle]] of scattering. It depends on the type of radiation involved.<br />
<br />
== X-ray scattering ==<br />
<br />
The scattering from a crystal of an X-ray beam results from the interaction between the electric component of the incident electromagnetic radiation and the electrons in the crystal. Tightly bound electrons scatter coherently (Rayleigh scattering); free electrons scatter incoherently (Compton scattering). The scattering process from atomic electrons in a crystal lattice has both coherent and incoherent components, and is described as Thomson scattering.<br />
<br />
The scattering amplitude from a neutral atom depends on the number of electrons (''Z'' = the atomic number) and also on the [[Bragg angle]] &theta; &ndash; destructive interference among waves scattered from the individual electrons reduces the intensity at other than zero scattering angle. For &theta; = 0 the scattering amplitude is normally equal to ''Z''. However, the scattering factor is modified by [[anomalous scattering]] if the incident wavelength is near an absorption edge of the scattering element.<br />
<br />
[[Category:Physical properties of crystals]]<br />
[[Category:Structure determination]]<br />
[[Category:X-rays]]<br />
<br />
The X-ray scattering factor is evaluated as the Fourier transform of the electron density distribution of an atom or ion, which is calculated from theoretical wavefunctions for free atoms.<br />
<br />
== See also ==<br />
<br />
Electron diffraction.<br />
C. Colliex, J. M. Cowley, S. L. Dudarev, M. Fink, J. Gjønnes, R. Hilderbrandt, A. Howie, D. F. Lynch, L. M. Peng, G. Ren, A. W. Ross, V. H. Smith Jr, J. C. H. Spence, J. W. Steeds, J. Wang, M. J. Whelan and B. B. Zvyagin. ''International Tables for Crystallography'' (2006). Vol. C, ch. 4.3, pp. 259-429 [http://dx.doi.org/10.1107/97809553602060000593 doi:10.1107/97809553602060000593] <br />
<br />
Intensity of diffracted intensities.<br />
P. J. Brown, A. G. Fox, E. N. Maslen, M. A. O'Keefe and B. T. M. Willis. ''International Tables for Crystallography'' (2006). Vol. C, ch. 6.1, pp. 554-595 [http://dx.doi.org/10.1107/97809553602060000600 doi:10.1107/97809553602060000600]<br />
<br />
Neutron techniques.<br />
I. S. Anderson, P. J. Brown, J. M. Carpenter, G. Lander, R. Pynn, J. M. Rowe, O. Schärpf, V. F. Sears and B. T. M. Willis. ''International Tables for Crystallography'' (2006). Vol. C, ch. 4.4, pp. 430-487 [http://dx.doi.org/10.1107/97809553602060000594 doi:10.1107/97809553602060000594]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Bragg_angle&diff=2680
Bragg angle
2008-03-31T15:50:44Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Angle de Bragg </Font>(''Fr'').<br />
<br />
== Definition ==<br />
<br />
[[Image:BraggLaw-1.gif|right]]<br />
<br />
In [[Bragg's law]] describing the condition for a plane wave to be diffracted from a family of lattice planes, the angle &theta; between the wavevector of the incident plane wave, '''k<sub>o</sub>''', and the lattice planes (Fig. 1).<br />
<br />
<br />
[[Category: X-rays]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Refinement&diff=2670
Refinement
2008-03-31T05:10:21Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Conditions de réflexion intégrales</Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
In [[structure determination]], the process of improving the parameters of an approximate (trial) structure until the best fit is achieved between an observed diffraction pattern and that calculated by Fourier transformation from the numerically parameterized trial structure.<br />
<br />
== Least-squares refinement ==<br />
<br />
The most common approach in the determination of inorganic or small-molecule structures is to minimize a function<br />
<br />
<math>\sum w (Y_o - Y_c)^2</math><br />
<br />
where <math>Y_o</math> represents the strength of an observed diffraction spot or reflection from a lattice plane of the crystal, <math>Y_c</math> is the value calculated from the structural model for the same reflection, and <math>w</math> is an assigned weight reflecting the importance that this reflection makes to the sum. The weights usually represent an estimate of the precision of the measured quantity. The sum is taken over all measured reflections.<br />
<br />
=== Refinable parameters ===<br />
<br />
The structural model describes a collection of scattering centres (atoms), each located at a fixed position in the crystal lattice, and with some degree of mobility or extension around that locus. In adjusting the structural model to improve the fit between calculated and observed diffraction patterns, the crystallographer may vary these and other parameters. ''Refinable'' parameters are those that may be varied in order to improve the fit. Usually they comprise atomic coordinates, atomic displacement parameters, a scale factor to bring the observed and calculated amplitudes or intensities to the same scale. They may also include extinction parameters, occupancy factors, twin component fractions, and even the assigned space group. Relations between the refinable parameters may be expressed as constraints or restraints that modify the function to be minimized.<br />
<br />
=== Constraints ===<br />
<br />
A '''constraint''' is an exact mathematical relationship that reduces the number of free parameters in a model. For example, the position of an atom on a general position is specified by three coordinates, all of which may be varied independently. However, an atom sitting on a special symmetry position has one or more positional coordinates determined by the symmetry (for example, an atom on an inversion centre in the unit cell has all three coordinates fixed). Constraints are rigid mathematical rules which must be adhered to during the refinement; they reduce the number of refinable parameters. A [[constrained refinement]] is one that includes constraints other than those arising from space group symmetry (since these are necessarily always present).<br />
<br />
=== Restraints ===<br />
<br />
A '''restraint''' is an additional condition that the model parameters must meet to satisfy some additional piece of knowledge appropriate to the structure. For example, if the chemical identities of certain atoms within a molecule are known, their intermolecular distance may be fit to a target value characteristic of bond lengths in other known chemical species of the same type. Restraints are therefore treated as if they were additional experimental observations, and have the effect of increasing the number of refinable parameters.<br />
<br />
=== Refinement against <math>F</math>, <math>F^2</math> or <math>I</math>? ===<br />
<br />
The function to minimize in least-squares refinement was given above in the general form<br />
<br />
<math>\sum w (Y_o - Y_c)^2</math><br />
<br />
and the quantity <math>Y</math> was referred to as a measure of the strength of a reflection. In practice, <math>Y</math>, sometimes known as the [[structure-factor coefficient]], may be either <math>I</math>, the intensity of the measured reflection, <math>|F|</math>, the magnitude of the structure factor, or <math>F^2</math>, the square of the structure factor.<br />
<br />
Refinement against <math>I</math>, the measured intensities, has the merit of using the raw measurements directly, although it requires the incorporation in the refinement of the correction factors (scale factor, Lorentz&ndash;polarization and absorption) that are applied during standard data reduction. There are, however, problems of high statistical correlation when refining absorption parameters against anisotropic displacement parameters.<br />
<br />
Refinement against <math>|F|</math> involves mathematical problems with very weak reflections or reflections with negative measured intensities. There are also difficulties in estimating standard uncertainties <math>\sigma(F)</math> from the <math>\sigma(F^2)</math> values for weak or zero measured intensities.<br />
<br />
Refinement against <math>F^2</math> avoids these difficulties, and also reduces the probability of the refinement iterations settling into a local minimum. It also simplifies the treatment of twinned and non-centrosymmetric structures. For these reasons, it is probably currently the most frequently used technique, although it does rely heavily on the assignment of reasonable weights to individual reflections.<br />
<br />
<br />
== See also ==<br />
<br />
Least squares.<br />
E. Prince and P. T. Boggs. ''International Tables for Crystallography'' (2006). Vol. C, ch. 8.1, pp. 678-688 [http://dx.doi.org/10.1107/97809553602060000609 doi:10.1107/97809553602060000609] <br />
<br />
Other refinement methods.<br />
E. Prince and D. M. Collins. ''International Tables for Crystallography '' (2006). Vol. C, ch. 8.2, pp. 689-692 [http://dx.doi.org/10.1107/97809553602060000610 doi:10.1107/97809553602060000610]<br />
<br />
[[Category:Structure determination]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Integral_reflection_conditions&diff=2669
Integral reflection conditions
2008-03-30T05:41:28Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Conditions de réflexion intégrales</Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The integral reflections are the general [[reflection conditions]] due to the centring of cells. They are given in the table below:<br />
<br />
<table border cellspacing=0 cellpadding=5 align=center><br />
<caption align=top> '''Integral reflection conditions for centred lattices.''' </caption><br />
<tr align=left><br />
<th> Reflection<br> condition </th><br />
<th> Centring type of cell </th><br />
<th>Centring symbol</th><br />
</tr><br />
<tr align=left><br />
<td>None</td> <td> Primitive</td> <td> ''P''<br><br />
''R'' (rhombohedral axes)</td><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'' = 2''n''</td> <td>''C''-face centred</td> <td>''C''</th><br />
</tr><br />
<tr align=left><br />
<td>''k'' + ''l'' = 2''n''</td> <td>''A''-face centred</td> <td>''A''</th><br />
</tr><br />
<tr align=left><br />
<td>''l'' + ''h'' = 2''n''</td> <td>''B''-face centred</td> <td>''B''</td><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'' + ''l'' = 2''n''</td> <td>body centred</td> <td>''I''</th><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'', ''h'' + ''l'' and<br> <br />
''k'' + ''l'' = 2''n'' or:<br><br />
''h'', ''k'', ''l'' all odd or all<br><br />
even (‘unmixed’)</td> <td>all-face centred</td> <td> ''F''</th><br />
</tr><br />
<tr align=left><br />
<td> &minus; ''h'' + ''k'' + ''l'' = 3''n''</td> <td> rhombohedrally<br><br />
centred, reverse<br><br />
setting </td><td rowspan=2>''R'' (hexagonal axes)</td></tr><br />
<tr align=left><br />
<td> ''h'' &minus; ''k'' + ''l'' = 3''n''</td> <td> rhombohedrally<br><br />
centred, obverse<br><br />
setting (standard)</td><br />
</tr><br />
<tr align=left><br />
<td> ''h'' &minus; ''k'' = 3''n''</td> <td>hexagonally centred</td> <td> ''H''</td><br />
</table><br />
<br />
==See also ==<br />
<br />
Section 2.2.13.1 of ''International Tables of Crystallography, Volume A''<br />
<br />
----<br />
[[Category:X-rays]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Integral_reflection_conditions&diff=2668
Integral reflection conditions
2008-03-30T05:40:01Z
<p>AndreAuthier: </p>
<hr />
<div>== Definition ==<br />
<br />
The integral reflections are the general [[reflection conditions]] due to the centring of cells. They are given in the table below:<br />
<br />
<table border cellspacing=0 cellpadding=5 align=center><br />
<caption align=top> '''Integral reflection conditions for centred lattices.''' </caption><br />
<tr align=left><br />
<th> Reflection<br> condition </th><br />
<th> Centring type of cell </th><br />
<th>Centring symbol</th><br />
</tr><br />
<tr align=left><br />
<td>None</td> <td> Primitive</td> <td> ''P''<br><br />
''R'' (rhombohedral axes)</td><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'' = 2''n''</td> <td>''C''-face centred</td> <td>''C''</th><br />
</tr><br />
<tr align=left><br />
<td>''k'' + ''l'' = 2''n''</td> <td>''A''-face centred</td> <td>''A''</th><br />
</tr><br />
<tr align=left><br />
<td>''l'' + ''h'' = 2''n''</td> <td>''B''-face centred</td> <td>''B''</td><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'' + ''l'' = 2''n''</td> <td>body centred</td> <td>''I''</th><br />
</tr><br />
<tr align=left><br />
<td>''h'' + ''k'', ''h'' + ''l'' and<br> <br />
''k'' + ''l'' = 2''n'' or:<br><br />
''h'', ''k'', ''l'' all odd or all<br><br />
even (‘unmixed’)</td> <td>all-face centred</td> <td> ''F''</th><br />
</tr><br />
<tr align=left><br />
<td> &minus; ''h'' + ''k'' + ''l'' = 3''n''</td> <td> rhombohedrally<br><br />
centred, reverse<br><br />
setting </td><td rowspan=2>''R'' (hexagonal axes)</td></tr><br />
<tr align=left><br />
<td> ''h'' &minus; ''k'' + ''l'' = 3''n''</td> <td> rhombohedrally<br><br />
centred, obverse<br><br />
setting (standard)</td><br />
</tr><br />
<tr align=left><br />
<td> ''h'' &minus; ''k'' = 3''n''</td> <td>hexagonally centred</td> <td> ''H''</td><br />
</table><br />
<br />
==See also ==<br />
<br />
Section 2.2.13.1 of ''International Tables of Crystallography, Volume A''<br />
<br />
----<br />
[[Category:X-rays]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Crystal_system&diff=2635
Crystal system
2007-08-21T07:59:03Z
<p>AndreAuthier: </p>
<hr />
<div><font color="blue">Système cristallin </font>(''Fr''); <Font color="black"> Sistema cristallino </Font>(''It''); <Font color="purple"> 晶系 </Font>(''Ja'')<br />
<br />
== Definition ==<br />
<br />
A crystal-class system, or '''crystal system''' for short, contains complete [[geometric crystal class]]es of space groups. All those geometric crystal classes belong to the the same crystal system which intersect exactly the same set of [[Bravais flock]]s.<br />
<br />
== Crystal systems in two and three dimensions ==<br />
In the two-dimensional space there exist four crystal systems:<br />
* oblique<br />
* rectangular<br />
* square<br />
* hexagonal<br />
<br />
In the three-dimensional space there exist seven crystal systems:<br />
* triclinic<br />
* monoclinic<br />
* orthorhombic<br />
* tetragonal<br />
* trigonal<br />
* hexagonal<br />
* cubic<br />
<br />
Note that the adjective ''rhombohedral'' refers to a [[lattice system]], not to a crystal system. Rhombohedral crystals belong to the trigonal crystal system, but trigonal crystals may belong to the rhombohedral or to the hexagonal [[lattice system]].<br />
<br />
== See also ==<br />
Section 8.2.8 in of ''International Tables of Crystallography, Volume A''<br />
<br />
[[category: Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Centred_lattice&diff=2634
Centred lattice
2007-07-25T04:35:59Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Réseaux centrés </Font>(''Fr''). <Font color="red">Zentrierte Gitter</Font> (''Ge''). <Font color="green">Redes centradas</Font> (''Sp''). <Font color="black"> Reticoli centrati </Font>(''It''). <Font color="purple"> 複合格子 </Font>(''Ja'')<br />
<br />
== Definition ==<br />
<br />
When the unit cell does not reflect the symmetry of the lattice, it is usual in crystallography to refer to a '[[conventional cell|conventional]]', non-primitive, crystallographic basis, '''a<sub>c</sub>''', '''b<sub>c</sub>''', '''c<sub>c</sub>''' instead of a [[primitive_cell| primitive basis]], '''a''', '''b''', '''c'''. This is done by adding lattice nodes at the center of the unit cell or at one or three faces. The vectors joining the origin of the unit cell to these additional nodes are called 'centring vectors'. In such a lattice '''a<sub>c</sub>''', '''b<sub>c</sub>''' and '''c<sub>c</sub>''' with all their integral linear combinations are lattice vectors again, but there exist other lattice vectors '''t''' &#8712; '''L''', '''t''' = ''t<sub>1</sub>'' '''a<sub>c</sub>''' + ''t<sub>2</sub>'' '''b<sub>c</sub>''' + ''t<sub>3</sub>'' '''c<sub>c</sub>'''; with at least two of the coefficients ''t<sub>1</sub>'', ''t<sub>2</sub>'', ''t<sub>3</sub>'' being fractional. The table below gives the various types of centring vectors and the corresponding types of centring. Each one is described by a letter, called the Bravais letter, which is to be found in the Hermann-Mauguin symbol of a space group.<br />
<br />
The 'multiplicity', ''m'', of the centred cell is the number of lattice nodes per unit cell (see table).<br />
<br />
The [[unit_cell|volume of the unit cell]], ''V<sub>c</sub>'' = ('''a<sub>c</sub>''', '''b<sub>c</sub>''', '''c<sub>c</sub>''') is given in terms of the volume of the primitive cell, ''V'' = ('''a''', '''b''', '''c'''), by:<br />
<div align="center"><br />
''V<sub>c</sub>'' = ''m V''<br />
</div><br />
==Centred cells vs. "centred lattices"==<br />
A lattice being an infinite, symmetric and periodic collection of zero-dimensional nodes, rigorously speaking it is neither primitive nor centred. The expression "centred lattice" has to be considered as a shortcut for "lattice whose [[conventional cell]] is centred".<br />
<br />
== Types of centred lattices ==<br />
{| border="1" cellpadding="2" cellspacing="2" align="center"<br />
! Bravais letter !! Centring type !! Centring vectors !! Multiplicity<br> (number of nodes per unit cell)!! Unit-cell volume <math>V_c</math> <br />
|-<br />
| ''P''|| Primitive|| 0|| 1|| ''V''<br />
|-<br />
| ''A''|| ''A''-face centred|| &#189;'''b<sub>c</sub>'''+&#189;'''c<sub>c</sub>'''|| 2|| 2''V''<br />
|-<br />
| ''B''|| ''B''-face centred|| &#189;'''c<sub>c</sub>'''+&#189;'''a<sub>c</sub>'''|| 2|| 2''V''<br />
|-<br />
| ''C''|| ''C''-face centred|| &#189;'''a<sub>c</sub>'''+&#189;'''b<sub>c</sub>'''|| 2|| 2''V''<br />
|-<br />
| ''I''|| body centred<br>(''Innenzentriert'')|| &#189;'''a<sub>c</sub>'''+&#189;'''b<sub>c</sub>'''+&#189;'''c<sub>c</sub>'''|| 2|| 2''V''<br />
|-<br />
|rowspan=3| ''F''<br />
|rowspan=3| All-face centred<br />
|| &#189;'''a<sub>c</sub>'''+&#189;'''b<sub>c</sub>'''<br />
|rowspan=3| ''4''<br />
|rowspan=3| 4''V''<br />
|-<br />
|| &#189;'''b<sub>c</sub>'''+&#189;'''c<sub>c</sub>'''<br />
|-<br />
|| &#189;'''c<sub>c</sub>'''+&#189;'''a<sub>c</sub>'''<br />
|-<br />
| ''R''|| Primitive<br>(rhombohedral axes)|| 0|| 1|| ''V''<br />
|-<br />
|rowspan=2| ''R''<br />
|rowspan=2| Rhombohedrally centred<br>(hexagonal axes)<br />
| &#8532;'''a<sub>c</sub>'''+&#8531;'''b<sub>c</sub>'''+&#8531;'''c<sub>c</sub>''' <br />
|rowspan=2| 3<br />
|rowspan=2| 3''V''<br />
|-<br />
||<br />
&#8531;'''a<sub>c</sub>'''+&#8532;'''b<sub>c</sub>'''+&#8532;'''c<sub>c</sub>'''<br />
<br />
|-<br />
|rowspan=2| ''[[H centred cell|H]]''<br />
|rowspan=2| [[H centred cell|Hexagonally centred]]<br />
|&#8532;'''a<sub>c</sub>'''+&#8531;'''b<sub>c</sub>'''<br />
|rowspan=2| 3<br />
|rowspan=2| 3''V''<br />
|-<br />
|| &#8531;'''a<sub>c</sub>'''+&#8532;'''b<sub>c</sub>'''<br />
|-<br />
|}<br />
<br />
<br />
The letter ''S'' is also used to indicate a single pair of centred faces. This happens in the monoclinic and orthorhombic [[crystal family|crystal families]].<br />
*In the monoclinic crystal family, b-unique axis, the centred cells ''mA'', ''mC'', ''mI'' and ''mF'' are equivalent in the sense that a different choice of axes in the (010) plane interchanges these centrings. The letter ''mS'' is sometimes used to collectively indicate any of these cells. The cell ''mB'' is instead equivalent to the cell ''mP''.<br />
*In the orthorhobic crystal family, the centred cells ''oA'', ''oB'' and ''oC'' are transformed one into the other when the axes are permuted. The symbol ''oS'' is sometimes used to collectively indicate these three equivalent cells.<br />
<br />
== See also ==<br />
<br />
*[[D centred cell]]<br />
*Sections 1.2 and 9 of ''International Tables of Crystallography, Volume A''<br />
*Section 1.1 of ''International Tables of Crystallography, Volume C''<br />
<br />
<br />
[[Category:Fundamental crystallography]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Primitive_basis&diff=2626
Primitive basis
2007-06-28T05:04:40Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Base primitive </Font> (''Fr''). <Font color="black"> Base primitiva </Font>(''It'')<br />
<br />
== Definition ==<br />
<br />
A primitive basis is a [[crystallographic basis]] of the vector lattice '''L''' such that every lattice vector '''t''' of '''L''' may be obtained as an integral linear combination of the basis vectors, '''a''', '''b''', '''c'''.<br />
<br />
== See also ==<br />
<br />
*[[direct lattice]]<br />
*[[primitive cell]]<br />
*Sections 8.1 and 9.1 of ''International Tables of Crystallography, Volume A''<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Aristotype&diff=2260
Aristotype
2007-01-30T05:50:45Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Aristotype</Font> (''Fr''). <br />
<br />
<br />
== Definition ==<br />
<br />
An arisotype is a high-symmetry structure type that can be viewed as an idealized version of a lower symmetry structure. It was introduced by Helen Megaw in relation to perovskites which it is where it is still mostly used, the cubic perovskite structure (which is adopted at most half a dozen compounds) is regarded as the aristotype for the vast array of other lower-symmetry perovskites.<br />
<br />
Originally, an aristotype is a printing-out process using paper coated with silver chloride in gelatin; now, any such process using silver salts in either collodion or gelatin; also, a print so made.<br />
<br />
== R eferences ==<br />
<br />
Megaw H. (1973). ''Crystal Structures'', London: W.B. Saunders, p. 216, 282<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Dual_basis&diff=2259
Dual basis
2007-01-14T07:30:44Z
<p>AndreAuthier: </p>
<hr />
<div><Font color = "blue">Base duale </font>(''Fr''). <Font color="black"> Base duale </Font>(''It'')<br />
<br />
== Definition ==<br />
<br />
The dual basis is a basis associated to the basis of a vector space. In three-dimensional space, it is isomorphous to the basis of the reciprocal lattice. It is mathematically defined as follows:<br />
<br />
Given a basis of ''n'' vectors '''e<sub>i</sub>''' spanning the [[direct space]] ''E<sup>n</sup>'', and a vector<br />
'''x''' = ''x<sup> i</sup>'' '''e<sub>i</sub>''', let us consider the ''n'' quantities defined by the<br />
scalar products of '''x''' with the basis vectors, '''e<sub>i</sub>''':<br />
<br />
''x<sub>i</sub>'' = '''x''' . '''e<sub>i</sub>''' = ''x<sup> j</sup>'' '''e<sub>j</sub>''' . '''e<sub>i</sub>''' = ''x<sup> j</sup> g<sub>ji</sub>'',<br />
<br />
where the ''g<sub>ji</sub>'' 's are the doubly covariant components of the [[metric tensor]].<br />
<br />
By solving these equations in terms of ''x<sup> j</sup>'', one gets:<br />
<br />
''x<sup> j</sup>'' = ''x<sub>i</sub> g<sup>ij</sup>''<br />
<br />
where the matrix of the ''g<sup>ij</sup>'' 's is inverse of that of the ''g<sub>ij</sub>'' 's (''g<sup>ik</sup>g<sub>jk</sub>'' = &#948;<sup>i</sup><sub>j</sub>). The development of vector '''x''' with respect to basis vectors '''e<sub>i</sub>''' can now also be written:<br />
<br />
'''x''' = ''x<sup> i</sup>'' '''e<sub>i</sub>''' = ''x<sub>i</sub> g<sup>ij</sup>'' '''e<sub>j</sub>'''<br />
<br />
The set of ''n'' vectors '''e<sup>i</sup>''' = ''g<sup>ij</sup>'' '''e<sub>j</sub>''' that span the space ''E<sup>n</sup>'' forms a basis since vector '''x''' can be written:<br />
<br />
'''x''' = ''x<sub>i</sub>'' '''e<sup>i</sup>'''<br />
<br />
This basis is the ''dual basis'' and the ''n'' quantities ''x<sub>i</sub>'' defined above are the<br />
coordinates of '''x''' with respect to the dual basis. In a similar way one can express the direct basis vectors in terms of the dual basis vectors:<br />
<br />
'''e<sub>i</sub>''' = ''g<sub>ij</sub>'' '''e<sup>j</sup>'''<br />
<br />
The scalar products of the basis vectors of the dual and direct bases are:<br />
<br />
''g<sup>i</sup><sub>j</sub>'' = '''e<sup>i</sup>''' . '''e<sub>j</sub>''' = ''g<sup>ik</sup>'' '''e<sub>k</sub>''' . '''e<sub>j</sub>''' = ''g<sup>ik</sup>g<sub>jk</sub>'' = &#948;<sup>i</sup><sub>j</sub>.<br />
<br />
One has therefore, since the matrices ''g<sup>ik</sup>'' and ''g<sub>ij</sub>'' are inverse:<br />
<br />
''g<sup>i</sup><sub>j</sub>'' = '''e<sup>i</sup>''' . '''e<sub>j</sub>''' = &#948;<sup>i</sup><sub>j</sub>.<br />
<br />
These relations show that the dual basis vectors satisfy the definition conditions of the reciprocal vectors. In a three-dimensional space the dual basis and the basis of [[reciprocal space]] are identical.<br />
<br />
== Change of basis ==<br />
<br />
In a change of basis where the direct basis vectors and coordinates transform like:<br />
<br />
'''e'<sub>j</sub>''' = ''A<sub>j</sub><sup>i</sup>'' '''e<sub>i</sub>'''; ''x'<sup>j</sup>'' = ''B<sub>i</sub><sup> j</sup>'' ''x<sup>i</sup>'',<br />
<br />
where ''A<sub>j</sub><sup>i</sup>'' and ''B<sub>i</sub><sup> j</sup>'' are transformation matrices, transpose of one another,<br />
the dual basis vectors '''e<sup>i</sup>''' and the coordinates ''x<sub>i</sub>'' transform according to:<br />
<br />
'''e'<sup>j</sup> ''' = ''B<sub>i</sub><sup> j</sup>'' '''e<sup>i</sup>'''; ''x'<sub>j</sub>'' = ''A<sub>j</sub><sup>i</sup>x<sub>i</sub>''.<br />
<br />
The coordinates of a vector in reciprocal space are therefore ''covariant'' and the dual basis vectors (or reciprocal vectors) ''contravariant''.<br />
<br />
=== See also ===<br />
<br />
[[metric tensor]]<br><br />
[[reciprocal space]]<br><br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/4/ The Reciprocal Lattice] (Teaching Pamphlet of the ''International Union of Crystallography'')<br />
<br />
Section 1.1.2 of ''International Tables of Crystallography, Volume D''<br />
<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]<br><br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Metric_tensor&diff=2258
Metric tensor
2007-01-12T14:23:22Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Tenseur métrique </Font>(''Fr''). <Font color="black"> Tensore metrico </Font>(''It'')<br />
<br />
== Definition ==<br />
<br />
Given a basis '''e<sub>i</sub>''' of a ''Euclidean space'', ''E<sup>n</sup>'', the metric tensor is a rank 2 tensor the components of <br />
which are:<br />
<br />
''g<sub>ij</sub>'' = '''e<sub>i</sub>''' . '''e<sub>j</sub>''' = '''e<sub>j</sub>'''.'''e<sub>i</sub>''' = ''g<sub>ji</sub>''.<br />
<br />
It is a symmetrical tensor. Using the metric tensor, the scalar product of two vectors, '''x''' = ''x<sup>i</sup>'' '''e<sub>i</sub>''' and '''y''' = ''y<sup>j</sup>'' '''e<sub>j</sub>''' is written:<br />
<br />
'''x''' . '''y''' = ''x<sup>i</sup>'' '''e<sub>i</sub>''' . ''y<sup>j</sup>'' '''e<sub>j</sub>''' = ''g<sub>ij</sub>'' ''x<sup>i</sup>'' ''y<sup>j</sup>''.<br />
<br />
In a three-dimensional space with basis vectors '''a''', '''b''', '''c''', the coefficients ''g<sub>ij</sub>'' of the metric tensor are:<br />
<br />
''g<sub>11</sub>,'' = '''a<sup>2</sup>'''; ''g<sub>12</sub>'' = '''a . b'''; ''g<sub>13</sub>'' = '''a . c''';<br><br />
''g<sub>21</sub>'' = '''b . a'''; ''g<sub>22</sub>'' = '''b<sup>2</sup>'''; ''g<sub>23</sub>'' = '''b . c''';<br><br />
''g<sub>31</sub>'' = '''c . a'''; ''g<sub>32</sub>'' = '''c . b'''; ''g<sub>33</sub>'' = '''c<sup>2</sup>''';<br />
<br />
The inverse matrix of ''g<sub>ij</sub>'', ''g<sup>ij</sup>'', (''g<sup>ik</sup>g<sub>kj</sub>'' = &#948;''<sup>k</sup><sub>j</sub>'', Kronecker symbol, = 0 if ''i'' &#8800; ''j'', = 1 if ''i'' = ''j'') relates the [[dual basis]], or [[reciprocal space]] vectors '''e<sup>i</sup>''' to the direct basis vectors '''e<sub>i</sub>''' through the relations:<br />
<br />
'''e<sup>j</sup>''' = ''g<sup>ij</sup>'' '''e<sub>j</sub>'''<br />
<br />
In three-dimensional space, the dual basis vectors are identical to the [[reciprocal space]] vectors and the components of ''g<sup>ij</sup>'' are:<br />
<br />
''g<sup>11</sup>'' = '''a*<sup>2</sup>'''; ''g<sup>12</sup>'' = '''a* . b*'''; ''g<sup>13</sup>'' = '''a* . c*''';<br><br />
''g<sup>21</sup>'' = '''b* . a*'''; ''g<sup>22</sup>'' = '''b*<sup>2</sup>'''; ''g<sup>23</sup>'' = '''b* . c*''';<br><br />
''g<sup>31</sup>'' = '''c* . a*'''; ''g<sup>32</sup>'' = '''c* . b*'''; ''g<sup>33</sup>'' = '''c*<sup>2</sup>''';<br />
<br />
with:<br />
<br />
''g<sup>11</sup>'' = ''b''<sup>2</sup>''c''<sup>2</sup> sin<sup>2</sup> &#945;/ V<sup>2</sup>;<br />
''g<sup>22</sup>'' = ''c''<sup>2</sup>''a''<sup>2</sup> sin<sup>2</sup> &#946;/ V<sup>2</sup>;<br />
''g<sup>33</sup>'' = ''a''<sup>2</sup>''b''<sup>2</sup> sin<sup>2</sup> &#947;/ V<sup>2</sup>;<br />
<br />
''g<sup>12</sup>'' = ''g<sup>21</sup>'' = (''abc''<sup>2</sup>/ V<sup>2</sup>)(cos &#945; cos &#946; - cos &#947;);<br />
''g<sup>23</sup>'' = ''g<sup>32</sup>'' = (''a<sup>2</sup>bc''/ V<sup>2</sup>)(cos &#946; cos &#947; - cos &#945;);<br />
''g<sup>31</sup>'' = ''g<sup>13</sup>'' = (''ab<sup>2</sup>c''/ V<sup>2</sup>)(cos &#947; cos &#945; - cos &#946;)<br />
<br />
where ''V'' is the volume of the unit cell ('''a''', '''b''', '''c''').<br />
<br />
== Change of basis ==<br />
<br />
In a change of basis the direct basis vectors and coordinates transform like:<br />
<br />
'''e'<sub>j</sub>''' = ''A<sub>j</sub><sup> i</sup>'' '''e<sub>i</sub>'''; ''x'<sup>j</sup>'' = ''B<sub>i</sub><sup> j</sup>'' ''x<sup> i</sup>'',<br />
<br />
where ''A<sub>j</sub><sup> i</sup>'' and ''B<sub>i</sub><sup> j</sup>'' are transformation matrices, transpose of one another. According to their<br />
definition, the components ''g<sub>ij</sub>,'' of the metric tensor transform like products of basis vectors:<br />
<br />
''g'<sub>kl</sub>'' = ''A<sub>k</sub><sup>i</sup>A<sub>l</sub><sup>j</sup>g<sub>ij</sub>''.<br />
<br />
They are the doubly covariant components of the metric tensor. <br />
<br />
The [[dual basis]] vectors and coordinates transform in the change of basis according to:<br />
<br />
'''e'<sup>j</sup>''' = ''B<sub>i</sub><sup> j</sup>'' '''e<sup>i</sup>'''; ''x'<sub>j</sub>'' = ''A<sub>j</sub><sup> i</sup>x<sub>i</sub>'',<br />
<br />
and the components ''g<sup>ij</sup>'' transform like products of dual basis vectors:<br />
<br />
''g'<sup>kl</sup>'' = ''A<sub>i</sub><sup>k</sup> A<sub>j</sub><sup>l</sup> g<sup>ij</sup>''.<br />
<br />
They are the doubly contravariant components of the metric tensor.<br />
<br />
The mixed components, ''g<sup>i</sup><sub>j</sub>'' = &#948;<sup>i</sup><sub>j</sub>, are once covariant and once contravariant and are invariant.<br />
<br />
== Properties of the metric tensor ==<br />
<br />
* The '''tensor nature''' of the metric tensor is demonstrated by the behaviour of its components in a change of basis. The components ''g<sub>ij</sub>'' and ''g<sup>ij</sup>'' are the components of a ''unique'' tensor.<br />
<br />
* The '''squares of the volumes''' ''V'' and ''V*'' of the direct space and reciprocal space unit cells are respectively equal to the determinants of the ''g<sub>ij</sub>'' 's and the ''g<sup>ij</sup>'' 's:<br />
<br />
''V''<sup> 2</sup> = &#916; (''g<sub>ij</sub>'') = ''abc''(1 - cos <sup>2</sup> &#945; - cos <sup>2</sup> &#946; - cos<sup>2</sup> &#947; + 2 cos &#945; cos &#945; cos &#945;)<br />
<br />
''V*''<sup>2</sup> = &#916; (''g<sup>ij</sup>'') = 1/ ''V''<sup> 2</sup>.<br />
<br />
* One changes the '''variance of a tensor''' by taking the contracted tensor product of the tensor by the suitable form of the metric tensor. For instance:<br />
<br />
''g<sub>im</sub>t<sup> ij..</sup><sub>kl..</sub>'' = ''t<sup> j..</sup><sub>klm..</sub>''<br />
<br />
Multiplying by the doubly covariant form of the metric tensor increases the covariance by one, multiplying by the doubly contravariant form increases the contravariance by one.<br />
<br />
== See also ==<br />
<br />
[[dual basis]]<br><br />
[[reciprocal space]]<br><br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/10/ Metric Tensor and Symmetry Operations in Crystallography] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 1.1.3 of ''International Tables of Crystallography, Volume B''<br><br />
Section 1.1.2 of ''International Tables of Crystallography, Volume D''<br><br />
<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]<br><br />
[[Category:Physical properties of crystals]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Metric_tensor&diff=2257
Metric tensor
2007-01-12T14:23:09Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Tenseur métrique </Font>(''Fr''). <Font color="black"> Tensore metrico </Font>(''It'')<br />
<br />
<br />
<br />
<br />
== Definition ==<br />
<br />
Given a basis '''e<sub>i</sub>''' of a ''Euclidean space'', ''E<sup>n</sup>'', the metric tensor is a rank 2 tensor the components of <br />
which are:<br />
<br />
''g<sub>ij</sub>'' = '''e<sub>i</sub>''' . '''e<sub>j</sub>''' = '''e<sub>j</sub>'''.'''e<sub>i</sub>''' = ''g<sub>ji</sub>''.<br />
<br />
It is a symmetrical tensor. Using the metric tensor, the scalar product of two vectors, '''x''' = ''x<sup>i</sup>'' '''e<sub>i</sub>''' and '''y''' = ''y<sup>j</sup>'' '''e<sub>j</sub>''' is written:<br />
<br />
'''x''' . '''y''' = ''x<sup>i</sup>'' '''e<sub>i</sub>''' . ''y<sup>j</sup>'' '''e<sub>j</sub>''' = ''g<sub>ij</sub>'' ''x<sup>i</sup>'' ''y<sup>j</sup>''.<br />
<br />
In a three-dimensional space with basis vectors '''a''', '''b''', '''c''', the coefficients ''g<sub>ij</sub>'' of the metric tensor are:<br />
<br />
''g<sub>11</sub>,'' = '''a<sup>2</sup>'''; ''g<sub>12</sub>'' = '''a . b'''; ''g<sub>13</sub>'' = '''a . c''';<br><br />
''g<sub>21</sub>'' = '''b . a'''; ''g<sub>22</sub>'' = '''b<sup>2</sup>'''; ''g<sub>23</sub>'' = '''b . c''';<br><br />
''g<sub>31</sub>'' = '''c . a'''; ''g<sub>32</sub>'' = '''c . b'''; ''g<sub>33</sub>'' = '''c<sup>2</sup>''';<br />
<br />
The inverse matrix of ''g<sub>ij</sub>'', ''g<sup>ij</sup>'', (''g<sup>ik</sup>g<sub>kj</sub>'' = &#948;''<sup>k</sup><sub>j</sub>'', Kronecker symbol, = 0 if ''i'' &#8800; ''j'', = 1 if ''i'' = ''j'') relates the [[dual basis]], or [[reciprocal space]] vectors '''e<sup>i</sup>''' to the direct basis vectors '''e<sub>i</sub>''' through the relations:<br />
<br />
'''e<sup>j</sup>''' = ''g<sup>ij</sup>'' '''e<sub>j</sub>'''<br />
<br />
In three-dimensional space, the dual basis vectors are identical to the [[reciprocal space]] vectors and the components of ''g<sup>ij</sup>'' are:<br />
<br />
''g<sup>11</sup>'' = '''a*<sup>2</sup>'''; ''g<sup>12</sup>'' = '''a* . b*'''; ''g<sup>13</sup>'' = '''a* . c*''';<br><br />
''g<sup>21</sup>'' = '''b* . a*'''; ''g<sup>22</sup>'' = '''b*<sup>2</sup>'''; ''g<sup>23</sup>'' = '''b* . c*''';<br><br />
''g<sup>31</sup>'' = '''c* . a*'''; ''g<sup>32</sup>'' = '''c* . b*'''; ''g<sup>33</sup>'' = '''c*<sup>2</sup>''';<br />
<br />
with:<br />
<br />
''g<sup>11</sup>'' = ''b''<sup>2</sup>''c''<sup>2</sup> sin<sup>2</sup> &#945;/ V<sup>2</sup>;<br />
''g<sup>22</sup>'' = ''c''<sup>2</sup>''a''<sup>2</sup> sin<sup>2</sup> &#946;/ V<sup>2</sup>;<br />
''g<sup>33</sup>'' = ''a''<sup>2</sup>''b''<sup>2</sup> sin<sup>2</sup> &#947;/ V<sup>2</sup>;<br />
<br />
''g<sup>12</sup>'' = ''g<sup>21</sup>'' = (''abc''<sup>2</sup>/ V<sup>2</sup>)(cos &#945; cos &#946; - cos &#947;);<br />
''g<sup>23</sup>'' = ''g<sup>32</sup>'' = (''a<sup>2</sup>bc''/ V<sup>2</sup>)(cos &#946; cos &#947; - cos &#945;);<br />
''g<sup>31</sup>'' = ''g<sup>13</sup>'' = (''ab<sup>2</sup>c''/ V<sup>2</sup>)(cos &#947; cos &#945; - cos &#946;)<br />
<br />
where ''V'' is the volume of the unit cell ('''a''', '''b''', '''c''').<br />
<br />
== Change of basis ==<br />
<br />
In a change of basis the direct basis vectors and coordinates transform like:<br />
<br />
'''e'<sub>j</sub>''' = ''A<sub>j</sub><sup> i</sup>'' '''e<sub>i</sub>'''; ''x'<sup>j</sup>'' = ''B<sub>i</sub><sup> j</sup>'' ''x<sup> i</sup>'',<br />
<br />
where ''A<sub>j</sub><sup> i</sup>'' and ''B<sub>i</sub><sup> j</sup>'' are transformation matrices, transpose of one another. According to their<br />
definition, the components ''g<sub>ij</sub>,'' of the metric tensor transform like products of basis vectors:<br />
<br />
''g'<sub>kl</sub>'' = ''A<sub>k</sub><sup>i</sup>A<sub>l</sub><sup>j</sup>g<sub>ij</sub>''.<br />
<br />
They are the doubly covariant components of the metric tensor. <br />
<br />
The [[dual basis]] vectors and coordinates transform in the change of basis according to:<br />
<br />
'''e'<sup>j</sup>''' = ''B<sub>i</sub><sup> j</sup>'' '''e<sup>i</sup>'''; ''x'<sub>j</sub>'' = ''A<sub>j</sub><sup> i</sup>x<sub>i</sub>'',<br />
<br />
and the components ''g<sup>ij</sup>'' transform like products of dual basis vectors:<br />
<br />
''g'<sup>kl</sup>'' = ''A<sub>i</sub><sup>k</sup> A<sub>j</sub><sup>l</sup> g<sup>ij</sup>''.<br />
<br />
They are the doubly contravariant components of the metric tensor.<br />
<br />
The mixed components, ''g<sup>i</sup><sub>j</sub>'' = &#948;<sup>i</sup><sub>j</sub>, are once covariant and once contravariant and are invariant.<br />
<br />
== Properties of the metric tensor ==<br />
<br />
* The '''tensor nature''' of the metric tensor is demonstrated by the behaviour of its components in a change of basis. The components ''g<sub>ij</sub>'' and ''g<sup>ij</sup>'' are the components of a ''unique'' tensor.<br />
<br />
* The '''squares of the volumes''' ''V'' and ''V*'' of the direct space and reciprocal space unit cells are respectively equal to the determinants of the ''g<sub>ij</sub>'' 's and the ''g<sup>ij</sup>'' 's:<br />
<br />
''V''<sup> 2</sup> = &#916; (''g<sub>ij</sub>'') = ''abc''(1 - cos <sup>2</sup> &#945; - cos <sup>2</sup> &#946; - cos<sup>2</sup> &#947; + 2 cos &#945; cos &#945; cos &#945;)<br />
<br />
''V*''<sup>2</sup> = &#916; (''g<sup>ij</sup>'') = 1/ ''V''<sup> 2</sup>.<br />
<br />
* One changes the '''variance of a tensor''' by taking the contracted tensor product of the tensor by the suitable form of the metric tensor. For instance:<br />
<br />
''g<sub>im</sub>t<sup> ij..</sup><sub>kl..</sub>'' = ''t<sup> j..</sup><sub>klm..</sub>''<br />
<br />
Multiplying by the doubly covariant form of the metric tensor increases the covariance by one, multiplying by the doubly contravariant form increases the contravariance by one.<br />
<br />
== See also ==<br />
<br />
[[dual basis]]<br><br />
[[reciprocal space]]<br><br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/10/ Metric Tensor and Symmetry Operations in Crystallography] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 1.1.3 of ''International Tables of Crystallography, Volume B''<br><br />
Section 1.1.2 of ''International Tables of Crystallography, Volume D''<br><br />
<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]<br><br />
[[Category:Physical properties of crystals]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Electrocaloric_effect&diff=2256
Electrocaloric effect
2007-01-12T09:34:19Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Effet électrocalorifique </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The electrocaloric effect is the converse of the pyroelectric effect: it describes the variation of entropy &delta;&sigma; of a material submitted to an applied electrical field ''E<sub>i</sub> '':<br />
<center><br />
''&delta;&sigma;'' = ''p<sub>i</sub><sup>T</sup>'' ''E<sub>i</sub> ''<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the electrocaloric coefficient at constant stress. It is equal to the pyroelectric coefficient.<br />
<br />
== See [[pyroelectricity]] ==<br />
<br />
== See also ==<br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 10.2 of ''International Tables of Crystallography, Volume A''<br><br />
Section 1.1.4 and part 3 of ''International Tables of Crystallography, Volume D''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Pyroelectricity&diff=2255
Pyroelectricity
2007-01-12T09:33:41Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Pyroélectricité </Font> (''Fr''). <Font color="red"> Pyroelectrizität </Font> (''Ge''). <font color="green">Pyroelectricidad </Font> (''Sp'').<Font color="black"> Piroelettricità </Font>(''It'')<br />
<br />
<br />
== Definition ==<br />
<br />
Pyroelectricity is the property presented by certain materials that exhibit an electric polarization ''P<sub>i</sub> '' when a temperature variation &delta;&Theta; is applied uniformly:<br />
<br />
<center><br />
''P<sub>i</sub> '' = ''p<sub>i</sub><sup>T</sup> ''&delta;&Theta;<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the pyroelectric coefficient at constant stress. Pyroelectric crystals actually have a spontaneous polarization, but the pyroelectric effect can only be observed during a temperature change. If the polarisation can be reversed by the application of an electric field, the crystal is ferroelectric.<br />
<br />
If the crystal is also piezoelectric, the polarization due to an applied temperature variation is also partly due to the piezoelectric effect. The coefficient describing the pure pyroelectric effect is the pyroelectric coefficient at constant strain, ''p<sub>i</sub>''<sup>''S''</sup>. The two coefficients are related by:<br />
<br />
<center><br />
''p<sub>i</sub><sup>T</sup> '' = ''c<sub>ijkl</sub>d<sub>kln</sub>''&alpha;''<sub>jn</sub>'' + ''p<sub>i</sub>''<sup>''S''</sup><br />
</center><br />
<br />
where the ''c<sub>ijkl</sub>'' are the elastic stiffnesses, the ''d<sub>kln</sub>'' the [[piezoelectricity| piezoelectric]] coefficients and the &alpha;''<sub>jn</sub>'' the linear [[thermal expansion]] coefficients.<br />
<br />
The converse effect is the [[electrocaloric effect]]. If a pyroelectric crystal is submitted to an electic field, it will undergo a change of entropy &Delta;&sigma;:<br />
<br />
<center><br />
&Delta;&sigma; = ''p<sub>i</sub> E<sup>i</sup> ''<br />
</center><br />
<br />
and will release or absorb a quantity of heat gien by &Theta;'' V'' &Delta;&sigma; where &Theta; is the temperature of the specimen and ''V'' its volume.<br />
<br />
== Pyroelectric point groups ==<br />
<br />
The [[geometric crystal classes]] for which the piezoelectric effect is possible are determined by symmetry considerations (see [[Curie laws]]). They are the classes of which the symmetry is a subgroup of the symmetry associated with that of the electric field, ''A''<sub>&infin;</sub> &infin;''M'':<br />
<br />
1, 2, 3, 4, 6, ''m'', 2''mm'', 3''m'', 4''mm'', 6''mm''<br />
<br />
== History ==<br />
<br />
The appearance of electrostatic charges upon changes of temperature has been observed since ancient times, in particular on tourmaline. It is Sir David Brewster (1781-1788) who coined the term 'pyroelectricity' (Brewster D., 1824, ''Edinburgh. J. Sci.'', '''1''', 208-215, ''Observations on the pyroelectricity of minerals'', translated into German, ''Poggendorf Ann. Phys.'', 1824, '''2''', 297-307, ''Beobachtungen über die, in den Mineralien, durch Wärme erregte Electricität'').<br />
<br />
== See also ==<br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 10.2 of ''International Tables of Crystallography, Volume A''<br><br />
Section 1.1.4 and part 3 of ''International Tables of Crystallography, Volume D''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Electrocaloric_effect&diff=2254
Electrocaloric effect
2007-01-12T09:32:29Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Effet électrocalorifique </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The electrocaloric effect is the converse of the pyroelectric effect: it describes the variation of entropy &delta;&sigma; of a material submitted to an electrical field ''E<sub>i</sub> '':<br />
<center><br />
''&delta;&sigma;'' = ''p<sub>i</sub><sup>T</sup>'' ''E<sub>i</sub> ''<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the electrocaloric coefficient at constant stress. It is equal to the pyroelectric coefficient.<br />
<br />
== See [[pyroelectricity]] ==<br />
<br />
== See also ==<br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 10.2 of ''International Tables of Crystallography, Volume A''<br><br />
Section 1.1.4 and part 3 of ''International Tables of Crystallography, Volume D''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Electrocaloric_effect&diff=2253
Electrocaloric effect
2007-01-12T09:30:33Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Effet électrocalorifique </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The electrocaloric effect is the converse of the pyroelectric effect: it describes the variation of entropy &delta;&sigma; of a material submitted to an electrical field ''E<sub>i</sub> '':<br />
<center><br />
''&delta;&sigma;'' = ''p<sub>i</sub><sup>T</sup>'' ''E<sub>i</sub> ''<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the electrocaloric coefficient at constant stress. It is equal to the pyroelectric coefficient.<br />
<br />
== See also ==<br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 10.2 of ''International Tables of Crystallography, Volume A''<br><br />
Section 1.1.4 and part 3 of ''International Tables of Crystallography, Volume D''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Electrocaloric_effect&diff=2252
Electrocaloric effect
2007-01-12T09:23:26Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Effet électrocalorifique </Font> (''Fr''). <br />
<br />
== Definition ==<br />
<br />
The electrocaloric effect is the converse of the pyroelectric effect: it describes the electrical response of a material to a thermal impetus. For instance, if the material is submitted uniformly to a temperature variation &delta;&Theta;, an electrical polarisation ''P<sub>i</sub> '' appears:<br />
<center><br />
''P<sub>i</sub> '' = ''p<sub>i</sub><sup>T</sup> ''&delta;&Theta;<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the electrocaloric coefficient at constant stress. It is equal to the pyroelectric coefficient.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=E&diff=2251
E
2007-01-12T09:12:47Z
<p>AndreAuthier: </p>
<hr />
<div>{| border="1" cellpadding="3" cellspacing="0" rules="all" <br />
| [[A]] || [[B]] || [[C]] || [[D]] || [[E]] || [[F]] || [[G]] || [[H]] || [[I]] || [[J]] || [[K]] || [[L]] || [[M]] || [[N]] || [[O]] || [[P]] || [[Q]] || [[R]] || [[S]] || [[T]] || [[U]] || [[V]] || [[W]] || [[X]] || [[Y]] || [[Z]] <br />
|}<br />
<br />
= E =<br />
<br />
[[eigensymmetry]]<br><br />
[[electrocaloric effect]]<br><br />
[[Ewald sphere]]<br><br />
[[extinctions]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Pyroelectricity&diff=2250
Pyroelectricity
2007-01-12T08:51:41Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue"> Pyroélectricité </Font> (''Fr''). <Font color="red"> Pyroelectrizität </Font> (''Ge''). <font color="green">Pyroelectricidad </Font> (''Sp'').<Font color="black"> Piroelettricità </Font>(''It'')<br />
<br />
<br />
== Definition ==<br />
<br />
Pyroelectricity is the property presented by certain materials that exhibit an electric polarization ''P<sub>i</sub> '' when a temperature variation &delta;&Theta; is applied uniformly:<br />
<br />
<center><br />
''P<sub>i</sub> '' = ''p<sub>i</sub><sup>T</sup> ''&delta;&Theta;<br />
</center><br />
<br />
where ''p<sub>i</sub><sup>T</sup>'' is the pyroelectric coefficient at constant stress. Pyroelectric crystals actually have a spontaneous polarization, but the pyroelectric effect can only be observed during a temperature change. If the polarisation can be reversed by the application of an electric field, the crystal is ferroelectric.<br />
<br />
If the crystal is also piezoelectric, the polarization due to an applied temperature variation is also partly due to the piezoelectric effect. The coefficient describing the pure pyroelectric effect is the pyroelectric coefficient at constant strain, ''p<sub>i</sub>''<sup>''S''</sup>. The two coefficients are related by:<br />
<br />
<center><br />
''p<sub>i</sub><sup>T</sup> '' = ''c<sub>ijkl</sub>d<sub>kln</sub>''&alpha;''<sub>jn</sub>'' + ''p<sub>i</sub>''<sup>''S''</sup><br />
</center><br />
<br />
where the ''c<sub>ijkl</sub>'' are the elastic stiffnesses, the ''d<sub>kln</sub>'' the [[piezoelectricity| piezoelectric]] coefficients and the &alpha;''<sub>jn</sub>'' the linear [[thermal expansion]] coefficients.<br />
<br />
The converse effect is the electrocaloric effect. If a pyroelectric crystal is submitted to an electic field, it will undergo a change of entropy &Delta;&sigma;:<br />
<br />
<center><br />
&Delta;&sigma; = ''p<sub>i</sub> E<sup>i</sup> ''<br />
</center><br />
<br />
and will release or absorb a quantity of heat gien by &Theta;'' V'' &Delta;&sigma; where &Theta; is the temperature of the specimen and ''V'' its volume.<br />
<br />
== Pyroelectric point groups ==<br />
<br />
The [[geometric crystal classes]] for which the piezoelectric effect is possible are determined by symmetry considerations (see [[Curie laws]]). They are the classes of which the symmetry is a subgroup of the symmetry associated with that of the electric field, ''A''<sub>&infin;</sub> &infin;''M'':<br />
<br />
1, 2, 3, 4, 6, ''m'', 2''mm'', 3''m'', 4''mm'', 6''mm''<br />
<br />
== History ==<br />
<br />
The appearance of electrostatic charges upon changes of temperature has been observed since ancient times, in particular on tourmaline. It is Sir David Brewster (1781-1788) who coined the term 'pyroelectricity' (Brewster D., 1824, ''Edinburgh. J. Sci.'', '''1''', 208-215, ''Observations on the pyroelectricity of minerals'', translated into German, ''Poggendorf Ann. Phys.'', 1824, '''2''', 297-307, ''Beobachtungen über die, in den Mineralien, durch Wärme erregte Electricität'').<br />
<br />
== See also ==<br />
<br />
[http://www.iucr.org/iucr-top/comm/cteach/pamphlets/18/ An introduction to crystal physics] (Teaching Pamphlet of the ''International Union of Crystallography'')<br><br />
Section 10.2 of ''International Tables of Crystallography, Volume A''<br><br />
Section 1.1.4 and part 3 of ''International Tables of Crystallography, Volume D''<br />
<br />
----<br />
<br />
[[Category:Physical properties of crystals]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=P&diff=2248
P
2006-10-31T07:37:38Z
<p>AndreAuthier: </p>
<hr />
<div>{| border="1" cellpadding="3" cellspacing="0" rules="all" <br />
| [[A]] || [[B]] || [[C]] || [[D]] || [[E]] || [[F]] || [[G]] || [[H]] || [[I]] || [[J]] || [[K]] || [[L]] || [[M]] || [[N]] || [[O]] || [[P]] || [[Q]] || [[R]] || [[S]] || [[T]] || [[U]] || [[V]] || [[W]] || [[X]] || [[Y]] || [[Z]] <br />
|}<br />
<br />
= P =<br />
<br />
[[piezoelectricity]]<br><br />
[[point symmetry]]<br><br />
[[polytypes]]<br><br />
[[polytypism]]<br><br />
[[preferred orientation]]<br><br />
[[primitive basis]]<br><br />
[[primitive cell]]<br><br />
[[pyroelectricity]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Polytypism&diff=2247
Polytypism
2006-10-28T05:07:32Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Polytypisme</Font> (''Fr'').<br />
<br />
== Definition ==<br />
<br />
An element or compound is '''polytypic''' if it occurs in several structural modifications, each of which can be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in their stacking sequence. Polytypism is a special case of polymorphism: the two-dimensional translations within the layers are essentially preserved.<br />
<br />
The complete definition is given in the Report of the International Union of Crystallography Ad-Hoc Committee on the Nomenclature of Disordered, Modulated and Polytype Structures:<br />
[http://dx.doi.org/10.1107/S0108767384000842 ''Acta Cryst.'' A'''40''', 399-404(1984)], "Nomenclature of Polytype Structures".<br />
<br />
==See also==<br />
Chapter 9.2 of ''International Tables of Crystallography, Volume C''<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Polytypism&diff=2246
Polytypism
2006-10-28T05:04:31Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Polytypisme</Font> (''Fr'').<br />
<br />
== Definition ==<br />
<br />
An element or compound is '''polytypic''' if it occurs in several structural modifications, each of which can be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in their stacking sequence. Polytypism is a special case of polymorphism: the two-dimensional translations within the layers are essentially preserved.<br />
<br />
<br />
[http://dx.doi.org/10.1107/S0108767384000842 ''Acta Cryst.'' A'''40''', 399-404].<br />
Acta Cryst. (1984). A40, 399-404; "Nomenclature of Polytype Structures"<br />
Report of the International Union of Crystallography Ad-Hoc Committee on the Nomenclature of Disordered, Modulated and Polytype Structures<br />
<br />
<br />
<br />
==See also==<br />
Chapter 9.2 of ''International Tables of Crystallography, Volume C''<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Polytypism&diff=2245
Polytypism
2006-10-28T04:52:23Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Polytypisme</Font> (''Fr'').<br />
<br />
== Definition ==<br />
<br />
An element or compound is '''polytypic''' if it occurs in several structural modifications, each of which can be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in their stacking sequence. Polytypism is a special case of polymorphism: the two-dimensional translations within the layers are essentially preserved.<br />
<br />
<br />
[http://dx.doi.org/10.1107/S0108768102003464 ''Acta Cryst.'' A'''40''', 399-404].<br />
Acta Cryst. (1984). A40, 399-404; "Nomenclature of Polytype Structures"<br />
Report of the International Union of Crystallography Ad-Hoc Committee on the Nomenclature of Disordered, Modulated and Polytype Structures<br />
<br />
<br />
<br />
==See also==<br />
Chapter 9.2 of ''International Tables of Crystallography, Volume C''<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Polytypism&diff=2244
Polytypism
2006-10-28T04:40:50Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Polytypisme</Font> (''Fr'').<br />
<br />
== Definition ==<br />
<br />
An element or compound is '''polytypic''' if it occurs in several structural modifications, each of which can be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in their stacking sequence. Polytypism is a special case of polymorphism: the two-dimensional translations within the layers are essentially preserved.<br />
<br />
Acta Cryst. (1984). A40, 399-404; "Nomenclature of Polytype Structures"<br />
Report of the International Union of Crystallography Ad-Hoc Committee on the Nomenclature of Disordered, Modulated and Polytype Structures<br />
<br />
<br />
<br />
==See also==<br />
Chapter 9.2 of ''International Tables of Crystallography, Volume C''<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Polytypism&diff=2243
Polytypism
2006-10-28T04:38:29Z
<p>AndreAuthier: </p>
<hr />
<div>== Definition<br />
<br />
An element or compound is '''polytypic''' if it occurs in several structural modifications, each of which can be regarded as built up by stacking layers of (nearly) identical structure and composition, and if the modifications differ only in their stacking sequence. Polytypism is a special case of polymorphism: the two-dimensional translations within the layers are essentially preserved.<br />
<br />
Acta Cryst. (1984). A40, 399-404; "Nomenclature of Polytype Structures"<br />
Report of the International Union of Crystallography Ad-Hoc Committee on the Nomenclature of Disordered, Modulated and Polytype Structures<br />
<br />
<br />
<br />
==See also==<br />
Chapter 9.2 of ''International Tables of Crystallography, Volume C''<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Aristotype&diff=2242
Aristotype
2006-10-21T05:41:13Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Aristotype</Font> (''Fr''). <br />
<br />
<br />
== Definition ==<br />
<br />
An arisotype is a high-symmetry structure type that can be viewed as an idealized version of a lower symmetry structure. It was introduced by Helen Megaw in relation to perovskites which it is where it is still mostly used, the cubic perovskite structure (which is adopted at most half a dozen compounds) is regarded as the aristotype for the vast array of other lower-symmetry perovskites.<br />
<br />
Originally, an aristotype is a printing-out process using paper coated with silver chloride in gelatin; now, any such process using silver salts in either collodion or gelatin; also, a print so made.<br />
<br />
----<br />
<br />
[[Category:Fundamental crystallography]]</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Aristotype&diff=2241
Aristotype
2006-10-21T05:39:16Z
<p>AndreAuthier: </p>
<hr />
<div><Font color="blue">Aristotype</Font> (''Fr''). <br />
<br />
<br />
== Definition ==<br />
<br />
An arisotype is a high-symmetry structure type that can be viewed as an idealized version of a lower symmetry structure. It was introduced by Helen Megaw in relation to perovskites which it is where it is still mostly used, the cubic perovskite structure (which is adopted at most half a dozen compounds) is regarded as the aristotype for the vast array of other lower-symmetry perovskites.<br />
<br />
Originally, an aristotype is a printing-out process using paper coated with silver chloride in gelatin; now, any such process using silver salts in either collodion or gelatin; also, a print so made.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Aristotype&diff=2240
Aristotype
2006-10-21T05:34:48Z
<p>AndreAuthier: </p>
<hr />
<div>An arisotype in crystallography is a high-symmetry structure type that can be viewed as an idealized version of a lower symmetry structure. I believe Helen Megaw introduced the term in relation to perovskites which it is where it is still mostly used, the cubic perovskite structure (which is adopted at most half a dozen compounds) is regarded as the aristotype for the vast array of other lower-symmetry perovskites.<br />
Orig., a printing-out process using paper coated with silver chloride in gelatin; now, any such process using silver salts in either collodion or gelatin; also, a print so made.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Aristotype&diff=2239
Aristotype
2006-10-21T05:33:49Z
<p>AndreAuthier: </p>
<hr />
<div>An arisotype in crystallography is a high-symmetry structure type that can be viewed as an idealized version of a lower symmetry structure. I believe Helen Megaw introduced the term in relation to perovskites which it is where it is still mostly used, the cubic perovskite structure (which is adopted at most half a dozen compounds) is regarded as the aristotype for the vast array of other lower-symmetry perovskites.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=A&diff=2238
A
2006-10-21T05:33:25Z
<p>AndreAuthier: </p>
<hr />
<div>{| border="1" cellpadding="3" cellspacing="0" rules="all" <br />
| [[A]] || [[B]] || [[C]] || [[D]] || [[E]] || [[F]] || [[G]] || [[H]] || [[I]] || [[J]] || [[K]] || [[L]] || [[M]] || [[N]] || [[O]] || [[P]] || [[Q]] || [[R]] || [[S]] || [[T]] || [[U]] || [[V]] || [[W]] || [[X]] || [[Y]] || [[Z]] <br />
|}<br />
<br />
= A =<br />
[[absolute structure]]<br><br />
[[absorption edge]]<br><br />
[[anomalous absorption]]<br><br />
[[anomalous dispersion]]<br><br />
[[anomalous transmission]]<br><br />
[[anomalous scattering]]<br><br />
[[aristotype]]<br><br />
[[arithmetic crystal classes]]<br></div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2233
Online Dictionary of Crystallography talk:About
2006-07-17T04:51:49Z
<p>AndreAuthier: /* APPENDIX: Membership of the Working Group */</p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold: on the one hand, to define the nature and scope of the Dictionary, and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''mediawiki'' software (see Technical Considerations). It was implemented by the Research and Development Officer, Brian McMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks, if it appears that there is a need for such a product. <br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' ''[[Bragg's law]]'', ''[[Ewald sphere]]''. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations, tables and figures are included where necessary (see, for instance, the entries ''[[Bragg's law]]'' and ''[[arithmetic crystal classes]]'').<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but the definitions should not be translated into other languages. The pilot demonstrates many translations into French, Spanish, Italian, German and Russian. Because it is impossible to collect a comprehensive set of translations at any one time, an advantage of the WiKi approach is the ability to extend the list of translations at any time.<br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are presented on a separate page that one accesses ''via'' a hyperlink (see for instance the page ''[[arithmetic crystal classes]]''). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF dictionaries, ''International Tables'', Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether such links will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (subscribers only or by buying the articles) and the entry ''[[Bragg's law]]'' to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry ''[[absolute structure]]'').<br />
<br />
The general pattern of a typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages<br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering by categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning ''Twinning''] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# ''Fundamental crystallography''].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. It is likely that individuals will need to be recruited and charged with populating specific topic areas with content if one wants the project to proceed at a reasonable pace. This may involve some financial incentive.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although it is managed as a separate virtual server, and so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed in the early stages to build a critical mass of content that will inspire more active involvement by volunteer contributors.<br />
<br />
= Technical Considerations=<br />
<br />
A major goal of the pilot project was to identify a software platform capable of supporting collaborative work on an online dictionary by the distributed authorship that the project required. Ideally the software chosen would also act as a dissemination mechanism, ''i.e.'' the contributors would be working directly on the pages that readers would view.<br />
<br />
== WiKi software ==<br />
<br />
The approach put forward at the Florence Congress and enthusiastically received by the Nomenclature Commission was the use of a 'WiKi'. A WiKi (from the Hawai'ian for 'quick' or 'fast') is a web-centric content management system designed to be lightweight and encourage rapid development of web sites by a collaboration of authors and editors. The public ''Wikipedia'' project is an example of a very large work of this sort (at the moment over one and a quarter million encyclopaedic entries in the English-language edition, written and edited by tens of thousands of users). Two software WiKi implementations were investigated, ''MoinMoin'', which is used in-house for technical documentation by the IUCr editorial staff, and ''mediawiki'', which is used in the Wikipedia project. Although ''MoinMoin'' had certain advantages in ease of set-up, maintenance and use, it proved to be too limited in its ability to handle images, mathematics, and complex page layouts. After a few months development on the ''MoinMoin'' platform, the content was transferred successfully to a ''mediawiki'' implementation, which will form the basis for future developments.<br />
<br />
== mediawiki ==<br />
<br />
The first ''mediawiki'' implementation (http://www.mediawiki.org) was set up in December 2005, and a reimplementation with updated software and appropriate access control mechanisms was launched in late January 2006. <br />
<br />
The main advantages of this implementation are:<br />
* native support for uploading of images and other non-text files<br />
* native support for TeX-based processing of suitable marked-up mathematics content<br />
* support for raw HTML markup, allowing the construction of complex tables and relatively complex page layout<br />
* support for a simple markup that is easy for a new author to learn, and is suitable for simple text-only entries<br />
* layered and extensible access rights, allowing different classes of user: 'reader', 'author', 'editor' and 'systems administrator'<br />
* support for categories<br />
* automated section numbering<br />
* numerous admin functions (collection of statistics, autoindexing of categories and of the entire site, identification of broken internal links ''etc.'')<br />
* support for automated rights metadata (the current pilot is advertising Creative Commons rights to copy, distribute, display, and perform the work, and to make derivative works)<br />
<br />
Its main disadvantages are:<br />
* sugnificantly greater administrative overhead than ''MoinMoin'' (although much of this is one-off setup or introduction of new features)<br />
* poor support for page templates (although templated data fields and transclusion will be useful features in the longer term)<br />
* poor local documentation<br />
<br />
''mediawiki'' offers many features that are suitable for the Online Dictionary project - ability to create and edit entries, store version histories, exercise editorial control to freeze definitions if necessary, internal hyperlinking, indexing and search engines, the ability to annotate and discuss articles. It is also suitable as a dissemination platform. It offers good support for maths and images, both of which are considered essential for an effective crystallography dictionary. It is therefore proposed to base the public Online Dictionary service on this software platform.<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the ''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, as observer, subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2232
Online Dictionary of Crystallography talk:About
2006-07-17T04:45:38Z
<p>AndreAuthier: /* The granularity of definitions */</p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold: on the one hand, to define the nature and scope of the Dictionary, and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''mediawiki'' software (see Technical Considerations). It was implemented by the Research and Development Officer, Brian McMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks, if it appears that there is a need for such a product. <br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' ''[[Bragg's law]]'', ''[[Ewald sphere]]''. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations, tables and figures are included where necessary (see, for instance, the entries ''[[Bragg's law]]'' and ''[[arithmetic crystal classes]]'').<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but the definitions should not be translated into other languages. The pilot demonstrates many translations into French, Spanish, Italian, German and Russian. Because it is impossible to collect a comprehensive set of translations at any one time, an advantage of the WiKi approach is the ability to extend the list of translations at any time.<br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are presented on a separate page that one accesses ''via'' a hyperlink (see for instance the page ''[[arithmetic crystal classes]]''). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF dictionaries, ''International Tables'', Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether such links will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (subscribers only or by buying the articles) and the entry ''[[Bragg's law]]'' to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry ''[[absolute structure]]'').<br />
<br />
The general pattern of a typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages<br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering by categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning ''Twinning''] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# ''Fundamental crystallography''].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. It is likely that individuals will need to be recruited and charged with populating specific topic areas with content if one wants the project to proceed at a reasonable pace. This may involve some financial incentive.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although it is managed as a separate virtual server, and so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed in the early stages to build a critical mass of content that will inspire more active involvement by volunteer contributors.<br />
<br />
= Technical Considerations=<br />
<br />
A major goal of the pilot project was to identify a software platform capable of supporting collaborative work on an online dictionary by the distributed authorship that the project required. Ideally the software chosen would also act as a dissemination mechanism, ''i.e.'' the contributors would be working directly on the pages that readers would view.<br />
<br />
== WiKi software ==<br />
<br />
The approach put forward at the Florence Congress and enthusiastically received by the Nomenclature Commission was the use of a 'WiKi'. A WiKi (from the Hawai'ian for 'quick' or 'fast') is a web-centric content management system designed to be lightweight and encourage rapid development of web sites by a collaboration of authors and editors. The public ''Wikipedia'' project is an example of a very large work of this sort (at the moment over one and a quarter million encyclopaedic entries in the English-language edition, written and edited by tens of thousands of users). Two software WiKi implementations were investigated, ''MoinMoin'', which is used in-house for technical documentation by the IUCr editorial staff, and ''mediawiki'', which is used in the Wikipedia project. Although ''MoinMoin'' had certain advantages in ease of set-up, maintenance and use, it proved to be too limited in its ability to handle images, mathematics, and complex page layouts. After a few months development on the ''MoinMoin'' platform, the content was transferred successfully to a ''mediawiki'' implementation, which will form the basis for future developments.<br />
<br />
== mediawiki ==<br />
<br />
The first ''mediawiki'' implementation (http://www.mediawiki.org) was set up in December 2005, and a reimplementation with updated software and appropriate access control mechanisms was launched in late January 2006. <br />
<br />
The main advantages of this implementation are:<br />
* native support for uploading of images and other non-text files<br />
* native support for TeX-based processing of suitable marked-up mathematics content<br />
* support for raw HTML markup, allowing the construction of complex tables and relatively complex page layout<br />
* support for a simple markup that is easy for a new author to learn, and is suitable for simple text-only entries<br />
* layered and extensible access rights, allowing different classes of user: 'reader', 'author', 'editor' and 'systems administrator'<br />
* support for categories<br />
* automated section numbering<br />
* numerous admin functions (collection of statistics, autoindexing of categories and of the entire site, identification of broken internal links ''etc.'')<br />
* support for automated rights metadata (the current pilot is advertising Creative Commons rights to copy, distribute, display, and perform the work, and to make derivative works)<br />
<br />
Its main disadvantages are:<br />
* sugnificantly greater administrative overhead than ''MoinMoin'' (although much of this is one-off setup or introduction of new features)<br />
* poor support for page templates (although templated data fields and transclusion will be useful features in the longer term)<br />
* poor local documentation<br />
<br />
''mediawiki'' offers many features that are suitable for the Online Dictionary project - ability to create and edit entries, store version histories, exercise editorial control to freeze definitions if necessary, internal hyperlinking, indexing and search engines, the ability to annotate and discuss articles. It is also suitable as a dissemination platform. It offers good support for maths and images, both of which are considered essential for an effective crystallography dictionary. It is therefore proposed to base the public Online Dictionary service on this software platform.<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the<br />
''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, <br />
as observer subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2231
Online Dictionary of Crystallography talk:About
2006-07-17T04:44:29Z
<p>AndreAuthier: </p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold: on the one hand, to define the nature and scope of the Dictionary, and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''mediawiki'' software (see Technical Considerations). It was implemented by the Research and Development Officer, Brian McMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks, if it appears that there is a need for such a product. <br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' ''[[Bragg's law]]'', ''[[Ewald sphere]]''. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations, tables and figures are included where necessary (see, for instance, the entries ''[[Bragg's law]]'' and ''[[arithmetic crystal classes]]'').<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but the definitions should not be translated into other languages. The pilot demonstrates many translations into French, Spanish, Italian, German and Russian. Because it is impossible to collect a comprehensive set of translations at any one time, an advantage of the WiKi approach is the ability to extend the list of translations at any time.<br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are presented on a separate page that one accesses ''via'' a hyperlink (see for instance the page ''[[arithmetic crystal classes]]''). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF dictionaries, ''International Tables'', Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether such links will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (subscribers only or by buying the articles) and the entry [[Bragg's law]] to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry ''[[absolute structure]]'').<br />
<br />
The general pattern of a typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages<br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering by categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning ''Twinning''] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# ''Fundamental crystallography''].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. It is likely that individuals will need to be recruited and charged with populating specific topic areas with content if one wants the project to proceed at a reasonable pace. This may involve some financial incentive.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although it is managed as a separate virtual server, and so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed in the early stages to build a critical mass of content that will inspire more active involvement by volunteer contributors.<br />
<br />
= Technical Considerations=<br />
<br />
A major goal of the pilot project was to identify a software platform capable of supporting collaborative work on an online dictionary by the distributed authorship that the project required. Ideally the software chosen would also act as a dissemination mechanism, ''i.e.'' the contributors would be working directly on the pages that readers would view.<br />
<br />
== WiKi software ==<br />
<br />
The approach put forward at the Florence Congress and enthusiastically received by the Nomenclature Commission was the use of a 'WiKi'. A WiKi (from the Hawai'ian for 'quick' or 'fast') is a web-centric content management system designed to be lightweight and encourage rapid development of web sites by a collaboration of authors and editors. The public ''Wikipedia'' project is an example of a very large work of this sort (at the moment over one and a quarter million encyclopaedic entries in the English-language edition, written and edited by tens of thousands of users). Two software WiKi implementations were investigated, ''MoinMoin'', which is used in-house for technical documentation by the IUCr editorial staff, and ''mediawiki'', which is used in the Wikipedia project. Although ''MoinMoin'' had certain advantages in ease of set-up, maintenance and use, it proved to be too limited in its ability to handle images, mathematics, and complex page layouts. After a few months development on the ''MoinMoin'' platform, the content was transferred successfully to a ''mediawiki'' implementation, which will form the basis for future developments.<br />
<br />
== mediawiki ==<br />
<br />
The first ''mediawiki'' implementation (http://www.mediawiki.org) was set up in December 2005, and a reimplementation with updated software and appropriate access control mechanisms was launched in late January 2006. <br />
<br />
The main advantages of this implementation are:<br />
* native support for uploading of images and other non-text files<br />
* native support for TeX-based processing of suitable marked-up mathematics content<br />
* support for raw HTML markup, allowing the construction of complex tables and relatively complex page layout<br />
* support for a simple markup that is easy for a new author to learn, and is suitable for simple text-only entries<br />
* layered and extensible access rights, allowing different classes of user: 'reader', 'author', 'editor' and 'systems administrator'<br />
* support for categories<br />
* automated section numbering<br />
* numerous admin functions (collection of statistics, autoindexing of categories and of the entire site, identification of broken internal links ''etc.'')<br />
* support for automated rights metadata (the current pilot is advertising Creative Commons rights to copy, distribute, display, and perform the work, and to make derivative works)<br />
<br />
Its main disadvantages are:<br />
* sugnificantly greater administrative overhead than ''MoinMoin'' (although much of this is one-off setup or introduction of new features)<br />
* poor support for page templates (although templated data fields and transclusion will be useful features in the longer term)<br />
* poor local documentation<br />
<br />
''mediawiki'' offers many features that are suitable for the Online Dictionary project - ability to create and edit entries, store version histories, exercise editorial control to freeze definitions if necessary, internal hyperlinking, indexing and search engines, the ability to annotate and discuss articles. It is also suitable as a dissemination platform. It offers good support for maths and images, both of which are considered essential for an effective crystallography dictionary. It is therefore proposed to base the public Online Dictionary service on this software platform.<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the<br />
''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, <br />
as observer subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2230
Online Dictionary of Crystallography talk:About
2006-07-17T04:37:36Z
<p>AndreAuthier: /* Scientific scope */</p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold: on the one hand, to define the nature and scope of the Dictionary, and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''mediawiki'' software (see Technical Considerations). It was implemented by the Research and Development Officer, Brian McMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks, if it appears that there is a need for such a product. <br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' ''[[Bragg's law]]'', ''[[Ewald sphere]]''. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations, tables and figures are included where necessary (see, for instance, the entry ''[[Bragg's law]]'').<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but the definitions should not be translated into other languages. The pilot demonstrates many translations into French, Spanish, Italian, German and Russian. Because it is impossible to collect a comprehensive set of translations at any one time, an advantage of the WiKi approach is the ability to extend the list of translations at any time.<br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are presented on a separate page that one accesses ''via'' a hyperlink (see for instance the page [[arithmetic crystal classes]]). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF dictionaries, ''International Tables'', Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether such links will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (subscribers only or by buying the articles) and the entry [[Bragg's law]] to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry ''[[absolute structure]]'').<br />
<br />
The general pattern of a typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages<br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering by categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning ''Twinning''] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# ''Fundamental crystallography''].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. It is likely that individuals will need to be recruited and charged with populating specific topic areas with content if one wants the project to proceed at a reasonable pace. This may involve some financial incentive.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although it is managed as a separate virtual server, and so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed in the early stages to build a critical mass of content that will inspire more active involvement by volunteer contributors.<br />
<br />
= Technical Considerations=<br />
<br />
A major goal of the pilot project was to identify a software platform capable of supporting collaborative work on an online dictionary by the distributed authorship that the project required. Ideally the software chosen would also act as a dissemination mechanism, ''i.e.'' the contributors would be working directly on the pages that readers would view.<br />
<br />
== WiKi software ==<br />
<br />
The approach put forward at the Florence Congress and enthusiastically received by the Nomenclature Commission was the use of a 'WiKi'. A WiKi (from the Hawai'ian for 'quick' or 'fast') is a web-centric content management system designed to be lightweight and encourage rapid development of web sites by a collaboration of authors and editors. The public ''Wikipedia'' project is an example of a very large work of this sort (at the moment over one and a quarter million encyclopaedic entries in the English-language edition, written and edited by tens of thousands of users). Two software WiKi implementations were investigated, ''MoinMoin'', which is used in-house for technical documentation by the IUCr editorial staff, and ''mediawiki'', which is used in the Wikipedia project. Although ''MoinMoin'' had certain advantages in ease of set-up, maintenance and use, it proved to be too limited in its ability to handle images, mathematics, and complex page layouts. After a few months development on the ''MoinMoin'' platform, the content was transferred successfully to a ''mediawiki'' implementation, which will form the basis for future developments.<br />
<br />
== mediawiki ==<br />
<br />
The first ''mediawiki'' implementation (http://www.mediawiki.org) was set up in December 2005, and a reimplementation with updated software and appropriate access control mechanisms was launched in late January 2006. <br />
<br />
The main advantages of this implementation are:<br />
* native support for uploading of images and other non-text files<br />
* native support for TeX-based processing of suitable marked-up mathematics content<br />
* support for raw HTML markup, allowing the construction of complex tables and relatively complex page layout<br />
* support for a simple markup that is easy for a new author to learn, and is suitable for simple text-only entries<br />
* layered and extensible access rights, allowing different classes of user: 'reader', 'author', 'editor' and 'systems administrator'<br />
* support for categories<br />
* automated section numbering<br />
* numerous admin functions (collection of statistics, autoindexing of categories and of the entire site, identification of broken internal links ''etc.'')<br />
* support for automated rights metadata (the current pilot is advertising Creative Commons rights to copy, distribute, display, and perform the work, and to make derivative works)<br />
<br />
Its main disadvantages are:<br />
* sugnificantly greater administrative overhead than ''MoinMoin'' (although much of this is one-off setup or introduction of new features)<br />
* poor support for page templates (although templated data fields and transclusion will be useful features in the longer term)<br />
* poor local documentation<br />
<br />
''mediawiki'' offers many features that are suitable for the Online Dictionary project - ability to create and edit entries, store version histories, exercise editorial control to freeze definitions if necessary, internal hyperlinking, indexing and search engines, the ability to annotate and discuss articles. It is also suitable as a dissemination platform. It offers good support for maths and images, both of which are considered essential for an effective crystallography dictionary. It is therefore proposed to base the public Online Dictionary service on this software platform.<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the<br />
''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, <br />
as observer subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2229
Online Dictionary of Crystallography talk:About
2006-07-16T16:15:42Z
<p>AndreAuthier: </p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold: on the one hand, to define the nature and scope of the Dictionary, and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''mediawiki'' software (see Technical Considerations). It was implemented by the Research and Development Officer, Brian McMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks, if it appears that there is a need for such a product. <br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' ''[[Bragg's law]]'', ''[[Ewald sphere]]''. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations and figures are included where necessary (see, for instance, the entry ''[[Bragg's law]]'').<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but the definitions should not be translated into other languages. The pilot demonstrates many translations into French, Spanish, Italian, German and Russian. Because it is impossible to collect a comprehensive set of translations at any one time, an advantage of the WiKi approach is the ability to extend the list of translations at any time.<br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are presented on a separate page that one accesses ''via'' a hyperlink (see for instance the page [[arithmetic crystal classes]]). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF dictionaries, ''International Tables'', Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether such links will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (subscribers only or by buying the articles) and the entry [[Bragg's law]] to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry ''[[absolute structure]]'').<br />
<br />
The general pattern of a typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages<br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering by categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning ''Twinning''] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# ''Fundamental crystallography''].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. It is likely that individuals will need to be recruited and charged with populating specific topic areas with content if one wants the project to proceed at a reasonable pace. This may involve some financial incentive.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although it is managed as a separate virtual server, and so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed in the early stages to build a critical mass of content that will inspire more active involvement by volunteer contributors.<br />
<br />
= Technical Considerations=<br />
<br />
A major goal of the pilot project was to identify a software platform capable of supporting collaborative work on an online dictionary by the distributed authorship that the project required. Ideally the software chosen would also act as a dissemination mechanism, ''i.e.'' the contributors would be working directly on the pages that readers would view.<br />
<br />
== WiKi software ==<br />
<br />
The approach put forward at the Florence Congress and enthusiastically received by the Nomenclature Commission was the use of a 'WiKi'. A WiKi (from the Hawai'ian for 'quick' or 'fast') is a web-centric content management system designed to be lightweight and encourage rapid development of web sites by a collaboration of authors and editors. The public ''Wikipedia'' project is an example of a very large work of this sort (at the moment over one and a quarter million encyclopaedic entries in the English-language edition, written and edited by tens of thousands of users). Two software WiKi implementations were investigated, ''MoinMoin'', which is used in-house for technical documentation by the IUCr editorial staff, and ''mediawiki'', which is used in the Wikipedia project. Although ''MoinMoin'' had certain advantages in ease of set-up, maintenance and use, it proved to be too limited in its ability to handle images, mathematics, and complex page layouts. After a few months development on the ''MoinMoin'' platform, the content was transferred successfully to a ''mediawiki'' implementation, which will form the basis for future developments.<br />
<br />
== mediawiki ==<br />
<br />
The first ''mediawiki'' implementation (http://www.mediawiki.org) was set up in December 2005, and a reimplementation with updated software and appropriate access control mechanisms was launched in late January 2006. <br />
<br />
The main advantages of this implementation are:<br />
* native support for uploading of images and other non-text files<br />
* native support for TeX-based processing of suitable marked-up mathematics content<br />
* support for raw HTML markup, allowing the construction of complex tables and relatively complex page layout<br />
* support for a simple markup that is easy for a new author to learn, and is suitable for simple text-only entries<br />
* layered and extensible access rights, allowing different classes of user: 'reader', 'author', 'editor' and 'systems administrator'<br />
* support for categories<br />
* automated section numbering<br />
* numerous admin functions (collection of statistics, autoindexing of categories and of the entire site, identification of broken internal links ''etc.'')<br />
* support for automated rights metadata (the current pilot is advertising Creative Commons rights to copy, distribute, display, and perform the work, and to make derivative works)<br />
<br />
Its main disadvantages are:<br />
* sugnificantly greater administrative overhead than ''MoinMoin'' (although much of this is one-off setup or introduction of new features)<br />
* poor support for page templates (although templated data fields and transclusion will be useful features in the longer term)<br />
* poor local documentation<br />
<br />
''mediawiki'' offers many features that are suitable for the Online Dictionary project - ability to create and edit entries, store version histories, exercise editorial control to freeze definitions if necessary, internal hyperlinking, indexing and search engines, the ability to annotate and discuss articles. It is also suitable as a dissemination platform. It offers good support for maths and images, both of which are considered essential for an effective crystallography dictionary. It is therefore proposed to base the public Online Dictionary service on this software platform.<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the<br />
''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, <br />
as observer subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier
https://dictionary.iucr.org/index.php?title=Online_Dictionary_of_Crystallography_talk:About&diff=2219
Online Dictionary of Crystallography talk:About
2006-07-14T12:24:35Z
<p>AndreAuthier: /* Structure of the work */</p>
<hr />
<div>The ''Dictionary Working Group'' of the Commission on Crystallographic Nomenclature (CCN) was formed during the 20th IUCr Congress in Florence to provide guidance on the establishment and conduct of a project undertaken under the aegis of the Commission, with the approval of the IUCr Executive Committee and the involvement of other Commissions and appropriate bodies of the IUCr, to provide online definitions of terms used in the practice of crystallography. <br />
<br />
The first stage of the action of the Working Group was two-fold, on one hand to define the nature and scope of the Dictionary and, on the other hand, to develop an appropriate tool for its implementation.<br />
<br />
The purpose of this report is to present the state of the project after nearly one year's experience and to give the Working Group's proposals on these two points and on the financial implications.<br />
<br />
= Nature and scope =<br />
<br />
== Motivation==<br />
<br />
Many definitions of crystallographic terms are scattered in the International Tables but there is, at present, no place where they are systematically compiled, as is the case, for instance, for the chemical terms defined in the various compendia published by IUPAC (the '[http://gold.zvon.org/ gold]', 'red', 'blue', 'purple', 'silver' books). The many questions received by the Commission on Crystallographic Nomenclature related to matters of definitions and nomenclature show that there is a real <br />
need for such a compendium for crystallography. The idea was received enthusiastically by the Executive Committee in Florence and the Working Group was set up to implement a pilot project for a dictionary of crystallographic terms.<br />
<br />
== Medium==<br />
<br />
It is proposed that the project should be executed initially as solely an online project because of the flexibility of the online medium, the fact that there is no limit on the number of entries, the possibility of hyperlinks to IUCr and other web resources. The present form of the project follows the ''Wikipedia'' pattern and makes use of the ''MediaWiki'' software (see Technical Considerations). It was implemented thanks to the unceasing and highly efficient efforts of the Research and<br />
Development Officer, Brian MacMahon.<br />
<br />
It will always be possible at a later stage to consider a physical book with a CD containing all the hyperlinks.<br />
<br />
== Scientific scope==<br />
<br />
Broadly speaking, the project should be confined to the subject of crystallography, the area of science over which the IUCr has authority. Terms selected for inclusion should have a clear crystallographic implication and terms from connected disciplines (mathematics, physics, chemistry, mineralogy, biology, computational data processing, ''etc.'') should be included insofar as they relate to crystallography, ''e.g.'' ''crystallographic group''. Names of chemical or biological substances or minerals should not be included at the present stage, but terms such as ''albite twin law'' should. Reference to computer programs ''per se'' should not be included, but there might be instances when it becomes essential, ''e.g.'' ''SHELX''. Names of people should only be included if they relate to crystallographic concepts, ''e.g.'' [[Bragg's law]], [[Ewald sphere]]. Double-word items such as “X-ray interferometry” should be entered as such. A search on “interferometry “ will automatically retrieve them. Equations and figures are included where necessary (see, for instance, the entry [[Bragg's law]]).<br />
<br />
The Working Group considers that translations of terms in other languages than English should be given, but not that of their definitions. <br />
<br />
== The granularity of definitions==<br />
<br />
The Working Group recommends a reference product that is a blend between “dictionary” and “encyclopaedia”: a list of terms with short definitions and cross-links to other entries in the work, with at times longer developments. These longer developments are to be written on a separate page that one accesses via a hyperlink (see for instance the page [[arithmetic crystal classes]]). Hyperlinks are also provided to other web resources of the IUCr (Teaching Pamphlets, CIF <br />
dictionaries, International Tables, Journals). For instance, in the entry ''[[reciprocal lattice]]'', hyperlinks are given to the corresponding pamphlet on the IUCr web site (open access) and to the appropriate chapters of ''IT Volumes A, B, C'' and ''D''; for these it is for the Executive Committee to decide (after recommendation from the Finance Committee) whether that link will be free access or not. As other examples, the entry ''[[CIF]]'' has links to Journal articles (suscribers only or by buying the articles) and the entry [[Bragg's law]] to [http://www.iucr.org/iucr-top/publ/50YearsOfXrayDiffraction/ 50 Years of X-ray Diffraction] (free access). Hyperlinks to other web sites such as the IUPAC web sites or educational web sites can also be provided, if appropriate (see, for instance the entry [[absolute structure]]).<br />
<br />
The general pattern of typical page is:<br />
<br />
* translation of the term in other languages,<br />
* main definition<br />
* examples or applications or special cases<br />
* history<br />
* list of links to other entries or to IUCr or other web pages <br />
<br />
== Structure of the work==<br />
<br />
The work will be structured in several ways to assist navigation. The terms are entered alphabetically and can be retrieved alphabetically, but the WiKi software allows an ordering in categories and subcategories. Each entry can be attached to one or more categories (and subcategories). At the time of writing, categories are being assigned to entries <br />
on an ''ad hoc'' basis in an attempt to determine suitable structuring mechanisms. A click on a category provides links to all the entries related to that category. The present list of categories is given on the Main Page. As an example the subcategory [http://reference.iucr.org/dictionary/Category:Twinning Twinning] has been introduced in the category <br />
[http://reference.iucr.org/dictionary/Category:Fundamental_crystallography# Fundamental crystallography].<br />
<br />
There are several advantages to having categories and subcategories. One is to allow searches on areas of interest, for instance if you are looking for a particular type of [[twinning]], but don’t remember its exact name. Another one is to make the work of preparing the dictionary easier by assigning editors and subeditors to categories and subcategories. Their duty would be to oversee the definitions and to check that there are no obvious omissions.<br />
<br />
Note that the Wiki software allows searches on headwords, but also full-text searching of the entire corpus, so that the user has available a large number of query-based informational retrieval strategies.<br />
<br />
==Level of definitions and audience==<br />
<br />
The primary goal of the dictionary is to be a reference for authors and referees of IUCr Journals and for research professionals in general: it will give the “official” IUCr acceptance of terms. As such it will also be useful to students and to the general public.<br />
<br />
== Organization of contributors==<br />
<br />
The Editorial Board should consist of the members of the CCN, with representatives from the other Commissions as consultants for the various fields of crystallography. It is clear that, as Editors of the various IUCr publications, the members of the CCN are the people whose duty is to say how crystallographic terms should be used. <br />
<br />
Efficiency, however, requires that the work should be done under the supervision of a Main Editor or Editor-in-Chief and and a small number of appointed Editors (and subeditors) for the various categories (and subcategories), chosen in priority among the CCN members and consultants.<br />
<br />
The initial experience of the Working Group has been, however, that even the greatest enthusiasts for the project are so busy that they find it difficult to spend the time necessary to make substantial contributions. The authoring privilege has been extended recently to the rest of the CCN. Early indications are that, again, the rate of accretion of new definitions is slower than we would like to see. One can but conclude than financial incitation is required if one wants the project to proceed at a reasonable pace.<br />
<br />
== Presentation==<br />
<br />
It is expected that the resource would appear as a single web site. However, it should also act as a companion to ''International Tables'' and to the Journals, as well as to educational resources such as the Teaching Pamphlets and any new educational initiatives arising from the Teaching Commission. As the ''Online Dictionary of Crystallography'' would be an important and useful service to researchers, students and authors, it is desirable that it should be open access, bearing in mind that most definitions have links to IT Volumes, which are not open access. This last point <br />
may encourage people to subscribe to ''International Tables Online''.<br />
<br />
= Financial implications =<br />
<br />
The project as initially envisaged will rely heavily on volunteer labour and existing hardware resources. The current pilot implementation shares the same hardware as the main IUCr web site (although is managed as a separate virtual server, so can easily be moved to its own server machine if required). Some additional software development will be required (''e.g.'' implementation of a reliable backup strategy, modifications to the style to conform with other IUCr web components); but so long as these are not time-critical, they can be absorbed within the existing workload of the R&D <br />
department. Significant software developments (such as creation of a hard-copy edition) would need to be assessed and costed separately. Note that hardware costs in the event of a migration to a separate server would be modest (''e.g.'' of the order of GBP 1000 would suffice for a powerful dedicated machine).<br />
<br />
Technical editing costs are ruled out at this stage (it is assumed that the invited contributors will have a high degree of literacy, and that there will be a measure of self-regulation as contributors edit each other's entries to correct minor spelling and typographic errors). Since each entry will be presented as a separate web page, minor inconsistencies of style and presentation will not be so important as they would be in a hard-copy publication. Conversely, however, the decision to produce a hard-copy publication would be likely to involve more rigorous technical editing, with subsequent <br />
added costs.<br />
<br />
The Finance Committee should monitor the possible need for payment of editorial honoraria. It is expected that the project will require an Editor-in-Chief responsible for its overall shape and direction (at present this role is filled by the project initiator, Professor Authier). The roles of such an Editor-in-Chief will also cover the possible appointment of subsidiary editors to supervise the collection of definitions in topic areas where they have particular expertise, and the commissioning of definitions or sets of definitions to address topics not currently covered. The <br />
number and roles of secondary editors will depend in part on the readiness of the volunteer pool of contributors to identify deficiencies and provide needed definitions without prompting. The experience of the ''Wikipedia'' project suggests that this is possible in principle, but the early experience of the pilot suggests that significant effort will be needed, at least in the early stages, to build an initial critical mass of content that will inspire more active <br />
involvement by volunteer contributors. It is intended to return to this point when the project produces its next report. In the mean time, it is not unreasonable to provide conservatively for the appointment of a small number - six to a dozen - of specialist Editors responsible for commissioning content within their fields of expertise, and possibly paid a modest honorarium in recognition of their successes (by analogy in some way with journal editors' handling of manuscripts).<br />
<br />
= Technical Considerations=<br />
<br />
= APPENDIX: Membership of the Working Group =<br />
<br />
The initial membership of the Working Group established in Florence consisted of:<br />
<br />
* Andre Authier (Chair)<br />
* John Helliwell<br />
* Bill Clegg<br />
* Paola Spadon<br />
* I. David Brown<br />
* Brian McMahon<br />
<br />
Giovanni Ferraris, as Chair of the ''Commission on Inorganic and Mineral Structures'', Massimo Nespolo, as Chair of the<br />
''Commission on Mathematical and Theoretical Crystallography'' and Peter Strickland, Managing Editor of IUCr publications, <br />
as observer subsequently joined the group. Howard Flack also provided sample entries and useful feedback.</div>
AndreAuthier